Changes in Escherichia coli rRNA Promoter Activity Correlate with Changes in Initiating Nucleoside Triphosphate and Guanosine 5′ Diphosphate 3′-Diphosphate Concentrations after Induction of Feedback Control of Ribosome Synthesis

ABSTRACT rRNA synthesis is the rate-limiting step in ribosome synthesis in Escherichia coli. Its regulation has been described in terms of a negative-feedback control loop in which rRNA promoter activity responds to the amount of translation. The feedback nature of this control system was demonstrated previously by artificially changing ribosome synthesis rates and observing responses of rRNA promoters. However, it has not been demonstrated previously that the initiating nucleoside triphosphate (iNTP) and guanosine 5′-diphosphate 3′-diphosphate (ppGpp), the molecular effectors responsible for controlling rRNA promoters in response to changes in the nutritional environment, are responsible for altering rRNA promoter activities under these feedback conditions. Here, we show that most feedback situations result in changes in the concentrations of both the iNTP and ppGpp and that the directions of these changes are consistent with a role for these two small-molecule regulators in feedback control of rRNA synthesis. In contrast, we observed no change in the level of DNA supercoiling under the feedback conditions examined.

[1]  R. Gourse,et al.  Defective antitermination of rRNA transcription and derepression of rRNA and tRNA synthesis in the nusB5 mutant of Escherichia coli. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[2]  C. Condon,et al.  Control of rRNA transcription in Escherichia coli. , 1995, Microbiological reviews.

[3]  E. Lund,et al.  Metabolism of guanosine tetraphosphate in Escherichia coli. , 1972, European journal of biochemistry.

[4]  R. Gourse,et al.  Activation of Escherichia coli rRNA Transcription by FIS during a Growth Cycle , 1998, Journal of bacteriology.

[5]  C. Condon,et al.  Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non‐ribosomal and ribosomal RNA antitermination , 2001, The EMBO journal.

[6]  R. Gourse,et al.  Stringent control and growth-rate-dependent control have nonidentical promoter sequence requirements. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[7]  R. Gourse,et al.  DNA determinants of rRNA synthesis in E. coli: Growth rate dependent regulation, feedback inhibition, upstream activation, antitermination , 1986, Cell.

[8]  Jeffrey H. Miller.  Experiments in molecular genetics , 1972 .

[9]  Dmitry Pokholok,et al.  The Feedback Response of Escherichia coli rRNA Synthesis Is Not Identical to the Mechanism of Growth Rate-Dependent Control , 2000, Journal of bacteriology.

[10]  A. Travers,et al.  FIS modulates growth phase‐dependent topological transitions of DNA in Escherichia coli , 1997, Molecular microbiology.

[11]  R. Gourse,et al.  Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. , 2001, Journal of molecular biology.

[12]  R. Gourse,et al.  A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. , 1993, Science.

[13]  R. Gourse,et al.  NTP-sensing by rRNA promoters in Escherichia coli is direct , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[14]  D. Friedman,et al.  Cooperative effects of bacterial mutations affecting lambda N gene expression. I. Isolation and characterization of a nusB mutant. , 1976, Virology.

[15]  R. Gourse,et al.  Expression of rRNA and tRNA genes in Escherichia coli: Evidence for feedback regulation by products of rRNA operons , 1983, Cell.

[16]  R. Gourse,et al.  Control of rRNA expression in Escherichia coli. , 2003, Current opinion in microbiology.

[17]  C. Ball,et al.  Isolation of the gene encoding the Hin recombinational enhancer binding protein. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[18]  R. Simons,et al.  Improved single and multicopy lac-based cloning vectors for protein and operon fusions. , 1987, Gene.

[19]  R. Gourse,et al.  rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli. , 1996, Annual Review of Microbiology.

[20]  O. Maaløe,et al.  Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium. , 1958, Journal of general microbiology.

[21]  A. T.,et al.  On Stringent Response , 1972, Nature.

[22]  R. Gourse,et al.  Control of rRNA expression by small molecules is dynamic and nonredundant. , 2003, Molecular cell.

[23]  L. Møller,et al.  Invariance of the Nucleoside Triphosphate Pools ofEscherichia coli with Growth Rate* , 2000, The Journal of Biological Chemistry.

[24]  R. Gourse,et al.  E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. , 1990, The EMBO journal.

[25]  R. Gourse,et al.  Feedback regulation of rRNA and tRNA synthesis and accumulation of free ribosomes after conditional expression of rRNA genes. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[26]  R. Gourse,et al.  Guanosine 3'-diphosphate 5'-diphosphate is not required for growth rate-dependent control of rRNA synthesis in Escherichia coli. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[27]  K. Sekimizu,et al.  Transient Relaxation of Plasmid DNA in Escherichia coli by Fluoroquinolones , 1996, The Journal of pharmacy and pharmacology.

[28]  M. Simon,et al.  Hin-mediated site-specific recombination requires two 26 by recombination sites and a 60 by recombinational enhancer , 1985, Cell.

[29]  R. Gourse,et al.  Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. , 1994, Journal of molecular biology.

[30]  P. Nygaard,et al.  Thin-layer chromatographic methods to isolate 32P-labeled 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP): determination of cellular PRPP pools and assay of PRPP synthetase activity. , 1979, Analytical biochemistry.

[31]  R. Gourse,et al.  RNA polymerase mutants that destabilize RNA polymerase-promoter complexes alter NTP-sensing by rrn P1 promoters. , 1998, Journal of molecular biology.

[32]  R. Gourse,et al.  Regulation of rRNA Transcription Correlates with Nucleoside Triphosphate Sensing , 2001, Journal of bacteriology.

[33]  Koreaki Ito,et al.  Insertional disruption of the nusB (ssyB) gene leads to cold-sensitive growth of Escherichia coli and suppression of the secY24 mutation , 1992, Molecular and General Genetics MGG.

[34]  C. Higgins,et al.  DNA supercoiling and the anaerobic and growth phase regulation of tonB gene expression , 1988, Journal of bacteriology.

[35]  C. Turnbough,et al.  Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria. , 1997, Science.

[36]  M. Cashel.  The control of ribonucleic acid synthesis in Escherichia coli. IV. Relevance of unusual phosphorylated compounds from amino acid-starved stringent strains. , 1969, The Journal of biological chemistry.

[37]  J. Wang,et al.  Transcription and DNA supercoiling. , 1993, Current opinion in genetics & development.

[38]  C. Condon,et al.  Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies. , 1993, The EMBO journal.

[39]  S. Aiyar,et al.  Contributions of UP Elements and the Transcription Factor FIS to Expression from the Seven rrn P1 Promoters inEscherichia coli , 2001, Journal of bacteriology.

[40]  R. Gourse,et al.  Growth rate-dependent control of the rrnB P1 core promoter in Escherichia coli , 1994, Journal of bacteriology.

[41]  R. Ebright,et al.  DNA-binding determinants of the alpha subunit of RNA polymerase: novel DNA-binding domain architecture. , 1996, Genes & development.