Skip to main content
RNA logoLink to RNA
. 2000 Aug;6(8):1079–1090. doi: 10.1017/s1355838200001023

Emerging features of mRNA decay in bacteria.

D A Steege 1
PMCID: PMC1369983  PMID: 10943888

Abstract

The problem of mRNA decay in E. coli has recently seen exciting progress, with the discoveries that key degradation enzymes are associated together in a high molecular weight degradosome and that polyadenylation promotes decay. Recent advances make it clear that mRNA decay in bacteria is far more interesting enzymatically than might have been predicted. In-depth study of specific mRNAs has revealed multiple pathways for degradation. Which pathway a given mRNA follows appears to depend in large part on the location of the initiating endonucleolytic cleavage within the mRNA. During the steps of mRNA decay, stable RNA structures pose formidable barriers to the 3' --> 5' exonucleases. However, polyadenylation is now emerging as a process that plays an important role in maintaining the momentum of exonucleolytic degradation by adding single-stranded extensions to the 3' ends of mRNAs and their decay intermediates, thereby facilitating further exonuclease digestion.

Full Text

The Full Text of this article is available as a PDF (303.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. AUGUST J. T., ORTIZ P. J., HURWITZ J. Ribonucleic acid-dependent ribonucleotide incorporation. I. Purification and properties of the enzyme. J Biol Chem. 1962 Dec;237:3786–3793. [PubMed] [Google Scholar]
  2. Anderson J. S., Parker R. P. The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex. EMBO J. 1998 Mar 2;17(5):1497–1506. doi: 10.1093/emboj/17.5.1497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arraiano C. M., Yancey S. D., Kushner S. R. Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12. J Bacteriol. 1988 Oct;170(10):4625–4633. doi: 10.1128/jb.170.10.4625-4633.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Babitzke P., Granger L., Olszewski J., Kushner S. R. Analysis of mRNA decay and rRNA processing in Escherichia coli multiple mutants carrying a deletion in RNase III. J Bacteriol. 1993 Jan;175(1):229–239. doi: 10.1128/jb.175.1.229-239.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bardwell J. C., Régnier P., Chen S. M., Nakamura Y., Grunberg-Manago M., Court D. L. Autoregulation of RNase III operon by mRNA processing. EMBO J. 1989 Nov;8(11):3401–3407. doi: 10.1002/j.1460-2075.1989.tb08504.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bessarab D. A., Kaberdin V. R., Wei C. L., Liou G. G., Lin-Chao S. RNA components of Escherichia coli degradosome: evidence for rRNA decay. Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):3157–3161. doi: 10.1073/pnas.95.6.3157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Binnie U., Wong K., McAteer S., Masters M. Absence of RNASE III alters the pathway by which RNAI, the antisense inhibitor of ColE1 replication, decays. Microbiology. 1999 Nov;145(Pt 11):3089–3100. doi: 10.1099/00221287-145-11-3089. [DOI] [PubMed] [Google Scholar]
  8. Blum E., Carpousis A. J., Higgins C. F. Polyadenylation promotes degradation of 3'-structured RNA by the Escherichia coli mRNA degradosome in vitro. J Biol Chem. 1999 Feb 12;274(7):4009–4016. doi: 10.1074/jbc.274.7.4009. [DOI] [PubMed] [Google Scholar]
  9. Blumer K. J., Steege D. A. mRNA processing in Escherichia coli: an activity encoded by the host processes bacteriophage f1 mRNAs. Nucleic Acids Res. 1984 Feb 24;12(4):1847–1861. doi: 10.1093/nar/12.4.1847. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Braun F., Hajnsdorf E., Régnier P. Polynucleotide phosphorylase is required for the rapid degradation of the RNase E-processed rpsO mRNA of Escherichia coli devoid of its 3' hairpin. Mol Microbiol. 1996 Mar;19(5):997–1005. doi: 10.1046/j.1365-2958.1996.440971.x. [DOI] [PubMed] [Google Scholar]
