title: Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity.
abstract: During active growth of Escherichia coli, majority of the transcriptional activity is carried out by the housekeeping sigma factor (sigma(70)), whose association with core RNAP is generally favoured because of its higher intracellular level and higher affinity to core RNAP. In order to facilitate transcription by alternative sigma factors during nutrient starvation, the bacterial cell uses multiple strategies by which the transcriptional ability of sigma(70) is diminished in a reversible manner. The facilitators of shifting the balance in favour of alternative sigma factors happen to be as diverse as a small molecule (p)ppGpp (represents ppGpp or pppGpp), proteins (DksA, Rsd) and a species of RNA (6S RNA). Although 6S RNA and (p)ppGpp were known in literature for a long time, their role in transcriptional switching has been understood only in recent years. With the elucidation of function of DksA, a new dimension has been added to the phenomenon of stringent response. As the final outcome of actions of (p)ppGpp, DksA, 6S RNA and Rsd is similar, there is a need to analyse these mechanisms in a collective manner. We review the recent trends in understanding the regulation of sigma(70) by (p)ppGpp, DksA, Rsd and 6S RNA and present a case for evolving a unified model of RNAP redistribution during starvation by modulation of sigma(70) activity in E. coli.
authors.affiliation: AstraZeneca R&D, 'Avishkar', Bellary Road, Hebbal, Bangalore 560 024, India. umender.sharma@astrazeneca.com
authors.forename: Umender K
authors.initials: UK
authors.lastname: Sharma
authors.forename: Dipankar
authors.initials: D
authors.lastname: Chatterji
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D015964:Gene Expression Regulation, Bacterial; D006159:Guanosine Tetraphosphate / Q000502:physiology; D012329:RNA, Bacterial / Q000502:physiology; D022661:RNA, Untranslated; D012097:Repressor Proteins / Q000502:physiology; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism*; D013312:Stress, Physiological / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: C411065:6S RNA; D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D012097:Repressor Proteins; C112239:Rsd protein, E coli; D012808:Sigma Factor; C090751:dksA protein, E coli; D006159:Guanosine Tetraphosphate; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases