{"entity": "journal", "iuid": "1848853d93bd41789c064efa881aa2c3", "timestamp": "2026-06-10T00:00:48.793Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Physiol%20Plantarum.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Physiol%20Plantarum"}}, "title": "Physiol Plantarum", "issn": "1399-3054", "issn-l": "0031-9317", "publications_count": 13, "publications": [{"entity": "publication", "iuid": "19188c6729144072978d9a3d01d09133", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19188c6729144072978d9a3d01d09133.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19188c6729144072978d9a3d01d09133"}}, "title": "Genetic Analysis of Apple Autumn Canopy Senescence in a Nordic Climate.", "authors": [{"family": "Skytte Af S\u00e4tra", "given": "Jonas", "initials": "J", "orcid": "0000-0002-2827-4842", "researcher": {"href": "https://publications.scilifelab.se/researcher/00b323220517477eb3c4acda1bb64c81.json"}}], "type": "journal article", "published": "2025-10-30", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "6", "pages": "e70599", "issn-l": "0031-9317"}, "abstract": "Autumn phenology traits are likely to be essential for the adaptation of apple to boreal climate. However, the genetic control of these traits is not well understood, and, for example, growth cessation does not appear to be controlled by day length as in many other boreal tree species. Here, I combine a quantitative genetic and population genomic approach to study autumn senescence in apple. I phenotyped a diverse germplasm collection for the timing of autumn senescence, performed quantitative trait loci (QTL) mapping in a multiparental population (MPP), and investigated genomic signals of selection to identify candidate genes. The timing of 50% autumn senescence was negatively correlated with adaptation to higher (boreal) climate zones. Two QTL were found to control the timing of autumn senescence in the MPP, exhibiting both dominance and epistatic interactions. The QTL on linkage group (LG) 17 was also variable in the diversity germplasm, while the QTL on LG11 was not. Cultivars adapted to boreal climate showed weak signals of selection at two loci within the genomic region of chromosome 17 corresponding to the LG17 QTL interval, consistent with a recent expansion to northern Sweden. These loci coincide with two predicted UGT85 genes and a possible copy number variation in PHYC, respectively. Thus, this study provides valuable information for further research and breeding of apple in light of the ongoing climate change.", "doi": "10.1111/ppl.70599", "pmid": "41164927", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573221"}], "notes": [], "created": "2025-11-07T07:26:45.450Z", "modified": "2025-11-14T11:08:25.063Z"}, {"entity": "publication", "iuid": "97dcd02768fa4b35be175ba383846812", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97dcd02768fa4b35be175ba383846812.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97dcd02768fa4b35be175ba383846812"}}, "title": "Comparative Study of the Mitochondrial Proteome From Mesophyll, Vascular, and Guard Cells in Response to Carbon Starvation.", "authors": [{"family": "Boussardon", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0001-8313-3535", "researcher": {"href": "https://publications.scilifelab.se/researcher/63dace73d3684bf3b48c13b58c5f777f.json"}}, {"family": "Hussain", "given": "Shah", "initials": "S", "orcid": "0000-0003-4977-1167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f9c2bc4a6094b52b13737f26051bbd3.json"}}, {"family": "Keech", "given": "Olivier", "initials": "O", "orcid": "0000-0002-0546-7721", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbfa829eb0b74b67aed7865dda0e15d3.json"}}], "type": "journal article", "published": "2025-08-30", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "5", "pages": "e70465", "issn-l": "0031-9317"}, "abstract": "A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.", "doi": "10.1111/ppl.70465", "pmid": "40873255", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12391860"}], "notes": [], "created": "2025-11-27T13:03:24.119Z", "modified": "2025-11-27T13:03:24.590Z"}, {"entity": "publication", "iuid": "e300a5100ec7443c9deaba850a878de7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e300a5100ec7443c9deaba850a878de7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e300a5100ec7443c9deaba850a878de7"}}, "title": "Metabolomic profiling of shade response and in silico analysis of PAL homologs imply the potential presence of bifunctional ammonia lyases in conifers.", "authors": [{"family": "Ranade", "given": "Sonali