{"entity": "researcher", "timestamp": "2026-07-19T07:06:22.813Z", "family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "affiliations": ["2Ume\u00e5 Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932"}}, "publications": [{"entity": "publication", "iuid": "8ed2bc92c9ef4a80aab66db3bcbdb8b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ed2bc92c9ef4a80aab66db3bcbdb8b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ed2bc92c9ef4a80aab66db3bcbdb8b1"}}, "title": "Wood-specific modification of glucuronoxylan can enhance growth in Populus.", "authors": [{"family": "Urbancsok", "given": "J\u00e1nos", "initials": "J", "orcid": "0000-0003-3237-6806", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6f0e25417543f49060959d3af92967.json"}}, {"family": "Donev", "given": "Evgeniy N", "initials": "EN", "orcid": "0000-0002-7279-0481", "researcher": {"href": "https://publications.scilifelab.se/researcher/26467c84e2664b4980a4ed04335860ad.json"}}, {"family": "Derba-Maceluch", "given": "Marta", "initials": "M", "orcid": "0000-0002-8034-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5be452cef9048e19a08fa8043b74329.json"}}, {"family": "Sivan", "given": "Pramod", "initials": "P", "orcid": "0000-0001-5297-2221", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bed5958298d4ca08df06860c94a3878.json"}}, {"family": "Barbut", "given": "F\u00e9lix R", "initials": "FR", "orcid": "0000-0001-5395-6776", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df5c17bbf0440fd8be22761c2df9a6f.json"}}, {"family": "Mitra", "given": "Madhusree", "initials": "M", "orcid": "0000-0002-8653-8770", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1827f45c7f4853888f15d857b7e414.json"}}, {"family": "Yassin", "given": "Zakiya", "initials": "Z", "orcid": "0000-0001-6878-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cd7ddc17274c0c9eabb07ae4e6c8e0.json"}}, {"family": "Cermanov\u00e1", "given": "Kate\u0159ina", "initials": "K"}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Karady", "given": "Michal", "initials": "M", "orcid": "0000-0002-5603-706X", "researcher": {"href": "https://publications.scilifelab.se/researcher/114911ccd31849e1a7584b5a52e9eb14.json"}}, {"family": "Scheepers", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-5630-1377", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a566216ee146d1bba50d7f8779a6f8.json"}}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2025-08-23", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "issn-l": "0022-0957"}, "abstract": "Xylem cells are surrounded by primary and secondary cell walls. Formation of primary walls is regulated by the cell wall integrity surveillance system, but it is unclear if the deposition of secondary walls is similarly regulated. To study this question, we introduced to aspen three different enzymes cleaving cell wall-localized xylan and we suppressed xylan synthase components either ubiquitously or specifically during secondary wall formation using Populus trichocarpa GT43B promoter. When xylan was ubiquitously altered, 95% of lines showed reduced growth, whereas when it was altered during secondary wall deposition, 30% of lines grew better with the rest having no growth impairment, suggesting opposite effects of primary and secondary wall disturbances. To detect mechanism of growth stimulation by disturbed deposition of secondary wall, we analyzed changes in wood quality traits, chemistry, transcriptomics, metabolomics and hormonomics in transgenic lines. We found increased tension wood production, reduced S- and H-lignin, and changes in several metabolites in common in these lines. Remorin REM1.3 and NRL2 (NPH3 family) transcripts increased and changes in jasmonates, ABA and SA occurred in secondary wall-forming xylem suggesting their involvement in secondary wall integrity surveyance and signaling. The data indicate that a unique program mediates responses to secondary wall impairment that induces growth.", "doi": "10.1093/jxb/eraf364", "pmid": "40847653", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "8240116"}], "notes": [], "created": "2025-11-18T12:16:27.291Z", "modified": "2025-11-18T12:16:27.407Z"}, {"entity": "publication", "iuid": "ce4033f0d9fc495bb5eaed500136d045", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce4033f0d9fc495bb5eaed500136d045.