The sequences and activities of RegB endoribonucleases of T4-related bacteriophages

Nucleic Acids Research

Volumn 32, Issue 18, 2004, Pages 5582-5595

  Piešiniene, Lina ^a   Truncaite, Lindija ^a   Zajančkauskaite, Aurelija ^a   Nivinskas, Rimas ^a  

^a VILNIUS UNIVERSITY   (Lithuania)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN REGB; RIBONUCLEASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL STRAIN; BACTERIOPHAGE T4; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME STRUCTURE; ESCHERICHIA COLI; GENETIC CODE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; BACTERIOPHAGE T4; BASE SEQUENCE; ENDORIBONUCLEASES; GENE EXPRESSION REGULATION, VIRAL; GENES, VIRAL; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); PROTEIN CONFORMATION; RNA, MESSENGER; RNA, VIRAL; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI; UNIDENTIFIED BACTERIOPHAGE;

EID: 9144271099     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh892     Document Type: Article

References (64)

1. Ueno,H. and Yonesaki,T. (2001) Recognition and specific degradation of bacteriophage T4 mRNAs. Genetics, 158, 7-17.
2. Miller,E.S., Kutter,E., Mosig,G., Arisaka,F., Kunisawa,T. and Rüger,W. (2003) Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 67, 86-156.
3. Otsuka,Y., Ueno,H. and Yonesaki,T. (2003) Escherichia coli endoribonucleases involved in cleavage of bacteriophage T4 mRNAs. J. Bacteriol., 185, 983-990.
4. Deutscher,M.P. and Li,Z. (2001) Exoribonucleases and their multiple roles in RNA metabolism. Prog. Nucleic Acid Res. Mol. Biol. 66, 67-105.
5. Zuo,Y. and Deutscher,M.P. (2001) Exoribonuclease superfamilies: structural analysis and phylogenetic, distribution. Nucleic Acids Res., 29, 1017-1026.
6. Deutscher,M.P. (1993) Ribonuclease multiplicity, diversity and complexity. J. Biol. Chem., 268, 13011-13014.
7. Kushner,S.R. (2002) mRNA decay in Escherichia coli comes of age. J. Mol. Biol., 184, 4658-4665.
8. Kennel,D. (2002) Processing endoribonucleases and mRNA degradation in bacteria. J. Bacteriol., 184, 4645-4657.
9. Mudd,E.A., Carpousis,A.J. and Krisch,H.M. (1990) E.coli RNase E has a role in the decay of bacteriophage T4 mRNA. Genes Dev. 4, 873-881.
10. Uzan,M., Favre,R. and Brody,E. (1988) A nuclease that cuts specifically in the ribosome binding site of some T4 mRNAs. Proc. Natl Acad. Sci. USA, 85, 8895-8899.
11. Ruckman,J., Parma,D., Tuerk,C., Hall,D.H. and Gold,L. (1989) Identification of a T4 gene required for bacteriophage mRNA processing. New Biol., 1, 54-65.
12. Sanson,B. and Uzan,M. (1993) Dual role of the sequence-specific bacteriophage T4 endoribonuclease RegB: mRNA inactivation and mRNA destabilization. J. Mol. Biol., 233, 429-446.
13. Sanson,B. and Uzan,M. (1995) Post-transcriptional controls in bacteriophage T4: roles of the sequence-specific endoribonuclease RegB. FEMS Microbiol. Rev., 17, 141-150.
14. Sanson,B., Hu,R.-M., Troitskaya,E., Mathy,N. and Uzan,M. (2000) Endoribonuclease RegB from bacteriophage T4 is necessary for the degradation of early but not middle or late mRNAs. J. Mol. Biol., 297, 1063-1074.
15. Truncaite,L. (2001) Deletional and transcriptional analysis of the genomic region between genes 30 and 31 of bacteriophage T4. PhD Thesis, Vilnius, Lithuania.
16. Ruckman,J., Ringquist,S., Brody,E. and Gold,L. (1994) The bacteriophage T4 regB ribonuclease. Stimulation of the purified enzyme by ribosomal protein S1. J. Biol. Chem., 269, 26655-26662.
17. Lebars,I., Hu,R.M., Lallemand,J.Y., Uzan,M. and Bontems,F. (2001) Role of the substrate conformation and of the S1 protein in the cleavage efficiency of the T4 endoribonuclease RegB. J. Biol. Chem. 276, 13264-13272.
18. Chace,K.V. and Hall,D.H. (1975) Characterization of new regulatory mutants of bacteriophage T4. II. New class of mutants. J. Virol., 15, 929-945.
19. Valerie,K., Stevens,J., Lynch,M., Henderson,E.E. and de Riel,J.K. (1986) Nucleotide sequence and analysis of the 58.3 to 65.5-kb early region of bacteriophage T4. Nucleic Acids Res., 14, 8637-8654.
20. Repoila,F., Tétart,F., Bouet,J.Y. and Krisch,H.M. (1994) Genomic polymorphism in the T-even bacteriophages. EMBO J., 13, 4181-4192.
21. Kutter,E., Gachechiladze,K., Poglazov,A., Marusich,E., Shneider,M., Aronsson,P., Napuli,A., Porter,D. and Mesyanzhinov,V. (1996) Evolution of T4-related phages. Virus Genes, 11, 285-297.
22. Ackermann,A.W. and Krisch,H.M. (1997) A catalogue of T4-type bacteriophages. Arch. Virol., 142, 2329-2345.
23. Loayza,D., Carpousis,A.J. and Krisch,H.M. (1991) Gene 32 transcription and mRNA processing in T4-related bacteriophages. Mol. Microbiol., 5, 715-725.
24. Selick,H.E., Stormo,G.D., Dyson,R.L. and Alberts,B.M. (1993) Analysis of five presumptive protein-coding sequences clustered between the primosome genes, 41 and 61, of bacteriophages T4, T2, and T6. J. Virol., 67, 2305-2316.
25. Monod,C., Repoila,F., Kutateladze,M., Tétart,F. and Krisch,H.M. (1997) The genome of the pseudo T-even bacteriophages, a diverse group that resembles T4. J. Mol. Biol., 267, 237-249.
26. Tétart,F., Desplats,C., Kutateladze,M., Monod,C., Ackermann,H.W. and Krisch,H.M. (2001) Phylogeny of the major head and tail genes of the wide-ranging T4-type bacteriophages. J. Bacteriol. 183, 358-366.
27. Hambly,E., Tétart,F., Desplats,C., Wilson,W.H., Krisch,H.M. and Mann,N.H. (2001) A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2. Proc. Natl Acad. Sci. USA, 98, 11411-11416.
28. Desplats,C. and Krisch,H.M. (2003) The diversity and evolution of the T4-type bacteriophages. Res. Microbiol., 154, 259-267.
29. Miroux,B. and Walker,J.E. (1996) Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J. Mol. Biol. 260, 289-298.
30. Kricker,M. (1994) Sequencing of genomic T4 DNA. In Karam,J.D. (editor-in-chief), Molecular Biology of Bacteriophage T4. ASM Press, Washington, DC, pp. 463-464.
31. Desplats,C., Dez,C., Tétart,F., Eleaume,H. and Krisch,H.M. (2002) Snapshot of the genome of the pseudo-T-even bacteriophage RB49. J. Bacteriol., 184, 2789-2804.
32. Sanger,F., Nicklen,S. and Coulson,A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463-5467.
33. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
34. Truncaite,L., Piešiniene,L., Kolesinskiene,G., Zajančkauskaite,A., Driukas,A., Klausa,V. and Nivinskas,R. (2003) Twelve new MotA-dependent middle promoters of bacteriophage T4: consensus sequence revised. J. Mol. Biol., 327, 335-346.
35. Saïda,F., Uzan,M. and Bontems,F. (2003) The phage T4 restriction endoribonuclease RegB: a cyclizing enzyme that requires two histidines to be fully active. Nucleic Acids Res., 31, 2751-2758.
36. Yeh,L.S., Hsu,T. and Karam,J.D. (1998) Divergence of a DNA replication gene cluster in the T4-related bacteriophage RB69. J. Bacteriol., 180, 2005-2013.
37. Miller,E.S., Heidelberg,J.F., Eisen,J.A., Nelson,W.C., Durkin,A.S., Ciecko,A., Feldblyum,T.V., White,O., Paulsen,I.T., Nierman,W.C., Lee,J., Szczypinski,B. and Fraser,C.M. (2003) Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J. Bacteriol., 185, 5220-5233.
38. Liebig,H.D. and Rüger,W. (1989) Bacteriophage T4 early promoter regions. Consensus sequences of promoters and ribosome-binding sites. J. Mol. Biol., 208, 517-536.
39. Wilkens,K. and Rüger,W. (1994) Transcription from early promoters. In Karam,J.D. (editor-in-chief), Molecular Biology of Bacteriophage T4. ASM Press, Washington, DC, pp. 132-141.
40. Wilkens,K. and Rüger,W. (1996) Characterization of bacteriophage T4 early promoters in vivo with a new promoter probe vector. Plasmid, 35, 108-120.
41. Sommer,N., Salniene,V., Gineikiene,E., Nivinskas,R. and Rüger,W. (2000) T4 early promoter strength probed in vivo with unribosylated and ADP-ribosylated Escherichia coli RNA polymerase: a mutation analysis. Microbiology, 146, 2643-2653.
42. Rosenberg,M. and Court,D. (1979) Regulatory sequences involved in the promotion and termination of RNA transcription. Annu. Rev. Genet., 13, 319-353.
43. Hawley,D.K. and McClure,W.R. (1983) Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11, 2237-2255.
44. Harley,C.B. and Reynolds,R.P. (1987) Analysis of E.coli promoter sequences. Nucleic Acids Res., 15, 2343-2361.
45. Lisser,S. and Margalit,H. (1993) Compilation of E.coli mRNA promoter sequences. Nucleic Acids Res., 21, 1507-1516.
46. Bardwell,J.C.A., Régnier,P., Chen,S.-M., Nakamura,Y., Grunberg-Manago,M. and Court,D.L. (1989) Autoregulation of RNase III operon by mRNA processing. EMBO J., 8, 3401-3407.
47. Matsunaga,J., Dyer,M., Simons,E.L. and Simons,R.W. (1996) Expression and regulation of the rnc and pdxJ operons of Escherichia coli. Mol. Microbiol., 22, 977-989.
48. Matsunaga,J., Simons,E.L. and Simons,R.W. (1997) Escherichia coli RNase III (rnc) autoregulation occurs independently of rnc gene translation. Mol. Microbiol., 26, 1125-1135.
49. Jain,C. and Belasco,J.G. (1995) RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity. Genes Dev., 9, 84-96.
50. Diwa,A., Bricker,A.L., Jain,C. and Belasco,J.G. (2000) An evolutionarily conserved RNA stem-loop functions as a sensor that directs feedback regulation of RNase E gene expression. Genes Dev., 14, 1249-1260.
51. Ow,M.C., Liu,Q., Mohanty,B.K., Andrew,M.E., Maples,V.F. and Kushner,S.R. (2002) RNase E levels in Escherichia coli are controlled by a complex regulatory system that involves transcription of the rne gene from three promoters. Mol. Microbiol., 43, 159-171.
52. Zilhão,R., Régnier,P. and Arraiano,C.M. (1995) The role of endonucleases in the expression of ribonuclease II in Escherichia coli. FEMS Microbiol. Lett., 130, 237-244.
53. Zilhão,R., Cairrão,F., Régnier,P. and Arraiano,C.M. (1996) PNPase modulates RNase II expression in Escherichia coli: implications for mRNA decay and cell metabolism. Mol. Microbiol., 20, 1033-1042.
54. Robert-LeMeur,M. and Portier,C. (1992) E.coli polynucleotide phosphorylase expression is autoregulated through an RNase III-dependent mechanism. EMBO J., 11, 2633-2641.
55. Robert-LeMeur,M. and Portier,C. (1994) Polynucleotide phosphorylase of Escherichia coli induces the degradation of its RNase III processed messenger by preventing its translation. Nucleic Acids Res., 22, 397-403.
56. Jarrige,A.C., Mathy,N. and Portier,C. (2001) PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader. EMBO J., 20, 6845-6855.
57. Mudd,E.A., Prentki,P., Belin,D. and Krisch,H.M. (1988) Processing of unstable bacteriophage T4 gene 32 mRNAs into a stable species requires Escherichia coli ribonuclease E. EMBO J., 7, 3601-3607.
58. Carpousis,A.J., Mudd,E.A. and Krisch,H.M. (1989) Transcription and messenger RNA processing upstream of bacteriophage T4 gene 32. Mol. Gen. Genet., 219, 39-48.
59. Ehretsmann,C.P., Carpousis,A.J. and Krisch,H.M. (1992) Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site. Genes Dev., 6, 149-159.
60. McDowall,K.J., Lin-Chao,S. and Cohen,S.N. (1994) A + U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. J. Biol. Chem., 269, 10790-10796.
61. Carpousis,A.J. and Krisch,H.M. (1994) mRNA processing and degradation. In Karam,J.D. (editor-in-chief), Molecular Biology of Bacteriophage T4. ASM Press, Washington, DC, pp. 176-181.
62. Jayasena,V.K., Brown,D., Shtatland,T. and Gold,L. (1996) In vitro selection of RNA specifically cleaved by bacteriophage T4 RegB endonuclease. Biochemistry, 35, 2349-2356.
63. Bisaglia,M., Laalami,S., Uzan,M. and Bontems,F. (2003) Activation of the RegB endoribonuclease by the S1 ribosomal protein is due to cooperation between the S1 four C-terminal modules in a substrate-dependent manner. J. Biol. Chem., 278, 15261-15271.
64. 15N double-isotopic labelling and two-dimensional heteronuclear spectra. Protein Expr. Purif., 34, 158-165.