title: Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon.
abstract: Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we used experimental and computational approaches to characterize Cmr's DNA binding properties and identify a putative regulon. Cmr binds a 16-bp palindromic site that includes four highly conserved nucleotides that are required for DNA binding. A total of 368 binding sites, distributed in clusters among ~200 binding regions throughout the Mycobacterium bovis BCG genome, were identified using ChIP-seq. One of the most enriched Cmr binding sites was located upstream of the cmr promoter, and we demonstrated that expression of cmr is autoregulated. cAMP affected Cmr binding at a subset of DNA loci in vivo and in vitro, including multiple sites adjacent to members of the DosR (DevR) dormancy regulon. Our findings of cooperative binding of Cmr to these DNA regions and the regulation by Cmr of the DosR-regulated virulence gene Rv2623 demonstrate the complexity of Cmr-mediated gene regulation and suggest a role for Cmr in the biology of persistent TB infection.
authors.affiliation: Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA.
authors.forename: Sridevi
authors.initials: S
authors.lastname: Ranganathan
authors.affiliation: Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA.
authors.forename: Guangchun
authors.initials: G
authors.lastname: Bai
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA 02215, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Lyubetskaya
authors.affiliation: Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA.
authors.forename: Gwendowlyn S
authors.initials: GS
authors.lastname: Knapp
authors.affiliation: Department of Microbiology, Boston University, Boston, MA 02215, USA.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Peterson
authors.affiliation: Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA.
authors.forename: Michaela
authors.initials: M
authors.lastname: Gazdik
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA 02215, USA.
authors.forename: Antonio L
authors.initials: AL
authors.lastname: C Gomes
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA 02215, USA Department of Microbiology, Boston University, Boston, MA 02215, USA Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA jgalag@bu.edu.
authors.forename: James E
authors.initials: JE
authors.lastname: Galagan
authors.affiliation: Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA kathleen.mcdonough@health.ny.gov.
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: McDonough
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D002417:Cattle; D047369:Chromatin Immunoprecipitation; D000242:Cyclic AMP / Q000378:metabolism*; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins; D015964:Gene Expression Regulation, Bacterial; D055786:Gene Knockout Techniques; D006801:Humans; D009163:Mycobacterium bovis / Q000235:genetics / Q000378:metabolism; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000378:metabolism*; D056510:Position-Specific Scoring Matrices; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D011494:Protein Kinases / Q000378:metabolism*; D055503:Protein Multimerization; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D052156:SELEX Aptamer Technique; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C542863:DosR protein, Mycobacterium tuberculosis; D011993:Recombinant Fusion Proteins; D014157:Transcription Factors; D004247:DNA; D000242:Cyclic AMP; D011494:Protein Kinases