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce4033f0d9fc495bb5eaed500136d045"}}, "title": "Glucuronoyl Esterase Expressed in Aspen Xylem Affects \u03b3-Ester Linkages Between Lignin and Glucuronoxylan Reducing Recalcitrance and Accelerating Growth.", "authors": [{"family": "Derba-Maceluch", "given": "Marta", "initials": "M", "orcid": "0000-0002-8034-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5be452cef9048e19a08fa8043b74329.json"}}, {"family": "Garc\u00eda Roma\u00f1ach", "given": "Laura", "initials": "L", "orcid": "0000-0003-1188-5193", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0a86fa91e6745e0ac048cf33e1ecda5.json"}}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M", "orcid": "0000-0002-0903-6662", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db0f81a369741b0847c6f79746d82aa.json"}}, {"family": "Mitra", "given": "Madhusree", "initials": "M", "orcid": "0000-0002-8653-8770", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1827f45c7f4853888f15d857b7e414.json"}}, {"family": "Donev", "given": "Evgeniy N", "initials": "EN", "orcid": "0000-0002-7279-0481", "researcher": {"href": "https://publications.scilifelab.se/researcher/26467c84e2664b4980a4ed04335860ad.json"}}, {"family": "Urbancsok", "given": "J\u00e1nos", "initials": "J", "orcid": "0000-0003-3237-6806", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6f0e25417543f49060959d3af92967.json"}}, {"family": "Yassin", "given": "Zakiya", "initials": "Z", "orcid": "0000-0001-6878-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cd7ddc17274c0c9eabb07ae4e6c8e0.json"}}, {"family": "Gandla", "given": "Madhavi L", "initials": "ML", "orcid": "0000-0003-2798-6298", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1e32323239243999cbb5f1dcc06279a.json"}}, {"family": "Sivan", "given": "Pramod", "initials": "P", "orcid": "0000-0001-5297-2221", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bed5958298d4ca08df06860c94a3878.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Scheepers", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-5630-1377", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a566216ee146d1bba50d7f8779a6f8.json"}}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ", "orcid": "0000-0003-3866-0111", "researcher": {"href": "https://publications.scilifelab.se/researcher/1769e674df8649ce82a0d058f0a309dc.json"}}, {"family": "Vilaplana", "given": "Francisco", "initials": "F", "orcid": "0000-0003-3572-7798", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ee4f3eaece8487fb5cb34ce6cfbbcbf.json"}}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2025-08-17", "journal": {"title": "Plant Biotechnol. J.", "issn": "1467-7652", "issn-l": "1467-7644"}, "abstract": "Wood is the most abundant renewable natural resource composed of different polysaccharides and lignin, but its utilisation is hampered by intermolecular linkages between these components forming lignin-carbohydrate complexes (LCCs) causing recalcitrance. The links between glucuronoxylan and the \u03b3-C of lignin (\u03b3-ester linkages) are thought to contribute to one-third of LCCs, but direct evidence for their natural occurrence and their role in recalcitrance has been scarce so far. To address these issues, Phanerochaete carnosa glucuronoyl esterase (PcGCE), hydrolysing \u03b3-ester linkages, was expressed in cell walls of developing wood in hybrid aspen (Populus tremula L. \u00d7 tremuloides Michx.). The enzyme reduced HSQC 2D NMR signals corresponding to the \u03b3-esters and xylan in dioxane-extracted LCCs without altering glucuronoxylan content or structure. This increased acid solubility of lignin and lignin content. Reduced wood recalcitrance was shown by increased sugar yields and glucose production rates (by approx. 20%) in saccharification without pretreatment and increased xylan extractability by subcritical water (by approx. 70%). Moreover, trees expressing PcGCE exhibited greater primary and secondary growth. Transcriptomics and metabolomics analyses in developing wood suggested that growth could have been induced by a higher transcription of SMR2 and RPOTmp, which was likely triggered by the secondary cell wall integrity signalling. The results provide evidence for the natural existence of LCC \u03b3-esters and their significant contribution to lignocellulose recalcitrance. Furthermore, they show that reducing \u03b3-ester linkages could increase plant productivity.", "doi": "10.1111/pbi.70301", "pmid": "40819283", "labels": {"Swedish NMR Centre": "Collaborative", "Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-10T14:26:46.012Z", "modified": "2025-11-18T12:07:29.246Z"}, {"entity": "publication", "iuid": "4e7a9e7c4d2c4b9f97fe7db41cc35680", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e7a9e7c4d2c4b9f97fe7db41cc35680.