  11. Braun F., Le Derout J., Régnier P. Ribosomes inhibit an RNase E cleavage which induces the decay of the rpsO mRNA of Escherichia coli. EMBO J. 1998 Aug 17;17(16):4790–4797. doi: 10.1093/emboj/17.16.4790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Cao G. J., Pogliano J., Sarkar N. Identification of the coding region for a second poly(A) polymerase in Escherichia coli. Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11580–11585. doi: 10.1073/pnas.93.21.11580. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Cao G. J., Sarkar N. Identification of the gene for an Escherichia coli poly(A) polymerase. Proc Natl Acad Sci U S A. 1992 Nov 1;89(21):10380–10384. doi: 10.1073/pnas.89.21.10380. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Cao G. J., Sarkar N. Poly(A) RNA in Escherichia coli: nucleotide sequence at the junction of the lpp transcript and the polyadenylate moiety. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7546–7550. doi: 10.1073/pnas.89.16.7546. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Carpousis A. J., Van Houwe G., Ehretsmann C., Krisch H. M. Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell. 1994 Mar 11;76(5):889–900. doi: 10.1016/0092-8674(94)90363-8. [DOI] [PubMed] [Google Scholar]
  16. Carpousis A. J., Vanzo N. F., Raynal L. C. mRNA degradation. A tale of poly(A) and multiprotein machines. Trends Genet. 1999 Jan;15(1):24–28. doi: 10.1016/s0168-9525(98)01627-8. [DOI] [PubMed] [Google Scholar]
  17. Cashman J. S., Webster R. E., Steege D. A. Transcription of bacteriophage fl. The major in vivo RNAs. J Biol Chem. 1980 Mar 25;255(6):2554–2562. [PubMed] [Google Scholar]
  18. Cheng Z. F., Zuo Y., Li Z., Rudd K. E., Deutscher M. P. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J Biol Chem. 1998 Jun 5;273(23):14077–14080. doi: 10.1074/jbc.273.23.14077. [DOI] [PubMed] [Google Scholar]
  19. Chow J., Dennis P. P. Coupling between mRNA synthesis and mRNA stability in Escherichia coli. Mol Microbiol. 1994 Mar;11(5):919–931. doi: 10.1111/j.1365-2958.1994.tb00371.x. [DOI] [PubMed] [Google Scholar]
  20. Coburn G. A., Mackie G. A. Degradation of mRNA in Escherichia coli: an old problem with some new twists. Prog Nucleic Acid Res Mol Biol. 1999;62:55–108. doi: 10.1016/s0079-6603(08)60505-x. [DOI] [PubMed] [Google Scholar]
  21. Coburn G. A., Mackie G. A. Differential sensitivities of portions of the mRNA for ribosomal protein S20 to 3'-exonucleases dependent on oligoadenylation and RNA secondary structure. J Biol Chem. 1996 Jun 28;271(26):15776–15781. doi: 10.1074/jbc.271.26.15776. [DOI] [PubMed] [Google Scholar]
  22. Coburn G. A., Mackie G. A. Overexpression, purification, and properties of Escherichia coli ribonuclease II. J Biol Chem. 1996 Jan 12;271(2):1048–1053. doi: 10.1074/jbc.271.2.1048. [DOI] [PubMed] [Google Scholar]
  23. Coburn G. A., Mackie G. A. Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes. J Mol Biol. 1998 Jun 26;279(5):1061–1074. doi: 10.1006/jmbi.1998.1842. [DOI] [PubMed] [Google Scholar]
  24. Coburn G. A., Miao X., Briant D. J., Mackie G. A. Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3' exonuclease and a DEAD-box RNA helicase. Genes Dev. 1999 Oct 1;13(19):2594–2603. doi: 10.1101/gad.13.19.2594. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Cohen S. N. Surprises at the 3' end of prokaryotic RNA. Cell. 1995 Mar 24;80(6):829–832. doi: 10.1016/0092-8674(95)90284-8. [DOI] [PubMed] [Google Scholar]
  26. Deutscher M. P. Promiscuous exoribonucleases of Escherichia coli. J Bacteriol. 1993 Aug;175(15):4577–4583. doi: 10.1128/jb.175.15.4577-4583.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Deutscher M. P., Reuven N. B. Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3277–3280. doi: 10.1073/pnas.88.8.3277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Deutscher M. P. Ribonuclease multiplicity, diversity, and complexity. J Biol Chem. 1993 Jun 25;268(18):13011–13014. [PubMed] [Google Scholar]
