Messenger RNA stability and its role in control of gene expression in bacteria and phages

Annual Review of Genetics

Volumn 33, Issue , 1999, Pages 193-227

  Grunberg Manago, Marianne ^a  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

Autoregulation; mRNA stability; PNPase; Poly(A) polymerase; RNAse E; RNase II; RNAse III

Indexed keywords

CIS ACTING ELEMENT; ENDONUCLEASE; EXONUCLEASE; MESSENGER RNA; POLYNUCLEOTIDE ADENYLYLTRANSFERASE; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; RIBONUCLEASE III; TRANS ACTING FACTOR;

AUTOREGULATION; BACTERIOPHAGE; BACTERIOPHAGE T4; COMPLEX FORMATION; GENE EXPRESSION REGULATION; GENETIC STABILITY; GROWTH RATE; PRIORITY JOURNAL; REVIEW; RNA CLEAVAGE; RNA DEGRADATION; RNA PROCESSING; RNA STRUCTURE;

BACTERIA; BACTERIOPHAGES; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, VIRAL; RIBONUCLEASES; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

PROKARYOTA; T4 BACTERIOPHAGE; UNIDENTIFIED BACTERIOPHAGE;

EID: 0033368475     PISSN: 00664197     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genet.33.1.193     Document Type: Review

References (202)

1. 1. Agaisse H, Lereclus D. 1996. STAB-SD: a Shine-Dalgarno sequence in the 5′ untranslated region is a determinant of mRNA stability. Mol. Microbiol. 20:633-43
2. 2. Ahnn J, March PE, Takiff HE, Inouye M. 1986. A GTP binding protein of Escherichia coli has homology to yeast RAS protein. Proc. Natl. Acad. Sci. USA 83:8849-53
3. 3. Alifano P, Rivellini F, Piscitelli C, Arraiano CM, Bruni CB, Carlomagno MS. 1994. Ribonuclease E provides substrates for ribonuclease P-dependent processing of a polycistronic mRNA. Genes Dev. 8:3021-31
4. 4. Altuvia S, Kornitzer D, Kobi S, Oppenheim AB. 1991. Functional and structural elements of the mRNA of the cIII gene of bacteriophage lambda. J. Mol Biol. 218:723-33
5. 5. Anderson PE, Matsunaga J, Simons EL, Simons RW. 1996. Structure and regulation of the Salmonella typhimurium rnc-era-recO operon. Biochimie 78:1025-34
6. 6. Apirion D. 1973. Degradation of RNA in Escherichia coli. A hypothesis. Mol. Gen. Genet. 122:313-22
7. 7. Apirion D, Gitelman DR. 1980. Decay of RNA in RNA processing mutants of Escherichia coli. Mol. Gen. Genet. 177: 339-43
8. 8. Apirion D, Lassar AB. 1978. A conditional lethal mutant of Escherichia coli which affects the processing of ribosomal RNA. J. Biol. Chem. 253:1738-42
9. 9. Arnold TE, Yu J, Belasco JG. 1998. mRNA stabilization by the ompA. 5′ untranslated region: Two protective elements hinder distinct pathways for mRNA degradation. RNA 4:319-30
10. 10. Babitzke P, Kushner SR. 1991. The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 88:1-5
11. 11. Baga M, Goransson M, Normark S, Uhlin BE. 1988. Processed mRNA with differential stability in the regulation of E. coli pilin gene expression. Cell 52:197-206
12. 12. Bardwell JC, Régnier P, Chen SM, Nakamura Y, Grunberg-Manago M, Court DL. 1989. Autoregulation of RNase III operon by mRNA processing. EMBO J. 8:3401-7
13. 13. Baumeister R, Flache P, Melefors O, von Gabain A, Hillen W. 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. 19:4595-600
14. 14. Belasco JG. 1993. mRNA degradation in prokaryotic cells: an overview of control of messenger RNA stability. See Ref. 15a, pp. 3-12
15. 15. Belasco JG, Beatty JT, Adams CW, von Gabain A, Cohen SN. 1985. Differential expression of photosynthesis genes in R. capsulata results from segmental differences in stability within the polycistronic rxcA transcript. Cell 40:171-81
16. 15a. Belasco JG, Brawerman G, eds. 1993. Control of mRNA Stability. New York: Academic
17. 16. Belasco JG, Higgins CF. 1988. Mechanisms of mRNA decay in bacteria: a perspective. Gene 72:15-23
18. 17. Belin D, Mudd EA, Prentki P, Yi-Yi Y, Krisch HM. 1987. Sense and anti-sense transcription of bacteriophage T4 gene 32. Processing and stability of the mRNAs. J. Mol. Biol. 194:231-43
19. 18. Bessarab DA, Kaberdin VR, Wei CL, Liou GG, Lin-Chao S. 1998. RNA components of Escherichia coli degradosome: evidence for rRNA decay. Proc. Natl. Acad. Sci. USA 95:3157-61
20. 19. Bilge SS, Apostol JM Jr, Aldape MA, Moseley SL. 1993. mRNA processing independent of RNase III and RNase E in the expression of the F1845 fimbrial adhesin of Escherichia coli. Proc. Natl. Acad. Sci. USA 90:1455-59
21. 20. Blum E, Py B, Carpousis AJ, Higgins CF. 1997. Polyphosphate kinase is a component of the Escherichia coli RNA degradosome. Mol. Microbiol. 26:387-98
22. 21. Bouvet P, Belasco JG. 1992. Control of RNase E-mediated RNA degradation by 5′-terminal base pairing in E. coli. Nature 360:488-91
23. 22. Braun F, Hajnsdorf E, Régnier P. 1996. 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. 19:997-1005
24. 23. Braun F, Le Dérout J, Régnier P. 1998. Ribosomes inhibit an RNase E cleavage which induces the decay of the rpsO mRNA of Escherichia coli. EMBO J. 17: 4790-97
25. 24. Bremer H, Dennis PP. 1987. Modulation of chemical composition and other parameters of the cell by growth rate. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, ed. FC Neidhardt, JL Ingraham, KB Low, B Magasanik, M Schaechter, HE Umbarger, pp. 1527-42. Washington, DC: Am. Soc. Microbiol.
