Regulation of transcription from two ssrS promoters in 6S RNA biogenesis

Molecules and Cells

Volumn 36, Issue 3, 2013, Pages 227-234

  Lee, Ji Young ^a   Park, Hongmarn ^a   Bak, Geunu ^a   Kim, Kwang Sun ^b   Lee, Younghoon ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

6S RNA; Feedback regulation; Fis; Promoter; Sigma factor

Indexed keywords

RNA; RNA 6S; SSRS PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; 6S RNA; BACTERIAL RNA; DNA DIRECTED RNA POLYMERASE; ESCHERICHIA COLI PROTEIN; FACTOR FOR INVERSION STIMULATION; FIS PROTEIN, E COLI; RNA POLYMERASE SIGMA 70; SIGMA FACTOR;

ARTICLE; BIOGENESIS; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; ENVIRONMENTAL CHANGE; ESCHERICHIA COLI; GENE OVEREXPRESSION; GROWTH CURVE; NEGATIVE FEEDBACK; NONHUMAN; PROMOTER REGION; TRANSCRIPTION REGULATION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; RNA PROCESSING;

ESCHERICHIA COLI;

DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FACTOR FOR INVERSION STIMULATION PROTEIN; GENE EXPRESSION REGULATION, BACTERIAL; PROMOTER REGIONS, GENETIC; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, BACTERIAL; SIGMA FACTOR; TRANSCRIPTION, GENETIC;

EID: 84898216207     PISSN: 10168478     EISSN: 02191032     Source Type: Journal    
DOI: 10.1007/s10059-013-0082-1     Document Type: Article

References (25)

1. Barrick, J.E., Sudarsan, N., Weinberg, Z., Ruzzo, W.L., and Breaker, R.R. (2005). 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA 11, 774-784.
2. Brownlee, G.G. (1971). Sequence of 6S RNA of E. coli. Nat. New Biol. 229, 147-149.
3. 70. Mol. Microbiol. 67, 1242-1256.
4. Cavanagh, A.T., Sperger, J.M., and Wassarman, K.M. (2012). Regulation of 6S RNA by pRNA synthesis is required for efficient recovery from stationary phase in E. coli and B. subtilis. Nucleic Acids Res. 40, 2234-2246.
5. Chae, H., Han, K., Kim, K.S., Park, H., Lee, J., and Lee, Y. (2011). Rho-dependent termination of ssrS (6S RNA) transcription in Escherichia coli: implication for 3′ processing of 6S RNA and expression of downstream ygfA (putative 5-formyl-tetrahydrofolate cyclo-ligase). J. Biol. Chem. 286, 114-122.
6. Gildehaus, N., Neusser, T., Wurm, R., and Wagner, R. (2007). Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts. Nucleic Acids Res. 35, 1885-1896.
7. Han, K., Kim, K.S., Bak, G., Park, H., and Lee, Y. (2010). Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family. Nucleic Acids Res. 38, 5851-5866.
8. Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K., and Pease, L.R. (1989). Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77, 51-59.
9. Kim, K.S., and Lee, Y. (2004). Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases. Nucleic Acids Res. 32, 6057-6068.
10. Kim, S., Kim, H.D., Park, I.W., and Lee, Y. (1996). Mutational analysis of RNA structures and sequences postulated to affect 3′ processing of M1 RNA, the RNA component of Escherichia coli RNase P. J. Biol. Chem. 271, 19330-19337.
11. Miller, J.H. (1992). A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria (New York: Cold Spring Harbor Laboratory Press).
12. Neusser, T., Gildehaus, N., Wurm, R., and Wagner, R. (2008). Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation. Biol. Chem. 389, 285-297.
13. Neusser, T., Polen, T., Geissen, R., and Wagner, R. (2010). Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery. BMC Genomics 11, 165.
14. Pepe, C.M., Suzuki, C., Laurie, C., and Simons, R.W. (1997). Regulation of the "tetCD" genes of transposon Tn10. J. Mol. Biol. 270, 14-25.
15. Powell, B.S., Rivas, M.P., Court, D.L., Nakamura, Y., and Turnbough, C.L. Jr. (1994). Rapid confirmation of single copy lambda prophage integration by PCR. Nucleic Acids Res. 22, 5765-5766.
16. Shephard, L., Dobson, N., and Unrau, P.J. (2010). Binding and release of the 6S transcriptional control RNA. RNA 16, 885-892.
17. Simons, R.W., Houman, F., and Kleckner, N. (1987). Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53, 85-96.
18. Stekel, D.J., and Jenkins, D.J. (2008). Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression. BMC Syst. Biol. 2, 6.
19. Trotochaud, A.E., and Wassarman, K.M. (2004). 6S RNA function enhances long-term cell survival. J. Bacteriol. 186, 4978-4985.
20. Trotochaud, A.E., and Wassarman, K.M. (2005). A highly conserved 6S RNA structure is required for regulation of transcription. Nat. Struct. Mol. Biol. 12, 313-319.
21. Trotochaud, A.E., and Wassarman, K.M. (2006). 6S RNA regulation of pspF transcription leads to altered cell survival at high pH. J. Bacteriol. 188, 3936-3943.
22. Wassarman, K.M. (2007). 6S RNA: a regulator of transcritpion. Mol. Microbiol. 65, 1425-1431.
23. Wassarman, K.M., and Storz, G. (2000). 6S RNA regulates E. coli RNA polymerase activity. Cell 101, 613-623.
24. Wassarman, K.M., Reopoila, F., Rosenow, C., Storz, G., and Gottesman, S. (2001). Identification of novel small RNAs using comparative genomics and microarray. Genes Dev. 15, 1637-1651.
25. Wurm, R., Neusser, T., and Wagner, R. (2010). 6S RNA-dependent inhibition of RNA polymerase is released by RNA-dependent synthesis of small de novo products. Biol. Chem. 391, 187-196.