  29. Donovan W. P., Kushner S. R. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1986 Jan;83(1):120–124. doi: 10.1073/pnas.83.1.120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Dunn J. J. RNase III cleavage of single-stranded RNA. Effect of ionic strength on the fideltiy of cleavage. J Biol Chem. 1976 Jun 25;251(12):3807–3814. [PubMed] [Google Scholar]
  31. GROS F., HIATT H., GILBERT W., KURLAND C. G., RISEBROUGH R. W., WATSON J. D. Unstable ribonucleic acid revealed by pulse labelling of Escherichia coli. Nature. 1961 May 13;190:581–585. doi: 10.1038/190581a0. [DOI] [PubMed] [Google Scholar]
  32. Ghosh S., Deutscher M. P. Oligoribonuclease is an essential component of the mRNA decay pathway. Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4372–4377. doi: 10.1073/pnas.96.8.4372. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Gilson E., Clément J. M., Brutlag D., Hofnung M. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 1984 Jun;3(6):1417–1421. doi: 10.1002/j.1460-2075.1984.tb01986.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Goodrich A. F., Steege D. A. Roles of polyadenylation and nucleolytic cleavage in the filamentous phage mRNA processing and decay pathways in Escherichia coli. RNA. 1999 Jul;5(7):972–985. doi: 10.1017/s1355838299990398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Granger L. L., O'Hara E. B., Wang R. F., Meffen F. V., Armstrong K., Yancey S. D., Babitzke P., Kushner S. R. The Escherichia coli mrsC gene is required for cell growth and mRNA decay. J Bacteriol. 1998 Apr;180(7):1920–1928. doi: 10.1128/jb.180.7.1920-1928.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Gupta R. S., Kasai T., Schlessinger D. Purification and some novel properties of Escherichia coli RNase II. J Biol Chem. 1977 Dec 25;252(24):8945–8949. [PubMed] [Google Scholar]
  37. Hajnsdorf E., Braun F., Haugel-Nielsen J., Régnier P. Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli. Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):3973–3977. doi: 10.1073/pnas.92.9.3973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Hajnsdorf E., Régnier P. E. coli RpsO mRNA decay: RNase E processing at the beginning of the coding sequence stimulates poly(A)-dependent degradation of the mRNA. J Mol Biol. 1999 Mar 5;286(4):1033–1043. doi: 10.1006/jmbi.1999.2547. [DOI] [PubMed] [Google Scholar]
  39. Hajnsdorf E., Steier O., Coscoy L., Teysset L., Régnier P. Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant. EMBO J. 1994 Jul 15;13(14):3368–3377. doi: 10.1002/j.1460-2075.1994.tb06639.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Haugel-Nielsen J., Hajnsdorf E., Regnier P. The rpsO mRNA of Escherichia coli is polyadenylated at multiple sites resulting from endonucleolytic processing and exonucleolytic degradation. EMBO J. 1996 Jun 17;15(12):3144–3152. [PMC free article] [PubMed] [Google Scholar]
  41. Hayes R., Kudla J., Schuster G., Gabay L., Maliga P., Gruissem W. Chloroplast mRNA 3'-end processing by a high molecular weight protein complex is regulated by nuclear encoded RNA binding proteins. EMBO J. 1996 Mar 1;15(5):1132–1141. [PMC free article] [PubMed] [Google Scholar]
  42. He L., Söderbom F., Wagner E. G., Binnie U., Binns N., Masters M. PcnB is required for the rapid degradation of RNAI, the antisense RNA that controls the copy number of ColE1-related plasmids. Mol Microbiol. 1993 Sep;9(6):1131–1142. doi: 10.1111/j.1365-2958.1993.tb01243.x. [DOI] [PubMed] [Google Scholar]