26. 25. Britton RA, Powell BS, Dasgupta S, Sun Q, Margolin W, et al. 1998. Cell cycle arrest in Era GTPase mutants: a potential growth rate-regulated checkpoint in Escherichia coli. Mol. Microbiol. 27:739-50. Erratum. 1998. Mol. Microbiol. 28(6):1391-93
27. 26. Burton ZF, Gross CA, Watanabe KK, Burgess RR. 1983. The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12. Cell 32: 335-49
28. 27. Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG. 1997. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell 88:235-42
29. 28. Cam K, Rome G, Krisch HM, Bouche JP. 1996. RNase E processing of essential cell division genes mRNA in Escherichia coli. Nucleic Acids Res. 24:3065-70
30. 29. Cao GJ, Pogliano J, Sarkar N. 1996. Identification of the coding region for a second poly(A) polymerase in Escherichia coli. Proc. Natl. Acad. Sci. USA 93:11580-85
31. 30. Cao GJ, Sarkar N. 1992. Identification of the gene for an Escherichia coli poly(A) polymerase. Proc. Natl. Acad. Sci. USA 89: 10380-44
32. 31. Carpousis AJ, Van Houwe G, Ehretsmann C, Krisch HM. 1994. Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76:889-900
33. 32. Casarégola S, Jacq A, Laoudj D, McGurk G, Margarson S, et al. 1992. Cloning and analysis of the entire Escherichia coli ams gene, ams is identical to hmp1 and encodes a 114 kDa protein that migrates as a 180 kDa protein. J. Mol. Biol. 228:30-40. Erratum. 1994. J. Mol. Biol. 238(5):867
34. 33. Cashman JS, Webster RE, Steege DA. 1980. Transcription of bacteriophage fl. The major in vivo RNAs. J. Biol. Chem. 255:2554-62
35. 34. Chen LH, Emory SA, Bricker AL, Bouvet P, Belasco JG. 1991. Structure and function of a bacterial mRNA stabilizer: analysis of the 5′ untranslated region of ompA mRNA. J. Bacteriol. 173:4578-86
36. 35. Chen SM, Takiff HE, Barber AM, Dubois GC, Bardwell JC, Court DL. 1990. Expression and characterization of RNase III and Era proteins. Products of the rnc operon of Escherichia coli. J. Biol. Chem. 265:2888-95
37. 36. Cheng ZF, Zuo Y, Li Z, Rudd KE, Deutscher MP. 1998. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J. Biol. Chem. 273:14077-80
38. 37. Cho KO, Yanofsky C. 1988. Sequence changes preceding a Shine-Dalgarno region influence trpE mRNA translation and decay. J. Mol. Biol. 204:51-60
39. 38. Claverie-Martin F, Diaz-Torres MR, Yancey SD, Kushner SR. 1991. Analysis of the altered mRNA stability (ams) gene from Escherichia coli. Nucleotide sequence, transcriptional analysis, and homology of its product to MRP3, a mitochondrial ribosomal protein from Neurospora crassa. J. Biol. Chem. 266:2843-51
40. 39. Coburn GA, Mackie GA. 1996. Differential sensitivities of portions of the mRNA for ribosomal protein S20 to 3′-exonucleases dependent on oligoadenylation and RNA secondary structure. J. Biol. Chem. 271:15776-81
41. 40. Coburn GA, Mackie GA. 1996. Overexpression, purification, and properties of Escherichia coli ribonuclease II. J. Biol. Chem. 271:1048-53
42. 41. Coburn GA, Mackie GA. 1999. Degradation of mRNA in Escherichia coli: an old problem with some new twists. Prog. Nucleic Acid Res. Mol. Biol. 62:55-108
43. 42. Cohen SN. 1995. Surprises at the 3′ end of prokaryotic RNA. Cell 80:829-32
44. 43. Cohen SN, McDowall KJ. 1997. RNase E: still a wonderfully mysterious enzyme. Mol. Microbiol. 23:1099-106
45. 44. Collins JJ, Roberts GP, Brill WJ. 1986. Posttranscriptional control of Klebsiella pneumoniae nif mRNA stability by the nifL product. J. Bacteriol. 168:173-78
46. 45. Condon C, Putzer H, Luo D, Grunberg-Manago M. 1997. Processing of the Bacillus subtilis thrS leader mRNA is RNase E-dependent mEscherichia coli. J. Mol. Biol. 268:235-42
47. 46. Cormack RS, Genereaux JL, Mackie GA. 1993. RNase E activity is conferred by a single polypeptide: overexpression, purification, and properties of the ams/rne/hmp1 gene product. Proc. Natl. Acad. Sci. USA 90:9006-10
48. 47. Court D. 1993. RNA processing and degradation by RNase III in control of mRNA stability. See Ref. 15a, pp. 71-116
49. 48. Dasgupta S, Fernandez L, Kameyama L, Inada T, Nakamura Y, et al. 1998. Genetic uncoupling of the dsRNA-binding and RNA cleavage activities of the Escherichia coli endoribonuclease RNase III - the effect of dsRNA binding on gene expression. Mol. Microbiol. 28:629-40. Erratum. 1998. Mol. Microbiol. 30(3):679
