title: OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants.
abstract: 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.
  
  
  CONCLUSIONS
  The proposed data evaluation strategy shows an efficient way of compiling complex, multi-platform datasets to obtain significant biological information.
authors.forename: Vaibhav
authors.initials: V
authors.lastname: Srivastava
authors.forename: Ogonna
authors.initials: O
authors.lastname: Obudulu
authors.forename: Joakim
authors.initials: J
authors.lastname: Bygdell
authors.forename: Tommy
authors.initials: T
authors.lastname: Löfstedt
authors.forename: Patrik
authors.initials: P
authors.lastname: Rydén
authors.forename: Robert
authors.initials: R
authors.lastname: Nilsson
authors.forename: Maria
authors.initials: M
authors.lastname: Ahnlund
authors.forename: Annika
authors.initials: A
authors.lastname: Johansson
authors.forename: Pär
authors.initials: P
authors.lastname: Jonsson
authors.forename: Eva
authors.initials: E
authors.lastname: Freyhult
authors.forename: Johanna
authors.initials: J
authors.lastname: Qvarnström
authors.forename: Jan
authors.initials: J
authors.lastname: Karlsson
authors.forename: Michael
authors.initials: M
authors.lastname: Melzer
authors.forename: Thomas
authors.initials: T
authors.lastname: Moritz
authors.forename: Johan
authors.initials: J
authors.lastname: Trygg
authors.forename: Torgeir R
authors.initials: TR
authors.lastname: Hvidsten
authors.affiliation: Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden. Gunnar.Wingsle@slu.se.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Wingsle
mesh_terms: D058506:Cambium / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D015999:Multivariate Analysis; D018384:Oxidative Stress; D030821:Plants, Genetically Modified / Q000235:genetics / Q000378:metabolism; D032107:Populus / Q000235:genetics* / Q000378:metabolism; D020543:Proteome; D017382:Reactive Oxygen Species / Q000378:metabolism; D013482:Superoxide Dismutase / Q000235:genetics / Q000378:metabolism; D049490:Systems Biology; D059467:Transcriptome
chemical_list: D020543:Proteome; D017382:Reactive Oxygen Species; D013482:Superoxide Dismutase