Sachin", "initials": "SS"}, {"family": "Garc\u00eda-Gil", "given": "Mar\u00eda Rosario", "initials": "MR", "orcid": "0000-0002-6834-6708", "researcher": {"href": "https://publications.scilifelab.se/researcher/774898d2b46f44cb8475be89ecd8b79d.json"}}], "type": "journal article", "published": "2025-03-28", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "2", "pages": "e70175", "issn-l": "0031-9317"}, "abstract": "Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.", "doi": "10.1111/ppl.70175", "pmid": "40148258", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11949857"}], "notes": [], "created": "2025-11-18T12:14:03.049Z", "modified": "2025-11-18T12:14:03.058Z"}, {"entity": "publication", "iuid": "067b61d871b748229c2cf96c89adeaa7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/067b61d871b748229c2cf96c89adeaa7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/067b61d871b748229c2cf96c89adeaa7"}}, "title": "A suitable strategy to find IAA metabolism mutants.", "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": "P\u011bn\u010d\u00edk", "given": "Ale\u0161", "initials": "A", "orcid": "0000-0002-1314-2249", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13dbbec35c441daa7ed84daa05cd6e7.json"}}, {"family": "Mu\u00f1oz-Viana", "given": "Rafael", "initials": "R", "orcid": "0000-0002-1363-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bd9a92a13fd4395aeae214b4930e55a.json"}}, {"family": "Brunoni", "given": "Federica", "initials": "F", "orcid": "0000-0003-1497-9419", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a28132c7a0e407da31e4d79698679c6.json"}}, {"family": "Pinto", "given": "Rui", "initials": "R", "orcid": "0000-0002-8527-4873", "researcher": {"href": "https://publications.scilifelab.se/researcher/58f5bd6ddde8458d927e78ef13efb67b.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Mateo-Bonmat\u00ed", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-2364-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1e96edf1a914d2f8ea8eb46c3ebacc4.json"}}], "type": "journal article", "published": "2025-03-21", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "2", "pages": "e70166", "issn-l": "0031-9317"}, "abstract": "Indole-3-acetic acid (IAA), the most common form of auxin, is involved in a great range of plant physiological processes. IAA is synthesized from the amino acid tryptophan and can be transported and inactivated in a myriad of ways. Despite intense research efforts, there are still dark corners in our comprehension of IAA metabolism and its interplays with other pathways. Genetic screens are a powerful tool for unbiasedly looking for new players in a given biological process. However, pleiotropism of auxin-related phenotypes and indirect effects make it necessary to incorporate additional screening steps to specifically find mutants affected in IAA homeostasis. We previously developed and validated a high-throughput methodology to simultaneously quantify IAA, key precursors, and inactive forms from as little as 10 mg of fresh tissue. We have carried out a genetic screening to identify mutants involved in IAA metabolism. Auxin reporters DR5pro:VENUS and 35Spro:DII-VENUS were EMS-mutagenized and subjected to a parallel morphological and reporter-signal pre-screen. We then obtained the auxin metabolite profile of 325 M3 selected lines and used multivariate data analysis to identify potential IAA-metabolism mutants. To test the screening design, we identified the causal mutations in three of the candidate lines by mapping-by-sequencing: dii365.3, dii571.1 and dr693. These carry new alleles of CYP83A1, MIAO, and SUPERROOT2, respectively, all of which have been previously involved in auxin homeostasis. Our results support the suitability of this approach to find new genes involved in IAA metabolism.", "doi": "10.1111/ppl.70166", "pmid": "40113441", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11925725"}], "notes": [], "created": "2025-11-18T12:07:26.876Z", "modified": "2025-11-18T12:07:27.054Z"}, {"entity": "publication", "iuid": "7910417a408d425d8241f2ab42cf38d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7910417a408d425d8241f2ab42cf38d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7910417a408d425d8241f2ab42cf38d8"}}, "title": "An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula.", "authors": [{"family": "Robinson", "given": "Kathryn M", "initials": "KM", "orcid": "0000-0002-5249-604X", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d40626e73d49799c175a2ea14f5626.json"}}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Liu", "given": "Hui", "initials": "H"}, {"family": "Rydman", "given": "Sara