Analysis of the role of trans-translation in the requirement of tmRNA for λimm(P22) growth in Escherichia coli

Journal of Bacteriology

Volumn 181, Issue 7, 1999, Pages 2148-2157

  Withey, Jeffrey ^a   Friedman, David ^a,b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; DNA BINDING PROTEIN; MESSENGER RNA; TM RNA; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GROWTH; BACTERIOPHAGE LAMBDA; CONTROLLED STUDY; ESCHERICHIA COLI; GENE FUNCTION; GENE LOCATION; GROWTH REGULATION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN RNA BINDING; REACTION ANALYSIS; RNA ANALYSIS; RNA TRANSLATION; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS;

BACTERIA (MICROORGANISMS); BACTERIOPHAGE LAMBDA; ESCHERICHIA COLI; PROKARYOTA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0032913245     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.181.7.2148-2157.1999     Document Type: Article

References (54)

1. Ando, H., M. Kitabatake, and H. Inokuchi. 1996. 10Sa RNA complements the temperature-sensitive phenotype caused by a mutation in the phosphoribosyl pyrophosphate synthetase (prs) gene in Escherichia coli. Genes Genet. Syst. 71:47-50.
2. Bear, S. E., D. L. Court, and D. I. Friedman. 1984 An accessory role for Escherichia coli integration host factor: characterization of a lambda mutant dependent upon integration host factor for DNA packaging. J. Virol. 52: 966-972.
3. Borukhov, S., V. Sagitov, and A. Goldfarb. 1993. Transcript cleavage factors from E. coli. Cell 72:459-466.
4. Brown, J. W., D. A. Hunt, and N. R. Pace. 1990. Nucleotide sequence of the 10Sa RNA gene of the beta-purple eubacterium Alcaligenes eutrophus. Nucleic Acids Res. 18:2820.
5. Felden, B., H. Himeno, A. Muto, J. P. McCutcheon, J. F. Atkins, and R. F. Gesteland. 1997. Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). RNA 3:89-103.
6. Friedman, D. I. 1992. Interaction between bacteriophage lambda and its Escherichia coli host. Curr. Opin. Genet. Dev. 2:727-738.
7. Friedman, D. I., E. R. Olson, L. L. Johnson, D. Alessi, and M. G. Craven. 1990. Transcription-dependent competition for a host factor: the function and optimal sequence of the phage lambda boxA transcription antitermination signal. Genes Dev. 4:2210-2222.
8. Gemski, P., Jr., L. S. Baron, and N. Yamamoto. 1972. Formation of hybrids between coliphage lambda and Salmonella phage P22 with a Salmonella typhimurium hybrid sensitive to these phages. Proc. Natl. Acad. Sci. USA 69:3110-3114.
9. Gottesman, S., W. P. Clark, V. de Crecy-Legard, and M. R. Maurizi. 1993. ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli. Sequence and in vivo activities. J. Biol. Chem. 258:22618-22626.
10. Gottesman, S., E. Roche, Y. Zhou, and R. T. Sauer. 1998. The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 12:1338-1347.
11. Gottesman, S., S. Wickner, and M. R. Maurizi. 1997. Protein quality control: triage by chaperones and proteases. Genes Dev. 11:815-823.
12. Haring, V., S. J. Billington, C. L. Wright, A. S. Huggins, M. E. Katz, and J. I. Rood. 1995. Delineation of the virulence-related locus (vrl) of Dichelobacter nodosus. Microbiology 141:2081-2089.
13. Herman, C., D. Thevenet, P. Bouloc, G. C. Walker, and R. D'Ari. 1998. Degradation of C-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH). Genes Dev. 12:1348-1355.
14. Hilliker, S., and D. Botstein. 1976. Specificity of genetic elements controlling regulation of early functions in temperate bacteriophages. J. Mol. Biol. 106:537-566.
15. Himeno, H., M. Sato, T. Tadaki, M. Fukushima, C. Ushida, and A. Muto. 1997. In vitro trans translation mediated by alanine-charged 10Sa RNA. J. Mol. Biol. 268:803-808.
16. Horton, R. M., H. D. Hunt, S. N. Ho, J. K. Pullen, and L. R. Pease. 1989. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77:61-68.
17. Hou, Y.-M., and P. Schimmel. 1988. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333:140-145.
18. Huang, C., et al. Unpublished data.
19. Keiler, K. C., P. R. Waller, and R. T. Sauer. 1996. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271:990-993.
20. Kirby, J. E., J. E. Trempy, and S. Gottesman. 1994. Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli. J. Bacteriol. 176:2068-2081.
21. Komine, Y., M. Kitabatake, and H. Inokuchi. 1996. 10Sa RNA is associated with 70S ribosome particles in Escherichia coli. J. Biochem. (Tokyo) 119: 463-467.
22. Komine, Y., M. Kitabatake, T. Yokogawa, K. Nishikawa, and H. Inokuchi. 1994. A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc. Natl. Acad. Sci. USA 91:9223-9227.
23. Lee, S. B., and J. E. Bailey. 1984. A mathematical model for lambda dv plasmid replication: analysis of wild-type plasmid. Plasmid 11:151-165.
24. Lee, S. Y., S. C. Baily, and D. Apirion. 1978. Small stable RNAs from Escherichia coli: evidence for the existence of new molecules and for a new ribonucleoprotein particle containing 6S RNA. J. Bacteriol. 133:1015-1023.
25. Makarov, E. M., and D. Apirion. 1992. 10Sa RNA: processing by and inhibition of RNase III. Biochem. Int. 26:1115-1124.
26. Matsubara, K. 1981. Replication control system in lambda dv. Plasmid 5:32-52.
27. Maurizi, M. R., W. P. Clark, Y. Katayama, S. Rudikoff, and J. Pumphrey. 1990. Sequence and structure of ClpP, the proteolytic subunit of the ATP-dependent Clp protease of Escherichia coli. J. Biol. Chem. 265:12536-12545.
28. McClain, W. H., and K. Foss. 1988. Changing the identity of a tRNA by introducing a G-U wobble pair near the 3′ acceptor end. Science 240:793-796.
29. Oh, B. K., and D. Apirion. 1991. 10Sa RNA, a small stable RNA of Escherichia coli, is functional. Mol. Gen. Genet. 229:52-56.
30. Oh, B. K., A. K. Chauhan, K. Isono, and D. Apirion. 1990. Location of a gene (ssrA) for a small, stable RNA (10Sa RNA) in the Escherichia coli chromosome. J. Bacteriol. 172:4708-4709.
31. Resnick, K., J. Withey, and D. Friedman. Unpublished data.
32. Retallack, D. M., and D. I. Friedman. 1995. A role for a small stable RNA in modulating the activity of DNA-binding proteins. Cell 83:227-235.
33. Retallack, D. M., L. L. Johnson, and D. I. Friedman. 1994. Role for 10Sa RNA in the growth of lambda-P22 hybrid phage. J. Bacteriol. 176:2082-2089.
34. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
35. L operon. J. Mol. Biol. 207:1-13.
36. Simons, R. W., F. Houman, and N. Kleckner. 1987. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53:85-96.
37. Srivastava, R. A., N. Srivastava, and D. Apirion. 1992. Characterization of the RNA processing enzyme RNase III from wild type and overexpressing Escherichia coli cells in processing natural RNA substrates. Int. J. Biochem. 24:737-749.
38. Srivastava, R. K., A. Miczak, and D. Apirion. 1990. Maturation of precursor 10Sa RNA in Escherichia coli is a two-step process: the first reaction is catalyzed by RNase III in presence of Mn2+. Biochimie 72:791-802.
39. Sternberg, N. L., and R. Maurer. 1991. Bacteriophage-mediated generalized transduction in Escherichia coli and Salmonella typhimurium. Methods Enzymol. 204:18-43.
40. Strauch, M. 1983. Ph.D. thesis. University of Michigan, Ann Arbor.
41. Strauch, M. A., M. Baumann, D. I. Friedman, and L. S. Baron. 1986. Identification and characterization of mutations in Escherichia coli that selectively influence the growth of hybrid lambda bacteriophages carrying the immunity region of bacteriophage P22. J. Bacteriol. 167:191-200.
42. Subbarao, M. N., and D. Apirion. 1989. A precursor for a small stable RNA (10Sa RNA) of Escherichia coli. Mol. Gen. Genet. 217:499-504.
43. Tadaki, T., M. Fukushima, C. Ushida, H. Himeno, and A. Muto. 1996. Interaction of 10Sa RNA with ribosomes in Escherichia coli. FEBS Lett. 399:223-226.
44. Tu, G. F., G. E. Reid, J. G. Zhang, R. L. Moritz, and R. J. Simpson. 1995. C-terminal extension of truncated recombinant proteins in Escherichia coli with a 10Sa RNA decapeptide. J. Biol. Chem. 270:9322-9326.
45. Ushida, C., H. Himeno, T. Watanabe, and A. Muto. 1994. tRNA-like structures in 10Sa RNAs of Mycoplasma capricolum and Bacillus subtilis. Nucleic Acids Res. 22:3392-3396.
46. Ushida, C., and A. Muto. 1993. Small stable RNAs in Mycoplasma capricolum. Nucleic Acids Symp. Ser. 29:157-158.
47. Wawrzynow, A., B. Banecki, and M. Zylicz. 1996. The Clp ATPases define a novel class of molecular chaperones. Mol. Microbiol. 21:895-899.
48. Williams, K. P., and D. P. Bartel. 1996. Phylogenetic analysis of tmRNA secondary structure. RNA 2:1306-1310.
49. Withey, J., and D. Friedman. Unpublished data.
50. Wojtkowiak, D., C. Georgopoulos, and M. Aylicz. 1993. Isolation and characterization of ClpX, a new ATP-dependent specificity component of the Clp protease of Escherichia coli. J. Biol. Chem. 268:22609-22617.
51. Womble, D. D., and R. H. Rownd. 1986. Regulation of lambda dv plasmid DNA replication. A quantitative model for control of plasmid lambda dv replication in the bacterial cell division cycle. J. Mol. Biol. 191:367-382.
52. Wulff, D. L., and M. Rosenberg. 1983. Establishment of repressor synthesis, p. 53-73. In R. W. Hendrix, J. W. Roberts, F. W. Stahl, and R. A. Weisberg (ed.), Lambda II. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
53. Yamamoto, N., J. A. Wohlheiter, P. Gemski, and L. S. Baron. 1978. Lambda immunity-P22 dis: a hybrid of coliphage lambda with both immunity regions of Salmonella phage P22. Mol. Gen. Genet. 166:233-243.
54. Yu, D., and D. Court. 1998. A new system to place single copies of genes, sites, and lacZ fusions on the Escherichia coli chromosome. Gene 223:77-81.