title: Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses.
abstract: Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including genes involved in maintaining redox equilibrium and in protein degradation. However, few of these are known to be directly regulated by SigH. The goal of this project is to comprehensively define the Mycobacterium tuberculosis genes and operons that are directly controlled by SigH in order to gain insight into the role of SigH in regulating M. tuberculosis physiology. We used ChIP-Seq to identify in vivo SigH binding sites throughout the M. tuberculosis genome, followed by quantification of SigH-dependent expression of genes linked to these sites and identification of SigH-regulated promoters. We identified 69 SigH binding sites, which are located both in intergenic regions and within annotated coding sequences in the annotated M. tuberculosis genome. 41 binding sites were linked to genes that showed greater expression following heat stress in a SigH-dependent manner. We identified several genes not previously known to be regulated by SigH, including genes involved in DNA repair, cysteine biosynthesis, translation, and genes of unknown function. Experimental and computational analysis of SigH-regulated promoter sequences within these binding sites identified strong consensus -35 and -10 promoter sequences, but with tolerance for non-consensus bases at specific positions. This comprehensive identification and validation of SigH-regulated genes demonstrates an extended SigH regulon that controls an unexpectedly broad range of stress response functions.
authors.affiliation: Division of Infectious Diseases, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States of America.
authors.forename: Jared D
authors.initials: JD
authors.lastname: Sharp
authors.affiliation: Division of Infectious Diseases, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States of America.
authors.forename: Atul K
authors.initials: AK
authors.lastname: Singh
authors.affiliation: National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts 02118, United States of America.
authors.forename: Sang Tae
authors.initials: ST
authors.lastname: Park
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts 02215, United States of America.
authors.forename: Anna
authors.initials: A
authors.lastname: Lyubetskaya
authors.affiliation: Department of Microbiology, Boston University, Boston, Massachusetts 02215, United States of America.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Peterson
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts 02215, United States of America.
authors.forename: Antonio L C
authors.initials: AL
authors.lastname: Gomes
authors.affiliation: Division of Infectious Diseases, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States of America.
authors.forename: Lakshmi-Prasad
authors.initials: LP
authors.lastname: Potluri
authors.affiliation: National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts 02118, United States of America.
authors.forename: Sahadevan
authors.initials: S
authors.lastname: Raman
authors.affiliation: National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts 02118, United States of America.|Bioinformatics Program, Boston University, Boston, Massachusetts 02215, United States of America.|Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States of America.|Department of Microbiology, Boston University, Boston, Massachusetts 02215, United States of America.
authors.forename: James E
authors.initials: JE
authors.lastname: Galagan
authors.affiliation: Division of Infectious Diseases, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States of America.
authors.forename: Robert N
authors.initials: RN
authors.lastname: Husson
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D009876:Operon / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D018085:Regulon / Q000235:genetics*; D012808:Sigma Factor / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; C120328:SigH protein, bacteria; D012808:Sigma Factor