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Publications (10 of 22) Show all publications
Liebsch, D., Juvany, M., Li, Z., Wang, H.-L., Ziolkowska, A., Chrobok, D., . . . Keech, O. (2022). Metabolic control of arginine and ornithine levels paces the progression of leaf senescence. Plant Physiology, 189(4), 1943-1960
Open this publication in new window or tab >>Metabolic control of arginine and ornithine levels paces the progression of leaf senescence
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2022 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 189, no 4, p. 1943-1960Article in journal (Refereed) Published
Abstract [en]

Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts—likely due to the lack of induction of amino acids (AAs) transport—can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.

Place, publisher, year, edition, pages
Oxford University Press, 2022
National Category
Botany Plant Biotechnology
Identifiers
urn:nbn:se:umu:diva-198906 (URN)10.1093/plphys/kiac244 (DOI)000803838800001 ()35604104 (PubMedID)2-s2.0-85135924586 (Scopus ID)
Funder
Swedish Research Council, 621-2014-4688The Kempe FoundationsCarl Tryggers foundation , CTS14-247Carl Tryggers foundation , CTS15-262Knut and Alice Wallenberg Foundation, 2016.0341Knut and Alice Wallenberg Foundation, 2016.0352Vinnova, 2016-00504
Available from: 2022-09-05 Created: 2022-09-05 Last updated: 2024-04-09Bibliographically approved
Bag, P., Lihavainen, J., Delhomme, N., Riquelme, T., Robinson, K. M. & Jansson, S. (2021). An atlas of the Norway spruce needle seasonal transcriptome. The Plant Journal, 108(6), 1815-1829
Open this publication in new window or tab >>An atlas of the Norway spruce needle seasonal transcriptome
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2021 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 108, no 6, p. 1815-1829Article in journal (Refereed) Published
Abstract [en]

Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.

Place, publisher, year, edition, pages
John Wiley & Sons, 2021
Keywords
conifers, Norway spruce, resource, seasonal adaptation, transcriptomics
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-188962 (URN)10.1111/tpj.15530 (DOI)000709512700001 ()34624161 (PubMedID)2-s2.0-85117463119 (Scopus ID)
Funder
EU, Horizon 2020, 675006VinnovaSwedish Research Council FormasKnut and Alice Wallenberg FoundationSwedish Research Council, 2018‐05973The Kempe Foundations
Available from: 2021-10-28 Created: 2021-10-28 Last updated: 2023-03-24Bibliographically approved
Mahmud, A. K., Delhomme, N., Nandi, S. & Fällman, M. (2021). ProkSeq for complete analysis of RNA-Seq data from prokaryotes. Bioinformatics, 37(1), 126-128
Open this publication in new window or tab >>ProkSeq for complete analysis of RNA-Seq data from prokaryotes
2021 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 37, no 1, p. 126-128Article in journal (Refereed) Published
Abstract [en]

Summary: Since its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, tools for studying gene expression, determination of differential gene expression, downstream pathway analysis and normalization of data collected in extreme biological conditions is still lacking. Here, we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data and visualizing data and results.

Availability and implementation: ProkSeq is implemented in Python and is published under the MIT source license. The pipeline is available as a Docker container https://hub.docker.com/repository/docker/snandids/prokseq-v2.0, or can be used through Anaconda: https://anaconda.org/snandiDS/prokseq. The code is available on Github: https://github.com/snandiDS/prokseq and a detailed user documentation, including a manual and tutorial can be found at https://prokseqV20.readthedocs.io.

Place, publisher, year, edition, pages
UK: Oxford University Press, 2021
National Category
Microbiology
Research subject
biology
Identifiers
urn:nbn:se:umu:diva-178930 (URN)10.1093/bioinformatics/btaa1063 (DOI)000649437800019 ()33367516 (PubMedID)2-s2.0-85134379041 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, 2016.0063Swedish Research Council, 2018-02855
Available from: 2021-01-21 Created: 2021-01-21 Last updated: 2023-03-23Bibliographically approved
Mahboubi, A., Delhomme, N., Häggström, S. & Hanson, J. (2021). Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture. Plant Methods, 17(1), Article ID 92.
Open this publication in new window or tab >>Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture
2021 (English)In: Plant Methods, E-ISSN 1746-4811, Vol. 17, no 1, article id 92Article in journal (Refereed) Published
Abstract [en]

Background: Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming.

Methods and results: Here we developed a platform for Ribo-Seq library construction and data analysis to enable rapid quality assessment of Ribo-Seq libraries with the help of a small-scale sequencer. Our data show that several qualitative features of a Ribo-Seq library, such as read length distribution, P-site distribution, reading frame and triplet periodicity, can be effectively evaluated using only the data generated by a benchtop sequencer with a very limited number of reads.

Conclusion: Our pipeline enables rapid evaluation of Ribo-Seq libraries, opening up possibilities for optimization of Ribo-Seq library construction from difficult samples, and leading to better decision making prior to more costly deep sequencing.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2021
Keywords
Evaluation of sequencing library quality, Ribo-Seq, Ribosomal profiling, Translation, Translational profiling
National Category
Biochemistry and Molecular Biology Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-187086 (URN)10.1186/s13007-021-00791-w (DOI)000687996100001 ()2-s2.0-85113340124 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, KAW 2016-0341Knut and Alice Wallenberg Foundation, KAW 2016-0352Knut and Alice Wallenberg Foundation, KAW 2016-0025Vinnova, 2016-00504
Available from: 2021-09-03 Created: 2021-09-03 Last updated: 2024-01-11Bibliographically 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
Zhang, B., Sztojka, B., Seyfferth, C., Escamez, S., Miskolczi, P., Chantreau, M., . . . Tuominen, H. (2020). The chromatin-modifying protein HUB2 is involved in the regulation of lignin composition in xylem vessels. Journal of Experimental Botany, 71(18), 5484-5494
Open this publication in new window or tab >>The chromatin-modifying protein HUB2 is involved in the regulation of lignin composition in xylem vessels
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2020 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 71, no 18, p. 5484-5494Article in journal (Refereed) Published
Abstract [en]

PIRIN2 (PRN2) was earlier reported to suppress syringyl (S)-type lignin accumulation of xylem vessels of Arabidopsis thaliana. In the present study, we report yeast two-hybrid results supporting the interaction of PRN2 with HISTONE MONOUBIQUITINATION2 (HUB2) in Arabidopsis. HUB2 has been previously implicated in several plant developmental processes, but not in lignification. Interaction between PRN2 and HUB2 was verified by β-galactosidase enzymatic and co-immunoprecipitation assays. HUB2 promoted the deposition of S-type lignin in the secondary cell walls of both stem and hypocotyl tissues, as analysed by pyrolysis-GC/MS. Chemical fingerprinting of individual xylem vessel cell walls by Raman and Fourier transform infrared microspectroscopy supported the function of HUB2 in lignin deposition. These results, together with a genetic analysis of the hub2 prn2 double mutant, support the antagonistic function of PRN2 and HUB2 in deposition of S-type lignin. Transcriptome analyses indicated the opposite regulation of the S-type lignin biosynthetic gene FERULATE-5-HYDROXYLASE1 by PRN2 and HUB2 as the underlying mechanism. PRN2 and HUB2 promoter activities co-localized in cells neighbouring the xylem vessel elements, suggesting that the S-type lignin-promoting function of HUB2 is antagonized by PRN2 for the benefit of the guaiacyl (G)-type lignin enrichment of the neighbouring xylem vessel elements.

Place, publisher, year, edition, pages
Oxford University Press, 2020
Keywords
Arabidopsis, cell wall chemistry, HUB2, lignin, PIRIN2, syringyl-type lignin, xylem vessels
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-176306 (URN)10.1093/jxb/eraa264 (DOI)000577073500017 ()32479638 (PubMedID)2-s2.0-85096472238 (Scopus ID)
Available from: 2020-11-05 Created: 2020-11-05 Last updated: 2023-03-24Bibliographically approved
Christie, N., Mannapperuma, C., Ployet, R., Van der Merwe, K., Mähler, N., Delhomme, N., . . . Myburg, A. A. (2020). The Eucalyptus Genome Integrative Explorer: an online resource for systems genetics in forest tree species. The Plant Journal
Open this publication in new window or tab >>The Eucalyptus Genome Integrative Explorer: an online resource for systems genetics in forest tree species
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2020 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313XArticle in journal (Other academic) Accepted
Place, publisher, year, edition, pages
John Wiley & Sons, 2020
National Category
Other Computer and Information Science Other Biological Topics
Identifiers
urn:nbn:se:umu:diva-170113 (URN)
Available from: 2020-04-27 Created: 2020-04-27 Last updated: 2023-05-02
Sullivan, A. R., Eldfjell, Y., Schiffthaler, B., Delhomme, N., Asp, T., Hebelstrup, K. H., . . . Wang, X.-R. (2020). The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants. Genome Biology and Evolution, 12(1), 3586-3598
Open this publication in new window or tab >>The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants
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2020 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 12, no 1, p. 3586-3598Article in journal (Refereed) Published
Abstract [en]

Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

Place, publisher, year, edition, pages
Oxford University Press, 2020
Keywords
mitogenome, repeats, recombination, rearrangement rates, structural variation
National Category
Earth and Related Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-168043 (URN)10.1093/gbe/evz263 (DOI)000522860800005 ()2-s2.0-85077489986 (Scopus ID)
Available from: 2020-02-14 Created: 2020-02-14 Last updated: 2023-09-05Bibliographically approved
Gil-Munoz, F., Delhomme, N., Quinones, A., Naval, M. d., Badenes, M. L. & Garcia-Gil, M. R. (2020). Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.). Agronomy, 10(11), Article ID 1703.
Open this publication in new window or tab >>Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.)
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2020 (English)In: Agronomy, E-ISSN 2073-4395, Vol. 10, no 11, article id 1703Article in journal (Refereed) Published
Abstract [en]

Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt--tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.

Place, publisher, year, edition, pages
MDPI, 2020
Keywords
Diospyros lotus L, salt stress, ion transport, persimmon, transmembrane electrochemical gradient, chloride channels, thermospermine
National Category
Botany Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-177780 (URN)10.3390/agronomy10111703 (DOI)000593583900001 ()2-s2.0-85109090541 (Scopus ID)
Available from: 2020-12-22 Created: 2020-12-22 Last updated: 2021-07-12Bibliographically approved
Law, S. R., Chrobok, D., Juvany, M., Delhomme, N., Lindén, P., Brouwer, B., . . . Keech, O. (2018). Darkened leaves use different metabolic strategies for senescence and survival. Plant Physiology, 177(1), 132-150
Open this publication in new window or tab >>Darkened leaves use different metabolic strategies for senescence and survival
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2018 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 177, no 1, p. 132-150Article in journal (Refereed) Published
Abstract [en]

In plants, an individually darkened leaf initiates senescence much more rapidly than a leaf from a whole darkened plant. Combining transcriptomic and metabolomic approaches in Arabidopsis (Arabidopsis thaliana), we present an overview of the metabolic strategies that are employed in response to different darkening treatments. Under darkened plant conditions, the perception of carbon starvation drove a profound metabolic readjustment in which branched-chain amino acids and potentially monosaccharides released from cell wall loosening became important substrates for maintaining minimal ATP production. Concomitantly, the increased accumulation of amino acids with a high nitrogen-carbon ratio may provide a safety mechanism for the storage of metabolically derived cytotoxic ammonium and a pool of nitrogen for use upon returning to typical growth conditions. Conversely, in individually darkened leaf, the metabolic profiling that followed our 13C-enrichment assays revealed a temporal and differential exchange of metabolites, including sugars and amino acids, between the darkened leaf and the rest of the plant. This active transport could be the basis for a progressive metabolic shift in the substrates fueling mitochondrial activities, which are central to the catabolic reactions facilitating the retrieval of nutrients from the senescing leaf. We propose a model illustrating the specific metabolic strategies employed by leaves in response to these two darkening treatments, which support either rapid senescence or a strong capacity for survival.

Keywords
Arabidopsis thaliana, senescence, metabolism, dark induced senescence, survival
National Category
Botany
Research subject
biology
Identifiers
urn:nbn:se:umu:diva-147675 (URN)10.1104/pp.18.00062 (DOI)000431347500015 ()29523713 (PubMedID)2-s2.0-85050218739 (Scopus ID)
Available from: 2018-05-14 Created: 2018-05-14 Last updated: 2024-04-09Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-3053-0796

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