A Comprehensive Resource for Escherichia coli Genomic Data and Tools

ABSTRACTEscherichia coli is the single most utilized cell in biology. It is the cornerstone of the biotechnology revolution,and the principal model organism for our understanding of bacterial molecular and cellular physiology. Despiteits central importance, there is no single resource providing access to the growing body of E. coli genomicsdata. RegulonDB is already the primary portal for curated knowledge of E. coli gene regulation. We propose toexpand RegulonDB to be a critically needed portal for E. coli genomic data in three key ways: (1) We willcurate all available E. coli highthroughput genomic data sets, analyze these data sets in a consistent fashion,and integrate the data into RegulonDB with tools for access, query, visualization, and analysis. The datasetswill include the first comprehensive map of the E. coli regulatory network based on ChIP-Seq and RNA-seqcurrently being generated by two of the PIs. (2) We will extend RegulonDB with comparative genomic dataspanning the Enterobacteriaceae. This will include genomic data for representatives of all majorEnterobacteriaceae genera. It will also include deep manual curation of the literature and genomic data sets forthree key pathogens related to E. coli: Salmonella enterica, Klebsiella pneumoniae, and Yersinia pestis. Inaddition, we will perform the first comparative ChIP-Seq mapping in a set of conserved TFs in these threespecies and E. coli. This will provide the first broad view of the evolution of regulation between E. coli andthese pathogens based on the comprehensive mapping of binding sites in conserved TFs. It will also provide aframework for generating complete regulatory maps in these and other Enterobacteriaceae species. (3) We willprovide an online server for bacterial ChIP-Seq analysis. The server will be specifically tailored to the uniquecharacteristics and pitfalls of ChIP-Seq in bacteria. The server will enable a new generation of microbiologistsaccess to the power of ChIPSeq for the comprehensive mapping of transcription factor-DNA binding.