{"entity": "journal", "iuid": "6460d1a6b04546e09d2e94fd6d7f0236", "timestamp": "2026-07-15T06:35:29.541Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/J.%20Biol.%20Chem..json"}, "display": {"href": "https://publications.scilifelab.se/journal/J.%20Biol.%20Chem."}}, "title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "publications_count": 54, "publications": [{"entity": "publication", "iuid": "c45c714869d64a00996f49c14d6bedab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c45c714869d64a00996f49c14d6bedab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c45c714869d64a00996f49c14d6bedab"}}, "title": "Minor hemolysin-coregulated proteins (Hcp) form heteromeric complexes and mediate effector secretion in Bacteroidales type VI secretion systems.", "authors": [{"family": "San-Miguel", "given": "Sergio G", "initials": "SG"}, {"family": "Hillier", "given": "Jessica B", "initials": "JB"}, {"family": "Saleh Al-Ammari", "given": "Manal Kamal", "initials": "MK"}, {"family": "Johansson", "given": "Emma", "initials": "E"}, {"family": "Kowalska", "given": "Anna", "initials": "A"}, {"family": "Sauer", "given": "Uwe", "initials": "U", "orcid": "0000-0002-3420-439X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d011e944ae54d47aed374d548007812.json"}}, {"family": "Batista", "given": "Paulo Ricardo", "initials": "PR"}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Uhlin", "given": "Bernt Eric", "initials": "BE", "orcid": "0000-0002-2991-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/9faa19d33fd84728bb6df987ba16475f.json"}}, {"family": "Cisneros", "given": "David A", "initials": "DA", "orcid": "0000-0001-9919-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/19f7a4aba7af436899b5d63f95f0dcda.json"}}], "type": "journal article", "published": "2026-04-16", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "pages": "111464", "volume": "302", "issue": "6", "issn-l": "0021-9258"}, "abstract": "The type VI secretion system (T6SS) is a protein complex found in Gram-negative bacteria that mediates intercellular antagonism. Hemolysin-coregulated proteins (Hcp) are major structural proteins in these systems. Hcp forms hexameric rings that stack to create an inner tube structure essential for translocating effector proteins into target cells. In gut Bacteroidales, T6SS loci encode multiple Hcp proteins with unknown function. The gut commensal Bacteroides fragilis encodes five Hcp subunits (sHcp and Hcp1-4) that have low sequence similarity. In this study, we investigated the roles of these proteins. Interaction studies showed that sHcp forms homohexamers, which is consistent with a major role of forming the bulk of the inner tube. In contrast, the less abundant minor Hcp1-4 were shown to form an interaction network involving heteromeric complexes. Biochemical and genetic analyses demonstrated that Hcp1 and Hcp2 assemble into heterohexamers and that this complex recognizes the secreted effector Bte1, contributing to its secretion. Finally, we showed that Hcp modules, which are encoded in highly syntenic regions in T6SS loci of Bacteroidales, cluster with effectors. These results imply that the minor Hcps genetically cosegregate with cognate effectors, contributing to effector cassette variability. Thus, minor Hcp subunits function as recognition particles for effectors to mediate secretion, which appears to be a conserved trait in Bacteroidales T6SSs. Exploiting these features could facilitate the characterization of unknown effectors by copurifying them with their cognate Hcps. This approach may reveal new insights into bacterial interactions and the mechanisms that establish gut biodiversity.", "doi": "10.1016/j.jbc.2026.111464", "pmid": "41999889", "labels": {"Structural Proteomics": "Service", "Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC13213661"}, {"db": "pii", "key": "S0021-9258(26)00336-4"}], "notes": [], "created": "2026-04-24T08:57:10.339Z", "modified": "2026-06-24T09:47:35.264Z"}, {"entity": "publication", "iuid": "e8e2a29927cd48e6bc32204e43189fbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8e2a29927cd48e6bc32204e43189fbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8e2a29927cd48e6bc32204e43189fbb"}}, "title": "SAG1.3-derived Frizzled-targeting small molecule compounds.", "authors": [{"family": "Gr\u00e4tz", "given": "Lukas", "initials": "L"}, {"family": "Turku", "given": "Ainoleena", "initials": "A"}, {"family": "Kozielewicz", "given": "Pawel", "initials": "P"}, {"family": "Bowin", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Scharf", "given": "Magdalena M", "initials": "MM"}, {"family": "Voss", "given": "Jan H", "initials": "JH"}, {"family": "Kinsolving", "given": "Julia", "initials": "J"}, {"family": "Shekhani", "given": "Rawan", "initials": "R"}, {"family": "Oliva-Vilarnau", "given": "Nuria", "initials": "N"}, {"family": "Koolmeister", "given": "Tobias", "initials": "T"}, {"family": "K\u00f6rber", "given": "Marlies", "initials": "M"}, {"family": "Lauschke", "given": "Volker M", "initials": "VM"}, {"family": "L\u00f6ber", "given": "Stefan", "initials": "S"}, {"family": "Gmeiner", "given": "Peter", "initials": "P"}, {"family": "Schulte", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2025-09-22", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "pages": "110751", "issn-l": "0021-9258"}, "abstract": "Exaggerated Wingless/Int1 (WNT)/Frizzled (FZD) signaling contributes to pathologies including fibrosis and different forms of cancers. Thus, targeting FZDs as WNT receptors for therapeutic purposes constitutes a promising intervention if the imminent risk of unwanted side effects caused by the involvement of WNT/FZD signaling in stem cell regulation and tissue homeostasis can be controlled. Here, we derivatize SAG1.3, which acts through FZD6 as a partial agonist. Screening of SAG1.3 derivatives identified compound 11 that competed with BODIPY-cyclopamine binding at different FZDs and inhibited WNT-induced FZD dynamics and \u03b2-catenin signaling in HEK293 cells. Furthermore, compound 11 blocked WNT-3A-induced Lgr5 gene expression in human primary hepatocyte spheroids and reduced the viability of RNF43-mutated but not RNF43-wildtype pancreatic cancer cells. Based on our data, we suggest that compound 11 acts on FZDs to limit WNT- and WNT-surrogate-induced receptor dynamics providing a valid proof-of-concept for targeting FZDs with small molecule compounds.", "doi": "10.1016/j.jbc.2025.110751", "pmid": "40992662", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0021-9258(25)02603-1"}], "notes": [], "created": "2025-10-14T15:26:07.354Z", "modified": "2025-10-17T13:04:26.480Z"}, {"entity": "publication", "iuid": "8f813a953a47489dbce089b11fc24f50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f813a953a47489dbce089b11fc24f50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f813a953a47489dbce089b11fc24f50"}}, "title": "Duplexed CeTEAM drug biosensors reveal determinants of PARP inhibitor selectivity in cells.", "authors": [{"family": "Pires", "given": "Maria J", "initials": "MJ"}, {"family": "Alam", "given": "Seher", "initials": "S"}, {"family": "Lovric", "given": "Alen", "initials": "A"}, {"family": "Fabbrizi", "given": "Emanuele", "initials": "E"}, {"family": "Rotili", "given": "Dante", "initials": "D"}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}, {"family": "Valerie", "given": "Nicholas C K", "initials": "NCK", "orcid": "0000-0002-9423-964X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d90c5a1f924c8b97409934dec74b0b.json"}}], "type": "journal article", "published": "2025-02-26", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "pages": "108361", "issn-l": "0021-9258"}, "abstract": "Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) targeting PARP1 and PARP2 have revolutionized cancer therapy by selectively killing cancer cells with defective DNA repair. However, achieving PARP1 or PARP2-selective inhibitors is difficult due to structural homology. Selectivity profiling is typically done with purified proteins, but these lack the complexity of intracellular environments and could therefore be inaccurate. Here, we duplex PARP1 L713F-GFP and PARP2 L269A-mCherry cellular target engagement by accumulation of mutant (CeTEAM) drug biosensors to systematically characterize binding and cell cycle alterations of 27 PARPi. Our results reveal that most PARPi are equipotent for both PARPs, including the next-generation drug, senaparib. However, benzimidazole carboxamide (niraparib) derivatives demonstrated PARP1-selective tendencies, while pthalazinones (olaparib) favored PARP2. AZD5305, a reported PARP1-selective inhibitor with characteristics of both series, was the exception and appears \u223c1600-fold more potent towards PARP1. In agreement with current understanding, we see that trapping-associated S/G2-phase transitions positively correlate with PARP1/2 binding potency, while some potent binders, such as veliparib, did not - likely reflecting their allosteric influence on DNA retention. We also assessed the effect of the PARP1/2 active site component, histone PARylation factor 1 (HPF1), on intracellular PARPi binding and see that HPF1 depletion elicits slight deviations in apparent binding potency, while contributing additively to trapping-like phenotypes. The PARP1/2 CeTEAM platform thus provides a structural roadmap for the development of selective PARPi and should facilitate the discovery of targeted therapies. Furthermore, our results highlight that multiplexing CeTEAM biosensors and layered genetic perturbations can systematically profile determinants of intracellular drug selectivity.", "doi": "10.1016/j.jbc.2025.108361", "pmid": "40021124", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(25)00210-8"}], "notes": [], "created": "2025-03-14T14:15:13.223Z", "modified": "2025-10-17T13:04:26.850Z"}, {"entity": "publication", "iuid": "e08c7e44cb4c4454bc432e35bd39d300", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e08c7e44cb4c4454bc432e35bd39d300.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e08c7e44cb4c4454bc432e35bd39d300"}}, "title": "Hematopoietic cells emerging from hemogenic endothelium exhibit lineage-specific oxidative stress responses.", "authors": [{"family": "Biezeman", "given": "Harmke", "initials": "H"}, {"family": "Nubi\u00e8", "given": "Martina", "initials": "M"}, {"family": "Oburoglu", "given": "Leal", "initials": "L"}], "type": "journal article", "published": "2024-09-24", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "300", "issue": "11", "pages": "107815", "issn-l": "0021-9258"}, "abstract": "During human embryogenesis, distinct waves of hematopoiesis give rise to various blood cell types, originating from hemogenic endothelial (HE) cells. As HE cells reside in hypoxic conditions in the embryo, we investigated the role of hypoxia in human endothelial to hematopoietic transition and subsequent hematopoiesis. Using single-cell RNA sequencing, we describe hypoxia-related transcriptional changes in different HE-derived blood lineages, which reveal that erythroid cells are particularly susceptible to oxidative stress, due to decreased NRF2 activity in hypoxia. In contrast, nonerythroid CD45+ cells exhibit increased proliferative rates in hypoxic conditions and enhanced resilience to oxidative stress. We find that even in normoxia, erythroid cells present a clear predisposition to oxidative stress, with low glutathione levels and high lipid peroxidation, in contrast to CD45+ cells. Intriguingly, reactive oxygen species are produced at different sites in GPA+ and CD45+ cells, revealing differences in oxidative phosphorylation and the use of canonical versus noncanonical tricarboxylic acid cycle in these lineages. Our findings elucidate how hypoxia and oxidative stress distinctly affect HE-derived hematopoietic lineages, uncovering critical transcriptional and metabolic pathways that influence blood cell development.", "doi": "10.1016/j.jbc.2024.107815", "pmid": "39326495", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11532904"}, {"db": "pii", "key": "S0021-9258(24)02316-0"}], "notes": [], "created": "2024-11-14T09:29:27.189Z", "modified": "2024-11-14T09:29:27.193Z"}, {"entity": "publication", "iuid": "b8144a1df1194cd194240a7128e3f674", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8144a1df1194cd194240a7128e3f674.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8144a1df1194cd194240a7128e3f674"}}, "title": "Cooperative folding as a molecular switch in an evolved antibody binder.", "authors": [{"family": "J\u00f6nsson", "given": "Malin", "initials": "M"}, {"family": "Mushtaq", "given": "Ameeq Ul", "initials": "AU"}, {"family": "Nagy", "given": "Tam\u00e1s Mil\u00e1n", "initials": "TM"}, {"family": "von Witting", "given": "Emma", "initials": "E"}, {"family": "L\u00f6fblom", "given": "John", "initials": "J"}, {"family": "Nam", "given": "Kwangho", "initials": "K"}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S"}], "type": "journal article", "published": "2024-09-19", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "300", "issue": "11", "pages": "107795", "issn-l": "0021-9258"}, "abstract": "Designing proteins with tunable activities from easily accessible external cues remains a biotechnological challenge. Here, we set out to create a small antibody-binding domain equipped with a molecular switch inspired by the allosteric response to calcium seen in naturally derived proteins like calmodulin. We have focused on one of the three domains of Protein G that show inherent affinity to antibodies. By combining a semi-rational protein design with directed evolution, we engineered novel variants containing a calcium-binding loop rendering the inherent antibody affinity calcium-dependent. The evolved variants resulted from a designed selection strategy subjecting them to negative and positive selection pressures focused on conditional antibody binding. Hence, these variants contains molecular \"on/off\" switches, controlling the target affinity towards antibody fragments simply by the presence or absence of calcium. From NMR spectroscopy we found that the molecular mechanism underlying the evolved switching behavior was a coupled calcium-binding and folding event where the target binding surface was intact and functional only in the presence of bound calcium. Notably, it was observed that the response to the employed selection pressures gave rise to the evolution of a cooperative folding mechanism. This observation illustrates why the cooperative folding reaction is an effective solution seen repeatedly in the natural evolution of fine-tuned macromolecular recognition. Engineering binding moieties to confer conditional target interaction has great potential due to the exquisite interaction control that is tunable to application requirements. Improved understanding of the molecular mechanisms behind regulated interactions is crucial to unlock how to engineer switchable proteins useful in a variety of biotechnological applications.", "doi": "10.1016/j.jbc.2024.107795", "pmid": "39305954", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11532951"}, {"db": "pii", "key": "S0021-9258(24)02296-8"}], "notes": [], "created": "2024-11-13T19:36:47.756Z", "modified": "2025-10-17T13:03:52.763Z"}, {"entity": "publication", "iuid": "79011bcedf334d5ba61693f646bdeae5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79011bcedf334d5ba61693f646bdeae5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79011bcedf334d5ba61693f646bdeae5"}}, "title": "A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors.", "authors": [{"family": "Menon", "given": "Indu", "initials": "I"}, {"family": "Sych", "given": "Taras", "initials": "T"}, {"family": "Son", "given": "Yeeun", "initials": "Y"}, {"family": "Morizumi", "given": "Takefumi", "initials": "T"}, {"family": "Lee", "given": "Joon", "initials": "J"}, {"family": "Ernst", "given": "Oliver P", "initials": "OP"}, {"family": "Khelashvili", "given": "George", "initials": "G"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E"}, {"family": "Levitz", "given": "Joshua", "initials": "J"}, {"family": "Menon", "given": "Anant K", "initials": "AK"}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "300", "issue": "2", "pages": "105649", "issn-l": "0021-9258"}, "abstract": "Class A G protein-coupled receptors (GPCRs), a superfamily of cell membrane signaling receptors, moonlight as constitutively active phospholipid scramblases. The plasma membrane of metazoan cells is replete with GPCRs yet has a strong resting trans-bilayer phospholipid asymmetry, with the signaling lipid phosphatidylserine confined to the cytoplasmic leaflet. To account for the persistence of this lipid asymmetry in the presence of GPCR scramblases, we hypothesized that GPCR-mediated lipid scrambling is regulated by cholesterol, a major constituent of the plasma membrane. We now present a technique whereby synthetic vesicles reconstituted with GPCRs can be supplemented with cholesterol to a level similar to that of the plasma membrane and show that the scramblase activity of two prototypical GPCRs, opsin and the \u03b21-adrenergic receptor, is impaired upon cholesterol loading. Our data suggest that cholesterol acts as a switch, inhibiting scrambling above a receptor-specific threshold concentration to disable GPCR scramblases at the plasma membrane.", "doi": "10.1016/j.jbc.2024.105649", "pmid": "38237683", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10874734"}, {"db": "pii", "key": "S0021-9258(24)00025-5"}], "notes": [], "created": "2024-08-27T08:28:09.931Z", "modified": "2024-08-27T08:28:09.936Z"}, {"entity": "publication", "iuid": "c7fa7c0f7e1641518831f53600f04e3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7fa7c0f7e1641518831f53600f04e3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7fa7c0f7e1641518831f53600f04e3a"}}, "title": "AdipoR2 recruits protein interactors to promote fatty acid elongation and membrane fluidity.", "authors": [{"family": "Ruiz", "given": "Mario", "initials": "M"}, {"family": "Devkota", "given": "Ranjan", "initials": "R"}, {"family": "Kaper", "given": "Delaney", "initials": "D"}, {"family": "Ruhanen", "given": "Hanna", "initials": "H"}, {"family": "Busayavalasa", "given": "Kiran", "initials": "K"}, {"family": "Radovi\u0107", "given": "Uro\u0161", "initials": "U"}, {"family": "Henricsson", "given": "Marcus", "initials": "M"}, {"family": "K\u00e4kel\u00e4", "given": "Reijo", "initials": "R"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Pilon", "given": "Marc", "initials": "M"}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "299", "issue": "6", "pages": "104799", "issn-l": "0021-9258"}, "abstract": "The human AdipoR2 and its Caenorhabditis elegans homolog PAQR-2 are multipass plasma membrane proteins that protect cells against membrane rigidification. However, how AdipoR2 promotes membrane fluidity mechanistically is not clear. Using 13C-labeled fatty acids, we show that AdipoR2 can promote the elongation and incorporation of membrane-fluidizing polyunsaturated fatty acids into phospholipids. To elucidate the molecular basis of these activities, we performed immunoprecipitations of tagged AdipoR2 and PAQR-2 expressed in HEK293 cells or whole C. elegans, respectively, and identified coimmunoprecipitated proteins using mass spectrometry. We found that several of the evolutionarily conserved AdipoR2/PAQR-2 interactors are important for fatty acid elongation and incorporation into phospholipids. We experimentally verified some of these interactions, namely, with the dehydratase HACD3 that is essential for the third of four steps in long-chain fatty acid elongation and ACSL4 that is important for activation of unsaturated fatty acids and their channeling into phospholipids. We conclude that AdipoR2 and PAQR-2 can recruit protein interactors to promote the production and incorporation of unsaturated fatty acids into phospholipids.", "doi": "10.1016/j.jbc.2023.104799", "pmid": "37164154", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10279913"}, {"db": "pii", "key": "S0021-9258(23)01827-6"}], "notes": [], "created": "2023-12-01T10:51:26.058Z", "modified": "2024-01-16T13:46:27.405Z"}, {"entity": "publication", "iuid": "d39855056cb449c0a66e776bb322d093", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d39855056cb449c0a66e776bb322d093.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d39855056cb449c0a66e776bb322d093"}}, "title": "Comprehensive characterization of complex glycosphingolipids in human pancreatic cancer tissues.", "authors": [{"family": "Ho\u0159ej\u0161\u00ed", "given": "Karel", "initials": "K"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Va\u0148kov\u00e1", "given": "Zuzana", "initials": "Z"}, {"family": "Jir\u00e1sko", "given": "Robert", "initials": "R"}, {"family": "Strouhal", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Melichar", "given": "Bohuslav", "initials": "B"}, {"family": "Teneberg", "given": "Susann", "initials": "S"}, {"family": "Hol\u010dapek", "given": "Michal", "initials": "M"}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "299", "issue": "3", "pages": "102923"}, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is one of the most common causes of cancer-related deaths worldwide, accounting for 90% of primary pancreatic tumors with an average 5-year survival rate of less than 10%. PDAC exhibits aggressive biology, which, together with late detection, results in most PDAC patients presenting with unresectable, locally advanced, or metastatic disease. In-depth lipid profiling and screening of potential biomarkers currently appear to be a promising approach for early detection of PDAC or other cancers. Here, we isolated and characterized complex glycosphingolipids (GSL) from normal and tumor pancreatic tissues of patients with PDAC using a combination of TLC, chemical staining, carbohydrate-recognized ligand-binding assay, and LC/ESI-MS2. The major neutral GSL identified were GSL with the terminal blood groups A, B, H, Lea, Leb, Lex, Ley, P1, and PX2 determinants together with globo- (Gb3 and Gb4) and neolacto-series GSL (nLc4 and nLc6). We also revealed that the neutral GSL profiles and their relative amounts differ between normal and tumor tissues. Additionally, the normal and tumor pancreatic tissues differ in type 1/2 core chains. Sulfatides and GM3 gangliosides were the predominant acidic GSL along with the minor sialyl-nLc4/nLc6 and sialyl-Lea/Lex. The comprehensive analysis of GSL in human PDAC tissues extends the GSL coverage and provides an important platform for further studies of GSL alterations; therefore, it could contribute to the development of new biomarkers and therapeutic approaches.", "doi": "10.1016/j.jbc.2023.102923", "pmid": "36681125", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9976472"}, {"db": "pii", "key": "S0021-9258(23)00055-8"}], "notes": [], "created": "2023-12-04T10:22:21.450Z", "modified": "2024-01-16T13:46:27.917Z"}, {"entity": "publication", "iuid": "8175d2c8812d4475a40501c87d36e35b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8175d2c8812d4475a40501c87d36e35b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8175d2c8812d4475a40501c87d36e35b"}}, "title": "Using reporters of different misfolded proteins reveals differential strategies in processing protein aggregates.", "authors": [{"family": "Schneider", "given": "Kara L", "initials": "KL"}, {"family": "Ahmadpour", "given": "Doryaneh", "initials": "D"}, {"family": "Keuenhof", "given": "Katharina S", "initials": "KS"}, {"family": "Eisele-B\u00fcrger", "given": "Anna Maria", "initials": "AM"}, {"family": "Berglund", "given": "Lisa Larsson", "initials": "LL"}, {"family": "Eisele", "given": "Frederik", "initials": "F"}, {"family": "Babazadeh", "given": "Roja", "initials": "R"}, {"family": "H\u00f6\u00f6g", "given": "Johanna L", "initials": "JL"}, {"family": "Nystr\u00f6m", "given": "Thomas", "initials": "T"}, {"family": "Widlund", "given": "Per O", "initials": "PO"}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "298", "issue": "11", "pages": "102476", "issn-l": "0021-9258"}, "abstract": "The accumulation of misfolded proteins is a hallmark of aging and many neurodegenerative diseases, making it important to understand how the cellular machinery recognizes and processes such proteins. A key question in this respect is whether misfolded proteins are handled in a similar way regardless of their genetic origin. To approach this question, we compared how three different misfolded proteins, guk1-7, gus1-3, and pro3-1, are handled by the cell. We show that all three are nontoxic, even though highly overexpressed, highlighting their usefulness in analyzing the cellular response to misfolding in the absence of severe stress. We found significant differences between the aggregation and disaggregation behavior of the misfolded proteins. Specifically, gus1-3 formed some aggregates that did not efficiently recruit the protein disaggregase Hsp104 and did not colocalize with the other misfolded reporter proteins. Strikingly, while all three misfolded proteins generally coaggregated and colocalized to specific sites in the cell, disaggregation was notably different; the rate of aggregate clearance of pro3-1 was faster than that of the other misfolded proteins, and its clearance rate was not hindered when pro3-1 colocalized with a slowly resolved misfolded protein. Finally, we observed using super-resolution light microscopy as well as immunogold labeling EM in which both showed an even distribution of the different misfolded proteins within an inclusion, suggesting that misfolding characteristics and remodeling, rather than spatial compartmentalization, allows for differential clearance of these misfolding reporters residing in the same inclusion. Taken together, our results highlight how properties of misfolded proteins can significantly affect processing.", "doi": "10.1016/j.jbc.2022.102476", "pmid": "36096201", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9636550"}, {"db": "pii", "key": "S0021-9258(22)00919-X"}], "notes": [], "created": "2023-02-16T08:26:24.796Z", "modified": "2023-02-16T08:26:24.810Z"}, {"entity": "publication", "iuid": "f31d14aaa42b47d58a36c9a3d82d7097", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f31d14aaa42b47d58a36c9a3d82d7097.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f31d14aaa42b47d58a36c9a3d82d7097"}}, "title": "Multi-transcriptome analysis following an acute skeletal muscle growth stimulus yields tools for discerning global and MYC regulatory networks.", "authors": [{"family": "Murach", "given": "Kevin A", "initials": "KA"}, {"family": "Liu", "given": "Zhengye", "initials": "Z"}, {"family": "Jude", "given": "Baptiste", "initials": "B"}, {"family": "Figueiredo", "given": "Vandre C", "initials": "VC"}, {"family": "Wen", "given": "Yuan", "initials": "Y"}, {"family": "Khadgi", "given": "Sabin", "initials": "S"}, {"family": "Lim", "given": "Seongkyun", "initials": "S"}, {"family": "Morena da Silva", "given": "Francielly", "initials": "F"}, {"family": "Greene", "given": "Nicholas P", "initials": "NP"}, {"family": "Lanner", "given": "Johanna T", "initials": "JT"}, {"family": "McCarthy", "given": "John J", "initials": "JJ"}, {"family": "Vechetti", "given": "Ivan J", "initials": "IJ"}, {"family": "von Walden", "given": "Ferdinand", "initials": "F"}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "298", "issue": "11", "pages": "102515"}, "abstract": "Myc is a powerful transcription factor implicated in epigenetic reprogramming, cellular plasticity, and rapid growth as well as tumorigenesis. Cancer in skeletal muscle is extremely rare despite marked and sustained Myc induction during loading-induced hypertrophy. Here, we investigated global, actively transcribed, stable, and myonucleus-specific transcriptomes following an acute hypertrophic stimulus in mouse plantaris. With these datasets, we define global and Myc-specific dynamics at the onset of mechanical overload-induced muscle fiber growth. Data collation across analyses reveals an under-appreciated role for the muscle fiber in extracellular matrix remodeling during adaptation, along with the contribution of mRNA stability to epigenetic-related transcript levels in muscle. We also identify Runx1 and Ankrd1 (Marp1) as abundant myonucleus-enriched loading-induced genes. We observed that a strong induction of cell cycle regulators including Myc occurs with mechanical overload in myonuclei. Additionally, in vivo Myc-controlled gene expression in the plantaris was defined using a genetic muscle fiber-specific doxycycline-inducible Myc-overexpression model. We determined Myc is implicated in numerous aspects of gene expression during early-phase muscle fiber growth. Specifically, brief induction of Myc protein in muscle represses Reverb\u03b1, Reverb\u03b2, and Myh2 while increasing Rpl3, recapitulating gene expression in myonuclei during acute overload. Experimental, comparative, and in silico analyses place Myc at the center of a stable and actively transcribed, loading-responsive, muscle fiber-localized regulatory hub. Collectively, our experiments are a roadmap for understanding global and Myc-mediated transcriptional networks that regulate rapid remodeling in postmitotic cells. We provide open webtools for exploring the five RNA-seq datasets as a resource to the field.", "doi": "10.1016/j.jbc.2022.102515", "pmid": "36150502", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9583450"}, {"db": "pii", "key": "S0021-9258(22)00958-9"}], "notes": [], "created": "2022-12-19T10:39:21.302Z", "modified": "2023-10-16T12:43:38.308Z"}, {"entity": "publication", "iuid": "82e90fe9450b4b63bb11a621bfbf5af2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82e90fe9450b4b63bb11a621bfbf5af2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82e90fe9450b4b63bb11a621bfbf5af2"}}, "title": "Characterization of novel nonacid glycosphingolipids as biomarkers of human gastric adenocarcinoma.", "authors": [{"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Teneberg", "given": "Susann", "initials": "S"}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "298", "issue": "4", "pages": "101732"}, "abstract": "Changes in glycosphingolipid structures have been shown to occur during the development of several types of human cancers, generating cancer-specific carbohydrate structures that could be used as biomarkers for diagnosis and therapeutic targeting. In this study, we characterized nonacid glycosphingolipids isolated from a human gastric adenocarcinoma by mass spectrometry, enzymatic hydrolysis, and by binding with a battery of carbohydrate-recognizing ligands. We show that the majority of the complex nonacid glycosphingolipids had type 2 (Gal\u03b24GlcNAc) core chains (neolactotetraosylceramide, the Lex, H type 2, x2, and the P1 pentaosylceramides, and the Ley, A type 2, and neolacto hexaosylceramides). We also found glycosphingolipids with type 1 (Gal\u03b23GlcNAc) core (lactotetraosylceramide and the H type 1 pentaosylceramide) and globo (Gal\u03b1Gal) core chains (globotriaosylceramide and globotetraosylceramide). Interestingly, we characterized two complex glycosphingolipids as a P1 heptaosylceramide (Gal\u03b14Gal\u03b24GlcNAc\u03b23Gal\u03b24GlcNAc\u03b23Gal \u03b24Glc\u03b21Cer) and a branched P1 decaosylceramide (Gal\u03b14Gal \u03b24GlcNAc\u03b23(Gal\u03b14Gal\u03b24GlcNAc\u03b26)Gal\u03b24GlcNAc\u03b23Gal\u03b24Glc \u03b21Cer). These are novel glycosphingolipid structures and the first reported cases of complex glycosphingolipids larger than pentaosylceramide carrying the P1 trisaccharide. We propose that these P1 glycosphingolipids may represent potential biomarkers for the early diagnosis of gastric cancer.", "doi": "10.1016/j.jbc.2022.101732", "pmid": "35176282", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8933711"}, {"db": "pii", "key": "S0021-9258(22)00172-7"}], "notes": [], "created": "2022-11-30T11:57:48.594Z", "modified": "2024-01-16T13:46:29.467Z"}, {"entity": "publication", "iuid": "b919fcbcfc42445690be42dfbb7fdfba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b919fcbcfc42445690be42dfbb7fdfba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b919fcbcfc42445690be42dfbb7fdfba"}}, "title": "ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism.", "authors": [{"family": "Widmark", "given": "Albin", "initials": "A"}, {"family": "Sagredo", "given": "Eduardo A", "initials": "EA"}, {"family": "Karlstr\u00f6m", "given": "Victor", "initials": "V"}, {"family": "Behm", "given": "Mikaela", "initials": "M"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Daniel", "given": "Chammiran", "initials": "C"}, {"family": "\u00d6hman", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "298", "issue": "3", "pages": "101682"}, "abstract": "miRNAs are short noncoding RNA molecules that regulate gene expression by inhibiting translation or inducing degradation of target mRNAs. miRNAs are often expressed as polycistronic transcripts, so-called miRNA clusters, containing several miRNA precursors. The largest mammalian miRNA cluster, the miR-379-410 cluster, is expressed primarily during embryonic development and in the adult brain; however, downstream regulation of this cluster is not well understood. Here, we investigated adenosine deamination to inosine (RNA editing) in the miR-379-410 cluster by adenosine deaminase acting on RNA (ADAR) enzymes as a possible mechanism modulating the expression and activity of these miRNAs in a brain-specific manner. We show that the levels of editing in the majority of mature miRNAs are lower than the editing levels of the corresponding site in primary miRNA precursors. However, for one miRNA, miR-376b-3p, editing was significantly higher in the mature form than in the primary precursor. We found miR-376b-3p maturation is negatively regulated by ADAR2 in an editing activity-independent manner, whereas ADAR1-mediated and ADAR2-mediated editing were observed to be competitive. In addition, the edited miR-376b-3p targets a different set of mRNAs than unedited miR-376b-3p, including 4-aminobutyrate aminotransferase, encoding the enzyme responsible for the catabolism of the neurotransmitter gamma aminobutyric acid (GABA). Expression of edited miR-376b-3p led to increased intracellular GABA levels as well as increased cell surface presentation of GABA type A receptors. Our results indicate that both editing and editing-independent effects modulate the expression of miR-376b-3p, with the potential to regulate GABAergic signaling in the brain.", "doi": "10.1016/j.jbc.2022.101682", "pmid": "35124003", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8892144"}, {"db": "pii", "key": "S0021-9258(22)00122-3"}], "notes": [], "created": "2022-03-29T13:47:29.079Z", "modified": "2024-01-16T13:48:37.394Z"}, {"entity": "publication", "iuid": "e51cc4ad20614595b24ca51fea3eb883", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e51cc4ad20614595b24ca51fea3eb883.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e51cc4ad20614595b24ca51fea3eb883"}}, "title": "The antimicrobial drug pyrimethamine inhibits STAT3 transcriptional activity by targeting the enzyme dihydrofolate reductase.", "authors": [{"family": "Heppler", "given": "Lisa N", "initials": "LN"}, {"family": "Attarha", "given": "Sanaz", "initials": "S"}, {"family": "Persaud", "given": "Rosanne", "initials": "R"}, {"family": "Brown", "given": "Jennifer I", "initials": "JI"}, {"family": "Wang", "given": "Peng", "initials": "P"}, {"family": "Petrova", "given": "Boryana", "initials": "B"}, {"family": "To\u0161i\u0107", "given": "Isidora", "initials": "I"}, {"family": "Burton", "given": "Foster B", "initials": "FB"}, {"family": "Flamand", "given": "Yael", "initials": "Y"}, {"family": "Walker", "given": "Sarah R", "initials": "SR"}, {"family": "Yeh", "given": "Jennifer E", "initials": "JE"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M"}, {"family": "Kanarek", "given": "Naama", "initials": "N"}, {"family": "Page", "given": "Brent D G", "initials": "BDG"}, {"family": "Frank", "given": "David A", "initials": "DA"}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "298", "issue": "2", "pages": "101531"}, "abstract": "Cancer is often characterized by aberrant gene expression patterns caused by the inappropriate activation of transcription factors. Signal transducer and activator of transcription 3 (STAT3) is a key transcriptional regulator of many protumorigenic processes and is persistently activated in many types of human cancer. However, like many transcription factors, STAT3 has proven difficult to target clinically. To address this unmet clinical need, we previously developed a cell-based assay of STAT3 transcriptional activity and performed an unbiased and high-throughput screen of small molecules known to be biologically active in humans. We identified the antimicrobial drug pyrimethamine as a novel and specific inhibitor of STAT3 transcriptional activity. Here, we show that pyrimethamine does not significantly affect STAT3 phosphorylation, nuclear translocation, or DNA binding at concentrations sufficient to inhibit STAT3 transcriptional activity, suggesting a potentially novel mechanism of inhibition. To identify the direct molecular target of pyrimethamine and further elucidate the mechanism of action, we used a new quantitative proteome profiling approach called proteome integral solubility alteration coupled with a metabolomic analysis. We identified human dihydrofolate reductase as a target of pyrimethamine and demonstrated that the STAT3-inhibitory effects of pyrimethamine are the result of a deficiency in reduced folate downstream of dihydrofolate reductase inhibition, implicating folate metabolism in the regulation of STAT3 transcriptional activity. This study reveals a previously unknown regulatory node of the STAT3 pathway that may be important for the development of novel strategies to treat STAT3-driven