Escherichia coli ribosomal RNA transcription: Regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein

Molecular Microbiology

Volumn 55, Issue 4, 2005, Pages 973-977

  Gralla, Jay D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; FACTOR FOR INVERSION STIMULATION; GUANOSINE 3' DIPHOSPHATE 5' DIPHOSPHATE; GUANOSINE TRIPHOSPHATE PYROPHOSPHOKINASE; HISTONE LIKE NUCLEOID STRUCTURING PROTEIN; HOLOENZYME; MESSENGER RNA; NUCLEASE; NUCLEOSIDE TRIPHOSPHATE; NUCLEOTIDE; PROTEIN DKSA; REGULATOR PROTEIN; RIBOSOME RNA; RNA POLYMERASE; SIGMA FACTOR; TRANSCRIPTION FACTOR RELA; UNCLASSIFIED DRUG;

BACTERIAL GROWTH; ESCHERICHIA COLI; MACROMOLECULE; NONHUMAN; NUTRIENT; NUTRITION; PRIORITY JOURNAL; PROMOTER REGION; RIBOSOME; RNA TRANSCRIPTION; SHORT SURVEY; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

BACTERIAL PROTEINS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GUANOSINE TETRAPHOSPHATE; RNA, BACTERIAL; RNA, RIBOSOMAL; TRANSCRIPTION, GENETIC;

EID: 14544287732     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2004.04455.x     Document Type: Short Survey

References (34)

1. Afflerbach, H., Schroder, O., and Wagner, R. (1998) Effects of the Escherichia coli DNA-binding protein H-NS on rRNA synthesis in vivo. Mol Microbiol 28: 641-653.
2. Ali Azam, T., Iwata, A., Nishimura, A., Ueda, S., and Ishihama, A. (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181: 6361-6370.
3. Artsimovitch, I., Patlan, V., Sekine, S., Vassylyeva, M.N., Hosaka, T., Ochi, K., et al. (2004) Structural basis for transcription regulation by alarmone ppGpp. Cell 117: 299-310.
4. Ball, C.A., Osuna, R., Ferguson, K.C., and Johnson, R.C. (1992) Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol 174: 8043-8056.
5. Brown, L., Gentry, D., Elliott, T., and Cashel, M. (2002) DksA affects ppGpp induction of RpoS at a translational level. J Bacteriol 184: 4455-4465.
6. Cabrera, J.E., and Jin, D.J. (2003) The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues. Mol Microbiol 50: 1493-1505.
7. Cashel, M., Gentry, D.R., Hernandez, V.J., and Vinella, D. (1996) The stringent response. In E. coli and Salmonella. Neidhardt F. (ed.). Washington DC: ASM press 1458-1496.
8. Dame, R.T., Wyman, C., Wurm, R., Wagner, R., and Goosen, N. (2002) Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1. J Biol Chem 277: 2146-2150.
9. Gourse, R.L. (1988) Visualization and quantitative analysis of complex formation between E. coli RNA polymerase and an rRNA promoter in vitro. Nucleic Acids Res 16: 9789-9809.
10. Hayes, C.S., and Sauer, R.T. (2003) Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol Cell 12:903-911.
11. Hogg, T., Mechold, U., Malke, H., Cashel, M., and Hilgenfeld, R. (2004) Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response [corrected]. Cell 117: 57-68.
12. Jishage, M., Kvint, K., Shingler, V., and Nystrom, T. (2002) Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev 16: 1260-1270.
13. Johansson, J., Balsalobre, C., Wang, S.Y., Urbonaviciene, J., Jin, D.J., Sonden, B., and Uhlin, B.E. (2000) Nucleoid proteins stimulate stringently controlled bacterial promoters: a link between the cAMP-CRP and the (p)ppGpp regulons in Escherichia coli. Cell 102: 475-485.
14. Jores, L., and Wagner, R. (2003) Essential steps in the ppGpp-dependent regulation of bacterial ribosomal RNA promoters can be explained by substrate competition. J Biol Chem 278: 16834-16843.
15. Lew, C.M., and Gralla, J.D. (2004a) Mechanism of stimulation of ribosomal promoters by binding of the +1 and +2 nucleotides. J Biol Chem 279: 19481-19485.
16. Lew, C.M., and Gralla, J.D. (2004b) Nucleotide dependent isomerization of E. coli RNA polymerase. Biochemistry 43: 12660-12666.
17. Mallik, P., Pratt, T.S., Beach, M.B., Bradley, M.D., Undamatla, J., and Osuna, R. (2004) Growth phase-dependent regulation and stringent control of fis are conserved processes in enteric bacteria and involve a single promoter (fis P) in Escherichia coli. J Bacteriol 186: 122-135.
18. Murray, H.D., Appleman, J.A., and Gourse, R.L. (2003a) Regulation of the Escherichia coli rrnB P2 promoter. J Bacteriol 185: 28-34.
19. Murray, H.D., Schneider, D.A., and Gourse, R.L. (2003b) Control of rRNA expression by small molecules is dynamic and nonredundant. Mol Cell 12: 125-134.
20. Ohlsen, K.L., and Gralla, J.D. (1992) DNA melting within stable closed complexes at the Escherichia coli rrnB P1 promoter. J Biol Chem 267: 19813-19818.
21. Paul, B.J., Ross, W., Gaal, T., and Gourse, R.L. (2004a) rRNA transcription in E. coli. Annu Rev Genet 38: 749-770.
22. Paul, B.J., Barker, M.M., Ross, W., Schneider, D.A., Webb, C., Foster, J.W., and Gourse, R.L. (2004b) DksA; a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 118: 311-322.
23. Pemberton, I.K., Muskhelishvili, G., Travers, A.A., and Buckle, M. (2000) The G+C-rich discriminator region of the tyrT promoter antagonises the formation of stable preinitiation complexes. J Mol Biol 299: 859-864.
24. Perederina, A., Svetlov, V., Vassylyeva, M.N., Tahirov, T.H., Yokoyama, S., Artsimovitch, I., and Vassylyev, D.G. (2004) Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription. Cell 118: 297-309.
25. Petersen, C., and Moller, L.B. (2000) Invariance of the nucleoside triphosphate pools of Escherichia coli with growth rate. J Biol Chem 275: 3931-3935.
26. Potrykus, K., Wegrzyn, G., and Hernandez, V.J. (2004) Direct stimulation of the lambdapaQ promoter by the transcription effector guanosine-3′, 5′-(bis)pyrophosphate in a defined in vitro system. J Biol Chem 279: 19860-19866.
27. Ross, W., Thompson, J.F., Newlands, J.T., and Gourse, R.L. (1990) E. coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J 9: 3733-3742.
28. Schneider, D.A., Gaal, T., and Gourse, R.L. (2002) NTP-sensing by rRNA promoters in Escherichia coli is direct. Proc Natl Acad Sci USA 99: 8602-8607.
29. Schneider, D.A., Ross, W., and Gourse, R.L. (2003) Control of rRNA expression in Escherichia coli. Curr Opin Microbiol 6: 151-156.
30. Schroder, O., and Wagner, R. (2000) The bacterial DNA-binding protein H-NS represses ribosomal RNA transcription by trapping RNA polymerase in the initiation complex. J Mol Biol 298: 737-748.
31. Squires, C.L., and Zaporojets, D. (2000) Proteins shared by the transcription and translation machines. Annu Rev Microbiol 54: 775-798.
32. Wendrich, T.M., Blaha, G., Wilson, D.N., Marahiel, M.A., and Nierhaus, K.H. (2002) Dissection of the mechanism for the stringent factor RelA. Mol Cell 10: 779-788.
33. Zhang, X., Dennis, P., Ehrenberg, M., and Bremer, H. (2002) Kinetic properties of rrn promoters in Escherichia coli. Biochimie 84: 981-996.
34. Zhi, H., Wang, X., Cabrera, J.E., Johnson, R.C., and Jin, D.J. (2003) Fis stabilizes the interaction between RNA polymerase and the ribosomal promoter rrnB P1, leading to transcriptional activation. J Biol Chem 278: 47340-47349.