{"entity": "researcher", "timestamp": "2026-07-12T08:37:25.585Z", "family": "Tuominen", "given": "Hannele", "initials": "H", "orcid": "0000-0002-4949-3702", "affiliations": ["Department of Plant Physiology Ume\u00e5 Plant Science Centre Ume\u00e5 University S\u2010901 87 Ume\u00e5 Sweden"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d"}}, "publications": [{"entity": "publication", "iuid": "a58a549ff82149ffa87c6ec256ec94ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a58a549ff82149ffa87c6ec256ec94ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a58a549ff82149ffa87c6ec256ec94ef"}}, "title": "Unraveling Nitrogen Uptake and Metabolism: Gene Families, Expression Dynamics, and Functional Insights in Aspen (Populus tremula).", "authors": [{"family": "Zhang", "given": "Yupeng", "initials": "Y", "orcid": "0000-0001-9461-8554", "researcher": {"href": "https://publications.scilifelab.se/researcher/307e4bb258054d37bda861e64d5f893f.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S"}, {"family": "Renstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Luomaranta", "given": "Mikko", "initials": "M"}, {"family": "Chantreau", "given": "Maxime", "initials": "M"}, {"family": "Fleig", "given": "Verena", "initials": "V"}, {"family": "Gaboreanu", "given": "Ioana", "initials": "I"}, {"family": "Grones", "given": "Carolin", "initials": "C"}, {"family": "Nilsson", "given": "Ove", "initials": "O", "orcid": "0000-0002-1033-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/729146afe5e24eb0a6f107db10e95e01.json"}}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "Tuominen", "given": "Hannele", "initials": "H", "orcid": "0000-0002-4949-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d.json"}}], "type": "journal article", "published": "2025-08-11", "journal": {"title": "Tree Physiol", "issn": "1758-4469", "issn-l": "0829-318X"}, "abstract": "The influence of nitrogen on wood formation is well established. To gain insight into the underlying molecular mechanism, we first identified genes in fourteen gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. This study provides insight into the genetic basis of nitrogen uptake and assimilation and its connection to wood formation, providing interesting targets for improving nitrogen use efficiency and growth of aspen trees.", "doi": "10.1093/treephys/tpaf099", "pmid": "40795931", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "8230290"}], "notes": [], "created": "2025-08-29T10:02:04.420Z", "modified": "2025-11-14T11:08:03.834Z"}, {"entity": "publication", "iuid": "94038f1bfdda49edbe15c90ae5ca3a68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94038f1bfdda49edbe15c90ae5ca3a68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94038f1bfdda49edbe15c90ae5ca3a68"}}, "title": "Systems genetic analysis of lignin biosynthesis in Populus tremula.", "authors": [{"family": "Luomaranta", "given": "Mikko", "initials": "M"}, {"family": "Grones", "given": "Carolin", "initials": "C", "orcid": "0000-0002-8962-3778", "researcher": {"href": "https://publications.scilifelab.se/researcher/2237d285735b40eea838eedfe54a4454.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S"}, {"family": "Milhinhos", "given": "Ana", "initials": "A", "orcid": "0000-0002-5699-0010", "researcher": {"href": "https://publications.scilifelab.se/researcher/383bc8fb6c434d2f8d7f4fbb0c5e9e4c.json"}}, {"family": "Kalman", "given": "Teitur Ahlgren", "initials": "TA"}, {"family": "Nilsson", "given": "Ove", "initials": "O", "orcid": "0000-0002-1033-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/729146afe5e24eb0a6f107db10e95e01.json"}}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM", "orcid": "0000-0002-5249-604X", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d40626e73d49799c175a2ea14f5626.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}, {"family": "Tuominen", "given": "Hannele", "initials": "H", "orcid": "0000-0002-4949-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "243", "issue": "6", "pages": "2157-2174", "issn-l": "0028-646X"}, "abstract": "The genetic control underlying natural variation in lignin content and composition in trees is not fully understood. We performed a systems genetic analysis to uncover the genetic regulation of lignin biosynthesis in a natural 'SwAsp' population of aspen (Populus tremula) trees. We analyzed gene expression by RNA sequencing (RNA-seq) in differentiating xylem tissues, and lignin content and composition using Pyrolysis-GC-MS in mature wood of 268 trees from 99 genotypes. Abundant variation was observed for lignin content and composition, and genome-wide association study identified proteins in the pentose phosphate pathway and arabinogalactan protein glycosylation among the top-ranked genes that are associated with these traits. Variation in gene expression and the associated genetic polymorphism was revealed