cancers.", "doi": "10.1016/j.jbc.2021.101531", "pmid": "34953855", "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0021-9258(21)01341-7"}, {"db": "pmc", "key": "PMC8800111"}], "notes": [], "created": "2022-01-01T15:15:16.728Z", "modified": "2024-01-18T23:31:55.905Z"}, {"entity": "publication", "iuid": "56847c644ddb4893a71cad8d4a8d4f6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56847c644ddb4893a71cad8d4a8d4f6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56847c644ddb4893a71cad8d4a8d4f6a"}}, "title": "A missense mutation converts the Na+,K+-ATPase into an ion channel and causes therapy-resistant epilepsy.", "authors": [{"family": "Ygberg", "given": "Sofia", "initials": "S"}, {"family": "Akkuratov", "given": "Evgeny E", "initials": "EE"}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Jans", "given": "Daniel C", "initials": "DC"}, {"family": "Mahato", "given": "Dhani R", "initials": "DR"}, {"family": "Katz", "given": "Adriana", "initials": "A"}, {"family": "Kinoshita", "given": "Paula F", "initials": "PF"}, {"family": "Portal", "given": "Benjamin", "initials": "B"}, {"family": "Nennesmo", "given": "Inger", "initials": "I"}, {"family": "Lindskog", "given": "Maria", "initials": "M"}, {"family": "Karlish", "given": "Steven J D", "initials": "SJD"}, {"family": "Andersson", "given": "Magnus", "initials": "M"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H"}, {"family": "Aperia", "given": "Anita", "initials": "A"}], "type": "journal article", "published": "2021-10-27", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "pages": "101355", "issn-l": "0021-9258"}, "abstract": "The ion pump Na+,K+-ATPase is a critical determinant of neuronal excitability; however, its role in the etiology of diseases of the central nervous system (CNS) is largely unknown. We describe here the molecular phenotype of a Trp931Arg mutation of the Na+,K+-ATPase catalytic \u03b11 subunit in an infant diagnosed with therapy-resistant lethal epilepsy. In addition to the pathological CNS phenotype, we also detected renal wasting of Mg2+. We found that membrane expression of the mutant \u03b11 protein was low, and ion pumping activity was lost. Arginine insertion into membrane proteins can generate water-filled pores in the plasma membrane, and our molecular dynamic (MD) simulations of the principle states of Na+,K+-ATPase transport demonstrated massive water inflow into mutant \u03b11, and destabilization of the ion binding sites. MD simulations also indicated that a water pathway was created between the mutant arginine residue and the cytoplasm, and analysis of oocytes expressing mutant \u03b11 detected a non-specific cation current. Finally, neurons expressing mutant \u03b11 were observed to be depolarized compared to neurons expressing wild type protein, compatible with a lowered threshold for epileptic seizures. The results imply that Na+,K+-ATPase should be considered a neuronal locus minoris resistentia in diseases associated with epilepsy and with loss of plasma membrane integrity.", "doi": "10.1016/j.jbc.2021.101355", "pmid": "34717959", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(21)01161-3"}], "notes": [], "created": "2021-11-22T19:30:19.112Z", "modified": "2021-11-22T19:30:19.118Z"}, {"entity": "publication", "iuid": "5b76361099394032a6d0345aca9e350b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b76361099394032a6d0345aca9e350b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b76361099394032a6d0345aca9e350b"}}, "title": "The IgGFc-binding protein FCGBP is secreted with all GDPH sequences cleaved but maintained by interfragment disulfide bonds.", "authors": [{"family": "Ehrencrona", "given": "Erik", "initials": "E"}, {"family": "van der Post", "given": "Sjoerd", "initials": "S"}, {"family": "Gallego", "given": "Pablo", "initials": "P"}, {"family": "Recktenwald", "given": "Christian V", "initials": "CV"}, {"family": "Rodriguez-Pineiro", "given": "Ana M", "initials": "AM"}, {"family": "Garcia-Bonete", "given": "Maria-Jose", "initials": "MJ"}, {"family": "Trillo-Muyo", "given": "Sergio", "initials": "S"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Malin", "initials": "M"}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC"}, {"family": "Johansson", "given": "Malin E V", "initials": "MEV"}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "297", "issue": "1", "pages": "100871", "issn-l": "0021-9258"}, "abstract": "Mucus forms an important protective barrier that minimizes bacterial contact with the colonic epithelium. Intestinal mucus is organized in a complex network with several specific proteins, including the mucin-2 (MUC2) and the abundant IgGFc-binding protein, FCGBP. FCGBP is expressed in all intestinal goblet cells and is secreted into the mucus. It is comprised of repeated von Willebrand D (vWD) domain assemblies, most of which have a GDPH amino acid sequence that can be autocatalytically cleaved, as previously observed in the mucins MUC2 and mucin-5AC. However, the functions of FCGBP in the mucus are not understood. We show that all vWD domains of FCGBP with a GDPH sequence are cleaved and that these cleavages occur early during biosynthesis in the endoplasmic reticulum. All cleaved fragments, however, remain connected via a disulfide bond within each vWD domain. This cleavage generates a C-terminal-reactive Asp-anhydride that could react with other molecules, such as MUC2, but this was not observed. Quantitative analyses by MS showed that FCGBP was mainly soluble in chaotropic solutions, whereas MUC2 was insoluble, and most of the secreted FCGBP was not covalently bound to MUC2. Although FCGBP has been suggested to bind immunoglobulin G, we were unable to reproduce this binding in vitro using purified proteins. In conclusion, while the function of FCGBP is still unknown, our results suggest that it does not contribute to covalent crosslinking in the mucus, nor incorporate immunoglobulin G into mucus, instead the single disulfide bond linking each fragment could mediate controlled dissociation.", "doi": "10.1016/j.jbc.2021.100871", "pmid": "34126068", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8267560"}, {"db": "pii", "key": "S0021-9258(21)00671-2"}], "notes": [], "created": "2023-02-16T08:15:57.453Z", "modified": "2023-02-16T08:15:57.466Z"}, {"entity": "publication", "iuid": "acc6906ee829461784859115db706458", "links": {"self": {"href": "https://publications.scilifelab.se/publication/acc6906ee829461784859115db706458.json"}, "display": {"href": "https://publications.scilifelab.se/publication/acc6906ee829461784859115db706458"}}, "title": "A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases.", "authors": [{"family": "Kmezik", "given": "Cathleen", "initials": "C"}, {"family": "Mazurkewich", "given": "Scott", "initials": "S"}, {"family": "Meents", "given": "Tomke", "initials": "T"}, {"family": "McKee", "given": "Lauren Sara", "initials": "LS"}, {"family": "Idstr\u00f6m", "given": "Alexander", "initials": "A"}, {"family": "Armeni", "given": "Marina", "initials": "M"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Br\u00e4nd\u00e9n", "given": "Gisela", "initials": "G"}, {"family": "Larsbrink", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2021-03-02", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "296", "issue": null, "pages": "100500"}, "abstract": "The gut microbiota plays a central role in human health by enzymatically degrading dietary fiber and concomitantly excreting short chain fatty acids that are associated with manifold health benefits. The polysaccharide xylan is abundant in dietary fiber but noncarbohydrate decorations hinder efficient cleavage by glycoside hydrolases (GHs) and need to be addressed by carbohydrate esterases (CEs). Enzymes from carbohydrate esterase families 1 and 6 (CE1 and 6) perform key roles in xylan degradation by removing feruloyl and acetate decorations, yet little is known about these enzyme families especially with regard to their diversity in activity. Bacteroidetes bacteria are dominant members of the microbiota and often encode their carbohydrate-active enzymes in multigene polysaccharide utilization loci (PULs). Here we present the characterization of three CEs found in a PUL encoded by the gut Bacteroidete Dysgonomonas mossii. We demonstrate that the CEs are functionally distinct, with one highly efficient CE6 acetyl esterase and two CE1 enzymes with feruloyl esterase activities. One multidomain CE1 enzyme contains two CE1 domains: an N-terminal domain feruloyl esterase, and a C-terminal domain with minimal activity on model substrates. We present the structure of the C-terminal CE1 domain with the carbohydrate-binding module that bridges the two CE1 domains, as well as a complex of the same protein fragment with methyl ferulate. The investment of D. mossii in producing multiple CEs suggests that improved accessibility of xylan for GHs and cleavage of covalent polysaccharide-polysaccharide and lignin-polysaccharide bonds are important enzyme activities in the gut environment.", "doi": "10.1016/j.jbc.2021.100500", "pmid": "33667545", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(21)00276-3"}, {"db": "pmc", "key": "PMC8040265"}], "notes": [], "created": "2022-06-30T09:17:50.958Z", "modified": "2023-04-13T09:08:47.343Z"}, {"entity": "publication", "iuid": "846d39f0d96e40b9b583e4a5b0420bef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/846d39f0d96e40b9b583e4a5b0420bef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/846d39f0d96e40b9b583e4a5b0420bef"}}, "title": "Obesity-associated microbiota contributes to mucus layer defects in genetically obese mice.", "authors": [{"family": "Schroeder", "given": "Bjoern O", "initials": "BO"}, {"family": "Birchenough", "given": "George M H", "initials": "GMH"}, {"family": "Pradhan", "given": "Meenakshi", "initials": "M"}, {"family": "Nystr\u00f6m", "given": "Elisabeth E L", "initials": "EEL"}, {"family": "Henricsson", "given": "Marcus", "initials": "M"}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2020-11-13", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "295", "issue": "46", "pages": "15712-15726", "issn-l": "0021-9258"}, "abstract": "The intestinal mucus layer is a physical barrier separating the tremendous number of gut bacteria from the host epithelium. Defects in the mucus layer have been linked to metabolic diseases, but previous studies predominantly investigated mucus function during high-caloric/low-fiber dietary interventions, thus making it difficult to separate effects mediated directly through diet quality from potential obesity-dependent effects. As such, we decided to examine mucus function in mouse models with metabolic disease to distinguish these factors. Here we show that, in contrast to their lean littermates, genetically obese (ob/ob) mice have a defective inner colonic mucus layer that is characterized by increased penetrability and a reduced mucus growth rate. Exploiting the coprophagic behavior of mice, we next co-housed ob/ob and lean mice to investigate if the gut microbiota contributed to these phenotypes. Co-housing rescued the defect of the mucus growth rate, whereas mucus penetrability displayed an intermediate phenotype in both mouse groups. Of note, non-obese diabetic mice with high blood glucose levels displayed a healthy colonic mucus barrier, indicating that the mucus defect is obesity- rather than glucose-mediated. Thus, our data suggest that the gut microbiota community of obesity-prone mice may regulate obesity-associated defects in the colonic mucosal barrier, even in the presence of dietary fiber.", "doi": "10.1074/jbc.RA120.015771", "pmid": "32900852", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7667970"}, {"db": "pii", "key": "S0021-9258(17)50399-3"}], "notes": [], "created": "2023-02-16T08:09:48.007Z", "modified": "2023-02-16T08:09:48.009Z"}, {"entity": "publication", "iuid": "d3262da1a3d84a52a3326fa53a0aa094", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3262da1a3d84a52a3326fa53a0aa094.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3262da1a3d84a52a3326fa53a0aa094"}}, "title": "A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.", "authors": [{"family": "Mart\u00ednez-Carranza", "given": "Markel", "initials": "M"}, {"family": "Jonna", "given": "Venkateswara Rao", "initials": "VR"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Sahlin", "given": "Margareta", "initials": "M"}, {"family": "Carlson", "given": "Lars-Anders", "initials": "LA"}, {"family": "Jemal", "given": "Newal", "initials": "N"}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M"}, {"family": "Sj\u00f6berg", "given": "Britt-Marie", "initials": "BM", "orcid": "0000-0001-5953-3360", "researcher": {"href": "https://publications.scilifelab.se/researcher/fab276f213364c2eaa6fe3dc5c9b01ff.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Hofer", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2020-11-13", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "295", "issue": "46", "pages": "15576-15587", "issn-l": "0021-9258"}, "abstract": "Ribonucleotide reductase (RNR) is a central enzyme for the synthesis of DNA building blocks. Most aerobic organisms, including nearly all eukaryotes, have class I RNRs consisting of R1 and R2 subunits. The catalytic R1 subunit contains an overall activity site that can allosterically turn the enzyme on or off by the binding of ATP or dATP, respectively. The mechanism behind the ability to turn the enzyme off via the R1 subunit involves the formation of different types of R1 oligomers in most studied species and R1-R2 octamers in Escherichia coli To better understand the distribution of different oligomerization mechanisms, we characterized the enzyme from Clostridium botulinum, which belongs to a subclass of class I RNRs not studied before. The recombinantly expressed enzyme was analyzed by size-exclusion chromatography, gas-phase electrophoretic mobility macromolecular analysis, EM, X-ray crystallography, and enzyme assays. Interestingly, it shares the ability of the E. coli RNR to form inhibited R1-R2 octamers in the presence of dATP but, unlike the E. coli enzyme, cannot be turned off by combinations of ATP and dGTP/dTTP. A phylogenetic analysis of class I RNRs suggests that activity regulation is not ancestral but was gained after the first subclasses diverged and that RNR subclasses with inhibition mechanisms involving R1 oligomerization belong to a clade separated from the two subclasses forming R1-R2 octamers. These results give further insight into activity regulation in class I RNRs as an evolutionarily dynamic process.", "doi": "10.1074/jbc.RA120.014895", "pmid": "32883811", "labels": {"Protein Science Facility (PSF)": "Service", "Cryo-EM": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(17)50390-7"}, {"db": "pmc", "key": "PMC7667963"}, {"db": "PDB", "key": "2RCC"}, {"db": "PDB", "key": "6W4X"}, {"db": "PDB", "key": "5CNS"}], "notes": [], "created": "2020-10-03T13:43:28.482Z", "modified": "2024-01-16T13:48:41.347Z"}, {"entity": "publication", "iuid": "e173e02b94644b7b8a5040986accb4a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e173e02b94644b7b8a5040986accb4a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e173e02b94644b7b8a5040986accb4a0"}}, "title": "Generation and validation of recombinant antibodies to study human aminoacyl-tRNA synthetases.", "authors": [{"family": "Preger", "given": "Charlotta", "initials": "C"}, {"family": "Wigren", "given": "Edvard", "initials": "E", "orcid": "0000-0002-7933-0939", "researcher": {"href": "https://publications.scilifelab.se/researcher/c844b8d4d0554443b369f6c0f128ea7e.json"}}, {"family": "Ossipova", "given": "Elena", "initials": "E"}, {"family": "Marks", "given": "Carolyn", "initials": "C"}, {"family": "Lengqvist", "given": "Johan", "initials": "J"}, {"family": "Hofstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Andersson", "given": "Oskar", "initials": "O"}, {"family": "Jakobsson", "given": "Per-Johan", "initials": "PJ", "orcid": "0000-0001-7665-9715", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb148e2233b4541bc7c8b340f0cf12c.json"}}, {"family": "Gr\u00e4slund", "given": "Susanne", "initials": "S"}, {"family": "Persson", "given": "Helena", "initials": "H", "orcid": "0000-0002-2965-0395", "researcher": {"href": "https://publications.scilifelab.se/researcher/971d18bca1874c9cb8630c15c530c11d.json"}}], "type": "journal article", "published": "2020-10-09", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "295", "issue": "41", "pages": "13981-13993"}, "abstract": "Aminoacyl-tRNA synthetases (aaRSs) have long been viewed as mere housekeeping proteins and have therefore often been overlooked in drug discovery. However, recent findings have revealed that many aaRSs have noncanonical functions, and several of the aaRSs have been linked to autoimmune diseases, cancer, and neurological disorders. Deciphering these roles has been challenging because of a lack of tools to enable their study. To help solve this problem, we have generated recombinant high-affinity antibodies for a collection of thirteen cytoplasmic and one mitochondrial aaRSs. Selected domains of these proteins were produced recombinantly in Escherichia coli and used as antigens in phage display selections using a synthetic human single-chain fragment variable library. All targets yielded large sets of antibody candidates that were validated through a panel of binding assays against the purified antigen. Furthermore, the top-performing binders were tested in immunoprecipitation followed by MS for their ability to capture the endogenous protein from mammalian cell lysates. For antibodies targeting individual members of the multi-tRNA synthetase complex, we were able to detect all members of the complex, co-immunoprecipitating with the target, in several cell types. The functionality of a subset of binders for each target was also confirmed using immunofluorescence. The sequences of these proteins have been deposited in publicly available databases and repositories. We anticipate that this open source resource, in the form of high-quality recombinant proteins and antibodies, will accelerate and empower future research of the role of aaRSs in health and disease.", "doi": "10.1074/jbc.RA120.012893", "pmid": "32817337", "labels": {"Autoimmunity and Serology Profiling": "Service", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0021-9258(17)49797-3"}, {"db": "pmc", "key": "PMC7549041"}], "notes": [], "created": "2020-12-02T15:16:20.268Z", "modified": "2025-10-17T13:05:07.951Z"}, {"entity": "publication", "iuid": "911de50d46654337a749860d7a8635b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/911de50d46654337a749860d7a8635b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/911de50d46654337a749860d7a8635b1"}}, "title": "Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target.", "authors": [{"family": "\u0160kerlov\u00e1", "given": "Jana", "initials": "J", "orcid": "0000-0002-9579-4047", "researcher": {"href": "https://publications.scilifelab.se/researcher/cde5c1c6ccb94ca3be0b092771e67524.json"}}, {"family": "Unterlass", "given": "Judith", "initials": "J"}, {"family": "G\u00f6ttmann", "given": "Mona", "initials": "M"}, {"family": "Marttila", "given": "Petra", "initials": "P", "orcid": "0000-0002-0115-8067", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3e92bdf843456784f98d3b521d2ccd.json"}}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS", "orcid": "0000-0002-7550-1833", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd07c6c543544af1a904e039f73ba857.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}], "type": "journal article", "published": "2020-08-14", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "295", "issue": "33", "pages": "11656-11668", "issn-l": "0021-9258"}, "abstract": "The bifunctional human enzyme phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase (PAICS) catalyzes two essential steps in the de novo purine biosynthesis pathway. PAICS is overexpressed in many cancers and could be a promising target for the development of cancer therapeutics. Here, using gene knockdowns and clonogenic survival and cell viability assays, we demonstrate that PAICS is required for growth and survival of prostate cancer cells. PAICS catalyzes the carboxylation of aminoimidazole ribonucleotide (AIR) and the subsequent conversion of carboxyaminoimidazole ribonucleotide (CAIR) and l-aspartate to N-succinylcarboxamide-5-aminoimidazole ribonucleotide (SAICAR). Of note, we present the first structures of human octameric PAICS in complexes with native ligands. In particular, we report the structure of PAICS with CAIR bound in the active sites of both domains and SAICAR bound in one of the SAICAR synthetase domains. Moreover, we report the PAICS structure with SAICAR and an ATP analog occupying the SAICAR synthetase active site. These structures provide insight into substrate and product binding and the architecture of the active sites, disclosing important structural information for rational design of PAICS inhibitors as potential anticancer drugs.", "doi": "10.1074/jbc.RA120.013695", "pmid": "32571877", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(17)48465-1"}, {"db": "pmc", "key": "PMC7450103"}, {"db": "PDB", "key": "5clj"}, {"db": "PDB", "key": "2h31"}, {"db": "PDB", "key": "4ja0"}, {"db": "PDB", "key": "3rgg"}, {"db": "PDB", "key": "2nsl"}, {"db": "PDB", "key": "2gqs"}, {"db": "PDB", "key": "4fe2"}, {"db": "PDB", "key": "4o7w"}, {"db": "PDB", "key": "2z02"}, {"db": "PDB", "key": "2cnv"}, {"db": "PDB", "key": "2cnu"}, {"db": "PDB", "key": "1obd"}], "notes": [], "created": "2020-10-03T09:58:37.898Z", "modified": "2021-11-10T12:48:19.342Z"}, {"entity": "publication", "iuid": "8e937f3dda6749c9b966dfb4fc501d72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e937f3dda6749c9b966dfb4fc501d72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e937f3dda6749c9b966dfb4fc501d72"}}, "title": "Unveiling the activation dynamics of a fold-switch bacterial glycosyltransferase by 19F NMR.", "authors": [{"family": "Liebau", "given": "Jobst", "initials": "J", "orcid": "0000-0003-4057-6699", "researcher": {"href": "https://publications.scilifelab.se/researcher/65f4fc23bfb94c66a696b10c9469dc56.json"}}, {"family": "Tersa", "given": "Montse", "initials": "M", "orcid": "0000-0002-2370-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd95e469b377450980c3e9db0ce63335.json"}}, {"family": "Trastoy", "given": "Beatriz", "initials": "B"}, {"family": "Patrick", "given": "Joan", "initials": "J"}, {"family": "Rodrigo-Unzueta", "given": "Ane", "initials": "A"}, {"family": "Corzana", "given": "Francisco", "initials": "F", "orcid": "0000-0001-5597-8127", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6fbae0b56747c08573c37ef5620244.json"}}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Guerin", "given": "Marcelo E", "initials": "ME"}, {"family": "M\u00e4ler", "given": "Lena", "initials": "L", "orcid": "0000-0002-9464-4311", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bfca98ce500442788b18afe2c656c53.json"}}], "type": "journal article", "published": "2020-07-17", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "295", "issue": "29", "pages": "9868-9878", "issn-l": "0021-9258"}, "abstract": "Fold-switch pathways remodel the secondary structure topology of proteins in response to the cellular environment. It is a major challenge to understand the dynamics of these folding processes. Here, we conducted an in-depth analysis of the \u03b1-helix-to-\u03b2-strand and \u03b2-strand-to-\u03b1-helix transitions and domain motions displayed by the essential mannosyltransferase PimA from mycobacteria. Using 19F NMR, we identified four functionally relevant states of PimA that coexist in dynamic equilibria on millisecond-to-second timescales in solution. We discovered that fold-switching is a slow process, on the order of seconds, whereas domain motions occur simultaneously but are substantially faster, on the order of milliseconds. Strikingly, the addition of substrate accelerated the fold-switching dynamics of PimA. We propose a model in which the fold-switching dynamics constitute a mechanism for PimA activation.", "doi": "10.1074/jbc.RA120.014162", "pmid": "32434931", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0021-9258(17)48929-0"}, {"db": "pmc", "key": "PMC7380196"}, {"db": "PDB", "key": "4NC9"}, {"db": "PDB", "key": "2GEJ"}], "notes": [], "created": "2020-11-24T20:27:10.865Z", "modified": "2025-10-17T13:03:56.779Z"}, {"entity": "publication", "iuid": "ca0a1a89785f44708ab634c2b1b2b13c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca0a1a89785f44708ab634c2b1b2b13c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca0a1a89785f44708ab634c2b1b2b13c"}}, "title": "MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool.", "authors": [{"family": "Scaletti", "given": "Emma Rose", "initials": "ER"}, {"family": "Vallin", "given": "Karl S", "initials": "KS"}, {"family": "Br\u00e4utigam", "given": "Lars", "initials": "L"}, {"family": "Sarno", "given": "Antonio", "initials": "A", "orcid": "0000-0002-9308-8018", "researcher": {"href": "https://publications.scilifelab.se/researcher/f47cb410dce04c30bf70b85c6633d72f.json"}}, {"family": "Warpman Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS", "orcid": "0000-0002-7550-1833", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd07c6c543544af1a904e039f73ba857.json"}}], "type": "journal article", "published": "2020-04-10", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "295", "issue": "15", "pages": "4761-4772", "issn-l": "0021-9258"}, "abstract": "MutT homologue 1 (MTH1) removes oxidized nucleotides from the nucleotide pool and thereby prevents their incorporation into the genome and thereby reduces genotoxicity. We previously reported that MTH1 is an efficient catalyst of O6-methyl-dGTP hydrolysis suggesting that MTH1 may also sanitize the nucleotide pool from other methylated nucleotides. We here show that MTH1 efficiently catalyzes the hydrolysis of N6-methyl-dATP to N6-methyl-dAMP and further report that N6-methylation of dATP drastically increases the MTH1 activity. We also observed MTH1 activity with N6-methyl-ATP, albeit at a lower level. We show that N6-methyl-dATP is incorporated into DNA in vivo, as indicated by increased N6-methyl-dA DNA levels in embryos developed from MTH1 knock-out zebrafish eggs microinjected with N6-methyl-dATP compared with noninjected embryos. N6-methyl-dATP activity is present in MTH1 homologues from distantly related vertebrates, suggesting evolutionary conservation and indicating that this activity is important. Of note, N6-methyl-dATP activity is unique to MTH1 among related NUDIX hydrolases. Moreover, we present the structure of N6-methyl-dAMP-bound human MTH1, revealing that the N6-methyl group is accommodated within a hydrophobic active-site subpocket explaining why N6-methyl-dATP is a good MTH1 substrate. N6-methylation of DNA and RNA has been reported to have epigenetic roles and to affect mRNA metabolism. We propose that MTH1 acts in concert with adenosine deaminase-like protein isoform 1 (ADAL1) to prevent incorporation of N6-methyl-(d)ATP into DNA and RNA. This would hinder potential dysregulation of epigenetic control and RNA metabolism via conversion of N6-methyl-(d)ATP to N6-methyl-(d)AMP, followed by ADAL1-catalyzed deamination producing (d)IMP that can enter the nucleotide salvage pathway.", "doi": "10.1074/jbc.RA120.012636", "pmid": "32144205", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(17)48573-5"}, {"db": "pmc", "key": "PMC7152754"}, {"db": "PDB", "key": "3ZR1"}, {"db": "PDB", "key": "3ZR0"}, {"db": "PDB", "key": "5OTM"}, {"db": "PDB", "key": "6QVO"}, {"db": "PDB", "key": "5OTN"}, {"db": "PDB", "key": "6FL4"}, {"db": "PDB", "key": "3A6T"}], "notes": [], "created": "2020-03-12T14:06:48.859Z", "modified": "2021-11-10T12:52:10.141Z"}, {"entity": "publication", "iuid": "9ff6a9ca6c4547029de2deb69bc4b826", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ff6a9ca6c4547029de2deb69bc4b826.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ff6a9ca6c4547029de2deb69bc4b826"}}, "title": "Structural and biochemical studies of the glucuronoyl esterase OtCE15A illuminate its interaction with lignocellulosic components.", "authors": [{"family": "Mazurkewich", "given": "Scott", "initials": "S"}, {"family": "Poulsen", "given": "Jens-Christian N", "initials": "JN"}, {"family": "Lo Leggio", "given": "Leila", "initials": "L"}, {"family": "Larsbrink", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2019-12-27", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "294", "issue": "52", "pages": "19978-19987", "issn-l": "0021-9258"}, "abstract": "Glucuronoyl esterases (GEs) catalyze the cleavage of ester linkages between lignin and glucuronic acid moieties on glucuronoxylan in plant biomass. As such, GEs represent promising biochemical tools in industrial processing of these recalcitrant resources. However, details on how GEs interact and catalyze degradation of their natural substrates are sparse, calling for thorough enzyme structure-function studies. Presented here is a structural and mechanistic investigation of the bacterial GE OtCE15A. GEs belong to the carbohydrate esterase family 15 (CE15), which is in turn part of the larger \u03b1/\u03b2-hydrolase superfamily. GEs contain a Ser-His-Asp/Glu catalytic triad, but the location of the catalytic acid in GEs has been shown to be variable, and OtCE15A possesses two putative catalytic acidic residues in the active site. Through site-directed mutagenesis, we demonstrate that these residues are functionally redundant, possibly indicating the evolutionary route toward new functionalities within the family. Structures determined with glucuronate, in both native and covalently bound intermediate states, and galacturonate provide insights into the catalytic mechanism of CE15. A structure of OtCE15A with the glucuronoxylooligosaccharide 23-(4-O-methyl-\u03b1-d-glucuronyl)-xylotriose (commonly referred to as XUX) shows that the enzyme can indeed interact with polysaccharides from the plant cell wall, and an additional structure with the disaccharide xylobiose revealed a surface binding site that could possibly indicate a recognition mechanism for long glucuronoxylan chains. Collectively, the results indicate that OtCE15A, and likely most of the CE15 family, can utilize esters of glucuronoxylooligosaccharides and support the proposal that these enzymes work on lignin-carbohydrate complexes in plant biomass.", "doi": "10.1074/jbc.RA119.011435", "pmid": "31740581", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "RA119.011435"}, {"db": "pmc", "key": "PMC6937553"}, {"db": "PDB", "key": "6GS0"}, {"db": "PDB", "key": "6HSW"}, {"db": "PDB", "key": "4G4G"}, {"db": "PDB", "key": "4G4J"}, {"db": "PDB", "key": "6SYR"}, {"db": "PDB", "key": "6SYV"}, {"db": "PDB", "key": "6T0E"}, {"db": "PDB", "key": "6SZ0"}, {"db": "PDB", "key": "6SZ4"}, {"db": "PDB", "key": "6SZO"}, {"db": "PDB", "key": "6T0I"}, {"db": "PDB", "key": "6SYU"}], "notes": [], "created": "2020-01-30T15:58:44.187Z", "modified": "2024-01-16T13:46:31.047Z"}, {"entity": "publication", "iuid": "ea5f24f5fbcb42c6b7012e20724fe78f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea5f24f5fbcb42c6b7012e20724fe78f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea5f24f5fbcb42c6b7012e20724fe78f"}}, "title": "Calcium-activated chloride channel regulator 1 (CLCA1) forms non-covalent oligomers in colonic mucus and has mucin 2-processing properties.", "authors": [{"family": "Nystr\u00f6m", "given": "Elisabeth E L", "initials": "EEL", "orcid": "0000-0002-6970-7894", "researcher": {"href": "https://publications.scilifelab.se/researcher/09bd302f8a1341f6a1a5aaf3bfe94a94.json"}}, {"family": "Arike", "given": "Liisa", "initials": "L"}, {"family": "Ehrencrona", "given": "Erik", "initials": "E"}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC", "orcid": "0000-0002-1900-1869", "researcher": {"href": "https://publications.scilifelab.se/researcher/44b3815603154322a6dac16f2fc1c1e9.json"}}, {"family": "Johansson", "given": "Malin E V", "initials": "MEV", "orcid": "0000-0002-4237-6677", "researcher": {"href": "https://publications.scilifelab.se/researcher/520dab35c19049c8b3f1083a92e60d56.json"}}], "type": "journal article", "published": "2019-11-08", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "294", "issue": "45", "pages": "17075-17089", "issn-l": "0021-9258"}, "abstract": "Calcium-activated chloride channel regulator 1 (CLCA1) is one of the major nonmucin proteins found in intestinal mucus. It is part of a larger family of CLCA proteins that share highly conserved features and domain architectures. The CLCA domain arrangement is similar to proteins belonging to the ADAM (a disintegrin and metalloproteinase) family, known to process extracellular matrix proteins. Therefore, CLCA1 is an interesting candidate in the search for proteases that process intestinal mucus. Here, we investigated CLCA1's biochemical properties both in vitro and in mucus from mouse and human colon biopsy samples. Using immunoblotting with CLCA1-specific antibodies and recombinant proteins, we observed that the CLCA1 C-terminal self-cleavage product forms a disulfide-linked dimer that noncovalently interacts with the N-terminal part of CLCA1, which further interacts to form oligomers. We also characterized a second, more catalytically active, N-terminal product of CLCA1, encompassing the catalytic domain together with its von Willebrand domain type A (VWA). This fragment was unstable but could be identified in freshly prepared mucus. Furthermore, we found that CLCA1 can cleave the N-terminal part of the mucus structural component MUC2. We propose that CLCA1 regulates the structural arrangement of the mucus and thereby takes part in the regulation of mucus processing.", "doi": "10.1074/jbc.RA119.009940", "pmid": "31570526", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(20)30545-7"}, {"db": "pmc", "key": "PMC6851300"}], "notes": [], "created": "2020-01-23T16:07:41.394Z", "modified": "2021-06-16T16:19:47.303Z"}, {"entity": "publication", "iuid": "104f03d669d3488e9f3326a8ef82542b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/104f03d669d3488e9f3326a8ef82542b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/104f03d669d3488e9f3326a8ef82542b"}}, "title": "The SH3 domains of the protein kinases ITK and LCK compete for adjacent sites on T cell-specific adapter protein.", "authors": [{"family": "Andersen", "given": "Thorny Cesilie Bie", "initials": "TCB"}, {"family": "Kristiansen", "given": "Per Eugen", "initials": "PE"}, {"family": "Huszenicza", "given": "Zsuzsa", "initials": "Z"}, {"family": "Johansson", "given": "Maria U", "initials": "MU"}, {"family": "Gopalakrishnan", "given": "Ramakrishna Prabhu", "initials": "RP"}, {"family": "Kjelstrup", "given": "Hanna", "initials": "H"}, {"family": "Boyken", "given": "Scott", "initials": "S"}, {"family": "Sundvold-Gjerstad", "given": "Vibeke", "initials": "V"}, {"family": "Granum", "given": "Stine", "initials": "S"}, {"family": "S\u00f8rli", "given": "Morten", "initials": "M"}, {"family": "Backe", "given": "Paul Hoff", "initials": "PH"}, {"family": "Fulton", "given": "D Bruce", "initials": "DB"}, {"family": "Karlsson", "given": "B G\u00f6ran", "initials": "BG"}, {"family": "Andreotti", "given": "Amy H", "initials": "AH"}, {"family": "Spurkland", "given": "Anne", "initials": "A", "orcid": "0000-0003-4421-0766", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fde22f7f7ef431c9beeea7e72139711.json"}}], "type": "journal article", "published": "2019-10-18", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "294", "issue": "42", "pages": "15480-15494", "issn-l": "0021-9258"}, "abstract": "T-cell activation requires stimulation of specific intracellular signaling pathways in which protein-tyrosine kinases, phosphatases, and adapter proteins interact to transmit signals from the T-cell receptor to the nucleus. Interactions of LCK proto-oncogene, SRC family tyrosine kinase (LCK), and the IL-2-inducible T cell kinase (ITK) with the T cell-specific adapter protein (TSAD) promotes LCK-mediated phosphorylation and thereby ITK activation. Both ITK and LCK interact with TSAD's proline-rich region (PRR) through their Src homology 3 (SH3) domains. Whereas LCK may also interact with TSAD through its SH2 domain, ITK interacts with TSAD only through its SH3 domain. To begin to understand on a molecular level how the LCK SH3 and ITK SH3 domains interact with TSAD in human HEK293T cells, here we combined biochemical analyses with NMR spectroscopy. We found that the ITK and LCK SH3 domains potentially have adjacent and overlapping binding sites within the TSAD PRR amino acids (aa) 239-274. Pulldown experiments and NMR spectroscopy revealed that both domains may bind to TSAD aa 239-256 and aa 257-274. Co-immunoprecipitation experiments further revealed that both domains may also bind simultaneously to TSAD aa 242-268. Accordingly, NMR spectroscopy indicated that the SH3 domains may compete for these two adjacent binding sites. We propose that once the associations of ITK and LCK with TSAD promote the ITK and LCK interaction, the interactions among TSAD, ITK, and LCK are dynamically altered by ITK phosphorylation status.", "doi": "10.1074/jbc.RA119.008318", "pmid": "31484725", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6802506"}, {"db": "pii", "key": "S0021-9258(20)33788-1"}, {"db": "PDB", "key": "2LMJ"}, {"db": "PDB", "key": "2RNA"}, {"db": "PDB", "key": "2YUQ"}], "notes": [], "created": "2023-05-31T16:50:17.060Z", "modified": "2025-10-17T13:03:57.461Z"}, {"entity": "publication", "iuid": "88baa504cc264b93ab15a9cc08b1f5d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88baa504cc264b93ab15a9cc08b1f5d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88baa504cc264b93ab15a9cc08b1f5d0"}}, "title": "E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2.", "authors": [{"family": "Anandapadamanaban", "given": "Madhanagopal", "initials": "M"}, {"family": "Kyriakidis", "given": "Nikolaos