M", "initials": "SM"}, {"family": "Rend\u00f3n-Anaya", "given": "Martha", "initials": "M"}, {"family": "Kalman", "given": "Teitur Ahlgren", "initials": "TA"}, {"family": "Kumar", "given": "Vikash", "initials": "V"}, {"family": "Canovi", "given": "Camilla", "initials": "C"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Jenkins", "given": "Jerry", "initials": "J"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Richau", "given": "Kerstin H", "initials": "KH"}, {"family": "Stokes", "given": "Victoria", "initials": "V"}, {"family": "A'Hara", "given": "Stuart", "initials": "S"}, {"family": "Cottrell", "given": "Joan", "initials": "J"}, {"family": "Coeck", "given": "Kizi", "initials": "K"}, {"family": "Diels", "given": "Tim", "initials": "T"}, {"family": "Vandepoele", "given": "Klaas", "initials": "K"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Park", "given": "Eung-Jun", "initials": "EJ"}, {"family": "Plaisance", "given": "Stephane", "initials": "S"}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}], "type": "journal article", "published": "2024-09-16", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "176", "issue": "5", "pages": "e14511", "issn-l": "0031-9317"}, "abstract": "Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Ume\u00e5 Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a ~177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.", "doi": "10.1111/ppl.14511", "pmid": "39279509", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-04T20:54:14.076Z", "modified": "2024-11-25T10:28:01.910Z"}, {"entity": "publication", "iuid": "1dfdd16ff95540f6b4d59ea2486a39bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1dfdd16ff95540f6b4d59ea2486a39bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1dfdd16ff95540f6b4d59ea2486a39bb"}}, "title": "Obscurity of chlorophyll tails - Is chlorophyll with farnesyl tail incorporated into PSII complexes?", "authors": [{"family": "Gra\u00e7a", "given": "Andr\u00e9 T", "initials": "AT", "orcid": "0000-0002-5502-1744", "researcher": {"href": "https://publications.scilifelab.se/researcher/d295844529f647bfb6fef295e6235f6a.json"}}, {"family": "Lihavainen", "given": "Jenna", "initials": "J", "orcid": "0000-0001-7979-8876", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab4d87f8aed74a9794dea29912031a93.json"}}, {"family": "Hussein", "given": "Rana", "initials": "R", "orcid": "0000-0001-6292-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/473c07367cf747faad5022538f0a9a4b.json"}}, {"family": "Schr\u00f6der", "given": "Wolfgang P", "initials": "WP", "orcid": "0000-0001-9831-1533", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2608c4b073e4056a51dd625189073cf.json"}}], "type": "journal article", "published": "2024-07-10", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "176", "issue": "4", "pages": "e14428", "issn-l": "0031-9317"}, "abstract": "Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.", "doi": "10.1111/ppl.14428", "pmid": "38981693", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-26T10:28:22.938Z", "modified": "2025-10-17T13:03:13.070Z"}, {"entity": "publication", "iuid": "6cf58ad1a0284e5d962d0794516d7d1d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cf58ad1a0284e5d962d0794516d7d1d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cf58ad1a0284e5d962d0794516d7d1d"}}, "title": "Overexpression of the plastidial pseudo-protease AtFtsHi3 enhances drought tolerance while sustaining plant growth.", "authors": [{"family": "Mishra", "given": "Laxmi S", "initials": "LS"}, {"family": "Cook", "given": "Sam D", "initials": "SD"}, {"family": "Kushwah", "given": "Sunita", "initials": "S"}, {"family": "Isaksson", "given": "Hanna", "initials": "H"}, {"family": "Straub", "given": "Isabella R", "initials": "IR"}, {"family": "Abele", "given": "Miriam", "initials": "M"}, {"family": "Mishra", "given": "Sanatkumar", "initials": "S"}, {"family": "Ludwig", "given": "Christina", "initials": "C"}, {"family": "Libby", "given": "Eric", "initials": "E"}, {"family": "Funk", "given": "Christiane", "initials": "C", "orcid": "0000-0002-7897-4038", "researcher": {"href": "https://publications.scilifelab.se/researcher/5db6c5fa2a754060b1583caf37bba1b8.json"}}], "type": "journal article", "published": "2024-05-31", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "176", "issue": "3", "pages": "e14370", "issn-l": "0031-9317"}, "abstract": "With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass and quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 (FtsHi3OE) enhances drought-tolerant phenotypes without compromising plant growth. AtFtsHi3 encodes a chloroplast envelope