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Hvidsten, Torgeir R.ORCID iD iconorcid.org/0000-0001-6097-2539
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Publications (10 of 40) Show all publications
Curci, P. L., Zhang, J., Mähler, N., Seyfferth, C., Mannapperuma, C., Diels, T., . . . Vandepoele, K. (2022). Identification of growth regulators using cross-species network analysis in plants. Plant Physiology, 190(4), 2350-2365
Open this publication in new window or tab >>Identification of growth regulators using cross-species network analysis in plants
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2022 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 190, no 4, p. 2350-2365Article in journal (Refereed) Published
Abstract [en]

With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.

Place, publisher, year, edition, pages
Oxford University Press, 2022
National Category
Botany Plant Biotechnology
Identifiers
urn:nbn:se:umu:diva-201619 (URN)10.1093/plphys/kiac374 (DOI)000844537500001 ()35984294 (PubMedID)2-s2.0-85143141934 (Scopus ID)
Funder
The Research Council of Norway, 287465
Available from: 2022-12-14 Created: 2022-12-14 Last updated: 2022-12-14Bibliographically approved
Gandla, M. L., Mähler, N., Escamez, S., Skotare, T., Obudulu, O., Möller, L., . . . Jönsson, L. J. (2021). Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees. Biotechnology for Biofuels, 14(1), Article ID 43.
Open this publication in new window or tab >>Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
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2021 (English)In: Biotechnology for Biofuels, ISSN 1754-6834, E-ISSN 1754-6834, Vol. 14, no 1, article id 43Article in journal (Refereed) Published
Abstract [en]

Background: 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.

Results: In this study, we report on transgenic hybrid aspen (Populus tremula × 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 × 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.

Conclusions: The 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.

Place, publisher, year, edition, pages
BioMed Central, 2021
Keywords
Bioprocessing, Growth, Metabolomics, Populus, Proteomics, Transcriptomics, VAMP, VAMP-associated protein, VAP27, Vesicle-associated membrane protein
National Category
Plant Biotechnology
Identifiers
urn:nbn:se:umu:diva-180984 (URN)10.1186/s13068-021-01895-0 (DOI)000620931600002 ()2-s2.0-85100873005 (Scopus ID)
Available from: 2021-03-05 Created: 2021-03-05 Last updated: 2023-11-06Bibliographically approved
Seyfferth, C., Wessels, B., Vahala, J., Kangasjärvi, J., Delhomme, N., Hvidsten, T. R., . . . Lundberg-Felten, J. (2021). PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen. Cells, 10(8), Article ID 1971.
Open this publication in new window or tab >>PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen
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2021 (English)In: Cells, E-ISSN 2073-4409, Vol. 10, no 8, article id 1971Article in journal (Refereed) Published
Abstract [en]

Secondary growth relies on precise and specialized transcriptional networks that determine cell division, differentiation, and maturation of xylem cells. We identified a novel role for the ethylene-induced Populus Ethylene Response Factor PtERF85 (Potri.015G023200) in balancing xylem cell expansion and secondary cell wall (SCW) formation in hybrid aspen (Populus tremula x tremuloides). Expression of PtERF85 is high in phloem and cambium cells and during the expansion of xylem cells, while it is low in maturing xylem tissue. Extending PtERF85 expression into SCW forming zones of woody tissues through ectopic expression reduced wood density and SCW thickness of xylem fibers but increased fiber diameter. Xylem transcriptomes from the transgenic trees revealed transcriptional induction of genes involved in cell expansion, translation, and growth. The expression of genes associated with plant vascular development and the biosynthesis of SCW chemical components such as xylan and lignin, was down-regulated in the transgenic trees. Our results suggest that PtERF85 activates genes related to xylem cell expansion, while preventing transcriptional activation of genes related to SCW formation. The importance of precise spatial expression of PtERF85 during wood development together with the observed phenotypes in response to ectopic PtERF85 expression suggests that PtERF85 contributes to the transition of fiber cells from elongation to secondary cell wall deposition.

Place, publisher, year, edition, pages
MDPI, 2021
Keywords
cell wall thickness, ERF85 (CRF4), lignin, ribosome biogenesis, wood development, xylem expansion
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-187903 (URN)10.3390/cells10081971 (DOI)000689001900001 ()34440740 (PubMedID)2-s2.0-85115043021 (Scopus ID)
Funder
Swedish Research Council, 213-2011-1148Swedish Research Council, 239-2011-1915The Kempe Foundations, SMK-1649The Kempe Foundations, SMK-1533Swedish Research Council Formas, 2018-01611Knut and Alice Wallenberg Foundation, 2016.0341Knut and Alice Wallenberg Foundation, 2016.0352Vinnova, 2016-00504
Available from: 2021-09-24 Created: 2021-09-24 Last updated: 2021-09-24Bibliographically approved
Abreu, I. N., Johansson, A. I., Sokolowska, K., Niittylä, T., Sundberg, B., Hvidsten, T. R., . . . Moritz, T. (2020). A metabolite roadmap of the wood-forming tissue in Populus tremula. New Phytologist, 228(5), 1559-1572
Open this publication in new window or tab >>A metabolite roadmap of the wood-forming tissue in Populus tremula
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2020 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 228, no 5, p. 1559-1572Article in journal (Refereed) Published
Abstract [en]

Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.

Place, publisher, year, edition, pages
John Wiley & Sons, 2020
Keywords
cambium, crysectioning, laser capture microdissection, metabolomics, Populus, wood
National Category
Botany Wood Science
Identifiers
urn:nbn:se:umu:diva-174877 (URN)10.1111/nph.16799 (DOI)000562922500001 ()32648607 (PubMedID)2-s2.0-85089866398 (Scopus ID)
Available from: 2020-09-16 Created: 2020-09-16 Last updated: 2023-03-24Bibliographically approved
Mannapperuma, C., Liu, H., Bel, M., Delhomme, N., Serrano, A., Schiffthaler, B., . . . Street, N. (2020). PlantGenIE-PLAZA: integrating orthology into the PlantGenIE.org resource using the PLAZA pipeline.
Open this publication in new window or tab >>PlantGenIE-PLAZA: integrating orthology into the PlantGenIE.org resource using the PLAZA pipeline
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2020 (English)Manuscript (preprint) (Other academic)
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-170114 (URN)
Available from: 2020-04-27 Created: 2020-04-27 Last updated: 2022-03-09
Schubert, M., Gronvold, L., Sandve, S. R., Hvidsten, T. R. & Fjellheim, S. (2019). Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae. Plant Physiology, 180(1), 404-419
Open this publication in new window or tab >>Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae
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2019 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 180, no 1, p. 404-419Article in journal (Refereed) Published
Abstract [en]

The grass subfamily Pooideae dominates the grass floras in cold temperate regions and has evolved complex physiological adaptations to cope with extreme environmental conditions like frost, winter, and seasonality. One such adaptation is cold acclimation, wherein plants increase their frost tolerance in response to gradually falling temperatures and shorter days in the autumn. However, understanding how complex traits like cold acclimation evolve remains a major challenge in evolutionary biology. Here, we investigated the evolution of cold acclimation in Pooideae and found that a phylogenetically diverse set of Pooideae species displayed cold acclimation capacity. However, comparing differential gene expression after cold treatment in transcriptomes of five phylogenetically diverse species revealed widespread species-specific responses of genes with conserved sequences. Furthermore, we studied the correlation between gene family size and number of cold-responsive genes as well as between selection pressure on coding sequences of genes and their cold responsiveness. We saw evidence of protein-coding and regulatory sequence evolution as well as the origin of novel genes and functions contributing toward evolution of a cold response in Pooideae. Our results reflect that selection pressure resulting from global cooling must have acted on already diverged lineages. Nevertheless, conservation of cold-induced gene expression of certain genes indicates that the Pooideae ancestor may have possessed some molecular machinery to mitigate cold stress. Evolution of adaptations to seasonally cold climates is regarded as particularly difficult. How Pooideae evolved to transition from tropical to temperate biomes sheds light on how complex traits evolve in the light of climate changes.

Place, publisher, year, edition, pages
American Society of Plant Biologists, 2019
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-159397 (URN)10.1104/pp.18.01448 (DOI)000466860800036 ()30850470 (PubMedID)2-s2.0-85065658810 (Scopus ID)
Available from: 2019-06-10 Created: 2019-06-10 Last updated: 2023-03-24Bibliographically approved
Obudulu, O., Mähler, N., Skotare, T., Bygdell, J., Abreu, I. N., Ahnlund, M., . . . Tuominen, H. (2018). A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees. BMC Genomics, 19, Article ID 11.
Open this publication in new window or tab >>A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees
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2018 (English)In: BMC Genomics, E-ISSN 1471-2164, Vol. 19, article id 11Article in journal (Refereed) Published
Abstract [en]

Background: 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).

Results: The 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.

Conclusions: Populus 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.

Place, publisher, year, edition, pages
Springer Publishing Company, 2018
Keywords
Secretory Carrier-Associated Membrane Protein (SCAMP), Populus, Wood chemistry, Wood density, Biomass, Bioprocessing, Cork, Multi-omics
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-143890 (URN)10.1186/s12864-017-4411-1 (DOI)000419232000004 ()2-s2.0-85042468619 (Scopus ID)
Projects
Bio4Energy
Funder
Swedish Research Council Formas, 232-2009-1698Bio4Energy
Available from: 2018-01-12 Created: 2018-01-12 Last updated: 2024-01-17Bibliographically approved
Felten, J., Vahala, J., Love, J., Gorzsás, A., Ruggeberg, M., Delhomme, N., . . . Sundberg, B. (2018). Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen. New Phytologist, 218(3), 999-1014
Open this publication in new window or tab >>Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen
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2018 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 218, no 3, p. 999-1014Article in journal (Refereed) Published
Abstract [en]

The phytohormone ethylene impacts secondary stem growth in plants by stimulating cambial activity, xylem development and fiber over vessel formation. We report the effect of ethylene on secondary cell wall formation and the molecular connection between ethylene signaling and wood formation. We applied exogenous ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to wild-type and ethylene-insensitive hybrid aspen trees (Populus tremulaxtremuloides) and studied secondary cell wall anatomy, chemistry and ultrastructure. We furthermore analyzed the transcriptome (RNA Seq) after ACC application to wild-type and ethylene-insensitive trees. We demonstrate that ACC and ethylene induce gelatinous layers (G-layers) and alter the fiber cell wall cellulose microfibril angle. G-layers are tertiary wall layers rich in cellulose, typically found in tension wood of aspen trees. A vast majority of transcripts affected by ACC are downstream of ethylene perception and include a large number of transcription factors (TFs). Motif-analyses reveal potential connections between ethylene TFs (Ethylene Response Factors (ERFs), ETHYLENE INSENSITIVE 3/ETHYLENE INSENSITIVE3-LIKE1 (EIN3/EIL1)) and wood formation. G-layer formation upon ethylene application suggests that the increase in ethylene biosynthesis observed during tension wood formation is important for its formation. Ethylene-regulated TFs of the ERF and EIN3/EIL1 type could transmit the ethylene signal.

Keywords
cell wall, ethylene signaling, gelatinous layer (G-layer), hybrid aspen, tension wood, transcriptome
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-147450 (URN)10.1111/nph.15078 (DOI)000430127000016 ()29528503 (PubMedID)2-s2.0-85043471933 (Scopus ID)
Projects
Bio4Energy
Funder
Swedish Research Council Formas, 213-2011-1148Swedish Research Council Formas, 239-2011-1915Bio4Energy
Available from: 2018-07-19 Created: 2018-07-19 Last updated: 2023-03-24Bibliographically approved
Lin, Y.-C., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., . . . Street, N. R. (2018). Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proceedings of the National Academy of Sciences of the United States of America, 115(46), E10970-E10978
Open this publication in new window or tab >>Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 46, p. E10970-E10978Article in journal (Refereed) Published
Abstract [en]

The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2018
Keywords
genome assembly, natural selection, coexpression, population genetics, Populus
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-154950 (URN)10.1073/pnas.1801437115 (DOI)000449934400020 ()30373829 (PubMedID)2-s2.0-85056516875 (Scopus ID)
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2020-05-13Bibliographically approved
Tylewicz, S., Petterle, A., Marttila, S., Miskolczi, P., Azeez, A., Singh, R. K., . . . Bhalerao, R. P. (2018). Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication. Science, 360(6385), 212-214
Open this publication in new window or tab >>Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication
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2018 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 360, no 6385, p. 212-214Article in journal (Refereed) Published
Abstract [en]

In temperate and boreal ecosystems, seasonal cycles of growth and dormancy allow perennial plants to adapt to winter conditions. We show, in hybrid aspen trees, that photoperiodic regulation of dormancy is mechanistically distinct from autumnal growth cessation. Dormancy sets in when symplastic intercellular communication through plasmodesmata is blocked by a process dependent on the phytohormone abscisic acid. The communication blockage prevents growth-promoting signals from accessing the meristem. Thus, precocious growth is disallowed during dormancy. The dormant period, which supports robust survival of the aspen tree in winter, is due to loss of access to growth-promoting signals.

Place, publisher, year, edition, pages
American Association for the Advancement of Science (AAAS), 2018
National Category
Forest Science Genetics
Identifiers
urn:nbn:se:umu:diva-147296 (URN)10.1126/science.aan8576 (DOI)000429805400048 ()29519919 (PubMedID)2-s2.0-85045283382 (Scopus ID)
Available from: 2018-05-25 Created: 2018-05-25 Last updated: 2023-03-24Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0001-6097-2539

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