C", "initials": "NC"}, {"family": "Csizm\u00f3k", "given": "Veronika", "initials": "V"}, {"family": "Wallenhammar", "given": "Am\u00e9lie", "initials": "A"}, {"family": "Espinosa", "given": "Alexander C", "initials": "AC"}, {"family": "Ahlner", "given": "Alexandra", "initials": "A"}, {"family": "Round", "given": "Adam R", "initials": "AR"}, {"family": "Trewhella", "given": "Jill", "initials": "J"}, {"family": "Moche", "given": "Martin", "initials": "M"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2019-07-26", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "294", "issue": "30", "pages": "11404-11419", "issn-l": "0021-9258"}, "abstract": "The E3 ubiquitin-protein ligase TRIM21, of the RING-containing tripartite motif (TRIM) protein family, is a major autoantigen in autoimmune diseases and a modulator of innate immune signaling. Together with ubiquitin-conjugating enzyme E2 E1 (UBE2E1), TRIM21 acts both as an E3 ligase and as a substrate in autoubiquitination. We here report a 2.82-\u00c5 crystal structure of the human TRIM21 RING domain in complex with the human E2-conjugating UBE2E1 enzyme, in which a ubiquitin-targeted TRIM21 substrate lysine was captured in the UBE2E1 active site. The structure revealed that the direction of lysine entry is similar to that described for human proliferating cell nuclear antigen (PCNA), a small ubiquitin-like modifier (SUMO)-targeted substrate, and thus differs from the canonical SUMO-targeted substrate entry. In agreement, we found that critical UBE2E1 residues involved in the capture of the TRIM21 substrate lysine are conserved in ubiquitin-conjugating E2s, whereas residues critical for SUMOylation are not conserved. We noted that coordination of the acceptor lysine leads to remodeling of amino acid side-chain interactions between the UBE2E1 active site and the E2-E3 direct interface, including the so-called \"linchpin\" residue conserved in RING E3s and required for ubiquitination. The findings of our work support the notion that substrate lysine activation of an E2-E3-connecting allosteric path may trigger catalytic activity and contribute to the understanding of specific lysine targeting by ubiquitin-conjugating E2s.", "doi": "10.1074/jbc.RA119.008485", "pmid": "31160341", "labels": {"Protein Science Facility (PSF)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "RA119.008485"}, {"db": "pmc", "key": "PMC6663867"}, {"db": "PDB", "key": "6FGA"}, {"db": "PDB", "key": "5LBN"}], "notes": [], "created": "2020-10-03T10:21:45.807Z", "modified": "2020-10-03T10:23:08.000Z"}, {"entity": "publication", "iuid": "f7dda86f0d594272a6715566780299cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f7dda86f0d594272a6715566780299cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f7dda86f0d594272a6715566780299cb"}}, "title": "Pyroglutamation of amyloid-\u03b2x-42 (A\u03b2x-42) followed by A\u03b21-40 deposition underlies plaque polymorphism in progressing Alzheimer's disease pathology.", "authors": [{"family": "Michno", "given": "Wojciech", "initials": "W"}, {"family": "Nystr\u00f6m", "given": "Sofie", "initials": "S"}, {"family": "Wehrli", "given": "Patrick", "initials": "P"}, {"family": "Lashley", "given": "Tammaryn", "initials": "T"}, {"family": "Brinkmalm", "given": "Gunnar", "initials": "G"}, {"family": "Guerard", "given": "Laurent", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "Stina", "initials": "S"}, {"family": "Sehlin", "given": "Dag", "initials": "D"}, {"family": "Kaya", "given": "Ibrahim", "initials": "I"}, {"family": "Brinet", "given": "Dimitri", "initials": "D"}, {"family": "Nilsson", "given": "K Peter R", "initials": "KPR"}, {"family": "Hammarstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Hanrieder", "given": "J\u00f6rg", "initials": "J", "orcid": "0000-0001-6059-198X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e65454100674f98bf8f2575093f2441.json"}}], "type": "journal article", "published": "2019-04-26", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "294", "issue": "17", "pages": "6719-6732", "issn-l": "0021-9258"}, "abstract": "Amyloid-\u03b2 (A\u03b2) pathology in Alzheimer's disease (AD) is characterized by the formation of polymorphic deposits comprising diffuse and cored plaques. Because diffuse plaques are predominantly observed in cognitively unaffected, amyloid-positive (CU-AP) individuals, pathogenic conversion into cored plaques appears to be critical to AD pathogenesis. Herein, we identified the distinct A\u03b2 species associated with amyloid polymorphism in brain tissue from individuals with sporadic AD (s-AD) and CU-AP. To this end, we interrogated A\u03b2 polymorphism with amyloid conformation-sensitive dyes and a novel in situ MS paradigm for chemical characterization of hyperspectrally delineated plaque morphotypes. We found that maturation of diffuse into cored plaques correlated with increased A\u03b21-40 deposition. Using spatial in situ delineation with imaging MS (IMS), we show that A\u03b21-40 aggregates at the core structure of mature plaques, whereas A\u03b21-42 localizes to diffuse amyloid aggregates. Moreover, we observed that diffuse plaques have increased pyroglutamated A\u03b2x-42 levels in s-AD but not CU-AP, suggesting an AD pathology-related, hydrophobic functionalization of diffuse plaques facilitating A\u03b21-40 deposition. Experiments in tgAPPSwe mice verified that, similar to what has been observed in human brain pathology, diffuse deposits display higher levels of A\u03b21-42 and that A\u03b2 plaque maturation over time is associated with increases in A\u03b21-40. Finally, we found that A\u03b21-40 deposition is characteristic for cerebral amyloid angiopathy deposition and maturation in both humans and mice. These results indicate that N-terminal A\u03b2x-42 pyroglutamation and A\u03b21-40 deposition are critical events in priming and maturation of pathogenic A\u03b2 from diffuse into cored plaques, underlying neurotoxic plaque development in AD.", "doi": "10.1074/jbc.RA118.006604", "pmid": "30814252", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(20)36610-2"}, {"db": "pmc", "key": "PMC6497931"}], "notes": [], "created": "2020-01-23T16:09:06.452Z", "modified": "2021-06-21T12:01:24.675Z"}, {"entity": "publication", "iuid": "e7af44ad2338461685c9091f4814e6d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7af44ad2338461685c9091f4814e6d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7af44ad2338461685c9091f4814e6d6"}}, "title": "The endoplasmic reticulum-resident collagen chaperone Hsp47 interacts with and promotes the secretion of decorin, fibromodulin, and lumican.", "authors": [{"family": "Ishikawa", "given": "Yoshihiro", "initials": "Y"}, {"family": "Rubin", "given": "Kristofer", "initials": "K"}, {"family": "B\u00e4chinger", "given": "Hans Peter", "initials": "HP"}, {"family": "Kalamajski", "given": "Sebastian", "initials": "S"}], "type": "journal article", "published": "2018-08-31", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "293", "issue": "35", "pages": "13707-13716", "issn-l": "0021-9258"}, "abstract": "The build-up of diversified and tissue-specific assemblies of extracellular matrix (ECM) proteins depends on secreted and cell surface-located molecular arrays that coordinate ECM proteins into discrete designs. The family of small leucine-rich proteins (SLRPs) associates with and dictates the structure of fibrillar collagens, which form the backbone of most ECM types. However, whether SLRPs form complexes with proteins other than collagens is unclear. Here, we demonstrate that heat shock protein 47 (Hsp47), a well-established endoplasmic reticulum-resident collagen chaperone, also binds the SLRPs decorin, lumican, and fibromodulin with affinities comparable with that in the Hsp47-type I collagen interaction. Furthermore, we show that a lack of Hsp47 inhibits the cellular secretion of decorin and lumican. Our results expand the understanding of the concerted molecular interactions that control the secretion and organization of a functional collagenous ECM.", "doi": "10.1074/jbc.RA117.000758", "pmid": "30002123", "labels": {"PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "RA117.000758"}, {"db": "pmc", "key": "PMC6120207"}], "notes": [], "created": "2020-01-07T14:47:20.430Z", "modified": "2023-04-14T13:56:03.188Z"}, {"entity": "publication", "iuid": "8ae151f05c28432eb5948e6c2e8dc8c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ae151f05c28432eb5948e6c2e8dc8c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ae151f05c28432eb5948e6c2e8dc8c3"}}, "title": "A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant.", "authors": [{"family": "Rozman Grinberg", "given": "Inna", "initials": "I"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Sahlin", "given": "Margareta", "initials": "M"}, {"family": "Crona", "given": "Mikael", "initials": "M"}, {"family": "Berggren", "given": "Gustav", "initials": "G"}, {"family": "Hofer", "given": "Anders", "initials": "A"}, {"family": "Sj\u00f6berg", "given": "Britt-Marie", "initials": "BM"}], "type": "journal article", "published": "2018-08-30", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": null, "issue": null, "issn-l": "0021-9258"}, "abstract": "Class I ribonucleotide reductase (RNR) consists of a catalytic subunit (NrdA) and a radical-generating subunit (NrdB) that together catalyze reduction of ribonucleotides to their corresponding deoxyribonucleotides. NrdB from the firmicute ", "doi": "10.1074/jbc.RA118.004991", "pmid": "30166338", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pii", "key": "RA118.004991"}], "notes": [], "created": "2018-09-07T09:22:41.717Z", "modified": "2018-09-07T09:22:41.720Z"}, {"entity": "publication", "iuid": "986a85ff0c9341799d534540d5a34c47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/986a85ff0c9341799d534540d5a34c47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/986a85ff0c9341799d534540d5a34c47"}}, "title": "LC-MS/MS characterization of xyloside-primed glycosaminoglycans with cytotoxic properties reveals structural diversity and novel glycan modifications.", "authors": [{"family": "Persson", "given": "Andrea", "initials": "A"}, {"family": "Gomez Toledo", "given": "Alejandro", "initials": "A"}, {"family": "Vorontsov", "given": "Egor", "initials": "E"}, {"family": "Nasir", "given": "Waqas", "initials": "W"}, {"family": "Will\u00e9n", "given": "Daniel", "initials": "D"}, {"family": "Noborn", "given": "Fredrik", "initials": "F"}, {"family": "Ellervik", "given": "Ulf", "initials": "U"}, {"family": "Mani", "given": "Katrin", "initials": "K"}, {"family": "Nilsson", "given": "Jonas", "initials": "J"}, {"family": "Larson", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2018-06-29", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "293", "issue": "26", "pages": "10202-10219", "issn-l": "0021-9258"}, "abstract": "Structural characterization of glycosaminoglycans remains a challenge but is essential for determining structure-function relationships between glycosaminoglycans and the biomolecules with which they interact and for gaining insight into the biosynthesis of glycosaminoglycans. We have recently reported that xyloside-primed chondroitin/dermatan sulfate derived from a human breast carcinoma cell line, HCC70, has cytotoxic effects and shown that it differs in disaccharide composition from nontoxic chondroitin/dermatan sulfate derived from a human breast fibroblast cell line, CCD-1095Sk. To further investigate the structural requirements for the cytotoxic effect, we developed a novel LC-MS/MS approach based on reversed-phase dibutylamine ion-pairing chromatography and negative-mode higher-energy collision dissociation and used it in combination with cell growth studies and disaccharide fingerprinting. This strategy enabled detailed structural characterization of linkage regions, internal oligosaccharides, and nonreducing ends, revealing not only differences between xyloside-primed chondroitin/dermatan sulfate from HCC70 cells and CCD-1095Sk cells, but also sialylation of the linkage region and previously undescribed methylation and sulfation of the nonreducing ends. Although the xyloside-primed chondroitin/dermatan sulfate from HCC70 cells was less complex in terms of presence and distribution of iduronic acid than that from CCD-1095Sk cells, both glucuronic acid and iduronic acid appeared to be essential for the cytotoxic effect. Our data have moved us one step closer to understanding the structure of the cytotoxic chondroitin/dermatan sulfate from HCC70 cells primed on xylosides and demonstrate the suitability of the LC-MS/MS approach for structural characterization of glycosaminoglycans.", "doi": "10.1074/jbc.RA118.002971", "pmid": "29739851", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "RA118.002971"}, {"db": "pmc", "key": "PMC6028968"}], "notes": [], "created": "2020-01-30T15:57:29.190Z", "modified": "2024-01-16T13:46:32.329Z"}, {"entity": "publication", "iuid": "3b356b5d45c644838c7145a377e726c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b356b5d45c644838c7145a377e726c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b356b5d45c644838c7145a377e726c5"}}, "title": "Granule-stored MUC5B mucins are packed by the non-covalent formation of N-terminal head-to-head tetramers.", "authors": [{"family": "Trillo-Muyo", "given": "Sergio", "initials": "S"}, {"family": "Nilsson", "given": "Harriet E", "initials": "HE"}, {"family": "Recktenwald", "given": "Christian V", "initials": "CV"}, {"family": "Ermund", "given": "Anna", "initials": "A"}, {"family": "Ridley", "given": "Caroline", "initials": "C"}, {"family": "Meiss", "given": "Lauren N", "initials": "LN"}, {"family": "B\u00e4hr", "given": "Andrea", "initials": "A"}, {"family": "Klymiuk", "given": "Nikolai", "initials": "N"}, {"family": "Wine", "given": "Jeffrey J", "initials": "JJ"}, {"family": "Koeck", "given": "Philip J B", "initials": "PJB"}, {"family": "Thornton", "given": "David J", "initials": "DJ"}, {"family": "Hebert", "given": "Hans", "initials": "H"}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC"}], "type": "journal article", "published": "2018-04-13", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "293", "issue": "15", "pages": "5746-5754", "issn-l": "0021-9258"}, "abstract": "Most MUC5B mucin polymers in the upper airways of humans and pigs are produced by submucosal glands. MUC5B forms N-terminal covalent dimers that are further packed into larger assemblies because of low pH and high Ca 2+ in the secretory granule of the mucin-producing cell. We purified the recombinant MUC5B N-terminal covalent dimer and used single-particle electron microscopy to study its structure under intracellular conditions. We found that, at intragranular pH, the dimeric MUC5B organized into head-to-head noncovalent tetramers where the von Willebrand D1-D2 domains hooked into each other. These N-terminal tetramers further formed long linear complexes from which, we suggest, the mucin domains and their C termini project radially outwards. Using conventional and video microscopy, we observed that, upon secretion into the submucosal gland ducts, a flow of bicarbonate-rich fluid passes the mucin-secreting cells. We suggest that this unfolds and pulls out the MUC5B assemblies into long linear threads. These further assemble into thicker mucin bundles in the glandular ducts before emerging at the gland duct opening. We conclude that the combination of intracellular packing of the MUC5B mucin and the submucosal gland morphology creates an efficient machine for producing linear mucin bundles.", "doi": "10.1074/jbc.RA117.001014", "pmid": "29440393", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9258(20)41867-8"}, {"db": "pmc", "key": "PMC5900763"}], "notes": [], "created": "2020-01-23T16:32:15.964Z", "modified": "2021-06-21T14:29:11.771Z"}, {"entity": "publication", "iuid": "c5a51272065d4a549accfb19495c629b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5a51272065d4a549accfb19495c629b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5a51272065d4a549accfb19495c629b"}}, "title": "A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors", "authors": [{"family": "Faraz", "given": "Mahmood", "initials": "M"}, {"family": "Herdenberg", "given": "Carl", "initials": "C"}, {"family": "Holmlund", "given": "Camilla", "initials": "C"}, {"family": "Henriksson", "given": "Roger", "initials": "R"}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H"}], "type": "journal-article", "published": "2018-01-09", "journal": {"volume": null, "issn": "1083-351X", "issue": null, "pages": "jbc.M117.807487", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": null, "doi": "10.1074/jbc.m117.807487", "pmid": "29317492", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-17T08:38:23.995Z", "modified": "2024-01-16T13:48:47.094Z"}, {"entity": "publication", "iuid": "2499bc475aae42a59bcc144af936e76f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2499bc475aae42a59bcc144af936e76f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2499bc475aae42a59bcc144af936e76f"}}, "title": "Characterization of the Ruler Protein Interaction Interface on the Substrate Specificity Switch Protein in the Yersinia Type III Secretion System.", "authors": [{"family": "Ho", "given": "Oanh", "initials": "O"}, {"family": "Rogne", "given": "Per", "initials": "P"}, {"family": "Edgren", "given": "Tomas", "initials": "T"}, {"family": "Wolf-Watz", "given": "Hans", "initials": "H"}, {"family": "Login", "given": "Fr\u00e9d\u00e9ric H", "initials": "FH"}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2017-02-24", "journal": {"volume": "292", "issn": "1083-351X", "issue": "8", "pages": "3299-3311", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Many pathogenic Gram-negative bacteria use the type III secretion system (T3SS) to deliver effector proteins into eukaryotic host cells. In Yersinia, the switch to secretion of effector proteins is induced first after intimate contact between the bacterium and its eukaryotic target cell has been established, and the T3SS proteins YscP and YscU play a central role in this process. Here we identify the molecular details of the YscP binding site on YscU by means of nuclear magnetic resonance (NMR) spectroscopy. The binding interface is centered on the C-terminal domain of YscU. Disrupting the YscU-YscP interaction by introducing point mutations at the interaction interface significantly reduced the secretion of effector proteins and HeLa cell cytotoxicity. Interestingly, the binding of YscP to the slowly self-cleaving YscU variant P264A conferred significant protection against autoproteolysis. The YscP-mediated inhibition of YscU autoproteolysis suggests that the cleavage event may act as a timing switch in the regulation of early versus late T3SS substrates. We also show that YscUC binds to the inner rod protein YscI with a dissociation constant (K ) of 3.8 \u03bcm and with 1:1 stoichiometry. The significant similarity among different members of the YscU, YscP, and YscI families suggests that the protein-protein interactions discussed in this study are also relevant for other T3SS-containing Gram-negative bacteria.d", "doi": "10.1074/jbc.M116.770255", "pmid": "28039361", "labels": {"Protein Science Facility (PSF)": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5336164"}, {"db": "pii", "key": "S0021-9258(20)41927-1"}, {"db": "PDB", "key": "2JLI"}], "notes": [], "created": "2017-10-23T10:56:36.771Z", "modified": "2025-10-17T13:03:59.984Z"}, {"entity": "publication", "iuid": "f00ddba0619e4b3a9feff7f71d09a120", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f00ddba0619e4b3a9feff7f71d09a120.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f00ddba0619e4b3a9feff7f71d09a120"}}, "title": "Phosphorylation of Leukotriene C4 Synthase at Serine 36 Impairs Catalytic Activity.", "authors": [{"family": "Ahmad", "given": "Shabbir", "initials": "S"}, {"family": "Ytterberg", "given": "A Jimmy", "initials": "AJ"}, {"family": "Thulasingam", "given": "Madhuranayaki", "initials": "M"}, {"family": "Tholander", "given": "Fredrik", "initials": "F"}, {"family": "Bergman", "given": "Tomas", "initials": "T"}, {"family": "Zubarev", "given": "Roman", "initials": "R", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}, {"family": "Wetterholm", "given": "Anders", "initials": "A"}, {"family": "Rinaldo-Matthis", "given": "Agnes", "initials": "A"}, {"family": "Haeggstr\u00f6m", "given": "Jesper Z", "initials": "JZ"}], "type": "journal article", "published": "2016-08-26", "journal": {"volume": "291", "issn": "1083-351X", "issue": "35", "pages": "18410-18418", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Leukotriene C4 synthase (LTC4S) catalyzes the formation of the proinflammatory lipid mediator leukotriene C4 (LTC4). LTC4 is the parent molecule of the cysteinyl leukotrienes, which are recognized for their pathogenic role in asthma and allergic diseases. Cellular LTC4S activity is suppressed by PKC-mediated phosphorylation, and recently a downstream p70S6k was shown to play an important role in this process. Here, we identified Ser(36) as the major p70S6k phosphorylation site, along with a low frequency site at Thr(40), using an in vitro phosphorylation assay combined with mass spectrometry. The functional consequences of p70S6k phosphorylation were tested with the phosphomimetic mutant S36E, which displayed only about 20% (20 \u03bcmol/min/mg) of the activity of WT enzyme (95 \u03bcmol/min/mg), whereas the enzyme activity of T40E was not significantly affected. The enzyme activity of S36E increased linearly with increasing LTA4 concentrations during the steady-state kinetics analysis, indicating poor lipid substrate binding. The Ser(36) is located in a loop region close to the entrance of the proposed substrate binding pocket. Comparative molecular dynamics indicated that Ser(36) upon phosphorylation will pull the first luminal loop of LTC4S toward the neighboring subunit of the functional homotrimer, thereby forming hydrogen bonds with Arg(104) in the adjacent subunit. Because Arg(104) is a key catalytic residue responsible for stabilization of the glutathione thiolate anion, this phosphorylation-induced interaction leads to a reduction of the catalytic activity. In addition, the positional shift of the loop and its interaction with the neighboring subunit affect active site access. Thus, our mutational and kinetic data, together with molecular simulations, suggest that phosphorylation of Ser(36) inhibits the catalytic function of LTC4S by interference with the catalytic machinery.", "doi": "10.1074/jbc.M116.735647", "pmid": "27365393", "labels": {"Advanced Mass Spectrometry Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0021-9258(20)32201-8"}, {"db": "pmc", "key": "PMC5000086"}, {"db": "PDB", "key": "2UUH"}, {"db": "PDB", "key": "2UUI"}, {"db": "PDB", "key": "5HV9"}], "notes": [], "created": "2017-05-03T13:02:25.688Z", "modified": "2021-07-08T08:58:46.694Z"}, {"entity": "publication", "iuid": "c09d047816424105b1a983d7235229eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c09d047816424105b1a983d7235229eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c09d047816424105b1a983d7235229eb"}}, "title": "Peroxisome Proliferator-activated Receptor \u03b3 Coactivator-1 \u03b1 Isoforms Selectively Regulate Multiple Splicing Events on Target Genes.", "authors": [{"family": "Mart\u00ednez-Redondo", "given": "Vicente", "initials": "V"}, {"family": "Jannig", "given": "Paulo R", "initials": "PR"}, {"family": "Correia", "given": "Jorge C", "initials": "JC"}, {"family": "Ferreira", "given": "Duarte M S", "initials": "DM"}, {"family": "Cervenka", "given": "Igor", "initials": "I"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Sinha", "given": "Indranil", "initials": "I"}, {"family": "Izadi", "given": "Manizheh", "initials": "M"}, {"family": "Pettersson-Klein", "given": "Amanda T", "initials": "AT"}, {"family": "Agudelo", "given": "Leandro Z", "initials": "LZ"}, {"family": "Gimenez-Cassina", "given": "Alfredo", "initials": "A"}, {"family": "Brum", "given": "Patricia C", "initials": "PC"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}, {"family": "Ruas", "given": "Jorge L", "initials": "JL"}], "type": "journal article", "published": "2016-07-15", "journal": {"volume": "291", "issn": "1083-351X", "issue": "29", "pages": "15169-15184", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Endurance and resistance exercise training induces specific and profound changes in the skeletal muscle transcriptome. Peroxisome proliferator-activated receptor \u03b3 coactivator-1 \u03b1 (PGC-1\u03b1) coactivators are not only among the genes differentially induced by distinct training methods, but they also participate in the ensuing signaling cascades that allow skeletal muscle to adapt to each type of exercise. Although endurance training preferentially induces PGC-1\u03b11 expression, resistance exercise activates the expression of PGC-1\u03b12, -\u03b13, and -\u03b14. These three alternative PGC-1\u03b1 isoforms lack the arginine/serine-rich (RS) and RNA recognition motifs characteristic of PGC-1\u03b11. Discrete functions for PGC-1\u03b11 and -\u03b14 have been described, but the biological role of PGC-1\u03b12 and -\u03b13 remains elusive. Here we show that different PGC-1\u03b1 variants can affect target gene splicing through diverse mechanisms, including alternative promoter usage. By analyzing the exon structure of the target transcripts for each PGC-1\u03b1 isoform, we were able to identify a large number of previously unknown PGC-1\u03b12 and -\u03b13 target genes and pathways in skeletal muscle. In particular, PGC-1\u03b12 seems to mediate a decrease in the levels of cholesterol synthesis genes. Our results suggest that the conservation of the N-terminal activation and repression domains (and not the RS/RNA recognition motif) is what determines the gene programs and splicing options modulated by each PGC-1\u03b1 isoform. By using skeletal muscle-specific transgenic mice for PGC-1\u03b11 and -\u03b14, we could validate, in vivo, splicing events observed in in vitro studies. These results show that alternative PGC-1\u03b1 variants can affect target gene expression both quantitatively and qualitatively and identify novel biological pathways under the control of this system of coactivators.", "doi": "10.1074/jbc.M115.705822", "pmid": "27231350", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "M115.705822"}, {"db": "pmc", "key": "PMC4946932"}], "notes": [], "created": "2017-05-08T07:58:40.937Z", "modified": "2021-07-05T12:48:16.046Z"}, {"entity": "publication", "iuid": "41ca68bbbb72487fbdfafa2619788d81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41ca68bbbb72487fbdfafa2619788d81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41ca68bbbb72487fbdfafa2619788d81"}}, "title": "Structural Analysis of a Complex between Small Ubiquitin-like Modifier 1 (SUMO1) and the ZZ Domain of CREB-binding Protein (CBP/p300) Reveals a New Interaction Surface on SUMO.", "authors": [{"family": "Diehl", "given": "Carl", "initials": "C"}, {"family": "Akke", "given": "Mikael", "initials": "M", "orcid": "0000-0002-2395-825X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e36b418e03154b90a8722670bed9e81a.json"}}, {"family": "Bekker-Jensen", "given": "Simon", "initials": "S"}, {"family": "Mailand", "given": "Niels", "initials": "N"}, {"family": "Streicher", "given": "Werner", "initials": "W"}, {"family": "Wikstr\u00f6m", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2016-06-10", "journal": {"volume": "291", "issn": "1083-351X", "issue": "24", "pages": "12658-12672", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "We have recently discovered that the ZZ zinc finger domain represents a novel small ubiquitin-like modifier (SUMO) binding motif. In this study we identify the binding epitopes in the ZZ domain of CBP (CREB-binding protein) and SUMO1 using NMR spectroscopy. The binding site on SUMO1 represents a unique epitope for SUMO interaction spatially opposite to that observed for canonical SUMO interaction motifs (SIMs). HADDOCK docking simulations using chemical shift perturbations and residual dipolar couplings was employed to obtain a structural model for the ZZ domain-SUMO1 complex. Isothermal titration calorimetry experiments support this model by showing that the mutation of key residues in the binding site abolishes binding and that SUMO1 can simultaneously and non-cooperatively bind both the ZZ domain and a canonical SIM motif. The binding dynamics of SUMO1 was further characterized using (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersions, which define the off rates for the ZZ domain and SIM motif and show that the dynamic binding process has different characteristics for the two cases. Furthermore, in the absence of bound ligands SUMO1 transiently samples a high energy conformation, which might be involved in ligand binding.", "doi": "10.1074/jbc.M115.711325", "pmid": "27129204", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "M115.711325"}, {"db": "pmc", "key": "PMC4933466"}, {"db": "PDB", "key": "1A5R"}, {"db": "PDB", "key": "1TOT"}, {"db": "PDB", "key": "2ASQ"}], "notes": [], "created": "2017-05-03T13:02:51.586Z", "modified": "2025-10-17T13:04:00.469Z"}, {"entity": "publication", "iuid": "e887236b9d6c40428b0fdcba35275b2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e887236b9d6c40428b0fdcba35275b2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e887236b9d6c40428b0fdcba35275b2a"}}, "title": "Regulation of Bone Morphogenetic Protein Signaling by ADP-ribosylation", "authors": [{"family": "Watanabe", "given": "Yukihide", "initials": "Y"}, {"family": "Papoutsoglou", "given": "Panagiotis", "initials": "P"}, {"family": "Maturi", "given": "Varun", "initials": "V"}, {"family": "Tsubakihara", "given": "Yutaro", "initials": "Y"}, {"family": "Hottiger", "given": "Michael O", "initials": "MO"}, {"family": "Heldin", "given": "Carl Henrik", "initials": "CH"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A"}], "type": "journal-article", "published": "2016-06-10", "journal": {"volume": "291", "issn": "1083-351X", "issue": "24", "pages": "12706-12723", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": null, "doi": "10.1074/jbc.m116.729699", "pmid": "27129221", "labels": {"PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T14:32:29.885Z", "modified": "2023-04-14T13:56:20.086Z"}, {"entity": "publication", "iuid": "29043aa893ee4780af9812c166522a99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29043aa893ee4780af9812c166522a99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29043aa893ee4780af9812c166522a99"}}, "title": "Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG.", "authors": [{"family": "Spoerry", "given": "Christian", "initials": "C"}, {"family": "Seele", "given": "Jana", "initials": "J"}, {"family": "Valentin-Weigand", "given": "Peter", "initials": "P"}, {"family": "Baums", "given": "Christoph G", "initials": "CG"}, {"family": "von Pawel-Rammingen", "given": "Ulrich", "initials": "U"}], "type": "journal article", "published": "2016-04-08", "journal": {"volume": "291", "issn": "1083-351X", "issue": "15", "pages": "7915-7925", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Streptococcus suisis a major endemic pathogen of pigs causing meningitis, arthritis, and other diseases. ZoonoticS. suisinfections are emerging in humans causing similar pathologies as well as severe conditions such as toxic shock-like syndrome. Recently, we discovered an IdeS family protease ofS. suisthat exclusively cleaves porcine IgM and represents the first virulence factor described, linkingS. suisto pigs as their natural host. Here we report the identification and characterization of a novel, unrelated protease ofS. suisthat exclusively targets porcine IgG. This enzyme, designated IgdE forimmunoglobulinG-degradingenzyme ofS. suis, is a cysteine protease distinct from previous characterized streptococcal immunoglobulin degrading proteases of the IdeS family and mediates efficient cleavage of the hinge region of porcine IgG with a high degree of specificity. The findings that allS. suisstrains investigated possess the IgG proteolytic activity and that piglet serum samples contain specific antibodies against IgdE strongly indicate that the protease is expressedin vivoduring infection and represents a novel and putative important bacterial virulence/colonization determinant, and a thus potential therapeutic target.", "doi": "10.1074/jbc.M115.711440", "pmid": "26861873", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "M115.711440"}, {"db": "pmc", "key": "PMC4824999"}], "notes": [], "created": "2017-05-03T13:00:42.410Z", "modified": "2020-01-21T13:53:21.265Z"}, {"entity": "publication", "iuid": "afcd3edfbfc644a0813d45d9c5044376", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afcd3edfbfc644a0813d45d9c5044376.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afcd3edfbfc644a0813d45d9c5044376"}}, "title": "Structural Studies of Lipopolysaccharide-defective Mutants from Brucella melitensis Identify a Core Oligosaccharide Critical in Virulence.", "authors": [{"family": "Fontana", "given": "Carolina", "initials": "C"}, {"family": "Conde-\u00c1lvarez", "given": "Raquel", "initials": "R"}, {"family": "St\u00e5hle", "given": "Jonas", "initials": "J"}, {"family": "Holst", "given": "Otto", "initials": "O"}, {"family": "Iriarte", "given": "Maite", "initials": "M"}, {"family": "Zhao", "given": "Yun", "initials": "Y"}, {"family": "Arce-Gorvel", "given": "Vilma", "initials": "V"}, {"family": "Hanniffy", "given": "Se\u00e1n", "initials": "S"}, {"family": "Gorvel", "given": "Jean-Pierre", "initials": "JP"}, {"family": "Moriy\u00f3n", "given": "Ignacio", "initials": "I"}, {"family": "Widmalm", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2016-04-01", "journal": {"volume": "291", "issn": "1083-351X", "issue": "14", "pages": "7727-7741", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The structures of the lipooligosaccharides fromBrucella melitensismutants affected in the WbkD and ManBcoreproteins have been fully characterized using NMR spectroscopy. The results revealed that disruption ofwbkDgives rise to a rough lipopolysaccharide (R-LPS) with a complete core structure (\u03b2-d-Glcp-(1\u21924)-\u03b1-Kdop-(2\u21924)[\u03b2-d-GlcpN-(1\u21926)-\u03b2-d-GlcpN-(1\u21924)[\u03b2-d-GlcpN-(1\u21926)]-\u03b2-d-GlcpN-(1\u21923)-\u03b1-d-Manp-(1\u21925)]-\u03b1-Kdop-(2\u21926)-\u03b2-d-GlcpN3N4P-(1\u21926)-\u03b1-d-GlcpN3N1P), in addition to components lacking one of the terminal \u03b2-d-GlcpN and/or the \u03b2-d-Glcpresidues (48 and 17%, respectively). These structures were identical to those of the R-LPS fromB. melitensisEP, a strain simultaneously expressing both smooth and R-LPS, also studied herein. In contrast, disruption ofmanBcoregives rise to a deep-rough pentasaccharide core (\u03b2-d-Glcp-(1\u21924)-\u03b1-Kdop-(2\u21924)-\u03b1-Kdop-(2\u21926)-\u03b2-d-GlcpN3N4P-(1\u21926)-\u03b1-d-GlcpN3N1P) as the major component (63%), as well as a minor tetrasaccharide component lacking the terminal \u03b2-d-Glcpresidue (37%). These results are in agreement with the predicted functions of the WbkD (glycosyltransferase involved in the biosynthesis of the O-antigen) and ManBcoreproteins (phosphomannomutase involved in the biosynthesis of a mannosyl precursor needed for the biosynthesis of the core and O-antigen). We also report that deletion ofB. melitensis wadCremoves the core oligosaccharide branch not linked to the O-antigen causing an increase in overall negative charge of the remaining LPS inner section. This is in agreement with the mannosyltransferase role predicted for WadC and the lack of GlcpN residues in the defective core oligosaccharide. Despite carrying the O-antigen essential inB. melitensisvirulence, the core deficiency in thewadCmutant structure resulted in a more efficient detection by innate immunity and attenuation, proving the role of the \u03b2-d-GlcpN-(1\u21926)-\u03b2-d-GlcpN-(1\u21924)[\u03b2-d-GlcpN-(1\u21926)]-\u03b2-d-GlcpN-(1\u21923)-\u03b1-d-Manp-(1\u21925) structure in virulence.", "doi": "10.1074/jbc.M115.701540", "pmid": "26867577", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "M115.701540"}, {"db": "pmc", "key": "PMC4817197"}], "notes": [], "created": "2017-05-03T13:02:51.267Z", "modified": "2025-10-17T13:04:00.556Z"}, {"entity": "publication", "iuid": "e0f21a44d89b48d5a29f17f773fc1729", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0f21a44d89b48d5a29f17f773fc1729.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0f21a44d89b48d5a29f17f773fc1729"}}, "title": "Structural basis for lack of ADP-ribosyltransferase activity in poly(ADP-ribose) polymerase-13/zinc finger antiviral protein.", "authors": [{"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Klepsch", "given": "Mirjam", "initials": "M"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "AG"}, {"family": "Andersson", "given": "C David", "initials": "CD"}, {"family": "Linusson", "given": "Anna", "initials": "A"}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H"}], "type": "journal article", "published": "2015-03-20", "journal": {"volume": "290", "issn": "1083-351X", "issue": "12", "pages": "7336-7344", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The mammalian poly(ADP-ribose) polymerase (PARP) family includes ADP-ribosyltransferases with diphtheria toxin homology (ARTD). Most members have mono-ADP-ribosyltransferase activity. PARP13/ARTD13, also called zinc finger antiviral protein, has roles in viral immunity and microRNA-mediated stress responses. PARP13 features a divergent PARP homology domain missing a PARP consensus sequence motif; the domain has enigmatic functions and apparently lacks catalytic activity. We used x-ray crystallography, molecular dynamics simulations, and biochemical analyses to investigate the structural requirements for ADP-ribosyltransferase activity in human PARP13 and two of its functional partners in stress granules: PARP12/ARTD12, and PARP15/BAL3/ARTD7. The crystal structure of the PARP homology domain of PARP13 shows obstruction of the canonical active site, precluding NAD(+) binding. Molecular dynamics simulations indicate that this closed cleft conformation is maintained in solution. Introducing consensus side chains in PARP13 did not result in 3-aminobenzamide binding, but in further closure of the site. Three-dimensional alignment of the PARP homology domains of PARP13, PARP12, and PARP15 illustrates placement of PARP13 residues that deviate from the PARP family consensus. Introducing either one of two of these side chains into the corresponding positions in PARP15 abolished PARP15 ADP-ribosyltransferase activity. Taken together, our results show that PARP13 lacks the structural requirements for ADP-ribosyltransferase activity.", "doi": "10.1074/jbc.M114.630160", "pmid": "25635049", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "M114.630160"}, {"db": "pmc", "key": "PMC4367243"}], "notes": [], "created": "2017-05-02T12:57:34.587Z", "modified": "2018-11-14T17:08:52.043Z"}, {"entity": "publication", "iuid": "cc9284765fcf434ba459a665c44443c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc9284765fcf434ba459a665c44443c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc9284765fcf434ba459a665c44443c6"}}, "title": "The Eph tyrosine kinase receptors EphB2 and EphA2 are novel proteolytic substrates of tissue factor/coagulation factor VIIa.", "authors": [{"family": "Eriksson", "given": "Oskar", "initials": "O"}, {"family": "Ramstr\u00f6m", "given": "Margareta", "initials": "M"}, {"family": "H\u00f6rnaeus", "given": "Katarina", "initials": "K"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Mokhtari", "given": "Dariush", "initials": "D"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}], "type": "journal article", "published": "2014-11-21", "journal": {"volume": "289", "issn": "1083-351X", "issue": "47", "pages": "32379-32391", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Tissue factor (TF) binds the serine protease factor VIIa (FVIIa) to form a proteolytically active complex that can trigger coagulation or activate cell signaling. Here we addressed the involvement of tyrosine kinase receptors (RTKs) in TF/FVIIa signaling by antibody array analysis and subsequently found that EphB2 and EphA2 of the Eph RTK family were cleaved in their ectodomains by TF/FVIIa. We used N-terminal Edman sequencing and LC-MS/MS analysis to characterize the cleaved Eph isoforms and identified a key arginine residue at the cleavage site, in agreement with the tryptic serine protease activity of FVIIa. Protease-activated receptor 2 (PAR2) signaling and downstream coagulation activity was non-essential in this context, in further support of a direct cleavage by TF/FVIIa. EphB2 was cleaved by FVIIa concentrations in the subnanomolar range in a number of TF expressing cell types, indicating that the active cellular pool of TF was involved. FVIIa caused potentiation of cell repulsion by the EphB2 ligand ephrin-B1, demonstrating a novel proteolytical event to control Eph-mediated cell segregation. These results define Eph RTKs as novel proteolytical targets of TF/FVIIa and provide new insights into how TF/FVIIa regulates cellular functions independently of PAR2.", "doi": "10.1074/jbc.M114.599332", "pmid": "25281742", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "M114.599332"}, {"db": "pmc", "key": "PMC4239594"}], "notes": [], "created": "2017-05-04T14:55:27.963Z", "modified": "2023-04-14T13:56:27.013Z"}, {"entity": "publication", "iuid": "b4376e6626754f4f94a5c1d7d774a005", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4376e6626754f4f94a5c1d7d774a005.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4376e6626754f4f94a5c1d7d774a005"}}, "title": "Structural basis for regulation of the human acetyl-CoA thioesterase 12 and interactions with the steroidogenic acute regulatory protein-related lipid transfer (START) domain.", "authors": [{"family": "Swarbrick", "given": "Crystall M D", "initials": "CM"}, {"family": "Roman", "given": "Noelia", "initials": "N"}, {"family": "Cowieson", "given": "Nathan", "initials": "N"}, {"family": "Patterson", "given": "Edward I", "initials": "EI"}, {"family": "Nanson", "given": "Jeffrey", "initials": "J"}, {"family": "Siponen", "given": "Marina I", "initials": "MI"}, {"family": "Berglund", "given": "Helena", "initials": "H"}, {"family": "Lehti\u00f6", "given": "Lari", "initials": "L"}, {"family": "Forwood", "given": "Jade K", "initials": "JK"}], "type": "journal article", "published": "2014-08-29", "journal": {"volume": "289", "issn": "1083-351X", "issue": "35", "pages": "24263-24274", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Acetyl-CoA plays a fundamental role in cell signaling and metabolic pathways, with its cellular levels tightly controlled through reciprocal regulation of enzymes that mediate its synthesis and catabolism. ACOT12, the primary acetyl-CoA thioesterase in the liver of human, mouse, and rat, is responsible for cleavage of the thioester bond within acetyl-CoA, producing acetate and coenzyme A for a range of cellular processes. The enzyme is regulated by ADP and ATP, which is believed to be mediated through the ligand-induced oligomerization of the thioesterase domains, whereby ATP induces active dimers and tetramers, whereas apo- and ADP-bound ACOT12 are monomeric and inactive. Here, using a range of structural and biophysical techniques, it is demonstrated that ACOT12 is a trimer rather than a tetramer and that neither ADP nor ATP exert their regulatory effects by altering the oligomeric status of the enzyme. Rather, the binding site and mechanism of ADP regulation have been determined to occur through two novel regulatory regions, one involving a large loop that links the thioesterase domains (Phe(154)-Thr(178)), defined here as RegLoop1, and a second region involving the C terminus of thioesterase domain 2 (Gln(304)-Gly(326)), designated RegLoop2. Mutagenesis confirmed that Arg(312) and Arg(313) are crucial for this mode of regulation, and novel interactions with the START domain are presented together with insights into domain swapping within eukaryotic thioesterases for substrate recognition. In summary, these experiments provide the first structural insights into the regulation of this enzyme family, revealing an alternate hypothesis likely to be conserved throughout evolution.", "doi": "10.1074/jbc.M114.589408", "pmid": "25002576", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "M114.589408"}, {"db": "pmc", "key": "PMC4148856"}, {"db": "PDB", "key": "1VPM"}, {"db": "PDB", "key": "1YLI"}, {"db": "PDB", "key": "2GVH"}, {"db": "PDB", "key": "2Q2B"}, {"db": "PDB", "key": "2V1O"}, {"db": "PDB", "key": "3B7K"}, {"db": "PDB", "key": "4MOB"}, {"db": "PDB", "key": "4MOC"}], "notes": [], "created": "2017-05-04T15:03:52.999Z", "modified": "2017-09-06T11:42:09.263Z"}, {"entity": "publication", "iuid": "c5d5ceb83acb4240a14def5ad6c0dba2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5d5ceb83acb4240a14def5ad6c0dba2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5d5ceb83acb4240a14def5ad6c0dba2"}}, "title": "Crystal structures of leukotriene C4 synthase in complex with product analogs: implications for the enzyme mechanism.", "authors": [{"family": "Niegowski", "given": "Damian", "initials": "D"}, {"family": "Kleinschmidt", "given": "Thea", "initials": "T"}, {"family": "Olsson", "given": "Ulrika", "initials": "U"}, {"family": "Ahmad", "given": "Shabbir", "initials": "S"}, {"family": "Rinaldo-Matthis", "given": "Agnes", "initials": "A"}, {"family": "Haeggstr\u00f6m", "given": "Jesper Z", "initials": "JZ"}], "type": "journal article", "published": "2014-02-21", "journal": {"volume": "289", "issn": "1083-351X", "issue": "8", "pages": "5199-5207", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Leukotriene (LT) C4 synthase (LTC4S) catalyzes the conjugation of the fatty acid LTA4 with the tripeptide GSH to produce LTC4, the parent compound of the cysteinyl leukotrienes, important mediators of asthma. Here we mutated Trp-116 in human LTC4S, a residue proposed to play a key role in substrate binding, into an Ala or Phe. Biochemical and structural characterization of these mutants along with crystal structures of the wild type and mutated enzymes in complex with three product analogs, viz. S-hexyl-, 4-phenyl-butyl-, and 2-hydroxy-4-phenyl-butyl-glutathione, provide new insights to binding of substrates and product, identify a new conformation of the GSH moiety at the active site, and suggest a route for product release, aided by Trp-116.", "doi": "10.1074/jbc.M113.534628", "pmid": "24366866", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "M113.534628"}, {"db": "pmc", "key": "PMC3931076"}, {"db": "PDB", "key": "4J7T"}, {"db": "PDB", "key": "4J7Y"}, {"db": "PDB", "key": "4JC7"}, {"db": "PDB", "key": "4JCZ"}, {"db": "PDB", "key": "4JRZ"}], "notes": [], "created": "2017-05-04T15:03:53.302Z", "modified": "2017-09-06T11:42:09.322Z"}, {"entity": "publication", "iuid": "0e3e7d2669db4343813208ec913c4d7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e3e7d2669db4343813208ec913c4d7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e3e7d2669db4343813208ec913c4d7c"}}, "title": "Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner.", "authors": [{"family": "\u00c5hsberg", "given": "Josefine", "initials": "J"}, {"family": "Ungerb\u00e4ck", "given": "Jonas", "initials": "J"}, {"family": "Strid", "given": "Tobias", "initials": "T", "orcid": "0000-0002-2166-5170", "researcher": {"href": "https://publications.scilifelab.se/researcher/8294f89150574803a12bc1944714d12b.json"}}, {"family": "Welinder", "given": "Eva", "initials": "E"}, {"family": "Stjernberg", "given": "Jenny", "initials": "J"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Sigvardsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2013-11-15", "journal": {"volume": "288", "issn": "1083-351X", "issue": "46", "pages": "33449-33461", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Transcription factor doses are of importance for normal and malignant B-lymphocyte development; however, the understanding of underlying mechanisms and functional consequences of reduced transcription factor levels is limited. We have analyzed progenitor and B-lineage compartments in mice carrying heterozygote mutations in the E2a, Ebf1, or Pax5 gene. Although lymphoid progenitors from Ebf1 or Pax5 heterozygote mice were specified and lineage-restricted in a manner comparable with Wt progenitors, this process was severely impaired in E2a heterozygote mutant mice. This defect was not significantly enhanced upon combined deletion of E2a with Ebf1 or Pax5. Analysis of the pre-B-cell compartment in Ebf1 heterozygote mice revealed a reduction in cell numbers. These cells expressed Pax5 and other B-lineage-associated genes, and global gene expression analysis suggested that the reduction of the pre-B-cell compartment was a result of impaired pre-B-cell expansion. This idea was supported by a reduction in IL2R\u03b1-expressing late pre-B-cells as well as by cell cycle analysis and by the finding that the complexity of the VDJ rearrangement patterns was comparable in Wt and Ebf1(+/-) pre-B-cells, although the number of progenitors was reduced. Heterozygote deletion of Ebf1 resulted in impaired response to IL7 in vitro and reduced expression levels of pre-BCR on the cell surface, providing possible explanations for the observed stage-specific reduction in cellular expansion. Thus, transcription factor doses are critical for specification as well as expansion of B-lymphoid progenitors, providing increased insight into the molecular regulation of B-cell development.", "doi": "10.1074/jbc.M113.506261", "pmid": "24078629", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0021-9258(19)54468-4"}, {"db": "pmc", "key": "PMC3829190"}], "notes": [], "created": "2017-05-04T14:56:24.274Z", "modified": "2021-07-06T15:17:27.838Z"}, {"entity": "publication", "iuid": "f860b4e98f3044179bb6ac075c1296ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f860b4e98f3044179bb6ac075c1296ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f860b4e98f3044179bb6ac075c1296ff"}}, "title": "Ebsulfur is a benzisothiazolone cytocidal inhibitor targeting the trypanothione reductase of Trypanosoma brucei.", "authors": [{"family": "Lu", "given": "Jun", "initials": "J"}, {"family": "Vodnala", "given": "Suman K", "initials": "SK"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Gustafsson", "given": "Tomas N", "initials": "TN"}, {"family": "Sj\u00f6berg", "given": "Birger", "initials": "B"}, {"family": "Johansson", "given": "Henrik A", "initials": "HA"}, {"family": "Kumar", "given": "Sangit", "initials": "S"}, {"family": "Tjernberg", "given": "Agneta", "initials": "A"}, {"family": "Engman", "given": "Lars", "initials": "L"}, {"family": "Rottenberg", "given": "Martin E", "initials": "ME"}, {"family": "Holmgren", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-09-20", "journal": {"volume": "288", "issn": "1083-351X", "issue": "38", "pages": "27456-27468", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Trypanosoma brucei is the causing agent of African trypanosomiasis. These parasites possess a unique thiol redox system required for DNA synthesis and defense against oxidative stress. It includes trypanothione and trypanothione reductase (TryR) instead of the thioredoxin and glutaredoxin systems of mammalian hosts. Here, we show that the benzisothiazolone compound ebsulfur (EbS), a sulfur analogue of ebselen, is a potent inhibitor of T. brucei growth with a favorable selectivity index over mammalian cells. EbS inhibited the TryR activity and decreased non-protein thiol levels in cultured parasites. The inhibition of TryR by EbS was irreversible and NADPH-dependent. EbS formed a complex with TryR and caused oxidation and inactivation of the enzyme. EbS was more toxic for T. brucei than for Trypanosoma cruzi, probably due to lower levels of TryR and trypanothione in T. brucei. Furthermore, inhibition of TryR produced high intracellular reactive oxygen species. Hydrogen peroxide, known to be constitutively high in T. brucei, enhanced the EbS inhibition of TryR. The elevation of reactive oxygen species production in parasites caused by EbS induced a programmed cell death. Soluble EbS analogues were synthesized and cured T. brucei brucei infection in mice when used together with nifurtimox. Altogether, EbS and EbS analogues disrupt the trypanothione system, hampering the defense against oxidative stress. Thus, EbS is a promising lead for development of drugs against African trypanosomiasis.", "doi": "10.1074/jbc.M113.495101", "pmid": "23900839", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0021-9258(20)49012-X"}, {"db": "pmc", "key": "PMC3779740"}], "notes": [], "created": "2017-10-20T14:49:29.162Z", "modified": "2025-10-17T13:04:30.291Z"}, {"entity": "publication", "iuid": "c18933a273324f8f820b0d8cb51b36eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c18933a273324f8f820b0d8cb51b36eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c18933a273324f8f820b0d8cb51b36eb"}}, "title": "Expression of fusion proteins of Aspergillus terreus reveals a novel allene oxide synthase.", "authors": [{"family": "Hoffmann", "given": "Inga", "initials": "I"}, {"family": "Jerner\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Oliw", "given": "Ernst H", "initials": "EH"}], "type": "journal article", "published": "2013-04-19", "journal": {"volume": "288", "issn": "1083-351X", "issue": "16", "pages": "11459-11469", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Aspergilli oxidize C18 unsaturated fatty acids by dioxygenase-cytochrome P450 fusion proteins to signal molecules involved in reproduction and host-pathogen interactions. Aspergillus terreus expresses linoleate 9R-dioxygenase (9R-DOX) and allene oxide synthase (AOS) activities in membrane fractions. The genome contains five genes (ATEG), which may code for a 9R-DOX-AOS fusion protein. The genes were cloned and expressed, but none of them oxidized 18:2n-6 to 9R-hydroperoxy-10(E),12(Z)-octadecadienoic acid (9R-HPODE). ATEG_02036 transformed 9R-HPODE to an unstable allene oxide, 9(R),10-epoxy-10,12(Z)-octadecadienoic acid. A substitution in the P450 domain (C1073S) abolished AOS activity. The N964V and N964D mutants both showed markedly reduced AOS activity, suggesting that Asn(964) may facilitate homolytic cleavage of the dioxygen bond of 9R-HPODE with formation of compound II in analogy with plant AOS (CYP74) and prostacyclin synthase (CYP8A1). ATEG_03992 was identified as 5,8-linoleate diol synthase (5,8-LDS). Replacement of Asn(878) in 5,8-LDS with leucine (N878L) mainly shifted ferryl oxygen insertion from C-5 toward C-6, but replacements of Gln(881) markedly affected catalysis. The Q881L mutant virtually abolished the diol synthase activity. Replacement of Gln(881) with Asn, Glu, Asp, or Lys residues augmented the homolytic cleavage of 8R-HPODE with formation of 10-hydroxy-8(9)-epoxy-12(Z)-octadecenoic acid (erythro/threo, 1-4:1) and/or shifted ferryl oxygen insertion from C-5 toward C-11. We conclude that homolysis and heterolysis of the dioxygen bond with formation of compound II in AOS and compound I in 5,8-LDS are influenced by Asn and Gln residues, respectively, of the I-helices. AOS of A. terreus appears to have evolved independently of CYP74 but with an analogous reaction mechanism.", "doi": "10.1074/jbc.M113.458257", "pmid": "23479731", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "M113.458257"}, {"db": "pmc", "key": "PMC3630850"}], "notes": [], "created": "2017-05-04T15:02:27.819Z", "modified": "2020-01-21T13:56:05.025Z"}, {"entity": "publication", "iuid": "f51ca77cdbe64ad19435f4e55f6cac26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f51ca77cdbe64ad19435f4e55f6cac26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f51ca77cdbe64ad19435f4e55f6cac26"}}, "title": "On the roles and regulation of chondroitin sulfate and heparan sulfate in zebrafish pharyngeal cartilage morphogenesis.", "authors": [{"family": "Holmborn", "given": "Katarina", "initials": "K"}, {"family": "Habicher", "given": "Judith", "initials": "J"}, {"family": "Kasza", "given": "Zsolt", "initials": "Z"}, {"family": "Eriksson", "given": "Anna S", "initials": "AS"}, {"family": "Filipek-Gorniok", "given": "Beata", "initials": "B", "orcid": "0000-0002-6757-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f0b7b3e0b045f082d2aff1dd23ec0e.json"}}, {"family": "Gopal", "given": "Sandeep", "initials": "S"}, {"family": "Couchman", "given": "John R", "initials": "JR"}, {"family": "Ahlberg", "given": "Per E", "initials": "PE"}, {"family": "Wiweger", "given": "Malgorzata", "initials": "M"}, {"family": "Spillmann", "given": "Dorothe", "initials": "D"}, {"family": "Kreuger", "given": "Johan", "initials": "J"}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}], "type": "journal article", "published": "2012-09-28", "journal": {"volume": "287", "issn": "1083-351X", "issue": "40", "pages": "33905-33916", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The present study addresses the roles of heparan sulfate (HS) proteoglycans and chondroitin sulfate (CS) proteoglycans in the development of zebrafish pharyngeal cartilage structures. uxs1 and b3gat3 mutants, predicted to have impaired biosynthesis of both HS and CS because of defective formation of the common proteoglycan linkage tetrasaccharide were analyzed along with ext2 and extl3 mutants, predicted to have defective HS polymerization. Notably, the effects on HS and CS biosynthesis in the respective mutant strains were shown to differ from what had been hypothesized. In uxs1 and b3gat3 mutant larvae, biosynthesis of CS was shown to be virtually abolished, whereas these mutants still were capable of synthesizing 50% of the HS produced in control larvae. extl3 and ext2 mutants on the other hand were shown to synthesize reduced amounts of hypersulfated HS. Further, extl3 mutants produced higher levels of CS than control larvae, whereas morpholino-mediated suppression of csgalnact1/csgalnact2 resulted in increased HS biosynthesis. Thus, the balance of the Extl3 and Csgalnact1/Csgalnact2 proteins influences the HS/CS ratio. A characterization of the pharyngeal cartilage element morphologies in the single mutant strains, as well as in ext2;uxs1 double mutants, was conducted. A correlation between HS and CS production and phenotypes was found, such that impaired HS biosynthesis was shown to affect chondrocyte intercalation, whereas impaired CS biosynthesis inhibited formation of the extracellular matrix surrounding chondrocytes.", "doi": "10.1074/jbc.M112.401646", "pmid": "22869369", "labels": {"Genome Engineering Zebrafish": null}, "xrefs": [{"db": "pii", "key": "S0021-9258(20)62888-5"}, {"db": "pmc", "key": "PMC3460485"}], "notes": [], "created": "2017-05-04T15:03:43.219Z", "modified": "2021-07-06T16:05:51.263Z"}, {"entity": "publication", "iuid": "2fdedc5402bb4246846cf6da7baf1e53", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fdedc5402bb4246846cf6da7baf1e53.