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e7a9e7c4d2c4b9f97fe7db41cc35680"}}, "title": "Modification of xylan in secondary walls alters cell wall biosynthesis and wood formation programs and improves saccharification.", "authors": [{"family": "Sivan", "given": "Pramod", "initials": "P", "orcid": "0000-0001-5297-2221", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bed5958298d4ca08df06860c94a3878.json"}}, {"family": "Urbancsok", "given": "J\u00e1nos", "initials": "J", "orcid": "0000-0003-3237-6806", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6f0e25417543f49060959d3af92967.json"}}, {"family": "Donev", "given": "Evgeniy N", "initials": "EN", "orcid": "0000-0002-7279-0481", "researcher": {"href": "https://publications.scilifelab.se/researcher/26467c84e2664b4980a4ed04335860ad.json"}}, {"family": "Derba-Maceluch", "given": "Marta", "initials": "M", "orcid": "0000-0002-8034-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5be452cef9048e19a08fa8043b74329.json"}}, {"family": "Barbut", "given": "F\u00e9lix R", "initials": "FR", "orcid": "0000-0001-5395-6776", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df5c17bbf0440fd8be22761c2df9a6f.json"}}, {"family": "Yassin", "given": "Zakiya", "initials": "Z", "orcid": "0000-0001-6878-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cd7ddc17274c0c9eabb07ae4e6c8e0.json"}}, {"family": "Gandla", "given": "Madhavi L", "initials": "ML", "orcid": "0000-0003-2798-6298", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1e32323239243999cbb5f1dcc06279a.json"}}, {"family": "Mitra", "given": "Madhusree", "initials": "M", "orcid": "0000-0002-8653-8770", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1827f45c7f4853888f15d857b7e414.json"}}, {"family": "Heinonen", "given": "Saara E", "initials": "SE", "orcid": "0000-0002-5069-2370", "researcher": {"href": "https://publications.scilifelab.se/researcher/3756b55888f745e6b7af3783e80b6037.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Cermanov\u00e1", "given": "Kate\u0159ina", "initials": "K", "orcid": "0009-0006-5809-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/16ca192806d6450fb69225e175eef629.json"}}, {"family": "Karady", "given": "Michal", "initials": "M", "orcid": "0000-0002-5603-706X", "researcher": {"href": "https://publications.scilifelab.se/researcher/114911ccd31849e1a7584b5a52e9eb14.json"}}, {"family": "Scheepers", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-5630-1377", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a566216ee146d1bba50d7f8779a6f8.json"}}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ", "orcid": "0000-0003-3866-0111", "researcher": {"href": "https://publications.scilifelab.se/researcher/1769e674df8649ce82a0d058f0a309dc.json"}}, {"family": "Master", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-6837-9817", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b15165d3c44d74a533948db1aa2d9a.json"}}, {"family": "Vilaplana", "given": "Francisco", "initials": "F", "orcid": "0000-0003-3572-7798", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ee4f3eaece8487fb5cb34ce6cfbbcbf.json"}}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Plant Biotechnol. J.", "issn": "1467-7652", "volume": "23", "issue": "1", "pages": "174-197", "issn-l": "1467-7644"}, "abstract": "Wood of broad-leaf tree species is a valued source of renewable biomass for biorefinery and a target for genetic improvement efforts to reduce its recalcitrance. Glucuronoxylan (GX) plays a key role in recalcitrance through its interactions with cellulose and lignin. To reduce recalcitrance, we modified wood GX by expressing GH10 and GH11 endoxylanases from Aspergillus nidulans in hybrid aspen (Populus tremula L. \u00d7 tremuloides Michx.) and targeting the enzymes to cell wall. The xylanases reduced tree height, modified cambial activity by increasing phloem and reducing xylem production, and reduced secondary wall deposition. Xylan molecular weight was decreased, and the spacing between acetyl and MeGlcA side chains was reduced in transgenic lines. The transgenic trees produced hypolignified xylem having thin secondary walls and deformed vessels. Glucose yields of enzymatic saccharification without pretreatment almost doubled indicating decreased recalcitrance. The transcriptomics, hormonomics and metabolomics data provided evidence for activation of cytokinin and ethylene signalling pathways, decrease in ABA levels, transcriptional suppression of lignification and a subset of secondary wall biosynthetic program, including xylan glucuronidation and acetylation machinery. Several candidate genes for perception of impairment in xylan integrity were detected. These candidates could provide a new target for uncoupling negative growth effects from reduced recalcitrance. In conclusion, our study supports the hypothesis that xylan modification generates intrinsic signals and evokes novel pathways regulating tree growth and secondary wall biosynthesis.", "doi": "10.1111/pbi.14487", "pmid": "39436777", "labels": {"Cryo-EM": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11672743"}], "notes": [], "created": "2024-11-26T10:43:47.363Z", "modified": "2025-11-18T12:14:05.231Z"}, {"entity": "publication", "iuid": "685add63cbd741ca860065bfa2d83316", "links": {"self": {"href": "https://publications.scilifelab.se/publication/685add63cbd741ca860065bfa2d83316.json"}, "display": {"href": "https://publications.scilifelab.se/publication/685add63cbd741ca860065bfa2d83316"}}, "title": "The Arabidopsis splicing factor PORCUPINE/SmE1 orchestrates temperature-dependent root development via auxin homeostasis maintenance.", "authors": [{"family": "El Arbi", "given": "Nabila", "initials": "N", "orcid": "0000-0001-5494-2229", "researcher": {"href": "https://publications.scilifelab.se/researcher/614aefe01caa48fdb17469924954fb77.json"}}, {"family": "Nardeli", "given": "Sarah Muniz", "initials": "SM", "orcid": "0000-0001-8858-807X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ad3aa41f7134bcf8679f7bd90be878f.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Schmid", "given": "Markus", "initials": "M", "orcid": "0000-0002-0068-2967", "researcher": {"href": "https://publications.scilifelab.se/researcher/8705d242aa8f4f92b930c2cdc23254f0.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "244", "issue": "4", "pages": "1408-1421", "issn-l": "0028-646X"}, "abstract": "Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.", "doi": "10.1111/nph.20153", "pmid": "39327913", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-25T10:27:56.725Z", "modified": "2025-10-17T13:03:12.817Z"}, {"entity": "publication", "iuid": "7075b2d10093427fbece11be1015664e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7075b2d10093427fbece11be1015664e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7075b2d10093427fbece11be1015664e"}}, "title": "Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development.", "authors": [{"family": "Urbancsok", "given": "J\u00e1nos", "initials": "J", "orcid": "0000-0003-3237-6806", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6f0e25417543f49060959d3af92967.json"}}, {"family": "Donev", "given": "Evgeniy N", "initials": "EN", "orcid": "0000-0002-7279-0481", "researcher": {"href": "https://publications.scilifelab.se/researcher/26467c84e2664b4980a4ed04335860ad.json"}}, {"family": "Sivan", "given": "Pramod", "initials": "P", "orcid": "0000-0001-5297-2221", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bed5958298d4ca08df06860c94a3878.json"}}, {"family": "van Zalen", "given": "Elena", "initials": "E", "orcid": "0000-0003-1621-3222", "researcher": {"href": "https://publications.scilifelab.se/researcher/00350ef0e2434baaa6d39f373a561a35.json"}}, {"family": "Barbut", "given": "F\u00e9lix R", "initials": "FR", "orcid": "0000-0001-5395-6776", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df5c17bbf0440fd8be22761c2df9a6f.json"}}, {"family": "Derba-Maceluch", "given": "Marta", "initials": "M", "orcid": "0000-0002-8034-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5be452cef9048e19a08fa8043b74329.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Yassin", "given": "Zakiya", "initials": "Z", "orcid": "0000-0001-6878-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cd7ddc17274c0c9eabb07ae4e6c8e0.json"}}, {"family": "Gandla", "given": "Madhavi L", "initials": "ML", "orcid": "0000-0003-2798-6298", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1e32323239243999cbb5f1dcc06279a.json"}}, {"family": "Karady", "given": "Michal", "initials": "M", "orcid": "0000-0002-5603-706X", "researcher": {"href": "https://publications.scilifelab.se/researcher/114911ccd31849e1a7584b5a52e9eb14.