  43. Kaberdin V. R., Miczak A., Jakobsen J. S., Lin-Chao S., McDowall K. J., von Gabain A. The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly. Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11637–11642. doi: 10.1073/pnas.95.20.11637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Kalapos M. P., Cao G. J., Kushner S. R., Sarkar N. Identification of a second poly(A) polymerase in Escherichia coli. Biochem Biophys Res Commun. 1994 Jan 28;198(2):459–465. doi: 10.1006/bbrc.1994.1067. [DOI] [PubMed] [Google Scholar]
  45. Kido M., Yamanaka K., Mitani T., Niki H., Ogura T., Hiraga S. RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. J Bacteriol. 1996 Jul;178(13):3917–3925. doi: 10.1128/jb.178.13.3917-3925.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Kokoska R. J., Blumer K. J., Steege D. A. Phage fl mRNA processing in Escherichia coli: search for the upstream products of endonuclease cleavage, requirement for the product of the altered mRNA stability (ams) locus. Biochimie. 1990 Nov;72(11):803–811. doi: 10.1016/0300-9084(90)90189-n. [DOI] [PubMed] [Google Scholar]
  47. Kokoska R. J., Steege D. A. Appropriate expression of filamentous phage f1 DNA replication genes II and X requires RNase E-dependent processing and separate mRNAs. J Bacteriol. 1998 Jun;180(12):3245–3249. doi: 10.1128/jb.180.12.3245-3249.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Kornberg A. Inorganic polyphosphate: toward making a forgotten polymer unforgettable. J Bacteriol. 1995 Feb;177(3):491–496. doi: 10.1128/jb.177.3.491-496.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. LITTAUER U. Z., KORNBERG A. Reversible synthesis of polyribonucleotides with an enzyme from Escherichia coli. J Biol Chem. 1957 Jun;226(2):1077–1092. [PubMed] [Google Scholar]
  50. Li Z., Pandit S., Deutscher M. P. Polyadenylation of stable RNA precursors in vivo. Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12158–12162. doi: 10.1073/pnas.95.21.12158. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Li Z., Pandit S., Deutscher M. P. RNase G (CafA protein) and RNase E are both required for the 5' maturation of 16S ribosomal RNA. EMBO J. 1999 May 17;18(10):2878–2885. doi: 10.1093/emboj/18.10.2878. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Lin-Chao S., Cohen S. N. The rate of processing and degradation of antisense RNAI regulates the replication of ColE1-type plasmids in vivo. Cell. 1991 Jun 28;65(7):1233–1242. doi: 10.1016/0092-8674(91)90018-t. [DOI] [PubMed] [Google Scholar]
  53. Liu J. D., Parkinson J. S. Genetic evidence for interaction between the CheW and Tsr proteins during chemoreceptor signaling by Escherichia coli. J Bacteriol. 1991 Aug;173(16):4941–4951. doi: 10.1128/jb.173.16.4941-4951.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Lopilato J., Bortner S., Beckwith J. Mutations in a new chromosomal gene of Escherichia coli K-12, pcnB, reduce plasmid copy number of pBR322 and its derivatives. Mol Gen Genet. 1986 Nov;205(2):285–290. doi: 10.1007/BF00430440. [DOI] [PubMed] [Google Scholar]
  55. Mackie G. A., Genereaux J. L., Masterman S. K. Modulation of the activity of RNase E in vitro by RNA sequences and secondary structures 5' to cleavage sites. J Biol Chem. 1997 Jan 3;272(1):609–616. [PubMed] [Google Scholar]
  56. Mackie G. A. Ribonuclease E is a 5'-end-dependent endonuclease. Nature. 1998 Oct 15;395(6703):720–723. doi: 10.1038/27246. [DOI] [PubMed] [Google Scholar]
  57. Mackie G. A. Stabilization of the 3' one-third of Escherichia coli ribosomal protein S20 mRNA in mutants lacking polynucleotide phosphorylase. J Bacteriol. 1989 Aug;171(8):4112–4120. doi: 10.1128/jb.171.8.4112-4120.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Margossian S. P., Li H., Zassenhaus H. P., Butow R. A. The DExH box protein Suv3p is a component of a yeast mitochondrial 3'-to-5' exoribonuclease that suppresses group I intron toxicity. Cell. 1996 Jan 26;84(2):199–209. doi: 10.1016/s0092-8674(00)80975-7. [DOI] [PubMed] [Google Scholar]