50. 49. Donovan WP, Kushner SR. 1986. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc. Natl. Acad. Sci. USA 83:120-24
51. 50. Dunn JJ, Studier FW. 1973. T7 early RNAs are generated by site-specific cleavages. Proc. Natl Acad. Sci. USA 70:1559-63
52. 51. Ehretsmann CP, Carpousis AJ, Krisch HM. 1992. mRNA degradation in procaryotes. FASEB J. 6:3186-92
53. 52. Ehretsmann CP, Carpousis AJ, Krisch HM. 1992. Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacterio-phage T4 mRNA processing site. Genes Dev. 6:149-59
54. 53. Emory SA, Belasco JG. 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. 172:4472-81
55. 54. Emory SA, Bouvet P, Belasco JG. 1992. A 5′-terminal stem-loop structure can stabilize mRNA in Escherichia coli. Genes Dev. 6:135-48
56. 55. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd [see comments]. Science 269:496-512
57. 56. Franzetti B, Sohlberg B, Zaccai G, von Gabain A. 1997. Biochemical and serological evidence for an RNase E-like activity in halophilic Archaea. J. Bacteriol. 179: 1180-85
58. 57. Gamper M, Ganter B, Polito MR, Haas D. 1992. RNA processing modulates the expression of the arcDABC operon in Pseudomonas aeruginosa. J. Mol. Biol. 226:943-57
59. 58. Georgellis D, Arvidson S, von Gabain A. 1992. Decay of ompA mRNA and processing of 9S RNA are immediately affected by shifts in growth rate, but in opposite manners. J. Bacteriol. 174:5382-90
60. 59. Godefroy-Colburn T, Grunberg-Manago M. 1972. Polynucleotide phosphorylase. In The Enzymes, 7:533-72. New York/ London: Academic. 3rd ed.
61. 60. Goldenberg D, Azar I, Oppenheim AB. 1996. Differential mRNA stability of the cspA gene in the cold-shockresponse of Escherichia coli. Mol. Microbiol. 19:241-48
62. 61. Guarneros G, Kameyama L, Orozco L, Velazquez F. 1988. Retroregulation of an intlacZ gene fusion in a plasmid system. Gene 72:129-30
63. 62. Guarneros G, Montanez C, Hernandez T, Court D. 1982. Posttranscriptional control of bacteriophage lambda gene expression from a site distal to the gene. Proc. Natl. Acad. Sci. USA 79:238-42
64. 63. Guarneros G, Portier C. 1990. Different specificities of ribonuclease II and polynucleotide phosphorylase in 3′ mRNA decay. Biochimie 72:771-77
65. 64. Gupta RS, Kasai T, Schlessinger D. 1977. Purification and some novel properties of Escherichia coli RNase II. J. Biol. Chem. 252:8945-49
66. 65. Hagege JM, Cohen SN. 1997. A developmentally regulated Streptomyces endoribonuclease resembles ribonuclease E of Escherichia coli. Mol. Microbiol. 25: 1077-90
67. 66. Hajnsdorf E, Braun F, Haugel-Nielsen J, Le Dérout J, Régnier P. 1996. Multiple degradation pathways of the rpsO mRNA of Escherichia coli. RNase E interacts with the 5′ and 3′ extremities of the primary transcript. Biochimie 78:416-24
68. 67. Hajnsdorf E, Braun F, Haugel-Nielsen J, Régnier P. 1995. Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli. Proc. Natl. Acad. Sci. USA 92:3973-77
69. 68. Hajnsdorf E, Carpousis AJ, Régnier P. 1994. Nucleolytic inactivation and degradation of the RNase III processed pnp message encoding polynucleotide phosphorylase of Escherichia coli. J. Mol. Biol. 239:439-54
70. 69. Hajnsdorf E, Régnier P. 1999. 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. 286:1033-43
71. 70. Hajnsdorf E, Steier O, Coscoy L, Teysset L, Régnier P. 1994. 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. 13:3368-77
72. 71. Hansen MJ, Chen LH, Fejzo ML, Belasco JG. 1994. The ompA 5′ untranslated region impedes a major pathway for mRNA degradation in Escherichia coli. Mol. Microbiol. 12:707-16
73. 72. Haugel-Nielsen J, Hajnsdorf E, Régnier P. 1996. The rpsO mRNA of Escherichia coli is polyadenylated at multiple sites resulting from endonucleolytic processing and exonucleolytic degradation. EMBO J. 15:3144-52
74. 73. He L, Soderbom F, Wagner EG, Binnie U, Binns N, Masters M. 1993. PcnB is required for the rapid degradation of RNAI, the antisense RNA that controls the copy number of ColE1-related plasmids. Mol. Microbiol. 9:1131-42