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Winestrand", "given": "Sandra", "initials": "S", "orcid": "0000-0001-8784-9696", "researcher": {"href": "https://publications.scilifelab.se/researcher/59e4a2ea1193426d939863a4b3188963.json"}}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ", "orcid": "0000-0003-3866-0111", "researcher": {"href": "https://publications.scilifelab.se/researcher/1769e674df8649ce82a0d058f0a309dc.json"}}, {"family": "Scheepers", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-5630-1377", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a566216ee146d1bba50d7f8779a6f8.json"}}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2023-12-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "240", "issue": "6", "pages": "2312-2334", "issn-l": "0028-646X"}, "abstract": "Stem bending in trees induces flexure wood but its properties and development are poorly understood. Here, we investigated the effects of low-intensity multidirectional stem flexing on growth and wood properties of hybrid aspen, and on its transcriptomic and hormonal responses. Glasshouse-grown trees were either kept stationary or subjected to several daily shakes for 5 wk, after which the transcriptomes and hormones were analyzed in the cambial region and developing wood tissues, and the wood properties were analyzed by physical, chemical and microscopy techniques. Shaking increased primary and secondary growth and altered wood differentiation by stimulating gelatinous-fiber formation, reducing secondary wall thickness, changing matrix polysaccharides and increasing cellulose, G- and H-lignin contents, cell wall porosity and saccharification yields. Wood-forming tissues exhibited elevated jasmonate, polyamine, ethylene and brassinosteroids and reduced abscisic acid and gibberellin signaling. Transcriptional responses resembled those during tension wood formation but not opposite wood formation and revealed several thigmomorphogenesis-related genes as well as novel gene networks including FLA and XTH genes encoding plasma membrane-bound proteins. Low-intensity stem flexing stimulates growth and induces wood having improved biorefinery properties through molecular and hormonal pathways similar to thigmomorphogenesis in herbaceous plants and largely overlapping with the tension wood program of hardwoods.", "doi": "10.1111/nph.19307", "pmid": "37857351", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2023-12-03T19:51:07.718Z", "modified": "2025-10-17T13:03:13.338Z"}, {"entity": "publication", "iuid": "2c5dd802fbf44ee5bed51c886ad791d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c5dd802fbf44ee5bed51c886ad791d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c5dd802fbf44ee5bed51c886ad791d3"}}, "title": "Changes in cell wall composition due to a pectin biosynthesis enzyme GAUT10 impact root growth.", "authors": [{"family": "Dash", "given": "Linkan", "initials": "L", "orcid": "0000-0003-4843-8653", "researcher": {"href": "https://publications.scilifelab.se/researcher/7af311e014b143dbad9136a979947356.json"}}, {"family": "Swaminathan", "given": "Sivakumar", "initials": "S", "orcid": "0000-0003-3931-275X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcd3993276c442f4b456f6486a29f0ae.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Gonzales", "given": "Caitlin Leigh P", "initials": "CLP", "orcid": "0009-0008-3055-8810", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0cb2a7468a74ff0bfc9935ee7894076.json"}}, {"family": "Montes", "given": "Christian", "initials": "C", "orcid": "0000-0003-1249-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/5766afbedb8c42ae97070a8fbb366e58.json"}}, {"family": "Solanki", "given": "Neel", "initials": "N"}, {"family": "Mejia", "given": "Ludvin", "initials": "L"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Zabotina", "given": "Olga A", "initials": "OA", "orcid": "0000-0001-6938-6923", "researcher": {"href": "https://publications.scilifelab.se/researcher/57bb9870ea5b49428f4f0134c9abd8c4.json"}}, {"family": "Kelley", "given": "Dior R", "initials": "DR", "orcid": "0000-0001-9186-4186", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8c76de8e1094308a0c236ee6c68110b.json"}}], "type": "journal article", "published": "2023-11-22", "journal": {"title": "Plant Physiol.", "issn": "1532-2548", "volume": "193", "issue": "4", "pages": "2480-2497", "issn-l": "0032-0889"}, "abstract": "Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as \u03b2-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short-root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan-I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short-root phenotype in gaut10 was linked to \u03b2-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.", "doi": "10.1093/plphys/kiad465", "pmid": "37606259", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10663140"}, {"db": "pii", "key": "7247419"}], "notes": [], "created": "2023-12-03T19:51:00.483Z", "modified": "2025-10-17T13:03:13.397Z"}, {"entity": "publication", "iuid": "5a695409066f48d7b8257d27f5949ea2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a695409066f48d7b8257d27f5949ea2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a695409066f48d7b8257d27f5949ea2"}}, "title": "Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit.", "authors": [{"family": "Casanova-S\u00e1ez", "given": "Rub\u00e9n", "initials": "R", "orcid": "0000-0001-5683-7051", "researcher": {"href": "https://publications.scilifelab.se/researcher/17868bb801534bd794ef1f5d2815a531.json"}}, {"family": "Mateo-Bonmat\u00ed", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-2364-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1e96edf1a914d2f8ea8eb46c3ebacc4.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "P\u011bn\u010d\u00edk", "given": "Ale\u0161", "initials": "A", "orcid": "0000-0002-1314-2249", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13dbbec35c441daa7ed84daa05cd6e7.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Staswick", "given": "Paul", "initials": "P", "orcid": "0000-0003-2798-0275", "researcher": {"href": "https://publications.scilifelab.se/researcher/4600c9bfb57f4146943a0fe71cde267b.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "235", "issue": "1", "pages": "263-275", "issn-l": "0028-646X"}, "abstract": "Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.", "doi": "10.1111/nph.18114", "pmid": "35322877", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9322293"}], "notes": [], "created": "2022-12-05T08:06:56.189Z", "modified": "2025-10-17T13:03:14.842Z"}, {"entity": "publication", "iuid": "7b45e3da656444be93f45f5707306a4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b45e3da656444be93f45f5707306a4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b45e3da656444be93f45f5707306a4e"}}, "title": "Broadening the roles of UDP-glycosyltransferases in auxin homeostasis and plant development.", "authors": [{"family": "Mateo-Bonmat\u00ed", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-2364-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1e96edf1a914d2f8ea8eb46c3ebacc4.json"}}, {"family": "Casanova-S\u00e1ez", "given": "Rub\u00e9n", "initials": "R", "orcid": "0000-0001-5683-7051", "researcher": {"href": "https://publications.scilifelab.se/researcher/17868bb801534bd794ef1f5d2815a531.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "232", "issue": "2", "pages": "642-654", "issn-l": "0028-646X"}, "abstract": "The levels of the important plant growth regulator indole-3-acetic acid (IAA) are tightly controlled within plant tissues to spatiotemporally orchestrate concentration gradients that drive plant growth and development. Metabolic inactivation of bioactive IAA is known to participate in the modulation of IAA maxima and minima. IAA can be irreversibly inactivated by oxidation and conjugation to aspartate and glutamate. Usually overlooked because of its reversible nature, the most abundant inactive IAA form is the IAA-glucose (IAA-glc) conjugate. Glycosylation of IAA in Arabidopsis thaliana is reported to be carried out by UDP-glycosyltransferase 84B1 (UGT84B1), while UGT74D1 has been implicated in the glycosylation of the irreversibly formed IAA catabolite oxIAA. Here we demonstrated that both UGT84B1 and UGT74D1 modulate IAA levels throughout plant development by dual IAA and oxIAA glycosylation. Moreover, we identified a novel UGT subfamily whose members redundantly mediate the glycosylation of oxIAA and modulate skotomorphogenic growth.", "doi": "10.1111/nph.17633", "pmid": "34289137", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-09T13:29:26.302Z", "modified": "2025-10-17T13:03:15.732Z"}, {"entity": "publication", "iuid": "c9d485a9f7dc4951954d7791279e86ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9d485a9f7dc4951954d7791279e86ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9d485a9f7dc4951954d7791279e86ff"}}, "title": "Studies of moss reproductive development indicate that auxin biosynthesis in apical stem cells may constitute an ancestral function for focal growth control.", "authors": [{"family": "Landberg", "given": "Katarina", "initials": "K", "orcid": "0000-0002-2945-8571", "researcher": {"href": "https://publications.scilifelab.se/researcher/20a571f6ca8340c0930261431100a33e.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Sundberg", "given": "Eva", "initials": "E", "orcid": "0000-0003-4228-434X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfcb8849bdf849328f4b82b435f5c98f.json"}}, {"family": "Thelander", "given": "Mattias", "initials": "M", "orcid": "0000-0002-6663-7405", "researcher": {"href": "https://publications.scilifelab.se/researcher/a35bfb87fd794e3d81c2908833cddb8c.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "229", "issue": "2", "pages": "845-860", "issn-l": "0028-646X"}, "abstract": "The plant hormone auxin is a key factor for regulation of plant development, and this function was probably reinforced during the evolution of early land plants. We have extended the available toolbox to allow detailed studies of how auxin biosynthesis and responses are regulated in moss reproductive organs, their stem cells and gametes to better elucidate the function of auxin in the morphogenesis of early land plants. We measured auxin metabolites and identified IPyA (indole-3-pyruvic acid) as the main biosynthesis pathway in Physcomitrium (Physcomitrella) patens and established knock-out, overexpressor and reporter lines for biosynthesis genes which were analyzed alongside previously reported auxin-sensing and transport reporters. Vegetative and reproductive apical stem cells synthesize auxin. Sustained stem cell activity depends on an inability to sense the auxin produced while progeny of the stem cells respond to the auxin, aiding in the control of cell division, expansion and differentiation. Gamete precursors are dependent on a certain degree of auxin sensing, while the final differentiation is a low auxin-sensing process. Tha data presented indicate that low auxin activity may represent a conserved hallmark of land plant gametes, and that local auxin biosynthesis in apical stem cells may be part of an ancestral mechanism to control focal growth.", "doi": "10.1111/nph.16914", "pmid": "32901452", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7821132"}], "notes": [], "created": "2021-12-09T13:29:38.769Z", "modified": "2025-10-17T13:03:16.435Z"}, {"entity": "publication", "iuid": "74c38ce26afa4ab181be8918dda27738", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74c38ce26afa4ab181be8918dda27738.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74c38ce26afa4ab181be8918dda27738"}}, "title": "A bacterial assay for rapid screening of IAA catabolic enzymes.", "authors": [{"family": "Brunoni", "given": "Federica", "initials": "F", "orcid": "0000-0003-1497-9419", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a28132c7a0e407da31e4d79698679c6.json"}}, {"family": "Collani", "given": "Silvio", "initials": "S", "orcid": "0000-0002-9603-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/0896530185b54e16824cd26658ccdfc8.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Schmid", "given": "Markus", "initials": "M", "orcid": "0000-0002-0068-2967", "researcher": {"href": "https://publications.scilifelab.se/researcher/8705d242aa8f4f92b930c2cdc23254f0.json"}}, {"family": "Bellini", "given": "Catherine", "initials": "C", "orcid": "0000-0003-2985-6649", "researcher": {"href": "https://publications.scilifelab.se/researcher/644f290e267f43fa9c5e76b2f159a62d.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}], "type": "journal article", "published": "2019-11-04", "journal": {"title": "Plant Methods", "issn": "1746-4811", "volume": "15", "issue": "1", "pages": "126", "issn-l": "1746-4811"}, "abstract": "Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl-l-aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and in planta feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays.\n\nIn this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC-ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein.\n\nThis new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.", "doi": "10.1186/s13007-019-0509-6", "pmid": "31700527", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "509"}, {"db": "pmc", "key": "PMC6827244"}], "notes": [], "created": "2020-01-07T15:51:28.889Z", "modified": "2025-10-17T13:03:17.248Z"}]}