Nascent RNA in transcription complexes interacts with CspE, a small protein in E. coli implicated in chromatin condensation

Journal of Molecular Biology

Volumn 282, Issue 2, 1998, Pages 227-239

  Hanna, Michelle M ^a   Liu, Kebin ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

CspE; Photocrosslinking nucleotide analogs; Q; RNA and DNA binding protein; Transcriptional antitermination

Indexed keywords

RNA; RNA BINDING PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHROMOSOME CONDENSATION; DNA TEMPLATE; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN CROSS LINKING; PROTEIN PURIFICATION; PROTEIN RNA BINDING;

ESCHERICHIA COLI;

EID: 0032544629     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2005     Document Type: Article

References (50)

1. Bernhard, S. L. & Meares, C. F. (1986). The sigma subunit of RNA polymerase contacts the leading ends of transcripts 9-13 bases long on the lambda pR promoter but not on T7 A1. Biochemistry, 25, 5914-5919.
2. Bowser, C. & Hanna, M. M. (1991). The sigma subunit of E. coli RNA polymerase loses contacts with the 3′ end of the nascent RNA after synthesis of a tetranucleotide. J. Mol. Biol. 220, 227-239.
3. Brandi, C. A., Pon, C. L. & Gualerzi, C. O. (1994). Interaction of the main cold shock protein CS7. 4 (CspA) of Escherichia coli with the promoter region of hns. Biochimie, 76, 1090-1098.
4. Briat, J.-F. & Chamberlin, M. J. (1984). Identification and characterization of a new transcriptional termination factor from Escherichia coli. Proc. Natl Acad. Sci. USA, 81, 7373-7377.
5. Brosius, J. (1984). Toxicity of an overproduced foreign gene product in E. coli and its use in plasmid vectors for the selection of transcription terminators. Gene, 27, 161-172.
6. Burgess, R. R. & Jendrisak, J. J. (1975). A procedure for the rapid, large-scale purification of Escherichia coli DNA-dependent RNA polymerase involving polymin P precipitation and DNA-cellulose chromatography. Biochemistry, 14, 4634-4638.
7. Das, A. (1992). How the phage lambda N gene product suppresses transcription termination of RNA polymerase with regulatory proteins mediated by signals in nascent RNA. J. Bacteriol. 174, 6711-6716.
8. Das, A. (1993). Control of transcription termination by RNA-binding proteins. Annu. Rev. Biochem. 62, 893-930.
9. DeRiemer, L. H. & Meares, C. F. (1981). Early steps in the path of nascent ribonucleic acid across the surface of ribonucleic acid polymerase, determined by photoaffinity labeling. Biochemistry, 20, 1612-1617.
10. Dissinger, S. & Hanna, M. M. (1990). Active site labeling of Escherichia coli transcription elongation complexes with 5-((4-azidophenacyl)thio)uridine 5′-triphosphate. J. Biol. Chem. 265, 7662-7668.
11. Dissinger, S. & Hanna, M. M. (1991). RNA-protein interactions in a NusA-containing Escherichia coli transcription complex paused at an RNA hairpin. J. Mol. Biol. 219, 11-25.
12. Friedman, D. I. & Court, D. L. (1995). Transcription antitermination: the λ paradigm updated. Mol. MicroBiol. 18, 191-200.
13. Goldstein, J., Pollitt, N. S. & Inouye, M. (1990). Major cold shock protein of Escherichia coli. Proc. Natl Acad. Sci. USA, 87, 283-287.
14. Grachev, M. A. & Zaychikov, E. F. (1981). Photo-modification studies of the contacts of the 5′-terminus of growing RNA with the subunits of RNA-polymerase. FEBS Letters, 130, 23-26.
15. Grayhack, E. J. & Roberts, J. W. (1982). The Phage lambda Q gene product: activity of a transcription antitermination in vitro. Cell, 30, 637-648.
16. Greenblatt, J. & Li, J. (1981). Interaction of the sigma factor and the nusA gene protein of E. coli with RNA polymerase in the initiation-termination cycle of transcription. Cell, 24, 421-428.
17. Gross, C. A., Lonetto, M. A. & Losick, R. (1992). Sigma factors. In Control of Transcription (Yamamoto, K. & McKnight, S., eds), pp. 129-176, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
18. R′ promoter. Methods Enzymol. 274, 402-418.
19. Hanna, M. M. & Meares, C. F. (1983a). Synthesis of a cleavable dinucleotide photoaffinity probe of RNA polymerase: application to trinucleotide labeling of an Escherichia coli transcription complex. Biochemistry, 22, 3546-3551.
20. Hanna, M. M. & Meares, C. F. (1983b). Topography of transcription: path of the leading end of nascent RNA through the Escherichia coli transcription complex. Proc. Natl Acad. Sci. USA, 80, 4238-4242.
21. Hanna, M. M., Dissinger, S., Williams, B. D. & Colston, J. E. (1989). Synthesis and characterization of 5-[(4-azidophenacyl)thio]uridine 5′-triphosphate, a cleavable photocross-linking nucleotide analogue. Biochemistry, 28, 5814-5820.
22. Hanna, M. M., Zhang, Y., Reidling, J. C., Thomas, M. J. & Jou, J. (1993). Synthesis and characterization of a new photocrosslinking CTP analog and its use in photoaffinity labeling E. coli and T7 polymerases. Nucl Acids Res. 21, 2073-2079.
23. Harrington, E. W. & Trun, N. J. (1997). Unfolding of the bacterial nucleoid both in vivo and in vitro as a result of exposure to camphor. J. Bacteriol. 179, 2435-2439.
24. Hu, K. H., Liu, E., Dean, K., Gingras, M., DeGraff, W. & Trun, N. J. (1996). Overexpression of three genes leads to camphor resistance and chromosome condensation in E. coli. Genetics, 143, 1521-1532.
25. Jiang, W., Hou, Y. & Inouye, M. (1997). CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone. J. Biol Chem. 272, 196-202.
26. Jones, P. G. & Inouye, M. (1994). The cold-shock response - a hot topic. Mol. Micribiol. 11, 811-818.
27. King, K., Benkovic, S. J. & Modrich, P. (1989). Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease. J. Biol. Chem. 264, 11807-11815.
28. Krummel, B. & Chamberlin, M. J. (1989). RNA Chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry, 28, 7829-7842.
29. Ladomery, M. & Sommerville, J. (1994). Binding of Y-box proteins to RNA: involvement of different protein domains. Nucl. Acids Res. 22, 5582-5589.
30. Li, S. C., Squires, C. & Squires, C. (1984). Antitermination of E. coli rRNA transcription is caused by a control region segment containing lambda nut-like sequences. Cell, 38, 851-860.
31. Liu, K. & Hanna, M. M. (1995a). NusA contacts nascent RNA in Escherichia coli transcription complexes. J. Mol. Biol. 247, 547-558.
32. Liu, K. & Hanna, M. M. (1995b). NusA interferes with interactions between the nascent RNA and the C-terminal domain of the α subunit in E. coli transcription complexes. Proc. Natl Acad. Sci. USA, 92, 5012-5016.
33. Liu, K., Zhang, Y., Severinov, K., Das, A. & Hanna, M. M. (1996). Role of Escherichia coli RNA polymerase alpha subunit in modulation of pausing, termination and anti-termination by the transcription elongation factor NusA. EMBO J. 15, 150-161.
34. Mogridge, J., Mah, T.-F. & Greenblatt, J. (1995). A protein-RNA interaction network facilitates the template-independent cooperative assembly on RNA polymerase of a stable antitermination complex containing the N protein. Genes Dev. 9, 2831-2844.
35. +-binding region (Rossmann fold). J. Biol. Chem. 270, 2755-2763.
36. Newkirk, K., Feng, W., Jiang, W., Tejero, R., Emerson, S. D., Inouye, M. & Montelione, G. T. (1994). Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA. Proc. Natl Acad. Sci. USA, 91, 5114-5118.
37. Pavco, P. A. & Steege, D. A. (1990). Elongation by Escherichia coli RNA polymerase is blocked in vitro by a site-specific DNA binding protein. J. Biol. Chem. 265, 9960-9969.
38. Picard, V., Ersdal-Badju, E., Lu, A. & Bock, S. C. (1994). A rapid and efficient one-tube PCR-based mutagenesis technique using pfu DNA polymerase. Nucl Acids Res. 22, 2587-2591.
39. Ring, B. Z., Yarnell, W. S. & Roberts, J. W. (1996). Function of E. coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing. Cell, 86, 485-493.
40. Roberts, J. W. (1992). Antitermination and the control of transcription elongation. In Transcription Regulation (Yamamoto, K. & McKnight, S., eds), pp. 389-406, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
41. Schagger, H. & von Jagow, G. (1987). Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal. Biochem. 166, 368-379.
42. Squires, C. L., Greenblatt, J., Li, J., Condon, C. & Squires, C. L. (1993). Ribosomal RNA antitermination in vitro: requirement for Nus factors and one or more unidentified cellular components. Proc. Natl Acad. Sci. USA, 90, 970-974.
43. Teana, A. L., Brandi, A., Falconi, M., Spurio, R., Pon, C. L. & Gualerzi, C. O. (1991). Identification of a cold shock transcriptional enhancer of the Escherichia coli gene encoding nucleoid protein H-NS. Proc. Natl Acad. Sci. USA, 88, 10907-10911.
44. 2. Mol. Gen. Genet. 199, 55-58.
45. Trun, N. J. & Marko, J. F. (1998). The architecture of a functional chromosome. ASM News.
46. Wolffe, A. P., Tafuri, S., Ranjan, M. & Familari, M. (1992). The Y-box factors: a familiar of nucleic acid binding proteins conserved from Escherichia coli to man. New Biol. 4, 290-298.
47. Wright, D. J., King, K. & Modrich, P. (1989). The negative charge of Glu-111 is required to activate the cleavage center of EcoRI endonuclease. J. Biol. Chem. 264, 11816-11821.
48. Yamanaka, K., Mitani, T., Ogura, T., Niki, H. & Hiraga, S. (1994). Cloning, sequencing, and characterization of multicopy suppressers of a mukB mutation in Escherichia coli. Mol. Microbiol. 13, 301-312.
49. Yarnell, W. S. & Roberts, J. W. (1992). The phage lambda gene Q transcription antiterminator binds DNA in the late gene promoter as it modifies RNA polymerase. Cell, 69, 1181-1189.
50. Zhang, Y. & Hanna, M. (1994). NusA changes the conformation of Escherichia coli RNA polymerase at the binding site for the 3′ end of the nascent RNA. J. Bacteriol. 176, 1787-1789.