  59. Martin G., Keller W. Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases. EMBO J. 1996 May 15;15(10):2593–2603. [PMC free article] [PubMed] [Google Scholar]
  60. McDowall K. J., Hernandez R. G., Lin-Chao S., Cohen S. N. The ams-1 and rne-3071 temperature-sensitive mutations in the ams gene are in close proximity to each other and cause substitutions within a domain that resembles a product of the Escherichia coli mre locus. J Bacteriol. 1993 Jul;175(13):4245–4249. doi: 10.1128/jb.175.13.4245-4249.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. McLaren R. S., Newbury S. F., Dance G. S., Causton H. C., Higgins C. F. mRNA degradation by processive 3'-5' exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J Mol Biol. 1991 Sep 5;221(1):81–95. [PubMed] [Google Scholar]
  62. Miczak A., Kaberdin V. R., Wei C. L., Lin-Chao S. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):3865–3869. doi: 10.1073/pnas.93.9.3865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Miczak A., Srivastava R. A., Apirion D. Location of the RNA-processing enzymes RNase III, RNase E and RNase P in the Escherichia coli cell. Mol Microbiol. 1991 Jul;5(7):1801–1810. doi: 10.1111/j.1365-2958.1991.tb01929.x. [DOI] [PubMed] [Google Scholar]
  64. Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Cell. 1997 Nov 14;91(4):457–466. doi: 10.1016/s0092-8674(00)80432-8. [DOI] [PubMed] [Google Scholar]
  65. Mohanty B. K., Kushner S. R. Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism. Mol Microbiol. 1999 Dec;34(5):1094–1108. doi: 10.1046/j.1365-2958.1999.01673.x. [DOI] [PubMed] [Google Scholar]
  66. Mohanty B. K., Kushner S. R. Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli. Mol Microbiol. 2000 May;36(4):982–994. doi: 10.1046/j.1365-2958.2000.01921.x. [DOI] [PubMed] [Google Scholar]
  67. Mohanty B. K., Kushner S. R. Residual polyadenylation in poly(A) polymerase I (pcnB ) mutants of Escherichia coli does not result from the activity encoded by the f310 gene. Mol Microbiol. 1999 Dec;34(5):1109–1119. doi: 10.1046/j.1365-2958.1999.01674.x. [DOI] [PubMed] [Google Scholar]
  68. Mott J. E., Galloway J. L., Platt T. Maturation of Escherichia coli tryptophan operon mRNA: evidence for 3' exonucleolytic processing after rho-dependent termination. EMBO J. 1985 Jul;4(7):1887–1891. doi: 10.1002/j.1460-2075.1985.tb03865.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Nierlich D. P., Murakawa G. J. The decay of bacterial messenger RNA. Prog Nucleic Acid Res Mol Biol. 1996;52:153–216. doi: 10.1016/s0079-6603(08)60967-8. [DOI] [PubMed] [Google Scholar]
  70. O'Hara E. B., Chekanova J. A., Ingle C. A., Kushner Z. R., Peters E., Kushner S. R. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1807–1811. doi: 10.1073/pnas.92.6.1807. [DOI] [PMC free article] [PubMed] [Google Scholar]
  71. Pepe C. M., Maslesa-Galić S., Simons R. W. Decay of the IS10 antisense RNA by 3' exoribonucleases: evidence that RNase II stabilizes RNA-OUT against PNPase attack. Mol Microbiol. 1994 Sep;13(6):1133–1142. doi: 10.1111/j.1365-2958.1994.tb00504.x. [DOI] [PubMed] [Google Scholar]
  72. Portier C., Dondon L., Grunberg-Manago M., Régnier P. The first step in the functional inactivation of the Escherichia coli polynucleotide phosphorylase messenger is a ribonuclease III processing at the 5' end. EMBO J. 1987 Jul;6(7):2165–2170. doi: 10.1002/j.1460-2075.1987.tb02484.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  73. Portier C. Quaternary structure of Escherichia coli polynucleotide phosphorylase: new evidence for a trimeric structure. FEBS Lett. 1975 Jan 15;50(1):79–81. doi: 10.1016/0014-5793(75)81045-3. [DOI] [PubMed] [Google Scholar]
