title: Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria.
abstract: Small RNAs (sRNAs) are molecules essential for a number of regulatory processes in the bacterial cell. Here we characterize Ms1, a sRNA that is highly expressed in Mycobacterium smegmatis during stationary phase of growth. By glycerol gradient ultracentrifugation, RNA binding assay, and RNA co-immunoprecipitation, we show that Ms1 interacts with the RNA polymerase (RNAP) core that is free of the primary sigma factor (σA) or any other σ factor. This contrasts with the situation in most other species where it is 6S RNA that interacts with RNAP and this interaction requires the presence of σA. The difference in the interaction of the two types of sRNAs (Ms1 or 6S RNA) with RNAP possibly reflects the difference in the composition of the transcriptional machinery between mycobacteria and other species. Unlike Escherichia coli, stationary phase M. smegmatis cells contain relatively few RNAP molecules in complex with σA. Thus, Ms1 represents a novel type of small RNAs interacting with RNAP.
authors.affiliation: Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic.
authors.forename: Jarmila
authors.initials: J
authors.lastname: Hnilicová
authors.affiliation: Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic.
authors.forename: Jitka
authors.initials: J
authors.lastname: Jirát Matějčková
authors.affiliation: Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic.
authors.forename: Michaela
authors.initials: M
authors.lastname: Šiková
authors.affiliation: Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Pospíšil
authors.affiliation: Department of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Halada
authors.affiliation: Department of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic.
authors.forename: Josef
authors.initials: J
authors.lastname: Pánek
authors.affiliation: Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic krasny@biomed.cas.cz.
authors.forename: Libor
authors.initials: L
authors.lastname: Krásný
mesh_terms: D002876:Chromosomes, Bacterial; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D009161:Mycobacterium / Q000235:genetics; D020102:Mycobacterium smegmatis / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D009690:Nucleic Acid Conformation; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012808:Sigma Factor / Q000378:metabolism; D026801:Synteny
chemical_list: D058727:RNA, Small Untranslated; D012808:Sigma Factor; D012321:DNA-Directed RNA Polymerases