through the identification of 312 705 local and 292 003 distant expression quantitative trait loci (eQTL). A co-expression network analysis suggested modularization of lignin biosynthesis and novel functions for the lignin-biosynthetic CINNAMYL ALCOHOL DEHYDROGENASE 2 and CAFFEOYL-CoA O-METHYLTRANSFERASE 3. PHENYLALANINE AMMONIA LYASE 3 was co-expressed with HOMEOBOX PROTEIN 5 (HB5), and the role of HB5 in stimulating lignification was demonstrated in transgenic trees. The systems genetic approach allowed linking natural variation in lignin biosynthesis to trees\u00b4 responses to external cues such as mechanical stimulus and nutrient availability.", "doi": "10.1111/nph.19993", "pmid": "39072753", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-25T10:27:46.343Z", "modified": "2025-02-28T14:20:36.843Z"}, {"entity": "publication", "iuid": "26d84ecc522b4511b3f194230afee366", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26d84ecc522b4511b3f194230afee366.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26d84ecc522b4511b3f194230afee366"}}, "title": "Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees.", "authors": [{"family": "Gandla", "given": "Madhavi Latha", "initials": "ML"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Escamez", "given": "Sacha", "initials": "S"}, {"family": "Skotare", "given": "Tomas", "initials": "T"}, {"family": "Obudulu", "given": "Ogonna", "initials": "O"}, {"family": "M\u00f6ller", "given": "Linus", "initials": "L"}, {"family": "Abreu", "given": "Ilka N", "initials": "IN"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Hertzberg", "given": "Magnus", "initials": "M"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Moritz", "given": "Thomas", "initials": "T"}, {"family": "Wingsle", "given": "Gunnar", "initials": "G"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Tuominen", "given": "Hannele", "initials": "H", "orcid": "0000-0002-4949-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d.json"}}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}], "type": "journal article", "published": "2021-02-16", "journal": {"title": "Biotechnol Biofuels", "issn": "1754-6834", "volume": "14", "issue": "1", "pages": "43", "issn-l": "1754-6834"}, "abstract": "Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth.\n\nIn this study, we report on transgenic hybrid aspen (Populus tremula \u00d7 tremuloides) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula \u00d7 tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20-44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26-50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control.\n\nThe results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.", "doi": "10.1186/s13068-021-01895-0", "pmid": "33593413", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s13068-021-01895-0"}, {"db": "pmc", "key": "PMC7885582"}], "notes": [], "created": "2021-12-09T20:06:46.824Z", "modified": "2025-10-17T13:03:16.368Z"}, {"entity": "publication", "iuid": "ab5a9cefcf044daba4246362a58f1356", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab5a9cefcf044daba4246362a58f1356.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab5a9cefcf044daba4246362a58f1356"}}, "title": "PIRIN2 suppresses S-type lignin accumulation in a noncell-autonomous manner in Arabidopsis xylem elements.", "authors": [{"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Sztojka", "given": "Bernadette", "initials": "B"}, {"family": "Escamez", "given": "Sacha", "initials": "S"}, {"family": "Vanholme", "given": "Ruben", "initials": "R"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Wang", "given": "Yin", "initials": "Y"}, {"family": "Turumtay", "given": "Halbay", "initials": "H"}, {"family": "Gorzs\u00e1s", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-2298-8844", "researcher": {"href": "https://publications.scilifelab.se/researcher/8070792ccead4c809c89943d84cf0e03.json"}}, {"family": "Boerjan", "given": "Wout", "initials": "W", "orcid": "0000-0003-1495-510X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8215f848a3047669e8896145e8db4b5.json"}}, {"family": "Tuominen", "given": "Hannele", "initials": "H", "orcid": "0000-0002-4949-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d.json"}}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "225", "issue": "5", "pages": "1923-1935", "issn-l": "0028-646X"}, "abstract": "PIRIN (PRN) genes encode cupin domain-containing proteins that function as transcriptional co-regulators in humans but that are poorly described in plants. A previous study in xylogenic cell cultures of Zinnia elegans suggested a role for a PRN protein in lignification. This study aimed to identify the function of Arabidopsis (Arabidopsis thaliana) PRN proteins in lignification of xylem tissues. Chemical composition of the secondary cell walls was analysed in Arabidopsis stems and/or hypocotyls