title: Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis.
abstract: One of the key developmental processes during photomorphogenesis is the differentiation of prolamellar bodies of proplastids into thylakoid membranes containing the photosynthetic pigment-protein complexes of chloroplasts. To study the regulatory events controlling pigment-protein complex assembly, including the biosynthesis of metabolic precursors and pigment end products, etiolated Arabidopsis thaliana seedlings were irradiated with continuous red light (Rc), which led to rapid greening, or continuous far-red light (FRc), which did not result in visible greening, and subjected to analysis by oligonucleotide microarrays and targeted metabolite profiling. An analysis using BioPathAt, a bioinformatic tool that allows the visualization of post-genomic data sets directly on biochemical pathway maps, indicated that in Rc-treated seedlings mRNA expression and metabolite patterns were tightly correlated (e.g., Calvin cycle, biosynthesis of chlorophylls, carotenoids, isoprenoid quinones, thylakoid lipids, sterols, and amino acids). K-means clustering revealed that gene expression patterns across various biochemical pathways were very similar in Rc- and FRc-treated seedlings (despite the visible phenotypic differences), whereas a principal component analysis of metabolite pools allowed a clear distinction between both treatments (in accordance with the visible phenotype). Our results illustrate the general importance of integrative approaches to correlate post-genomic data sets with phenotypic outcomes.
authors.affiliation: Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA.
authors.forename: Majid
authors.initials: M
authors.lastname: Ghassemian
authors.forename: Jason
authors.initials: J
authors.lastname: Lutes
authors.forename: James M
authors.initials: JM
authors.lastname: Tepperman
authors.forename: Hur-Song
authors.initials: HS
authors.lastname: Chang
authors.forename: Tong
authors.initials: T
authors.lastname: Zhu
authors.forename: Xun
authors.initials: X
authors.lastname: Wang
authors.forename: Peter H
authors.initials: PH
authors.lastname: Quail
authors.forename: B Markus
authors.initials: BM
authors.lastname: Lange
mesh_terms: D017360:Arabidopsis / Q000502:physiology* / Q000528:radiation effects*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D003198:Computer Simulation; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology / Q000528:radiation effects; D008027:Light; D008954:Models, Biological; D009024:Morphogenesis / Q000502:physiology* / Q000528:radiation effects; D018462:Photobiology / Q000379:methods; D010788:Photosynthesis / Q000502:physiology* / Q000528:radiation effects; D015398:Signal Transduction / Q000502:physiology* / Q000528:radiation effects; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D014157:Transcription Factors