An evolutionarily conserved RNA stem-loop functions as a sensor that directs feedback regulation of RNase E gene expression

Genes and Development

Volumn 14, Issue 10, 2000, Pages 1249-1260

  Diwa, Alexis ^a   Bricker, Angela L ^b   Jain, Chaitanya ^a   Belasco, Joel G ^a,b  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Autoregulation; E. coli; mRNA degradation; Phylogenetic comparison; RNA secondary structure; RNase E

Indexed keywords

ENDONUCLEASE; MESSENGER RNA; RIBONUCLEASE E; UNCLASSIFIED DRUG;

5' UNTRANSLATED REGION; ALKYLATION; ARTICLE; AUTOREGULATION; ENZYME ACTIVITY; ENZYME SYNTHESIS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN SECONDARY STRUCTURE; RNA DEGRADATION; RNA STRUCTURE; SEQUENCE ANALYSIS;

5' UNTRANSLATED REGIONS; ALKYLATION; AMINO ACID SEQUENCE; BASE PAIRING; BASE SEQUENCE; CONSERVED SEQUENCE; ENDORIBONUCLEASES; ESCHERICHIA COLI; FEEDBACK; GENE EXPRESSION REGULATION, BACTERIAL; HALF-LIFE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA STABILITY; RNA, BACTERIAL; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0034657405     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (29)

1. Apirion, D. 1978. Isolation, genetic mapping, and some characterization of a mutation in Escherichia coli that affects the processing of ribonucleic acids. Genetics 90: 659-671.
2. Arnold, T.E., J. Yu, and J.G. Belasco. 1998. mRNA stabilization by the ompA 5′ untranslated region: Two protective elements hinder distinct pathways for mRNA degradation. RNA 4: 319-330.
3. Babitzke, P. and S.R. Kushner. 1991. The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli. Proc. Natl. Acad. Sci. 88: 1-5.
4. Baumeister, R., P. Flache, Ö. Melefors, A. von Gabain, and W. Hillen. 1991. Lack of a 5′ non-coding region in Tn1721 encoded tetR mRNA is associated with a low efficiency of translation and a short half-life in Escherichia coli. Nucleic Acids Res. 19: 4595-4600.
5. Belasco, J.G. 1993. mRNA degradation in prokaryotic cells: An overview. In Control of messenger RNA stability. pp. 3-12. Academic Press, San Diego, CA.
6. Blattner, F.R., G. Plunkett, C.A. Bloch, N.T. Perna, V. Burland, M. Riley, J. Collado-Vides, J.D. Glasner, C.K. Rode, G.F. Mayhew et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474.
7. Bouvet, P. and J.G. Belasco. 1992. Control of RNase E-mediated RNA degradation by 5′-terminal base pairing in E. coli. Nature 360: 488-491.
8. Carpousis, A.J., G. Van Houwe, C. Ehretsmann, and H.M. Krisch. 1994. Co-purification of E. coli RNase E and PNPase: Evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76: 889-900.
9. Chen, L.-H., S.A. Emory, A.L. Bricker, P. Bouvet, and J.G. Belasco. 1991. Structure and function of a bacterial mRNA stabilizer: Analysis of the 5′ untranslated region of ompA mRNA. J. Bacteriol. 173: 4578-4586.
10. Claverie-Martin, F., M.R. Diaz-Torres, S.D. Yancey, and S.R. Kushner. 1991. Analysis of the altered mRNA stability (ams) gene from Escherichia coli. J. Biol. Chem. 266: 2843-2851.
11. Emory, S.A. and J.G. Belasco. 1990. The ompA 5′ untranslated RNA segment functions in Escherichia coli as a growth-rate-regulated mRNA stabilizer whose activity is unrelated to translational efficiency. J. Bacteriol. 172: 4472-4481.
12. Fleischmann, R.D., M.D. Adams, O. White, R.A. Clayton, E.F. Kirkness, A.R. Kerlavage, C.J. Bult, J.F. Tomb, B.A. Dougherty, and J.M. Merrick. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
13. Jain, C. and J.G. Belasco. 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.
14. Jain, C. and N. Kleckner. 1993. IS10 mRNA stability and steady state levels in Escherichia coli: Indirect effects of translation and role of rne function. Mol. Microbiol. 9: 233-247.
15. Lin-Chao, S., T.-T. Wong, K.J. McDowall, and S.N. Cohen. 1994. Effects of nucleotide sequence on the specificity of rne-dependent and RNase E-mediated cleavages of RNA I encoded by the pBR322 plasmid. J. Biol. Chem. 269: 10797-10803.
16. Mackie, G.A. 1998. Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395: 720-723.
17. Mak, Y.M. and K.K. Ho. 1992. An improved method for the isolation of chromosomal DNA from various bacteria and cyanobacteria. Nucleic Acids Res. 20: 4101-4102.
18. McDowall, K.J., S. Lin-Chao, and S.N. Cohen. 1994. A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. J. Biol. Chem. 269: 10790-10796.
19. Melefors, Ö. and A. von Gabain. 1991. Genetic studies of cleavage-initiated mRNA decay and processing of ribosomal 9S RNA show that the Escherichia coli ams and rne loci are the same. Mol. Microbiol. 5: 857-864.
20. Miczak, A., V.R. Kaberdin, C.L. Wei, and S. Lin-Chao. 1996. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc. Natl. Acad. Sci. 93: 3865-3869.
21. Moazed, D., S. Stern, and H.F. Noller. 1986. Rapid chemical probing of conformation in 16S ribosomal RNA and 30S ribosomal subunits using primer extension. J. Mol. Biol. 187: 399-416.
22. Mudd, E.A. and C.F. Higgins. 1993. Escherichia coli endoribonuclease RNase E: Autoregulation of expression and site-specific cleavage of mRNA. Mol. Microbiol. 9: 557-568.
23. Mudd, E.A., H.M. Krisch, and C.F. Higgins. 1990. RNase E, an endoribonuclease, has a general role in the chemical decay of E. coli mRNA: Evidence that rne and ams are the same genetic locus. Mol. Microbiol. 4: 2127-2135.
24. Noller, H.F. and C.R. Woese. 1981. Secondary structure of 16S ribosomal RNA. Science 212: 403-411.
25. Ono, M. and M. Kuwano. 1979. A conditional lethal mutation in an Escherichia coli strain with a longer chemical lifetime of mRNA. J. Mol. Biol. 129: 343-357.
26. Py, B., C.F. Higgins, H.M. Krisch, and A.J. Carpousis. 1996. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381: 169-172.
27. Schnare, M.N., S.H. Damberger, M.W. Gray, and R.R. Gutell. 1996. Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA. J. Mol. Biol. 256: 701-719.
28. Taraseviciene, L., A. Miczak, and D. Apirion. 1991. The gene specifying RNase E (rne) and a gene affecting mRNA stability (ams) are the same gene. Mol. Microbiol. 5: 851-855.
29. Yarchuk, O., N. Jacques, J. Guillerez, and M. Dreyfus. 1992. Interdependence of translation, transcription and mRNA degradation in the lacZ gene. J. Mol. Biol. 226: 581-596.