pseudo-protease; knock-down mutants (ftshi3-1) are found to be drought tolerant but exhibit stunted growth. Altered AtFtsHi3 expression therefore leads to drought tolerance, while only diminished expression of this gene leads to growth retardation. To understand the underlying mechanisms of the enhanced drought tolerance, we compared the proteomes of ftshi3-1 and pFtsHi3-FtsHi3OE (pFtsHi3-OE) to wild-type plants under well-watered and drought conditions. Drought-related processes like osmotic stress, water transport, and abscisic acid response were enriched in pFtsHi3-OE and ftshi3-1 mutants following their enhanced drought response compared to wild-type. The knock-down mutant ftshi3-1 showed an increased abundance of HSP90, HSP93, and TIC110 proteins, hinting at a potential downstream role of AtFtsHi3 in chloroplast pre-protein import. Mathematical modeling was performed to understand how variation in the transcript abundance of AtFtsHi3 can, on the one hand, lead to drought tolerance in both overexpression and knock-down lines, yet, on the other hand, affect plant growth so differently. The results led us to hypothesize that AtFtsHi3 may form complexes with at least two other protease subunits, either as homo- or heteromeric structures. Enriched amounts of AtFtsH7/9, AtFtsH11, AtFtsH12, and AtFtsHi4 in ftshi3-1 suggest a possible compensation mechanism for these proteases in the hexamer.", "doi": "10.1111/ppl.14370", "pmid": "38818570", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-26T10:43:37.939Z", "modified": "2025-10-17T13:03:13.192Z"}, {"entity": "publication", "iuid": "90c6743864c749ea88a615065315621f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90c6743864c749ea88a615065315621f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90c6743864c749ea88a615065315621f"}}, "title": "The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation.", "authors": [{"family": "Renstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0009-0004-8104-3228", "researcher": {"href": "https://publications.scilifelab.se/researcher/b63f6ee710ba4b0a980e29a1689d24cf.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S"}, {"family": "Gandla", "given": "Madhavi Latha", "initials": "ML"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "J\u00e4mtg\u00e5rd", "given": "Sandra", "initials": "S"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2024-02-21", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "issn-l": "0031-9317", "volume": "176", "issue": "1", "pages": "e14219"}, "abstract": "Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR <0.01) respond to added NO3 - , the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.", "doi": "10.1111/ppl.14219", "pmid": "38380723", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-03-12T15:49:46.223Z", "modified": "2025-10-17T13:03:53.118Z"}, {"entity": "publication", "iuid": "f8669acb0cd84c8d91bc8a7db440e1c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8669acb0cd84c8d91bc8a7db440e1c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8669acb0cd84c8d91bc8a7db440e1c4"}}, "title": "Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not.", "authors": [{"family": "Fataftah", "given": "Nazeer", "initials": "N"}, {"family": "Edlund", "given": "Erik", "initials": "E"}, {"family": "Lihavainen", "given": "Jenna", "initials": "J", "orcid": "0000-0001-7979-8876", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab4d87f8aed74a9794dea29912031a93.json"}}, {"family": "Bag", "given": "Pushan", "initials": "P"}, {"family": "Bj\u00f6rk\u00e9n", "given": "Lars", "initials": "L"}, {"family": "N\u00e4sholm", "given": "Torgny", "initials": "T"}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "174", "issue": "3", "pages": "e13690", "issn-l": "0031-9317"}, "abstract": "Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N ( ) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO NO 3 -3 - and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3 - and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3 - and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.", "doi": "10.1111/ppl.13690", "pmid": "35460591", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9323471"}], "notes": [], "created": "2022-12-05T08:10:26.521Z", "modified": "2025-10-17T13:03:15.052Z"}, {"entity": "publication", "iuid": "72435e06eae5420599adccd125018768", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72435e06eae5420599adccd125018768.