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fdedc5402bb4246846cf6da7baf1e53"}}, "title": "Catalytic convergence of manganese and iron lipoxygenases by replacement of a single amino acid.", "authors": [{"family": "Wennman", "given": "Anneli", "initials": "A"}, {"family": "Jerner\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Hamberg", "given": "Mats", "initials": "M"}, {"family": "Oliw", "given": "Ernst H", "initials": "EH"}], "type": "journal article", "published": "2012-09-14", "journal": {"volume": "287", "issn": "1083-351X", "issue": "38", "pages": "31757-31765", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Lipoxygenases (LOXs) contain a hydrophobic substrate channel with the conserved Gly/Ala determinant of regio- and stereospecificity and a conserved Leu residue near the catalytic non-heme iron. Our goal was to study the importance of this region (Gly(332), Leu(336), and Phe(337)) of a lipoxygenase with catalytic manganese (13R-MnLOX). Recombinant 13R-MnLOX oxidizes 18:2n-6 and 18:3n-3 to 13R-, 11(S or R)-, and 9S-hydroperoxy metabolites (\u223c80-85, 15-20, and 2-3%, respectively) by suprafacial hydrogen abstraction and oxygenation. Replacement of Phe(337) with Ile changed the stereochemistry of the 13-hydroperoxy metabolites of 18:2n-6 and 18:3n-3 (from \u223c100% R to 69-74% S) with little effect on regiospecificity. The abstraction of the pro-S hydrogen of 18:2n-6 was retained, suggesting antarafacial hydrogen abstraction and oxygenation. Replacement of Leu(336) with smaller hydrophobic residues (Val, Ala, and Gly) shifted the oxygenation from C-13 toward C-9 with formation of 9S- and 9R-hydroperoxy metabolites of 18:2n-6 and 18:3n-3. Replacement of Gly(332) and Leu(336) with larger hydrophobic residues (G332A and L336F) selectively augmented dehydration of 13R-hydroperoxyoctadeca-9Z,11E,15Z-trienoic acid and increased the oxidation at C-13 of 18:1n-6. We conclude that hydrophobic replacements of Leu(336) can modify the hydroperoxide configurations at C-9 with little effect on the R configuration at C-13 of the 18:2n-6 and 18:3n-3 metabolites. Replacement of Phe(337) with Ile changed the stereospecific oxidation of 18:2n-6 and 18:3n-3 with formation of 13S-hydroperoxides by hydrogen abstraction and oxygenation in analogy with soybean LOX-1.", "doi": "10.1074/jbc.M112.364331", "pmid": "22822060", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "M112.364331"}, {"db": "pmc", "key": "PMC3442510"}], "notes": [], "created": "2017-05-04T14:57:36.883Z", "modified": "2020-01-21T13:56:10.330Z"}, {"entity": "publication", "iuid": "de1f1172b5fa4a0a94e02ce36e84a68e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de1f1172b5fa4a0a94e02ce36e84a68e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de1f1172b5fa4a0a94e02ce36e84a68e"}}, "title": "MicroRNA-125b down-regulates matrix metallopeptidase 13 and inhibits cutaneous squamous cell carcinoma cell proliferation, migration, and invasion.", "authors": [{"family": "Xu", "given": "Ning", "initials": "N"}, {"family": "Zhang", "given": "Lingyun", "initials": "L"}, {"family": "Meisgen", "given": "Florian", "initials": "F"}, {"family": "Harada", "given": "Masako", "initials": "M"}, {"family": "Heilborn", "given": "Johan", "initials": "J"}, {"family": "Homey", "given": "Bernhard", "initials": "B"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "St\u00e5hle", "given": "Mona", "initials": "M"}, {"family": "Sonkoly", "given": "Enik\u00f6", "initials": "E"}, {"family": "Pivarcsi", "given": "Andor", "initials": "A"}], "type": "clinical trial", "published": "2012-08-24", "journal": {"volume": "287", "issn": "1083-351X", "issue": "35", "pages": "29899-29908", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Cutaneous squamous cell carcinoma (cSCC) is the second most common human cancer. Although dysregulation of microRNAs (miRNAs) is known to be involved in a variety of cancers, the role of miRNAs in cSCC is unclear. In this study, we aimed to identify tumor suppressive and oncogenic miRNAs involved in the pathogenesis of cSCC. MiRNA expression profiles in healthy skins (n = 4) and cSCCs (n = 4) were analyzed using MicroRNA Low Density Array. MiR-125b expression was analyzed by quantitative real-time PCR and in situ hybridization in skin biopsies from 40 healthy donors, 13 actinic keratosis, and 74 cSCC patients. The effect of miR-125b was analyzed in wound closure, colony formation, migration, and invasion assays in two cSCC cell lines, UT-SCC-7 and A431. The genes regulated by miR-125b in cSCC were identified by microarray analysis and its direct target was validated by luciferase reporter assay. Comparing cSCC with healthy skin, we identified four up-regulated miRNAs (miR-31, miR-135b, miR-21, and miR-223) and 54 down-regulated miRNAs, including miR-125b, whose function was further examined. We found that miR-125b suppressed proliferation, colony formation, migratory, and invasive capacity of cSCC cells. Matrix metallopeptidase 13 (MMP13) was identified as a direct target suppressed by miR-125b, and there was an inverse relationship between the expression of miR-125b and MMP13 in cSCC. Knockdown of MMP13 expression phenocopied the effects of miR-125b overexpression. These findings provide a novel molecular mechanism by which MMP13 is up-regulated in cSCCs and indicate that miR-125b plays a tumor suppressive role in cSCC.", "doi": "10.1074/jbc.M112.391243", "pmid": "22782903", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "M112.391243"}, {"db": "pmc", "key": "PMC3436131"}], "notes": [], "created": "2017-05-04T15:03:11.960Z", "modified": "2017-05-30T12:40:35.114Z"}, {"entity": "publication", "iuid": "d7bd1c5050d3453eb235b0dd54f012bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7bd1c5050d3453eb235b0dd54f012bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7bd1c5050d3453eb235b0dd54f012bc"}}, "title": "Identification of Bacterial Target Proteins for the Salicylidene Acylhydrazide Class of Virulence-blocking Compounds", "authors": [{"family": "Wang", "given": "Dai", "initials": "D"}, {"family": "Zetterstr\u00f6m", "given": "Caroline E", "initials": "CE"}, {"family": "Gabrielsen", "given": "Mads", "initials": "M"}, {"family": "Beckham", "given": "Katherine S H", "initials": "KSH"}, {"family": "Tree", "given": "Jai J", "initials": "JJ"}, {"family": "Macdonald", "given": "Sarah E", "initials": "SE"}, {"family": "Byron", "given": "Olwyn", "initials": "O"}, {"family": "Mitchell", "given": "Tim J", "initials": "TJ"}, {"family": "Gally", "given": "David L", "initials": "DL"}, {"family": "Herzyk", "given": "Pawel", "initials": "P"}, {"family": "Mahajan", "given": "Arvind", "initials": "A"}, {"family": "Uvell", "given": "Hanna", "initials": "H"}, {"family": "Burchmore", "given": "Richard", "initials": "R"}, {"family": "Smith", "given": "Brian O", "initials": "BO"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Roe", "given": "Andrew J", "initials": "AJ"}], "type": "journal-article", "published": "2011-08-26", "journal": {"volume": "286", "issn": "1083-351X", "issue": "34", "pages": "29922-29931", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": null, "doi": "10.1074/jbc.m111.233858", "pmid": "21724850", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:36.719Z", "modified": "2025-10-17T13:04:30.765Z"}, {"entity": "publication", "iuid": "e43e7e015dec4e649c76420282600e5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e43e7e015dec4e649c76420282600e5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e43e7e015dec4e649c76420282600e5a"}}, "title": "Identification of noncoding transcripts from within CENP-A chromatin at fission yeast centromeres.", "authors": [{"family": "Choi", "given": "Eun Shik", "initials": "ES"}, {"family": "Str\u00e5lfors", "given": "Annelie", "initials": "A"}, {"family": "Castillo", "given": "Araceli G", "initials": "AG"}, {"family": "Durand-Dubief", "given": "Micka\u00ebl", "initials": "M"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Allshire", "given": "Robin C", "initials": "RC"}], "type": "journal article", "published": "2011-07-01", "journal": {"volume": "286", "issn": "1083-351X", "issue": "26", "pages": "23600-23607", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The histone H3 variant CENP-A is the most favored candidate for an epigenetic mark that specifies the centromere. In fission yeast, adjacent heterochromatin can direct CENP-A(Cnp1) chromatin establishment, but the underlying features governing where CENP-A(Cnp1) chromatin assembles are unknown. We show that, in addition to centromeric regions, a low level of CENP-A(Cnp1) associates with gene promoters where histone H3 is depleted by the activity of the Hrp1(Chd1) chromatin-remodeling factor. Moreover, we demonstrate that noncoding RNAs are transcribed by RNA polymerase II (RNAPII) from CENP-A(Cnp1) chromatin at centromeres. These analyses reveal a similarity between centromeres and a subset of RNAPII genes and suggest a role for remodeling at RNAPII promoters within centromeres that influences the replacement of histone H3 with CENP-A(Cnp1).", "doi": "10.1074/jbc.M111.228510", "pmid": "21531710", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "M111.228510"}, {"db": "pmc", "key": "PMC3123123"}], "notes": [], "created": "2017-05-04T14:57:20.723Z", "modified": "2020-01-21T13:56:05.862Z"}, {"entity": "publication", "iuid": "3288a254cd004acaac77dcacd80433e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3288a254cd004acaac77dcacd80433e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3288a254cd004acaac77dcacd80433e1"}}, "title": "Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum.", "authors": [{"family": "Boesler", "given": "Carsten", "initials": "C"}, {"family": "Kruse", "given": "Janis", "initials": "J"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}, {"family": "Hammann", "given": "Christian", "initials": "C"}], "type": "journal article", "published": "2011-05-20", "journal": {"volume": "286", "issn": "1083-351X", "issue": "20", "pages": "17693-17703", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The amoeba Dictyostelium discoideum is a well established model organism for studying numerous aspects of cellular and developmental functions. Its ribosomal RNA (rRNA) is encoded in an extrachromosomal palindrome that exists in \u223c100 copies in the cell. In this study, we have set out to investigate the sequence of the expressed rRNA. For this, we have ligated the rRNA ends and performed RT-PCR on these circular RNAs. Sequencing revealed that the mature 26 S, 17 S, 5.8 S, and 5 S rRNAs have sizes of 3741, 1871, 162, and 112 nucleotides, respectively. Unlike the published data, all mature rRNAs of the same type uniformly display the same start and end nucleotides in the analyzed AX2 strain. We show the existence of a short lived primary transcript covering the rRNA transcription unit of 17 S, 5.8 S, and 26 S rRNA. Northern blots and RT-PCR reveal that from this primary transcript two precursor molecules of the 17 S and two precursors of the 26 S rRNA are generated. We have also determined the sequences of these precursor molecules, and based on these data, we propose a model for the maturation of the rRNAs in Dictyostelium discoideum that we compare with the processing of the rRNA transcription unit of Saccharomyces cerevisiae.", "doi": "10.1074/jbc.M110.208306", "pmid": "21454536", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "M110.208306"}, {"db": "pmc", "key": "PMC3093845"}, {"db": "GENBANK", "key": "FR733593"}, {"db": "GENBANK", "key": "FR733594"}, {"db": "GENBANK", "key": "FR733595"}, {"db": "GENBANK", "key": "FR733596"}, {"db": "GENBANK", "key": "FR733598"}, {"db": "GENBANK", "key": "FR733599"}, {"db": "GENBANK", "key": "FR733600"}], "notes": [], "created": "2017-05-04T14:57:20.426Z", "modified": "2020-01-21T13:56:01.411Z"}, {"entity": "publication", "iuid": "c78777ade0d647c8bb89f2dbabcd3ba7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c78777ade0d647c8bb89f2dbabcd3ba7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c78777ade0d647c8bb89f2dbabcd3ba7"}}, "title": "Cys-X scanning for expansion of active-site residues and modulation of catalytic functions in a glutathione transferase.", "authors": [{"family": "Norrg\u00e5rd", "given": "Malena A", "initials": "MA"}, {"family": "Hellman", "given": "Ulf", "initials": "U"}, {"family": "Mannervik", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2011-05-13", "journal": {"volume": "286", "issn": "1083-351X", "issue": "19", "pages": "16871-16878", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "We propose Cys-X scanning as a semisynthetic approach to engineer the functional properties of recombinant proteins. As in the case of Ala scanning, key residues in the primary structure are identified, and one of them is replaced by Cys via site-directed mutagenesis. The thiol of the residue introduced is subsequently modified by alternative chemical reagents to yield diverse Cys-X mutants of the protein. This chemical approach is orthogonal to Ala or Cys scanning and allows the expansion of the repertoire of amino acid side chains far beyond those present in natural proteins. In its present application, we have introduced Cys-X residues in human glutathione transferase (GST) M2-2, replacing Met-212 in the substrate-binding site. To achieve selectivity of the modifications, the Cys residues in the wild-type enzyme were replaced by Ala. A suite of simple substitutions resulted in a set of homologous Met derivatives ranging from normethionine to S-heptyl-cysteine. The chemical modifications were validated by HPLC and mass spectrometry. The derivatized mutant enzymes were assayed with alternative GST substrates representing diverse chemical reactions: aromatic substitution, epoxide opening, transnitrosylation, and addition to an ortho-quinone. The Cys substitutions had different effects on the alternative substrates and differentially enhanced or suppressed catalytic activities depending on both the Cys-X substitution and the substrate assayed. As a consequence, the enzyme specificity profile could be changed among the alternative substrates. The procedure lends itself to large-scale production of Cys-X modified protein variants.", "doi": "10.1074/jbc.M111.230078", "pmid": "21454564", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "M111.230078"}, {"db": "pmc", "key": "PMC3089530"}], "notes": [], "created": "2017-05-04T15:01:58.898Z", "modified": "2020-01-21T13:56:05.144Z"}, {"entity": "publication", "iuid": "2053235d85a7403f82a48f1034ca4dac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2053235d85a7403f82a48f1034ca4dac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2053235d85a7403f82a48f1034ca4dac"}}, "title": "A chromatin-remodeling protein is a component of fission yeast mediator.", "authors": [{"family": "Khorosjutina", "given": "Olga", "initials": "O"}, {"family": "Wanrooij", "given": "Paulina H", "initials": "PH"}, {"family": "Walfridsson", "given": "Julian", "initials": "J"}, {"family": "Szilagyi", "given": "Zsolt", "initials": "Z"}, {"family": "Zhu", "given": "Xuefeng", "initials": "X"}, {"family": "Baraznenok", "given": "Vera", "initials": "V"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Gustafsson", "given": "Claes M", "initials": "CM"}], "type": "journal article", "published": "2010-09-24", "journal": {"volume": "285", "issn": "1083-351X", "issue": "39", "pages": "29729-29737", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The multiprotein Mediator complex is an important regulator of RNA polymerase II-dependent genes in eukaryotic cells. In contrast to the situation in many other eukaryotes, the conserved Med15 protein is not a stable component of Mediator isolated from fission yeast. We here demonstrate that Med15 exists in a protein complex together with Hrp1, a CHD1 ATP-dependent chromatin-remodeling protein. The Med15-Hrp1 subcomplex is not a component of the core Mediator complex but can interact with the L-Mediator conformation. Deletion of med15(+) and hrp1(+) causes very similar effects on global steady-state levels of mRNA, and genome-wide analyses demonstrate that Med15 associates with a distinct subset of Hrp1-bound gene promoters. Our findings therefore indicate that Mediator may directly influence histone density at regulated promoters.", "doi": "10.1074/jbc.M110.153858", "pmid": "20622008", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "M110.153858"}, {"db": "pmc", "key": "PMC2943280"}], "notes": [], "created": "2017-05-04T15:03:06.026Z", "modified": "2017-05-30T12:39:09.916Z"}], "created": "2017-05-09T09:12:14.505Z", "modified": "2020-11-27T13:14:00.950Z"}