title: Integrated omics analyses of retrograde signaling mutant delineate interrelated stress-response strata.
abstract: To maintain homeostasis in the face of intrinsic and extrinsic insults, cells have evolved elaborate quality control networks to resolve damage at multiple levels. Interorganellar communication is a key requirement for this maintenance, however the underlying mechanisms of this communication have remained an enigma. Here we integrate the outcome of transcriptomic, proteomic, and metabolomics analyses of genotypes including ceh1, a mutant with constitutively elevated levels of both the stress-specific plastidial retrograde signaling metabolite methyl-erythritol cyclodiphosphate (MEcPP) and the defense hormone salicylic acid (SA), as well as the high MEcPP but SA deficient genotype ceh1/eds16, along with corresponding controls. Integration of multi-omic analyses enabled us to delineate the function of MEcPP from SA, and expose the compartmentalized role of this retrograde signaling metabolite in induction of distinct but interdependent signaling cascades instrumental in adaptive responses. Specifically, here we identify strata of MEcPP-sensitive stress-response cascades, among which we focus on selected pathways including organelle-specific regulation of jasmonate biosynthesis; simultaneous induction of synthesis and breakdown of SA; and MEcPP-mediated alteration of cellular redox status in particular glutathione redox balance. Collectively, these integrated multi-omic analyses provided a vehicle to gain an in-depth knowledge of genome-metabolism interactions, and to further probe the extent of these interactions and delineate their functional contributions. Through this approach we were able to pinpoint stress-mediated transcriptional and metabolic signatures and identify the downstream processes modulated by the independent or overlapping functions of MEcPP and SA in adaptive responses.
authors.affiliation: Department of Plant Biology, University of California, Davis, CA, 95616, USA.|Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Marta
authors.initials: M
authors.lastname: Bjornson
authors.affiliation: Department of Physics, University of California, Davis, CA, 95616, USA.
authors.forename: Gerd Ulrich
authors.initials: GU
authors.lastname: Balcke
authors.affiliation: Department of Plant Biology, University of California, Davis, CA, 95616, USA.
authors.forename: Yanmei
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: Department of Plant Biology, University of California, Davis, CA, 95616, USA.
authors.forename: Amancio
authors.initials: A
authors.lastname: de Souza
authors.affiliation: Department of Plant Biology, University of California, Davis, CA, 95616, USA.
authors.forename: Jin-Zheng
authors.initials: JZ
authors.lastname: Wang
authors.affiliation: Department of Computer Science, University of California, Davis, CA, 95616, USA.
authors.forename: Dina
authors.initials: D
authors.lastname: Zhabinskaya
authors.affiliation: Department of Cell and Metabolic Biology, Leibniz-Institute of Plant Biochemistry, Halle, Germany.
authors.forename: Ilias
authors.initials: I
authors.lastname: Tagkopoulos
authors.affiliation: Department of Physics, University of California, Davis, CA, 95616, USA.
authors.forename: Alain
authors.initials: A
authors.lastname: Tissier
authors.affiliation: Department of Plant Biology, University of California, Davis, CA, 95616, USA.
authors.forename: Katayoon
authors.initials: K
authors.lastname: Dehesh
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D003517:Cyclopentanes / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D005978:Glutathione / Q000378:metabolism; D055432:Metabolomics / Q000379:methods; D054883:Oxylipins / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D020156:Salicylic Acid / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology; D059467:Transcriptome / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D003517:Cyclopentanes; D054883:Oxylipins; C011006:jasmonic acid; D005978:Glutathione; D020156:Salicylic Acid
keywords: 
  Arabidopsis thaliana
  ; glutathione redox status; jasmonate biosynthesis; metabolic signature of stress; methyl-erythritol cyclodiphosphate (MEcPP); multi-omics; plastidial retrograde signaling; salicylic acid (SA)