Genome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulon

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dc.contributor.authorStringer, Anne M.
dc.contributor.authorCurrenti, Salvatore
dc.contributor.authorBonocora, Richard P.
dc.contributor.authorBaranowski, Catherine
dc.contributor.authorPetrone, Brianna L.
dc.contributor.authorPalumbo, Michael J.
dc.contributor.authorReilly, Andrew A.
dc.contributor.authorZhang, Zhen
dc.contributor.authorErill, Ivan
dc.contributor.authorWade, Joseph T.
dc.date.accessioned2021-03-08T19:23:13Z
dc.date.available2021-03-08T19:23:13Z
dc.date.issued2013-11-22
dc.description.abstractEscherichia coli AraC is a well-described transcription activator of genes involved in arabinose metabolism. Using complementary genomic approaches, chromatin immunoprecipitation (ChIP)-chip, and transcription profiling, we identify direct regulatory targets of AraC, including five novel target genes: ytfQ, ydeN, ydeM, ygeA, and polB. Strikingly, only ytfQ has an established connection to arabinose metabolism, suggesting that AraC has a broader function than previously described. We demonstrate arabinose-dependent repression of ydeNM by AraC, in contrast to the well-described arabinose-dependent activation of other target genes. We also demonstrate unexpected read-through of transcription at the Rho-independent terminators downstream of araD and araE, leading to significant increases in the expression of polB and ygeA, respectively. AraC is highly conserved in the related species Salmonella enterica. We use ChIP sequencing (ChIP-seq) and RNA sequencing (RNA-seq) to map the AraC regulon in S. enterica. A comparison of the E. coli and S. enterica AraC regulons, coupled with a bioinformatic analysis of other related species, reveals a conserved regulatory network across the family Enterobacteriaceae comprised of 10 genes associated with arabinose transport and metabolism.en_US
dc.description.sponsorshipWe thank David Grainger, members of the Wade laboratory, Robert Schleif, and members of Keith Derbyshire and Todd Gray's group for helpful discussions. We thank David Grainger, Todd Gray, Keith Derbyshire, and Rick Wolf for comments on the manuscript. We thank Chunhong Mao for assistance with RNA-seq analysis. We thank the Wadsworth Center Bioinformatics Core, the Wadsworth Center Applied Genomic Technologies Core, and the University at Buffalo Next Generation Sequencing Core Facility for technical assistance. This work was supported by National Institutes of Health (NIH) grant 1DP2OD007188 and Wadsworth Center start-up funds (J.W.), U.S. National Science Foundation grant MCB-1158056 (I.E.), and appointments (C.B. and B.P.) to the Emerging Infectious Diseases (EID) Fellowship Program administered by the Association of Public Health Laboratories (APHL) and funded by the Centers for Disease Control and Prevention (CDC).en_US
dc.description.urihttps://jb.asm.org/content/196/3/660.longen_US
dc.format.extent12 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/m2gdxi-sx70
dc.identifier.citationAnne M. Stringer, Salvatore Currenti et al., Genome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulon,Journal of Bacteriology, 196 (3) 660-671; DOI: 10.1128/JB.01007-13en_US
dc.identifier.urihttps://doi.org/10.1128/JB.01007-13
dc.identifier.urihttp://hdl.handle.net/11603/21099
dc.language.isoen_USen_US
dc.publisherAmerican Society for Microbiologyen_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Biological Sciences Department Collection
dc.relation.ispartofUMBC Faculty Collection
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.
dc.subjectescherichia colien_US
dc.subjectRNAen_US
dc.subjecttranscription factorsen_US
dc.subjectbioinformaticsen_US
dc.subjectbacteriologyen_US
dc.subjectgenomicsen_US
dc.titleGenome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulonen_US
dc.typeTexten_US

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