by pyrolysis-gas chromatography/mass spectrometry, 2D-nuclear magnetic resonance and phenolic profiling. Secondary cell walls of individual xylem elements were chemotyped by Fourier transform infrared and Raman microspectroscopy. Arabidopsis PRN2 suppressed accumulation of S-type lignin in Arabidopsis stems and hypocotyls. PRN2 promoter activity and PRN2:GFP fusion protein were localised specifically in cells next to the vessel elements, suggesting a role for PRN2 in noncell-autonomous lignification of xylem vessels. Accordingly, PRN2 modulated lignin chemistry in the secondary cell walls of the neighbouring vessel elements. These results indicate that PRN2 suppresses S-type lignin accumulation in the neighbourhood of xylem vessels to bestow G-type enriched lignin composition on the secondary cell walls of the vessel elements. Gene expression analyses suggested that PRN2 function is mediated by regulation of the expression of the lignin-biosynthetic genes.", "doi": "10.1111/nph.16271", "pmid": "31625609", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7027918"}, {"db": "GENBANK", "key": "At3g59220"}, {"db": "GENBANK", "key": "At2g43120"}, {"db": "GENBANK", "key": "At3g59260"}, {"db": "GENBANK", "key": "At1g50590"}, {"db": "GENBANK", "key": "At2g37040"}, {"db": "GENBANK", "key": "At2g30490"}, {"db": "GENBANK", "key": "At1g51680"}, {"db": "GENBANK", "key": "At2g40890"}, {"db": "GENBANK", "key": "At5g48930"}, {"db": "GENBANK", "key": "At4g34050"}, {"db": "GENBANK", "key": "At1g15950"}, {"db": "GENBANK", "key": "At4g36220"}, {"db": "GENBANK", "key": "At5g54160"}, {"db": "GENBANK", "key": "At4g34230"}, {"db": "GENBANK", "key": "At5g62380"}, {"db": "GENBANK", "key": "At1g71930"}, {"db": "GENBANK", "key": "At2g46770"}, {"db": "GENBANK", "key": "At3g61910"}, {"db": "GENBANK", "key": "At1g32770"}, {"db": "GENBANK", "key": "At5g12870"}, {"db": "GENBANK", "key": "At3g08500"}, {"db": "GENBANK", "key": "At1g16490"}, {"db": "GENBANK", "key": "At1g79180"}, {"db": "GENBANK", "key": "At4g22680"}, {"db": "GENBANK", "key": "At1g09540"}, {"db": "GENBANK", "key": "At1g63910"}], "notes": [], "created": "2019-11-22T14:28:02.623Z", "modified": "2025-10-17T13:03:57.081Z"}, {"entity": "publication", "iuid": "89f85b8150ec4621b3e38e5f6146d691", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89f85b8150ec4621b3e38e5f6146d691.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89f85b8150ec4621b3e38e5f6146d691"}}, "title": "A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of\u200b \u200b\u200bPopulus\u200b\u200b \u200btrees.", "authors": [{"family": "Obudulu", "given": "Ogonna", "initials": "O"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Skotare", "given": "Tomas", "initials": "T"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Abreu", "given": "Ilka N", "initials": "IN"}, {"family": "Ahnlund", "given": "Maria", "initials": "M"}, {"family": "Latha Gandla", "given": "Madhavi", "initials": "M"}, {"family": "Petterle", "given": "Anna", "initials": "A"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}, {"family": "Wingsle", "given": "Gunnar", "initials": "G"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Tuominen", "given": "Hannele", "initials": "H", "orcid": "0000-0002-4949-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d.json"}}], "type": "journal article", "published": "2018-01-03", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "19", "issue": "1", "pages": "11", "issn-l": "1471-2164"}, "abstract": "Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32-38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri.019G104000).\n\nThe woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with a tendency towards increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. Multivariate OnPLS (orthogonal projections to latent structures) modeling of five different omics datasets (the transcriptome, proteome, GC-MS metabolome, LC-MS metabolome and pyrolysis-GC/MS metabolome) collected from the secondary xylem tissues of the stem revealed systemic variation in the different variables in the transgenic lines, including changes that correlated with the changes in the secondary cell wall composition. The OnPLS model also identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis.\n\nPopulus SCAMP proteins were shown to influence accumulation of secondary cell wall components, including polysaccharides and phenolic compounds, in the woody tissues of Populus tree stems. Our multi-omics analyses combined with the OnPLS modelling suggest that this function is mediated by changes in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues.", "doi": "10.1186/s12864-017-4411-1", "pmid": "29298676", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-4411-1"}, {"db": "pmc", "key": "PMC5753437"}], "notes": [], "created": "2019-01-10T10:03:22.571Z", "modified": "2025-10-17T13:03:18.332Z"}]}