(646e) Integrating Multiple Omics Studies to Uncover Underlying Post-Transcriptional Regulatory Networks

An important challenge in gene regulation studies is to identify the targets and effects of global regulators. A single global regulator can often control hundreds of targets and impact multiple levels of cellular process (transcription, translation, metabolite profile, etc). In our studies, we explore these key issues using the Escherichia coli carbon storage regulator (Csr) system as a case study. The Csr system is a well-studied posttranscriptional regulatory system that responds to various extracellular stresses. The system has four major regulatory elements, two proteins, CsrA and CsrD, and two small RNAs, csrB and csrC. CsrA, the main effector of the system, can affect a wide variety of cellular mRNAs and differentially regulate their translation via multiple mechanisms. Many CsrA targets have been suggested and studied in the literature, but further characterization for the majority of these targets is lacking and novel targets likely remain unknown; this largely limits our ability to exploit this powerful system for any engineering application. Furthermore, the experiments performed to identify CsrA targets have been performed in a highly traditional manner, at a single time point while ignoring potential dynamic network reconfigurations. To address these knowledge gaps, we performed a time-resolved of transcriptomic, proteomic, and pull-down study of the Csr response in E. coli to environmental stress in various genetic backgrounds. Using this new approach, we discovered that signature patterns on the proteomics, transcriptomics, and pull-down assays can be used to confidently predict a more complete set of real Csr targets. Additionally, we have experimentally validated and characterized these predicted omics targets using a combination of fluorescence and traditional biochemical approaches. As a result of these studies, we identified a number of novel Csr targets for which we have predicted and tested potential mechanisms of control. This large scale studies provides new insights on how to use global omics studies to identify new regulatory targets and suggest possible mechanisms of action for these targets.