title: DksA guards elongating RNA polymerase against ribosome-stalling-induced arrest.
abstract: In bacteria, translation-transcription coupling inhibits RNA polymerase (RNAP) stalling. We present evidence suggesting that, upon amino acid starvation, inactive ribosomes promote rather than inhibit RNAP stalling. We developed an algorithm to evaluate genome-wide polymerase progression independently of local noise and used it to reveal that the transcription factor DksA inhibits promoter-proximal pausing and increases RNAP elongation when uncoupled from translation by depletion of charged tRNAs. DksA has minimal effect on RNAP elongation in vitro and on untranslated RNAs in vivo. In these cases, transcripts can form RNA structures that prevent backtracking. Thus, the effect of DksA on transcript elongation may occur primarily upon ribosome slowing/stalling or at promoter-proximal locations that limit the potential for RNA structure. We propose that inactive ribosomes prevent formation of backtrack-blocking mRNA structures and that, in this circumstance, DksA acts as a transcription elongation factor in vivo.
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Mooney
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Grass
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Priya
authors.initials: P
authors.lastname: Sivaramakrishnan
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Christophe
authors.initials: C
authors.lastname: Herman
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: landick@bact.wisc.edu.
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: wang@bact.wisc.edu.
authors.forename: Jue D
authors.initials: JD
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D047369:Chromatin Immunoprecipitation; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial; D015971:Gene Expression Regulation, Enzymologic; D016366:Open Reading Frames; D012343:RNA, Transfer / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism*; D012808:Sigma Factor / Q000737:chemistry; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D012808:Sigma Factor; D035602:Transcriptional Elongation Factors; C090751:dksA protein, E coli; D012343:RNA, Transfer; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases