Morphing molecular specificities between Arm-peptide and NUT-RNA in the antitermination complexes of bacteriophages λ and P22

Molecular Microbiology

Volumn 52, Issue 3, 2004, Pages 815-822

  Franklin, Naomi C ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE NUCLEOTIDE BINDING PROTEIN; PEPTIDE; PEPTIDE ARM; RNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE LAMBDA; BACTERIOPHAGE P22; COMPLEX FORMATION; CONTROLLED STUDY; MOLECULAR DYNAMICS; MORPHOLOGICAL TRAIT; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; BACTERIOPHAGE LAMBDA; BACTERIOPHAGE P22; BASE SEQUENCE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, VIRAL; TRANSCRIPTION, GENETIC; VIRAL REGULATORY PROTEINS;

BACTERIOPHAGE LAMBDA; UNIDENTIFIED BACTERIOPHAGE;

EID: 2442595009     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2004.04018.x     Document Type: Article

References (42)

1. Austin, R.J., Xia, T., Ren, J., Takahashi, T., and Roberts, R.W. (2002) Designed arginine-rich RNA-binding peptides with picomolar affinity. J Am Chem Soc 124: 10966-10967.
2. Barrick, J.E., Takahashi, T.T., Ren. J., Xia, T., and Roberts, R.W. (2001) Large libraries reveal diverse solutions to an RNA recognition problem. Proc Natl Acad Sci USA 98: 12374-12378.
3. Cai, Z., Gorin, A., Frederick, R., Ye, X., Hu, W., Majumdar, A., et al. (1998) Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex. Nature Struct Biol 5: 203-212.
4. Campbell, A. (1961) Sensitive mutants of bacteriophage λ. Virology 14: 22-32.
5. Chattopadhyay, S., Garcia-Mena, J., DeVito, J., Wolska, K., and Das, A. (1995) Bipartite function of a small RNA hairpin in transcription antitermination in bacteriophage lambda. Proc Natl Acad Sci USA 92: 12131-12135.
6. Cilley, C.D., and Williamson, J.R. (1997) An analysis of bacteriophage N protein and peptide binding to boxB RNA using polyacrylamide gel coelectrophoresis (PACE). RNA 3: 57-67.
7. Cilley, C.D., and Williamson, J.R. (2003) Structural mimicry in the phage φ21 N peptide-boxB RNA complex. RNA 9: 663-676.
8. Craven, M.G., Granston, A.E., Schauer, A.T., Zheng, C., Gray, T.A., and Friedman, D.I. (1994) Escherichia coli-Salmonella typhimurium hybrid nusA genes: identification of a short motif required for action of the λ N transcription antitermination protein. J Bacteriol 176: 1394-1404.
9. Doelling, J.H., and Franklin, N.C. (1989a) Effect of all single base substitutions in the loop of boxB on antitermination of transcription by bacteriophage λ's N protein. Nucleic Acids Res 17: 5565-5577.
10. Echols, H. (1971) Regulation of lytic development. In The Bacteriophage Lambda. Hershey, A.D. (ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 247-270.
11. Faber, C., Scharpf, M., Becker, T., Sticht, H., and Rosch, P. (2001) The structure of the coliphage HK022 Nun protein-λ-phage boxB RNA complex. J Biol Chem 276: 32064-32070.
12. Frankel, A.D., and Smith, C.A. (1998) Induced folding in RNA-protein recognition: more than a simple molecular handshake. Cell 92: 149-151.
13. Franklin, N.C. (1985) Conservation of genome form but not sequence in the transcription antitermination determinants of bacteriophages λ, Φ21 and P22. J Mol Biol 181: 75-84.
14. Franklin, N.C. (1989) A plasmid to visualize and assay termination and antitermination of transcription in Escherichia coli. Plasmid 21: 31-42.
15. Franklin, N.C. (1993) Clustered arginine residues of bacteriophage λ N protein are essential to antitermination of transcription, but their locale cannot compensate for boxB Loop defects. J Mol Biol 231: 343-360.
16. Franklin, N.C., and Doelling, J.H. (1989) Overexpression of N antitermination proteins of bacteriophages λ, 21 and P22: loss of N protein specificity. J Bacteriol 171: 2513-2522.
17. Friedman, D.I. (1988) Regulation of phage gene expression by termination and antitermination of transcription. In The Viruses. Calendar, R. (ed.). New York: Plenum Press, pp. 263-319.
18. Harada, K., Martin, S.S., and Frankel, A.D. (1996) Selection of RNA-binding peptides in vivo. Nature 380: 175-179.
19. Harada, K., Martin, S.S., Tan, R., and Frankel, A.D. (1997) Molding of a peptide into an RNA site by in vivo peptide evolution. Proc Natl Acad Sci USA 94: 11887-11892.
20. Henthorn, K.S., and Friedman, D.I. (1996) Identification of functional regions of the Nun transcription termination protein of phage HK022 and the N antitermination protein of phage λ using hybrid nun-N genes. J Mol Biol 257: 9-20.
21. Jain, C., and Belasco, J.G. (1996) A structural model for the HIV-1 Rev-RRE complex deduced from alte red-specificity Rev variants isolated by a rapid genetic strategy. Cell 87: 115-125.
22. Kourilsky, P., Bourguignon, M.-F., and Gros, F. (1971) Kinetics of viral transcription after induction of prophage. In The Bacteriophage Lambda. Hershey, A.D. (ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 647-666.
23. Lazinski, D., Grzadzielska, E., and Das, A. (1989) Sequence-specific recognition of RNA hairpins by bacteriophage anti-terminators requires a conserved arginine-rich motif. Cell 59: 207-218.
24. Legault, P., Li, J., Mogridge, J., Kay, L.E., and Greenblatt, J. (1998) NMR Structure of the bacteriophage λ N peptide/ boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell 93: 289-299.
25. Luk, K.-C., and Szybalski, W. (1983) The L2 cluster of transcription termination sites between genes bet and ral of coliphage lambda. Virology 125: 403-418.
26. Patel, D.J. (1999) Adaptive recognition in RNA complexes with peptides and protein modules. Curr Opin Struct Biol 9: 74-87.
27. Rees, W.A., Weitzel, S.E., Yager, T.D., Das, A., and von Hippel, P.H. (1996) Bacteriophage λ N protein alone can induce transcription antitermination in vitro. Proc Natl Acad Sci USA 93: 342-346.
28. Roberts, J.W. (1969) Termination factor for RNA synthesis. Nature 224: 1168-1174.
29. - : a unique class of mutants defective in the site of gene N product utilization for antitermination of leftward transcription. J Mol Biol 124: 195-221.
30. Salstrom, J.S., and Szybalski, W. (1978b) Transcription termination sites in the major leftward operon of coliphage lambda. Virology 88: 252-262.
31. Scharpf, M., Sticht, H., Schweimer, K., Boehm, M., Hoffmann, S., and Rosch, P. (2000) Antitermination in bacteriophage λ. The structure of the N36 peptide-boxB RNA complex. Eur J Biochem 267: 2397-2408.
32. Smith, C.A., Crotty, S., Harada, Y., and Frankel, A.D. (1998) Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins. Biochemistry 37: 10808-10814.
33. Smith, C.A., Calabro, V., and Frankel, A.D. (2000) An RNA-binding chameleon. Mol Cell 6: 1067-1076.
34. Su, L., Radek, J.T., Labeots, L.A., Hallenga, K., Hermanto, P., Chen, H., et al. (1997a) An RNA enhancer in a phage transcriptional antitermination complex functions as a structural switch. Genes Dev 11: 2214-2226.
35. Su, L., Radek, J.T., Hallenga, K., Hermanto, K., Chan, G., Labeots, L.A., and Weiss, M.A. (1997b) RNA recognition by a bent α-helix regulates transcriptional antitermination in phage λ. Biochem 36: 12722-12732.
36. Tan, R., and Frankel, A.D. (1995) Structural variety of arginine-rich RNA-binding peptides. Proc Natl Acad Sci USA 92: 5282-5286.
37. Van Gilst, M.R., Rees, W.A., Das, A., and von Hippel, P.H. (1997) Complexes of N antitermination protein of phage λ with specific and nonspecific RNA target sites on the nascent transcript. Biochemistry 36: 1514-1524.
38. Watnick, R.S., and Gottesman, M.E. (1999) Binding of transcription termination protein Nun to nascent RNA and template DNA. Science 286: 2337-2339.
39. Weisberg, R.A., and Gottesman, M.E. (1999) Processive antitermination. J Bacteriol 181: 359-367.
40. Weisberg, R.A., Gottesman, M.E., Hendrix, R.W., and Little, J.W. (1999) Family values in the age of genomics: Comparative analysis of bacteriophage HKO22. Annu Rev Genet 33: 565-602.
41. Williamson, J.R. (2000) Induced fit in RNA-protein recognition. Nature Struct Biol 7: 834-837.
42. Xia, T., Frankel, A., Takahashi, T.T., Ren, J., and Roberts, R.W. (2003) Context and conformation dictate the function of a transcriptional switch. Nature Struct Biol 10: 812-819.