title: Growth rate regulation in Escherichia coli.
abstract: Growth rate regulation in bacteria has been an important issue in bacterial physiology for the past 50 years. This review, using Escherichia coli as a paradigm, summarizes the mechanisms for the regulation of rRNA synthesis in the context of systems biology, particularly, in the context of genome-wide competition for limited RNA polymerase (RNAP) in the cell under different growth conditions including nutrient starvation. The specific location of the seven rrn operons in the chromosome and the unique properties of the rrn promoters contribute to growth rate regulation. The length of the rrn transcripts, coupled with gene dosage effects, influence the distribution of RNAP on the chromosome in response to growth rate. Regulation of rRNA synthesis depends on multiple factors that affect the structure of the nucleoid and the allocation of RNAP for global gene expression. The magic spot ppGpp, which acts with DksA synergistically, is a key effector in both the growth rate regulation and the stringent response induced by nutrient starvation, mainly because the ppGpp level changes in response to environmental cues. It regulates rRNA synthesis via a cascade of events including both transcription initiation and elongation, and can be explained by an RNAP redistribution (allocation) model.
authors.affiliation: Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA. djjin@helix.nih.gov
authors.forename: Ding Jun
authors.initials: DJ
authors.lastname: Jin
authors.forename: Cedric
authors.initials: C
authors.lastname: Cagliero
authors.forename: Yan Ning
authors.initials: YN
authors.lastname: Zhou
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D012335:RNA, Ribosomal / Q000235:genetics / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D012335:RNA, Ribosomal; D012321:DNA-Directed RNA Polymerases