  74. Py B., Causton H., Mudd E. A., Higgins C. F. A protein complex mediating mRNA degradation in Escherichia coli. Mol Microbiol. 1994 Nov;14(4):717–729. doi: 10.1111/j.1365-2958.1994.tb01309.x. [DOI] [PubMed] [Google Scholar]
  75. Py B., Higgins C. F., Krisch H. M., Carpousis A. J. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature. 1996 May 9;381(6578):169–172. doi: 10.1038/381169a0. [DOI] [PubMed] [Google Scholar]
  76. Raynal L. C., Carpousis A. J. Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation. Mol Microbiol. 1999 May;32(4):765–775. doi: 10.1046/j.1365-2958.1999.01394.x. [DOI] [PubMed] [Google Scholar]
  77. Régnier P., Grunberg-Manago M. Cleavage by RNase III in the transcripts of the met Y-nus-A-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA. J Mol Biol. 1989 Nov 20;210(2):293–302. doi: 10.1016/0022-2836(89)90331-8. [DOI] [PubMed] [Google Scholar]
  78. Régnier P., Hajnsdorf E. Decay of mRNA encoding ribosomal protein S15 of Escherichia coli is initiated by an RNase E-dependent endonucleolytic cleavage that removes the 3' stabilizing stem and loop structure. J Mol Biol. 1991 Jan 20;217(2):283–292. doi: 10.1016/0022-2836(91)90542-e. [DOI] [PubMed] [Google Scholar]
  79. SPAHR P. F. PURIFICATION AND PROPERTIES OF RIBONUCLEASE II FROM ESCHERICHIA COLI. J Biol Chem. 1964 Nov;239:3716–3726. [PubMed] [Google Scholar]
  80. Sarkar N. Polyadenylation of mRNA in prokaryotes. Annu Rev Biochem. 1997;66:173–197. doi: 10.1146/annurev.biochem.66.1.173. [DOI] [PubMed] [Google Scholar]
  81. Soreq H., Littauer U. Z. Purification and characterization of polynucleotide phosphorylase from Escherichia coli. Probe for the analysis of 3' sequences of RNA. J Biol Chem. 1977 Oct 10;252(19):6885–6888. [PubMed] [Google Scholar]
  82. Stern M. J., Ames G. F., Smith N. H., Robinson E. C., Higgins C. F. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell. 1984 Jul;37(3):1015–1026. doi: 10.1016/0092-8674(84)90436-7. [DOI] [PubMed] [Google Scholar]
  83. Tock M. R., Walsh A. P., Carroll G., McDowall K. J. The CafA protein required for the 5'-maturation of 16 S rRNA is a 5'-end-dependent ribonuclease that has context-dependent broad sequence specificity. J Biol Chem. 2000 Mar 24;275(12):8726–8732. doi: 10.1074/jbc.275.12.8726. [DOI] [PubMed] [Google Scholar]
  84. Vanzo N. F., Li Y. S., Py B., Blum E., Higgins C. F., Raynal L. C., Krisch H. M., Carpousis A. J. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 1998 Sep 1;12(17):2770–2781. doi: 10.1101/gad.12.17.2770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. Wachi M., Umitsuki G., Nagai K. Functional relationship between Escherichia coli RNase E and the CafA protein. Mol Gen Genet. 1997 Jan 27;253(4):515–519. doi: 10.1007/s004380050352. [DOI] [PubMed] [Google Scholar]
  86. Wang R. F., O'Hara E. B., Aldea M., Bargmann C. I., Gromley H., Kushner S. R. Escherichia coli mrsC is an allele of hflB, encoding a membrane-associated ATPase and protease that is required for mRNA decay. J Bacteriol. 1998 Apr;180(7):1929–1938. doi: 10.1128/jb.180.7.1929-1938.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  87. Xu F., Cohen S. N. RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation. Nature. 1995 Mar 9;374(6518):180–183. doi: 10.1038/374180a0. [DOI] [PubMed] [Google Scholar]
  88. Xu F., Lin-Chao S., Cohen S. N. The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6756–6760. doi: 10.1073/pnas.90.14.6756. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Yue D., Maizels N., Weiner A. M. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA. 1996 Sep;2(9):895–908. [PMC free article] [PubMed] [Google Scholar]
  90. Zhang X., Zhu L., Deutscher M. P. Oligoribonuclease is encoded by a highly conserved gene in the 3'-5' exonuclease superfamily. J Bacteriol. 1998 May;180(10):2779–2781. doi: 10.1128/jb.180.10.2779-2781.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES