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OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants
Umeå University, Faculty of Science and Technology, Department of Chemistry. Computational life science cluster (CLiC), Umeå University and Swedish University of Agricultural Sciences.
Umeå University, Faculty of Science and Technology, Department of Chemistry. Computational life science cluster (CLiC), Umeå University.
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2013 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 14, Article Number: 893- p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
BioMed Central, 2013. Vol. 14, Article Number: 893- p.
Keyword [en]
Statistical integration, OnPLS, Poplar, Oxidative stress, Systems biology
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Genetics
Identifiers
URN: urn:nbn:se:umu:diva-85515DOI: 10.1186/1471-2164-14-893PubMedID: 24341908OAI: oai:DiVA.org:umu-85515DiVA: diva2:694129
Funder
Swedish Foundation for Strategic Research Swedish Research Council
Available from: 2014-02-05 Created: 2014-02-05 Last updated: 2017-12-06Bibliographically approved

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Obudulu, OgonnaLöfstedt, TommyRyden, PatrikJonsson, PärFreyhult, EvaKarlsson, JanTrygg, JohanHvidsten, Torgeir R
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Department of ChemistryDepartment of Mathematics and Mathematical StatisticsDepartment of Plant PhysiologyUmeå Plant Science Centre (UPSC)
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BMC Genomics
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)Genetics

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