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72435e06eae5420599adccd125018768"}}, "title": "Loss of Arabidopsis matrix metalloproteinase-5 affects root development and root bacterial communities during drought stress.", "authors": [{"family": "Mishra", "given": "Laxmi S", "initials": "LS", "orcid": "0000-0002-7212-3785", "researcher": {"href": "https://publications.scilifelab.se/researcher/f55ca038e10d4239b8bb18e90ed103d5.json"}}, {"family": "Kim", "given": "Sung-Yong", "initials": "SY"}, {"family": "Caddell", "given": "Daniel F", "initials": "DF"}, {"family": "Coleman-Derr", "given": "Devin", "initials": "D"}, {"family": "Funk", "given": "Christiane", "initials": "C", "orcid": "0000-0002-7897-4038", "researcher": {"href": "https://publications.scilifelab.se/researcher/5db6c5fa2a754060b1583caf37bba1b8.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "172", "issue": "2", "pages": "1045-1058", "issn-l": "0031-9317"}, "abstract": "Matrix metalloproteinases (MMPs) are zinc-dependent endo-peptidases that in mammals are known to be involved in remodeling the extracellular matrix (ECM) in developmental and pathological processes. In this study, we report At5-MMP of Arabidopsis thaliana to be important for root development and root bacterial communities. At5-MMP is mainly localized in the root vasculature and lateral root, an At5-MMP T-DNA insertion mutant (mmp5 KO) showed reduced root growth and a lower number of root apexes, causing reduced water uptake from the soil. Subsequently, mmp5 KO is sensitive to drought stress. Inhibited auxin transport was accompanied with resistance to indole-3-acetic acid (IAA), 2, 4-dichlorophenoxyacetic acid (2, 4-D), and 1-naphthaleneacetic acid (NAA). The content of endogenous abscisic acid (ABA) was lower in roots of mmp5 KO than in wild type. Genes responsive to ABA as well as genes encoding enzymes of the proline biosynthesis were expressed to a lower extent in mmp5 KO than in wild type. Moreover, drought stress modulated root-associated bacterial communities of mmp5 KO: the number of Actinobacteria increased. Therefore, At5-MMP modulates auxin/ABA signaling rendering the plant sensitive to drought stress and recruiting differential root bacterial communities.", "doi": "10.1111/ppl.13299", "pmid": "33616955", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8247326"}], "notes": [], "created": "2021-01-12T12:46:50.454Z", "modified": "2025-10-17T13:03:16.083Z"}, {"entity": "publication", "iuid": "c483356da7bf44ef98bbf720dd5b2471", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c483356da7bf44ef98bbf720dd5b2471.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c483356da7bf44ef98bbf720dd5b2471"}}, "title": "Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals.", "authors": [{"family": "Lihavainen", "given": "Jenna", "initials": "J", "orcid": "0000-0001-7979-8876", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab4d87f8aed74a9794dea29912031a93.json"}}, {"family": "Edlund", "given": "Erik", "initials": "E"}, {"family": "Bj\u00f6rk\u00e9n", "given": "Lars", "initials": "L"}, {"family": "Bag", "given": "Pushan", "initials": "P", "orcid": "0000-0003-3858-4606", "researcher": {"href": "https://publications.scilifelab.se/researcher/033b97dc712047a294d3e801ba750787.json"}}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM", "orcid": "0000-0002-5249-604X", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d40626e73d49799c175a2ea14f5626.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "172", "issue": "1", "pages": "201-217", "issn-l": "0031-9317"}, "abstract": "Autumn senescence in aspen (Populus tremula) is precisely timed every year to relocate nutrients from leaves to storage organs before winter. Here we demonstrate how stem girdling, which leads to the accumulation of photosynthates in the crown, influences senescence. Girdling resulted in an early onset of senescence, but the chlorophyll degradation was slower and nitrogen more efficiently resorbed than during normal autumn senescence. Girdled stems accumulated or retained anthocyanins potentially providing photoprotection in senescing leaves. Girdling of one stem in a clonal stand sharing the same root stock did not affect senescence in the others, showing that the stems were autonomous in this respect. One girdled stem with unusually high chlorophyll and nitrogen contents maintained low carbon-to-nitrogen (C/N) ratio and did not show early senescence or depleted chlorophyll level unlike the other girdled stems suggesting that the responses depended on the genotype or its carbon and nitrogen status. Metabolite analysis highlighted that the tricarboxylic acid (TCA) cycle, salicylic acid pathway, and redox homeostasis are involved in the regulation of girdling-induced senescence. We propose that disrupted sink-source relation and C/N status can provide cues through the TCA cycle and phytohormone signaling to override the phenological control of autumn senescence in the girdled stems.", "doi": "10.1111/ppl.13319", "pmid": "33368469", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8248097"}], "notes": [], "created": "2021-01-12T12:46:49.376Z", "modified": "2025-10-17T13:03:16.148Z"}, {"entity": "publication", "iuid": "10971b3610c243aaaf7fe9b336cc58a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10971b3610c243aaaf7fe9b336cc58a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10971b3610c243aaaf7fe9b336cc58a2"}}, "title": "Dynamic pH-induced conformational changes of the PsbO protein in the fluctuating acidity of the thylakoid lumen.", "authors": [{"family": "Carius", "given": "Anke B", "initials": "AB"}, {"family": "Rogne", "given": "Per", "initials": "P"}, {"family": "Duchoslav", "given": "Milo\u0161", "initials": "M"}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M"}, {"family": "Samuelsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Shutova", "given": "Tatyana", "initials": "T", "orcid": "0000-0002-4095-9609", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec5a10e3ad274526b819f24961ab015e.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "166", "issue": "1", "pages": "288-299", "issn-l": "0031-9317"}, "abstract": "The PsbO protein is an essential extrinsic subunit of photosystem II, the pigment-protein complex responsible for light-driven water splitting. Water oxidation in photosystem II supplies electrons to the photosynthetic electron transfer chain and is accompanied by proton release and oxygen evolution. While the electron transfer steps in this process are well defined and characterized, the driving forces acting on the liberated protons, their dynamics and their destiny are all largely unknown. It was suggested that PsbO undergoes proton-induced conformational changes and forms hydrogen bond networks that ensure prompt proton removal from the catalytic site of water oxidation, i.e. the Mn 4 CaO5 cluster. This work reports the purification and characterization of heterologously expressed PsbO from green algae Chlamydomonas reinhardtii and two isoforms from the higher plant Solanum tuberosum (PsbO1 and PsbO2). A comparison to the spinach PsbO reveals striking similarities in intrinsic protein fluorescence and CD spectra, reflecting the near-identical secondary structure of the proteins from algae and higher plants. Titration experiments using the hydrophobic fluorescence probe ANS revealed that eukaryotic PsbO proteins exhibit acid-base hysteresis. This hysteresis is a dynamic effect accompanied by changes in the accessibility of the protein's hydrophobic core and is not due to reversible oligomerization or unfolding of the PsbO protein. These results confirm the hypothesis that pH-dependent dynamic behavior at physiological pH ranges is a common feature of PsbO proteins and causes reversible opening and closing of their \u03b2-barrel domain in response to the fluctuating acidity of the thylakoid lumen.", "doi": "10.1111/ppl.12948", "pmid": "30793329", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-20T16:14:55.880Z", "modified": "2025-10-17T13:03:57.950Z"}, {"entity": "publication", "iuid": "ba325afcd24341c0b0d35e40d4d9596e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba325afcd24341c0b0d35e40d4d9596e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba325afcd24341c0b0d35e40d4d9596e"}}, "title": "Tissue-specific hormone profiles from woody poplar roots under bending stress.", "authors": [{"family": "De Zio", "given": "Elena", "initials": "E", "orcid": "0000-0002-5696-922X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dbd7bca12934992a397c695f9fbdb42.json"}}, {"family": "Trupiano", "given": "Dalila", "initials": "D"}, {"family": "Karady", "given": "Michal", "initials": "M"}, {"family": "Antoniadi", "given": "Ioanna", "initials": "I"}, {"family": "Montagnoli", "given": "Antonio", "initials": "A"}, {"family": "Terzaghi", "given": "Mattia", "initials": "M"}, {"family": "Chiatante", "given": "Donato", "initials": "D"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Scippa", "given": "Gabriella S", "initials": "GS"}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "165", "issue": "1", "pages": "101-113", "issn-l": "0031-9317"}, "abstract": null, "doi": "10.1111/ppl.12830", "pmid": "30187489", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-10T11:29:19.052Z", "modified": "2025-10-17T13:03:17.861Z"}], "created": "2019-01-10T11:29:19.065Z", "modified": "2020-11-27T13:14:02.284Z"}