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OnPLS integration o...
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Srivastava, VaibhavSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,KTH,Glykovetenskap,Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden;Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden,Umeå University, KTH,Institutionen för skoglig genetik och växtfysiologi,Department of Forest Genetics and Plant Physiology,AlbaNova University Center
(author)
OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants
- Article/chapterEnglish2013
Publisher, publication year, extent ...
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2013-12-17
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BioMed Central,2013
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electronicrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:umu-85515
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https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-85515URI
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https://doi.org/10.1186/1471-2164-14-893DOI
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https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-139153URI
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https://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-10716URI
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-214341URI
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https://res.slu.se/id/publ/52736URI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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QC 20140108
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Upprättat; 2013; 20131219 (robnil)
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BACKGROUND: Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.RESULTS: The main categories that appear to be significantly influenced in the transgenic plants were pathways related to redox regulation, carbon metabolism and protein degradation, e.g. the glycolysis and pentose phosphate pathways (PPP). The results provide system-level information on ROS metabolism and responses to oxidative stress, and indicate that some initial responses to oxidative stress may share common pathways.CONCLUSION: The proposed data evaluation strategy shows an efficient way of compiling complex, multi-platform datasets to obtain significant biological information.
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Obudulu, OgonnaSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Umeå universitet,Kemiska institutionen,Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden;Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden,Institutionen för skoglig genetik och växtfysiologi,Department of Forest Genetics and Plant Physiology,Umeå University(Swepub:slu)48345
(author)
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Bygdell, JoakimSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för skoglig genetik och växtfysiologi,Department of Forest Genetics and Plant Physiology(Swepub:slu)48658
(author)
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Löfstedt, TommyUmeå universitet,Kemiska institutionen,Department of Chemistry, Umeå University, Umeå, Sweden;Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden(Swepub:umu)toklot02
(author)
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Rydén, PatrikUmeå universitet,Institutionen för matematik och matematisk statistik,Kemiska institutionen,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden;Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden(Swepub:umu)pary0001
(author)
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Nilsson, RobertSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Luleå tekniska universitet,Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden,Institutionen för skoglig genetik och växtfysiologi,Department of Forest Genetics and Plant Physiology,Luleå University of Technology(Swepub:slu)52630
(author)
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Ahnlund, MariaSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för skoglig genetik och växtfysiologi,Department of Forest Genetics and Plant Physiology(Swepub:slu)50268
(author)
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Johansson, AnnikaSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för skoglig genetik och växtfysiologi,Department of Forest Genetics and Plant Physiology(Swepub:slu)50633
(author)
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Jonsson, PärUmeå universitet,Kemiska institutionen,Department of Chemistry, Umeå University, Umeå, Sweden;Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden(Swepub:umu)parjon95
(author)
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Freyhult, EvaUmeå universitet,Kemiska institutionen,Klinisk bakteriologi,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden;Department of Clinical Microbiology, Clinical Bacteriology, Umeå University, Umeå, Sweden(Swepub:uu)evfre192
(author)
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Qvarnström, JohannaUmeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
(author)
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Karlsson, JanUmeå universitet,Institutionen för fysiologisk botanik,Umeå Plant Science Centre (UPSC),Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden(Swepub:umu)jaka0002
(author)
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Melzer, MichaelDepartment of Molecular Cell Biology, Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
(author)
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Moritz, ThomasSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för skoglig genetik och växtfysiologi,Department of Forest Genetics and Plant Physiology(Swepub:slu)49634
(author)
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Trygg, JohanUmeå universitet,Kemiska institutionen,Computational life science cluster (CLiC), Umeå University,Department of Chemistry, Umeå University, Umeå, Sweden(Swepub:umu)jotr0001
(author)
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Hvidsten, Torgeir RUmeå universitet,Institutionen för fysiologisk botanik,Umeå Plant Science Centre (UPSC),Kemiska institutionen,Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden;Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden;Department of Chemistry, Biotechnology and Food Science, Norwegian, University of Life Sciences, Norway(Swepub:umu)tokv0002
(author)
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Wingsle, GunnarSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för skoglig genetik och växtfysiologi,Department of Forest Genetics and Plant Physiology(Swepub:slu)48677
(author)
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KTHGlykovetenskap
(creator_code:org_t)
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Sveriges lantbruksuniversitet
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In:BMC Genomics: BioMed Central141471-2164
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Srivastava, Vaib ...
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Obudulu, Ogonna
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Bygdell, Joakim
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Löfstedt, Tommy
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Rydén, Patrik
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Nilsson, Robert
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Ahnlund, Maria
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Johansson, Annik ...
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Jonsson, Pär
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Freyhult, Eva
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Qvarnström, Joha ...
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Karlsson, Jan
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Melzer, Michael
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Moritz, Thomas
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Trygg, Johan
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Hvidsten, Torgei ...
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Wingsle, Gunnar
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