title: Integrative FourD omics approach profiles the target network of the carbon storage regulatory system.
abstract: Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets.
authors.affiliation: Microbiology Graduate Program, University of Texas at Austin, 100 E. 24th Street Stop A6500, Austin, TX 78712, USA.
authors.forename: Steven W
authors.initials: SW
authors.lastname: Sowa
authors.affiliation: McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
authors.forename: Grant
authors.initials: G
authors.lastname: Gelderman
authors.affiliation: McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
authors.forename: Abigail N
authors.initials: AN
authors.lastname: Leistra
authors.affiliation: Biological Sciences Program College of Natural Sciences, University of Texas at Austin, 120 Inner Campus Drive Stop G2500, Austin, TX 78712, USA.
authors.forename: Aishwarya
authors.initials: A
authors.lastname: Buvanendiran
authors.affiliation: McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Lipp
authors.affiliation: McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
authors.forename: Areen
authors.initials: A
authors.lastname: Pitaktong
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Vakulskas
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA.
authors.forename: Tony
authors.initials: T
authors.lastname: Romeo
authors.affiliation: McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Baldea
authors.affiliation: McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
authors.forename: Lydia M
authors.initials: LM
authors.lastname: Contreras
mesh_terms: D002244:Carbon / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D015964:Gene Expression Regulation, Bacterial; D023281:Genomics / Q000379:methods; D060847:Metabolic Engineering / Q000379:methods; D055442:Metabolome; D055432:Metabolomics / Q000379:methods; D008954:Models, Biological; D020543:Proteome; D040901:Proteomics / Q000379:methods; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: C093587:CsrA protein, E coli; D029968:Escherichia coli Proteins; D020543:Proteome; D016601:RNA-Binding Proteins; D012097:Repressor Proteins; D002244:Carbon