sRNA-Mediated Control of Transcription Termination in E. coli.
Bacterial small RNAs (sRNAs) have been implicated in various aspects of post-transcriptional gene regulation. Here, we demonstrate that sRNAs also act at the level of transcription termination. We use the rpoS gene, which encodes a general stress sigma factor σ(S), as a model system, and show that sRNAs DsrA, ArcZ, and RprA bind the rpoS 5'UTR to suppress premature Rho-dependent transcription termination, both in vitro and in vivo. sRNA-mediated antitermination markedly stimulates transcription of rpoS during the transition to the stationary phase of growth, thereby facilitating a rapid adjustment of bacteria to global metabolic changes. Next generation RNA sequencing and bioinformatic analysis indicate that Rho functions as a global "attenuator" of transcription, acting at the 5'UTR of hundreds of bacterial genes, and that its suppression by sRNAs is a widespread mode of bacterial gene regulation.
Department of Biochemistry and Cellbiology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
Nadezda
N
Sedlyarova
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
Ilya
I
Shamovsky
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA.
Binod K
BK
Bharati
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
Vitaly
V
Epshtein
Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
Jiandong
J
Chen
Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
Susan
S
Gottesman
Department of Biochemistry and Cellbiology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria.
Renée
R
Schroeder
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA. Electronic address: evgeny.nudler@nyumc.org.
Evgeny
E
Nudler
D020121:5' Untranslated Regions; D001426:Bacterial Proteins / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D058727:RNA, Small Untranslated / Q000378:metabolism*; D012808:Sigma Factor / Q000378:metabolism*; D061806:Transcription Termination, Genetic
D020121:5' Untranslated Regions; D001426:Bacterial Proteins; C405431:DsrA RNA, E coli; D058727:RNA, Small Untranslated; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria
Rho; Transcription termination; antitermination; sRNA; sigma factor; stress response
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