75. 74. Heck C, Rothfuchs R, Jager A, Rauhut R, Klug G. 1996. Effect of the pufQ-pufB intercistronic region on puf mRNA stability in Rhodobacter capsulatus. Mol. Microbiol. 20:1165-78
76. 75. Huang H, Liao J, Cohen SN. 1998. Poly(A)- and poly(U)-specific RNA 3′ tail shortening by E. coli ribonuclease E. Nature 391:99-102
77. 76. Hue KK, Bechhofer DH. 1991. Effect of ermC leader region mutations on induced mRNA stability. J. Bacteriol. 173:3732-40
78. 77. Inada T, Kawakami K, Chen SM, Takiff HE, Court DL, Nakamura Y. 1989. Temperature-sensitive lethal mutant of era, a G protein in Escherichia coli. J. Bacteriol. 171:5017-24
79. 78. Iost I, Dreyfus M. 1994. mRNAs can be stabilized by DEAD-box proteins. Nature 372:193-96
80. 79. Iost I, Dreyfus M. 1995. The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation. EMBO J. 14:3252-61
81. 80. Jain C, Belasco JG. 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
82. 81. Jain C, Kleckner N. 1993. IS10 mRNA stability and steady state levels in Escherichia coli: indirect effects of translation and role of rne function. Mol. Microbiol. 9:233-47
83. 82. Jayasena VK, Brown D, Shtatland T, Gold L. 1996. In vitro selection of RNA specifically cleaved by bacteriophage T4 RegB endonuclease. Biochemistry 35:2349-56
84. 83. Jordi BJ, op den Camp IE, de Haan LA, van der Zeijst BA, Gaastra W. 1993. Differential decay of RNA of the CFA/I fimbrial operon and control of relative gene expression. J. Bacteriol. 175:7976-81
85. 84. Joyce SA, Dreyfus M. 1998. In the absence of translation, RNase E can bypass 5′ mRNA stabilizers in Escherichia coli. J. Mol. Biol. 282:241-54
86. 85. Kaberdin VR, Miczak A, Jakobsen JS, Lin-Chao S, McDowall KJ, von Gabain A. 1998. 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. USA 95: 11637-42
87. 86. Kalapos MP, Cao GJ, Kushner SR, Sarkar N. 1994. Identification of a second poly(A) polymerase in Escherichia coli. Biochem. Biophys. Res. Commun. 198:459-65
88. 87. Kameyama L, Fernandez L, Court DL, Guarneros G. 1991. RNaselll activation of bacteriophage lambda N synthesis. Mol. Microbiol. 5:2953-63
89. 88. Kido M, Yamanaka K, Mitani T, Niki H, Ogura T, Hiraga S. 1996. RNase Epolypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. J. Bacteriol. 178:3917-25
90. 89. Klug G. 1991. Endonucleolytic degradation of puf mRNA in Rhodobacter capsulatus is influenced by oxygen. Proc. Natl. Acad. Sci. USA 88:1765-69
91. 90. Klug G, Cohen SN. 1990. Combined actions of multiple hairpin loop structures and sites of rate-limiting endonucleolytic cleavage determine differential degradation rates of individual segments within polycistronic puf operon mRNA. J. Bacteriol. 172:5140-46
92. 91. Klug G, Cohen SN. 1991. Effects of translation on degradation of mRNA segments transcribed from the polycistronic puf operon of Rhodobacter capsulatus. J. Bacteriol. 173:1478-84
93. 92. Kokoska RJ, Steege DA. 1998. Appropriate expression of filamentous phage fl DNA replication genes II and X requires RNase E-dependent processing and separate mRNAs. J. Bacteriol. 180:3245-49
94. 93. Kolodner R, Fishel RA, Howard M. 1985. Genetic recombination of bacterial plasmid DNA: effect of RecF pathway mutations on plasmid recombination in Escherichia coli. J. Bacteriol. 163:1060-66
95. 94. Kornitzer D, Teff D, Altuvia S, Oppenheim AB. 1989. Genetic analysis of bacteriophage lambda cIII gene: mRNA structural requirements for translation initiation. J. Bacteriol. 171:2563-72
96. 95. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis [see comments]. Nature 390:249-56
97. 96. Kuwano M, Ono M, Endo H, Hori K, Nakamura K, et al. 1977. Gene affecting longevity of messenger RNA: a mutant of Escherichia coli with altered mRNA stability. Mol. Gen. Genet. 154:279-85
98. 97. Li H, Nicholson AW. 1996. Defining the enzyme binding domain of a ribonuclease III processing signal. Ethylation interference and hydroxyl radical footprinting using catalytically inactive RNase III mutants. EMBO J. 15:1421-33
99. 97a. Li Z, Pandit S, Deutscher MP. 1999. Rnase G (CafA protein) and Rnase E are both required for the 5′ maturation of 16S ribosomal RNA. EMBO J. 18:2878-85
100. 98. Lin-Chao S, Cohen SN. 1991. The rate of processing and degradation of antisense RNAI regulates the replication of ColE1-type plasmids in vivo. Cell 65:1233-42
101. 99. Lin-Chao S, Wong TT, McDowall KJ, Cohen SN. 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. 269:10797-803
102. 100. Littauer UZ, Grunberg-Manago M. 1998. Polynucleotide phosphorylase. In The Encyclopedia of Molecular Biology, ed. TE Creighton. New York: Wiley. In press
103. 101. Liu J, Barnell WO, Conway T. 1992. The polycistronic mRNA of the Zymomonas mobilis glf-zwf-edd-glk operon is subject to complex transcript processing. J. Bacteriol. 174:2824-33
104. 102. Liu JD, Parkinson JS. 1989. Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control. J. Bacteriol. 171: 1254-61
105. 103. Lopez PJ, Marchand I, Yarchuk O, Dreyfus M. 1998. Translation inhibitors stabilize Escherichia coli mRNAs independently of ribosome protection. Proc. Natl. Acad. Sci. USA 95:6067-72
106. 104. Lopez PL, Marchand I, Joyce SA, Dreyfus M. 1999. The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Mol. Microbiol. 33:188-99
107. 105. Lundberg U, Nilsson G, von Gabain A. 1988. The differential stability of the Escherichia coli ompA and bla mRNA at various growth rates is not correlated to the efficiency of translation. Gene 72: 141-49
108. 106. Luttinger A, Hahn J, Dubnau D. 1996. Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis. Mol. Microbiol. 19:343-56
109. 107. Mackie GA. 1991. Specific endonucleolytic cleavage of the mRNA for ribosomal protein S20 of Escherichia coli requires the product of the ams gene in vivo and in vitro. J. Bacteriol. 173:2488-97
110. 108. Mackie GA. 1998. Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395:720-23
111. 109. Mackie GA, Genereaux JL. 1993. The role of RNA structure in determining RNase E-dependent cleavage sites in the mRNA for ribosomal protein S20 in vitro. J. Mol. Biol. 234:998-1012
112. 110. Mackie GA, Genereaux JL, Masterman SK. 1997. Modulation of the activity of RNase E in vitro by RNA sequences and secondary structures 5′ to cleavage sites. J. Biol. Chem. 272:609-16
113. 111. Makarova OV, Makarov EM, Sousa R, Dreyfus M. 1995. Transcribing of Escherichia coli genes with mutant T7 RNA polymerases: Stability of lacZ mRNA inversely correlates with polymerase speed. Proc. Natl. Acad. Sci. USA 92:12250-54
114. 112. March PE, Ahnn J, Inouye M. 1985. The DNA sequence of the gene (rnc) encoding ribonuclease III of Escherichia coli. Nucleic Acids Res. 13:4677-85
115. 113. March PE, Lerner CG, Ahnn J, Cui X, Inouye M. 1988. The Escherichia coli Ras-like protein (Era) has GTPase activity and is essential for cell growth. Oncogene 2:539-44
116. 114. Masters M, Colloms MD, Oliver IR, He L, Macnaughton EJ, Charters Y. 1993. The pcnB gene of Escherichia coli, which is required for ColE1 copy number maintenance, is dispensable. J. Bacteriol. 175: 4405-13
117. 115. Matsunaga J, Dyer M, Simons EL, Simons RW. 1996. Expression and regulation of the rnc and pdxJ operons of Escherichia coli. Mol. Microbiol. 22:977-89
118. 116. Matsunaga J, Simons EL, Simons RW. 1996. RNase III autoregulation: structure and function of rncO, the posttranscriptional "operator". RNA 2:1228-40
119. 117. Matsunaga J, Simons EL, Simons RW. 1997. Escherichia coli RNase III (rnc) autoregulation occurs independently of rnc gene translation. Mol. Microbiol. 26: 1125-35
120. 118. McCormick JR, Zengel JM, Lindahl L. 1994. Correlation of translation efficiency with the decay of lacZ mRNA in Escherichia coli. J. Mol. Biol. 239:608-22
121. 119. McDowall KJ, Cohen SN. 1996. The N-terminal domain of the rne gene product has RNase E activity and is non-overlapping with the arginine-rich RNA-binding site. J. Mol. Biol. 255:349-55
122. 120. McDowall KJ, Lin-Chao S, Cohen SN. 1994. A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. J. Biol. Chem. 269:10790-96
123. 121. McLaren RS, Newbury SF, Dance GS, Causton HC, Higgins CF. 1991. mRNA degradation by processive 3′-5′ exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J. Mol. Biol. 221:81-95
124. 122. Melefors O, von Gabain A. 1988. Site-specific endonucleolytic cleavages and the regulation of stability of E. coli ompA mRNA. Cell 52:893-901
125. 123. Melefors O, von Gabain A. 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: 857-64
126. 124. Melin L, Friden H, Dehlin E, Rutberg L, von Gabain A. 1990. The importance of the 5′-region in regulating the stability of sdh mRNA in Bacillus subtilis. Mol. Microbiol. 4:1881-89
127. 125. Miczak A, Kaberdin VR, Wei CL, Lin-Chao S. 1996. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc. Natl. Acad. Sci. USA 93:3865-69
128. 126. Miczak A, Srivastava RA, Apirion D. 1991. Location of the RNA-processing enzymes RNase III, RNase E and RNase P in the Escherichia coli cell. Mol. Microbiol. 5:1801-10
129. 127. Misra TK, Apirion D. 1979. RNase E, an RNA processing enzyme from Escherichia coli. J. Biol. Chem. 254:11154-59
130. 128. Mitra S, Bechhofer DH. 1994. Substrate specificity of an RNase III-like activity from Bacillus subtilis. J. Biol. Chem. 269:31450-56
131. 129. Mitra S, Hue K, Bechhofer DH. 1996. In vitro processing activity of Bacillus subtilis polynucleotide phosphorylase. Mol. Microbiol. 19:329-42
132. 130. Morrison PT, Lovett ST, Gilson LE, Kolodner R. 1989. Molecular analysis of the Escherichia coli recO gene. J. Bacteriol. 171:3641-49
133. 131. Morse DE, Yanofsky C. 1969. Polarity and the degradation of mRNA. Nature 224:329-31
134. 132. Mudd EA, Carpousis AJ, Krisch HM. 1990. Escherichia coli RNase E has a role in the decay of bacteriophage T4 mRNA. Genes Dev. 4:873-81. Erratum. 1990. Genes Dev. 4(6):1078
135. 133. Mudd EA, Higgins CF. 1993. Escherichia coli endoribonuclease RNase E: autoregulation of expression and site-specific cleavage of mRNA. Mol. Microbiol. 9: 557-68
136. 134. Mudd EA, Krisch HM, Higgins CF. 1990. RNase E, an endoribonuclease, has a general role in the chemical decay of Escherichia coli mRNA: Evidence that rne and ams are the same genetic locus. Mol. Microbiol. 4:2127-35
137. 135. Mudd EA, Prentki P, Belin D, Krisch HM. 1988. Processing of unstable bacteriophage T4 gene 32 mRNAs into a stable species requires Escherichia coli ribonuclease E. EMBO J. 7:3601-7
138. 136. Nakazato H, Venkatesan S, Edmonds M. 1975. Polyadenylic acid sequences in E. coli messenger RNA. Nature 256:144-46
139. 137. Naureckiene S, Uhlin BE. 1996. In vitro analysis of mRNA processing by RNase E in the pap operon of Escherichia coli. Mol. Microbiol. 21:55-68
140. 138. Newbury SF, Smith NH, Higgins CF. 1987. Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell 51:1131-43
141. 139. Nierlich DP, Murakawa GJ. 1996. The decay of bacterial messenger RNA. Prog. Nucleic Acid Res. Mol. Biol. 52:153-216
142. 140. Nilsson G, Belasco JG, Cohen SN, von Gabain A. 1984. Growth-rate dependent regulation of mRNA stability in Escherichia coli. Nature 312:75-77
143. 141. Nilsson G, Belasco JG, Cohen SN, von Gabain A. 1987. Effect of premature termination of translation on mRNA stability depends on the site of ribosome release. Proc. Natl. Acad. Sci. USA 84:4890-94
144. 142. Nilsson P, Naureckiene S, Uhlin BE. 1996. Mutations affecting mRNA processing and fimbrial biogenesis in the Escherichia coli pap operon. J. Bacteriol. 178:683-90
145. 143. Nilsson P, Uhlin BE. 1991. Differential decay of a polycistronic Escherichia coli transcript is initiated by RNaseE-dependent endonucleolytic processing. Mol. Microbiol. 5:1791-99
146. 144. O'Hara EB, Chekanova JA, Ingle CA, Kushner ZR, Peters E, Kushner SR. 1995. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc. Natl. Acad. Sci. USA 92:1807-11
147. 145. Ono M, Kuwano M. 1979. A conditional lethal mutation in an Escherichia coli strain with a longer chemical lifetime of messenger RNA. J. Mol. Biol. 129:343-57
148. 146. Pato ML, Bennett PM, Meyenburg KV. 1973. Messenger ribonucleic acid synthesis and degradation in Escherichia coli during inhibition of translation. J. Bacteriol. 116:710-18
149. 147. Pepe CM, Maslesa-Galic S, Simons RW. 1994. Decay of the IS10 antisense RNA by 3′ exoribonucleases: evidence that RNase II stabilizes RNA-OUT against PNPase attack. Mol. Microbiol. 13:1133-42
150. 148. Petersen C. 1993. Translation and mRNA stability in bacteria: a complex relationship. See Ref. 15a, pp. 117-47
151. 149. Plamann MD, Stauffer GV. 1990. Escherichia coli gly A mRNA decay: the role of 3′ secondary structure and the effects of the pnp and rnb mutations. Mol. Gen. Genet. 220:301-6
152. 150. Portier C. 1980. Isolation of a polynucleotide phosphorylase mutant using a kanamycin resistant determinant. Mol. Gen. Genet. 178:343-49
153. 151. Portier C, Dondon L, Grunberg-Manago M, Régnier P. 1987. 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. 6:2165-70
154. 152. Portier C, Régnier P. 1984. Expression of the rpsO and pnp genes: structural analysis of a DNA fragment carrying their control regions. Nucleic Acids Res. 12:6091-102
155. 153. Py B, Causton H, Mudd EA, Higgins CF. 1994. A protein complex mediating mRNA degradation in Escherichia coli. Mol. Microbiol. 14:717-29
156. 154. Py B, Higgins CF, Krisch HM, Carpousis AJ. 1996. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381:169-72
157. 155. Rapaport LR, Mackie GA. 1994. Influence of translational efficiency on the stability of the mRNA for ribosomal protein S20 in Escherichia coli. J. Bacteriol. 176:992-98
158. 156. Rauhut R, Jager A, Conrad C, Klug G. 1996. Identification and analysis of the rnc gene for RNase III in Rhodobacter capsulatus. Nucleic Acids Res. 24:1246-51
159. 157. Ray PN, Pearson ML. 1974. Evidence for post-transcriptional control of the morphogenetic genes of bacteriophage lambda. J. Mol. Biol. 85:163-75
160. 158. Ray PN, Pearson ML. 1975. Functional inactivation of bacteriophage lambda morphogenetic gene in RNA. Nature 253: 647-50
161. 159. Raynal LC, Krisch HM, Carpousis AJ. 1996. Bacterial poly(A) polymerase: an enzyme that modulates RNA stability. Biochimie 78:390-98
162. 160. Régnier P, Grunberg-Manago M, Portier C. 1987. Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1. J. Biol. Chem. 262:63-68
163. 161. Régnier P, Hajnsdorf E. 1991. 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. 217: 283-92
164. 162. Robert-Le Meur M, Portier C. 1992. E.coli polynucleotide phosphorylase expression is autoregulated through an RNase III-dependent mechanism. EMBO J. 11:2633-41
165. 163. Robert-Le Meur M, 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
166. 164. Ruckman J, Parma D, Tuerk C, Hall DH, Gold L. 1989. Identification of a T4 gene required for bacteriophage mRNA processing. New Biol. 1:54-65
167. 165. Ruckman J, Ringquist S, Brody E, Gold L. 1994. The bacteriophage T4 regB ribonuclease. Stimulation of the purified enzyme by ribosomal protein S1. J. Biol. Chem. 269:26655-62
168. 166. Sandler P, Weisblum B. 1989. Erythromycin-induced ribosome stall in the ermA leader: a barricade to 5′-to-3′ nucleolytic cleavage of the ermA transcript. J. Bacteriol. 171:6680-88
169. 167. Sanson B, Uzan M. 1993. Dual role of the sequence-specific bacteriophage T4 endoribonuclease RegB. mRNA inactivation and mRNA destabilization. J. Mol. Biol. 233:429-46
170. 168. Sanson B, Uzan M. 1995. Posttranscriptional controls in bacteriophage T4: roles of the sequence-specific endoribonuclease RegB. FEMS Microbiol. Rev. 17:141-50
171. 169. Sarkar B, Cao GJ, Sarkar N. 1997. Identification of two poly(A) polymerases in Bacillus subtilis. Biochem. Mol. Biol. Int. 41:1045-50
172. 170. Sarkar N. 1997. Polyadenylation of mRNA in prokaryotes. Annu. Rev. Biochem. 66:173-97
173. 171. Schneider E, Blundell M, Kennen D. 1978. Translation and mRNA decay. Mol. Gen. Genet. 160:121-29
174. 172. Segal G, Ron EZ. 1995. The groESL operon of Agrobacterium tumefaciens: evidence for heat shock-dependent m RNA cleavage. J. Bacteriol. 177:750-77
175. 173. Srinivasan PR, Ramanarayanan M, Rabbani E. 1975. Presence of polyriboadenylate sequences in pulse-labeled RNA of Escherichia coli. Proc. Natl. Acad. Sci. USA 72:2910-14
176. 174. Studier FW, Dunn JJ, Buzash-Pollert E. 1979. Processing of bacteriophage T7 RNAs by RNase III. In From Gene to Protein: Information Transfer in Normal and Abnormal Cells, ed. TR Russell, K Brew, H Farber, T Schultz, pp. 261-69. New York: Academic
177. 175. Stump MD, Steege DA. 1996. Functional analysis of filamentous phage f1 mRNA processing sites. RNA 2:1286-94
178. 176. Sulewski M, Marchese-Ragona SP, Johnson KA, Benkovic SJ. 1989. Mechanism of polynucleotide phosphorylase. Biochemistry 28:5855-64
179. 177. Takata R, Izuhara M, Akiyama K. 1992. Processing in the 5′ region of the pnp transcript facilitates the site-specific endonucleolytic cleavages of mRNA. Nucleic Acids Res. 20:847-50
180. 178. Takiff HE, Baker T, Copeland T, Chen SM, Court DL. 1992. Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon. J. Bacteriol. 174:1544-53
181. 179. Takiff HE, Chen SM, Court DL. 1989. Genetic analysis of the rnc operon of Escherichia coli. J. Bacteriol. 171:2581-90
182. 180. Taraseviciene L, Bjork GR, Uhlin BE. 1995. Evidence for an RNA binding region in the Escherichia coli processing endoribonuclease RNase E. J. Biol. Chem. 270:26391-98
183. 181. Taraseviciene L, Miczak A, Apirion D. 1991. The gene specifying RNase E (rne) and a gene affecting mRNA stability (ams) are the same gene. Mol. Microbiol. 5:851-55
184. 182. Thang MN, Guschelbauer W, Zachau HG, Grunberg-Manago M. 1967. Degradation of transfer ribonucleic acid by polynucleotide phosphorylase. J. Mol. Biol. 26:403-21
185. 183. Tomesanyi T, Apirion D. 1985. Processing enzyme ribonuclease E specifically cleaves RNA I. An inhibitor of primer formation in plasmid DNA synthesis. J. Mol. Biol. 185:713-20
186. 184. Uzan M, Favre R, Brody E. 1988. A nuclease that cuts specifically in the ribosome binding site of some T4 mRNAs. Proc. Natl. Acad. Sci. USA 85:8895-99
187. 185. Vanzo NF, Li YS, Py B, Blum E, Higgins CF, et al. 1998. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 12:2770-81
188. 186. Vytvytska O, Jakobsen JS, Balcunaite G, Andersen JS, Baccarini M, von Gabain A. 1998. Host factor I, Hfq, binds to Escherichia coli ompA mRNA in a growth rate-dependent fashion and regulates its stability. Proc. Natl. Acad. Sci. USA 95: 14118-23
189. 187. Wagner LA, Gesteland RF, Dayhuff TJ, Weiss RB. 1994. An efficient Shine-Dalgarno sequence but not translation is necessary for lacZ mRNA stability in Escherichia coli. J. Bacteriol. 176:1683-88
190. 188. Wang W, Bechhofer DH. 1996. Properties of a Bacillus subtilis polynucleotide phosphorylase deletion strain. J. Bacteriol. 178:2375-82
191. 189. Wang W, Bechhofer DH. 1997. Bacillus subtilis RNase III gene: cloning, function of the gene in Escherichia coli, and construction of Bacillus subtilis strains with altered rnc loci. J. Bacteriol. 179:7379-85
192. 190. Wilder DA, Lozeron HA. 1979. Differential modes of processing and decay for the major N-dependent RNA transcript of coliphage lambda. Virology 99:241-56
193. 191. Woo WM, Lin-Chao S. 1997. Processing of the rne transcript by an RNase E-independent amino acid-dependent mechanism. J. Biol. Chem. 272:15516-20
194. 192. Xu F, Cohen SN. 1995. RNA degradation in Escherichia coli regulated by 3′ adenylation and 5′ phosphorylation. Nature 374:180-83
195. 193. Xu F, Lin-Chao S, Cohen SN. 1993. 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. USA 90:6756-60
196. 194. Yajnik V, Godson GN. 1993. Selective decay of Escherichia coli dnaG messenger RNA is initiated by RNase E. J. Biol. Chem. 268:13253-60
197. 195. Yarchuk O, Iost I, Dreyfus M. 1991. The relation between translation and mRNA degradation in the lacZ gene. Biochimie 73: 1533-41
198. 196. Zhang K, Nicholson AW. 1997. Regulation of ribonuclease III processing by double-helical sequence antideterminants. Proc. Natl Acad. Sci. USA 94: 13437-41
199. 197. Zilhao R, Caillet J, Régnier P, Arraiano CM. 1995. Precise physical mapping of the Escherichia coli rnb gene, encoding ribonuclease II. Mol. Gen. Genet. 248: 242-46
200. 198. Zilhao R, Cairrao F, Régnier P, Arraiano CM. 1996. PNPase modulates RNase II expression in Escherichia coli: implications for mRNA decay and cell metabolism. Mol. Microbiol. 20:1033-42
201. 199. Zilhao R, Régnier P, Arraiano CM. 1995. The role of endonucleases in the expression of ribonuclease II in Escherichia coli. FEMS Microbiol. Lett. 130:237-44
202. 200. Zuber M, Hoover TA, Powell BS, Court DL. 1994. Analysis of the rnc locus of Coxiella burnetii. Mol. Microbiol. 14: 291-300