Escherichia coli RNA polymerase mutations located near the upstream edge of an RNA:DNA hybrid and the beginning of the RNA-exit channel are defective for transcription antitermination by the N protein from lambdoid phage H-19B

Journal of Molecular Biology

Volumn 352, Issue 1, 2005, Pages 28-43

  Cheeran, Anoop ^a   Suganthan, Rajan Babu ^a   Swapna, G ^a   Bandey, Irfan ^a   Achary, M Sridhar ^a   Nagarajaram, H A ^a   Sen, Ranjan ^a  

^a Center for DNA Fingerprinting and Diagnostics   (India)

Author keywords

H 19B N protein; Mutagenesis; RNA polymerase; RNA:DNA hybrid; Transcription antitermination

Indexed keywords

AMINO ACID; BACTERIAL ENZYME; DNA HYBRID; GUANINE NUCLEOTIDE BINDING PROTEIN; HOLOENZYME; MUTANT PROTEIN; PROTEIN SUBUNIT; RNA; RNA POLYMERASE;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL GENETICS; BACTERIOPHAGE; CARBOXY TERMINAL SEQUENCE; ENZYME ACTIVITY; ENZYME PURIFICATION; ESCHERICHIA COLI; GENE CLUSTER; GENE LOCATION; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; TRANSCRIPTION TERMINATION;

BACTERIOPHAGE H-19B; ESCHERICHIA COLI;

EID: 23944518352     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.06.052     Document Type: Article

References (43)

1. K.M. Arndt, and M.J. Chamberlin RNA chain elongation by Escherichia coli RNA polymerase. Factors affecting the stability of elongating ternary complexes J. Mol. Biol. 213 1990 79 108
2. E. Nudler, E. Avetissova, V. Markovtsov, and A. Goldfarb Transcription processivity: protein-DNA interactions holding together the elongation complex Science 273 1996 211 217
3. I. Sidorenkov, N. Komissarova, and M. Kashlev Crucial role of the RNA: DNA hybrid in the processivity of transcription Mol. Cell 2 1998 55 64
4. N. Korzheva, A. Mustaev, M. Kozlov, A. Malhotra, V. Nikiforov, A. Goldfarb, and S.A. Darst A structural model of transcription elongation Science 289 2000 619 625
5. S.A. Darst Bacterial RNA polymerase Curr. Opin. Struct. Biol. 11 2001 155 162
6. A.L. Gnatt, P. Cramer, J. Fu, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution Science 292 2001 1876 1882
7. S.M. Uptain, C.M. Kane, and M.J. Chamberlin Basic mechanisms of transcript elongation and its regulation Annu. Rev. Biochem. 66 1997 117 172
8. P.H. von Hippel An integrated model of the transcription complex in elongation, termination, and editing Science 281 1998 660 665
9. E. Nudler, and M.E. Gottesman Transcription termination and anti-termination in E. coli Genes Cells 7 2002 755 768
10. J.P. Richardson Rho-dependent termination and ATPases in transcript termination Biochim. Biophys. Acta 1577 2002 251 260
11. D.I. Friedman, and D.L. Court Transcription antitermination: the lambda paradigm updated Mol. Microbiol. 18 1995 191 200
12. R.A. Weisberg, and M.E. Gottesman Processive antitermination J. Bacteriol. 181 1999 359 367
13. D. Lazinski, E. Grzadzielska, and A. Das Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine rich motif Cell 59 1989 207 218
14. S. Chattopadhyay, J. Garcia-Mena, J. DeVito, K. Wolska, and A. Das Bipartite function of a small RNA hairpin in transcription antitermination in bacteriophage lambda Proc. Natl Acad. Sci. USA 92 1995 4061 4065
15. J. Greenblatt, J.R. Nodell, and S.W. Mason Transcriptional antitermination Nature 364 1993 401 406
16. A. Das Control of transcription termination by RNA binding proteins Annu. Rev. Biochem. 62 1993 893 930
17. J. Mogridge, T.F. Mah, and J. Greenblatt Involvement of boxA nucleotides in the formation of a stable ribonucleoprotein complex containing the bacteriophage lambda N protein J. Biol. Chem. 273 1998 4143 4148
18. J. Mogridge, P. Legault, J. Li, M.D. Van Oene, L.E. Kay, and J. Greenblatt Independent ligand-induced folding of the RNA-binding domain and two functionally distinct antitermination regions in the phage λ N protein Mol. Cell 1 1998 265 275
19. C.P. Georgopoulos Bacterial mutants in which the gene N function of bacteriophage lambda is blocked have an altered RNA Polymerase Proc. Natl Acad. Sci. USA 68 1971 2977 2981
20. A. Ghysen, and M. Pironio Relationship between the N function of bacteriophage lambda and host RNA polymerase J. Mol. Biol. 65 1972 259 272
21. R RNA polymerase mutations that interferes with the expression of coliphage λ late genes Virology 73 1976 139 154
22. J.D. Jin, M. Cashel, D.I. Friedman, Y. Nakamura, A.W. Walter, and C.A. Gross Effects of Rifampicin resistant rpoB mutations on antitermination and interaction with nusA in Escherichia coli J. Mol. Biol. 204 1988 247 261
23. A.T. Schauer, S.W.C. Cheng, C. Zheng, L.S. Pierre, D. Alessi, and D.L. Hidayetoglu The alpha subunit of RNA polymerase and transcription Antitermination Mol. Microbiol. 21 1996 839 851
24. M. Obuchowski, A. Wegrzyn, A. Szalewska-Palasz, M.S. Thomas, and G. Wegrzyn An RNA polymerase a-subunit mutant impairs N-dependent transcriptional antitermination in Escherichia coli Mol. Microbiol. 23 1997 211 222
25. A. Szalewska-Palasz, B. Strzelczyk, A. Herman-Antosiewicz, G. Wegrzyn, and M.S. Thomas Genetic analysis of bacteriophage λN-dependent antitermination suggests a possible role for the RNA polymerase alpha subunit in facilitating specific functions of NusA and NusE Arch. Microbiol. 180 2003 161 168
26. N.M. Neely, and D.I. Friedman Functional and genetic analysis of regulatory regions of coliphage H-19B: location of shiga like toxin and lysis genes suggest a role for phage functions in toxin release Mol. Microbiol. 28 1998 1255 1267
27. N.M. Neely, and D.I. Friedman N-mediated transcription antitermination in lambdoid phage H-19B is characterized by alternative NUT RNA structures and a reduced requirement for host factors Mol. Microbiol. 38 2000 1074 1085
28. G. Zhang, E.A. Campbell, L. Minakhin, C. Richter, K. Severinov, and S.A. Darst Crystal structure of Thermus acquaticus core RNA Polymerase at 3.3 Å resolution Cell 98 1999 811 824
29. Y. Zhou, J.J. Filter, D.L. Court, M.E. Gottesman, and D.I. Friedman Requirement for NusG for transcription antitermination in vivo by the λ N protein J. Bacteriol. 184 2002 3416 3418
30. W.A. Rees, S.E. Weitzel, A. Das, and P.H. vonHippel Regulation of elongation-termination decision at intrinsic terminators by antitermination protein N of phage λ J. Mol. Biol. 273 1997 797 813
31. J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucl. Acids Res. 24 1997 4876 4882
32. K. Kuznedelov, N. Korzheva, A. Mustaev, and K. Severinov Structure-based analysis of RNA polymerase function: the largest subunit's rudder contributes critically to elongation complex stability and is not involved in the maintenance of RNA-DNA hybrid length EMBO J. 21 2002 1369 1378
33. R. Sen, R.A. King, and R.A. Weisberg Modification of the properties of elongating RNA Polymerase by persistent association with nascent antiterminator RNA Mol. Cell 7 2001 993 1001
34. R.A. King, R. Sen, and R.A. Weisberg Using a lac repressor roadblock to analyze the E. coli transcription elongation complex Methods Enzymol. 371 2003 207 218
35. N. Komissarova, J. Backer, S. Solter, M. Kireeva, and M. Kashlev Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination Mol. Cell 10 2002 1151 1162
36. I. Gusarov, and E. Nudler Control of intrinsic transcription termination by N and NusA: The basic mechanisms Cell 107 2001 437 449
37. R.W. Simons, F. Houman, and N. Kleckner Improved single and multicopy lac- based cloning vectors for protein and operon fusions Gene 53 1987 85 96
38. J.H. Miller, I.V. Claeys, J.B. Kirschbaum, S. Nasi, S. Van den Elsacker, and B. Molholt Altered RNA polymerases resulting from temperature-sensitive mutations in the rif region of the E. coli chromosome R.M. Losick M. Chamberlin RNA Polymerase 1976 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY 519 538
39. D. Markov, T. Naryshkina, A. Mustaev, and K. Severinov A zinc-binding site in the largest subunit of DNA dependent RNA polymerase is involved in enzyme assembly Genes Dev. 13 1999 2439 2448
40. R. Sen, R.A. King, M. Mzhavia, P.L. Madsen, and R.A. Weisberg Sequence-specific interaction of nascent antiterminator RNA with the zinc-finger motif of Escherichia coli RNA polymerase Mol. Microbiol. 46 2002 215 222
41. J.H. Miller A Short Course in Bacterial Genetics: a Laboratory Manual and Handbook for Escherichia coli and Related Bacteria 1992 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
42. M. Kashlev, E. Nudler, K. Severinov, S. Borukhov, N. Komissarova, and A. Goldfarb Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase Methods Enzymol. 274 1996 326 334
43. A. Das, P. Mahadeb, J.G. Mena, W. Whalen, K. Wolska, and R. Crossley Components of multiprotein-RNA complex that controls transcription elongation in Escherichia coli phage lambda Methods Enzymol. 274 1996 390 392