Chapter 4 Poly(A)-Assisted RNA Decay and Modulators of RNA Stability

Progress in Molecular Biology and Translational Science

Volumn 85, Issue C, 2009, Pages 137-185

  Régnier, Philippe ^a   Hajnsdorf, Eliane ^a  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

POLYADENYLIC ACID;

ENVIRONMENT; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYADENYLATION; REVIEW; RNA STABILITY;

BASE SEQUENCE; ENVIRONMENT; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; POLY A; POLYADENYLATION; RNA STABILITY;

EID: 64049113602     PISSN: 18771173     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0079-6603(08)00804-0     Document Type: Review

References (329)

1. Dreyfus M., and Régnier P. The poly(A) tail of mRNAs: Bodyguard in eukaryotes, scavenger in bacteria. Cell 111 (2002) 611-613
2. Mathy N., Benard L., Pellegrini O., Daou R., Wen T., and Condon C. 5′-3′ exoribonuclease activity in bacteria: Role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129 (2007) 681-692
3. Deana A., Celesnik H., and Belasco J.G. The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451 (2008) 355-358
4. Celesnik H., Deana A., and Belasco J.G. Initiation of RNA decay in Escherichia coli by 5′ pyrophosphate removal. Mol Cell 27 (2007) 79-90
5. Takayama K., and Kjelleberg S. The role of RNA stability during bacterial stress responses and starvation. Environ Microbiol 2 (2000) 355-365
6. Bernstein J.A., Khodursky A.B., Lin P., Lin-Chao S., and Cohen S.N. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA 99 (2002) 9697-9702
7. Nilsson G., Belasco J.G., Cohen S.N., and von Gabain A. Growth-rate dependent regulation of mRNA stability in Escherichia coli. Nature 312 (1984) 75-77
8. Melefors O., and von Gabain A. Site specific endonucleolytic cleavages and the regulation of stability of E. coli ompA mRNA. Cell 52 (1988) 893-901
9. Udekwu K.I., Darfeuille F., Vogel J., Reimegard J., Holmqvist E., and Wagner E. Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev 19 (2005) 2355-2366
10. Vytvytska O., Moll I., Kaberdin V.R., von Gabain A., and Bläsi U. HFq (HFI) stimulates ompA mRNA decay by interfering with ribosomes binding. Genes Dev 14 (2000) 1109-1118
11. Papenfort K., Pfeiffer V., Mika F., Lucchini S., Hinton J.C., and Vogel J. SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay. Mol Microbiol 62 (2006) 1674-1688
12. Johansen J., Rasmussen A.A., Overgaard M., and Valentin-Hansen P. Conserved small noncoding RNAs that belong to the sigmaE regulon: Role in down-regulation of outer membrane proteins. J Mol Biol 364 (2006) 1-8
13. Figueroa-Bossi N., Lemire S., Maloriol D., Balbontin R., Casadesus J., and Bossi L. Loss of Hfq activates the sigmaE-dependent envelope stress response in Salmonella enterica. Mol Microbiol 62 (2006) 838-852
14. Guisbert E., Rhodius V.A., Ahuja N., Witkin E., and Gross C.A. Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli. J Bacteriol 189 (2007) 1963-1973
15. Melin L., Rutberg L., and von Gabain A. Transcriptional and posttranscriptional control of the Bacillus subtilis succinate dehydrogenase operon. J Bacteriol 171 (1989) 2110-2115
16. Resnekov O., Rutberg L., and von Gabain A. Changes in the stability of specific mRNA species in response to growth stage in Bacillus subtilis. Proc Natl Acad Sci USA 87 (1990) 8355-8359
17. Paesold G., and Krause M. Analysis of rpoS mRNA in Salmonella dublin: Identification of multiple transcripts with growth-phase-dependent variation in transcript stability. J Bacteriol 181 (1999) 1264-1268
18. Aiso T., Yoshida H., Wada A., and Ohki R. Modulation of mRNA stability participates in stationary-phase-specific expression of ribosome modulation factor. J Bacteriol 187 (2005) 1951-1958
19. Kusz A.E., Medberry P.S., and Schottel J.L. Stationary phase, amino acid limitation and recovery from stationary phase modulate the stability and translation of chloramphenicol acetyltransferase mRNA and total mRNA in Escherichia coli. Microbiology 144 (1998) 739-750
20. Soltes-Rak E., Kushner D.J., Williams D.D., and Coleman J.R. Factors regulating cryIVB expression in the cyanobacterium-Synechococcus PCC 7942. Mol Gen Genet 246 (1995) 301-308
21. Barnett T.C., Bugrysheva J.V., and Scott J.R. Role of mRNA stability in growth phase regulation of gene expression in the group A streptococcus. J Bacteriol 189 (2007) 1866-1873
22. Ueno H., and Yonesaki T. Phage-induced change in the stability of mRNAs. Virology 329 (2004) 134-141
23. Marchand I., Nicholson A.W., and Dreyfus M. Bacteriophage T7 protein kinase phosphorylates RNase E and stabilizes mRNAs synthesized by T7 RNA polymerase. Mol Microbiol 42 (2001) 767-776
24. Sanson B., Hu R.M., Troitskayadagger E., Mathy N., and Uzan M. Endoribonuclease RegB from bacteriophage T4 is necessary for the degradation of early but not middle or late mRNAs. J Mol Biol 297 (2000) 1063-1074
25. Romeo J.M., and Zusman D.R. Determinants of an unusually stable mRNA in the bacterium Myxococcus xanthus. Mol Microbiol 6 (1992) 2975-2988
26. Morita T., El-Kazzaz W., Tanaka Y., Inada T., and Aiba H. Accumulation of glucose 6-phosphate or fructose 6-phosphate is responsible for destabilization of glucose transporter mRNA in Escherichia coli. J Biol Chem 278 (2003) 15608-15614
27. Kawamoto H., Morita T., Shimizu A., Inada T., and Aiba H. Implication of membrane localization of target mRNA in the action of a small RNA: Mechanism of posttranscriptional regulation of glucose transporter in Escherichia coli. Genes Dev 19 (2005) 328-338
28. Albertson N.H., and Nystrom T. Effects of starvation for exogenous carbon on functional mRNA stability and rate of peptide chain elongation in Escherichia coli. FEMS Microbiol Lett 117 (1994) 181-187
29. Redon E., Loubiere P., and Cocaign-Bousquet M. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280 (2005) 36380-36385
30. Jurgen B., Schweder T., and Hecker M. The stability of mRNA gsiB of Bacillus subtilis is dependent on the presence of a strong ribosome binding site. Mol Gen Genet 258 (1998) 538-545
31. Jager A., Samorski R., Pfeifer F., and Klug G. Individual gvp transcript segments in Haloferax mediterranei exhibit varying half-lives, which are differentially affected by salt concentration and growth phase. Nucleic Acids Res 30 (2002) 5436-5443
32. Collins J.J., Roberts G.P., and Brill W.J. Posttranscriptional control of Klebsiella pneumoniae nif mRNA stability by the nifL product. J Bacteriol 168 (1986) 173-178
33. Condon C., Putzer H., and Grunberg-Manago M. Processing of the leader mRNA plays a major role in the induction of the thrS espression following threonine starvation in Bacillus subtilis. Proc Natl Acad Sci USA 93 (1996) 6992-6997
34. Even S., Pellegrini O., Zig L., Labas V., Vinh J., Brechemmier-Baey D., et al. Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res 33 (2005) 2141-2152
35. Dubrac S., and Touati D. Fur positive regulation of iron superoxide dismutase in Escherichia coli: Functional analysis of the sodB promoter. J Bacteriol 182 (2000) 3802-3808
36. Masse E., Salvail H., Desnoyers G., and Arguin M. Small RNAs controlling iron metabolism. Curr Opin Microbiol 10 (2007) 140-145
37. Masse E., Vanderpool C.K., and Gottesman S. Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 187 (2005) 6962-6971
38. Massé E., and Gottesman S. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci USA 99 (2002) 4620-4625
39. Aiba H. Mechanism of RNA silencing by Hfq-binding small RNAs. Curr Opin Microbiol 10 (2007) 134-139
40. Bovy A., de Vrieze G., Lugones L., van Horssen P., van den Berg C., Borrias M., et al. Iron-dependent stability of the ferredoxin I transcripts from the cyanobacterial strains Synechococcus species PCC 7942 and Anabaena species PCC 7937. Mol Microbiol 7 (1993) 429-439
41. Bechhofer D.H., and Dubnau D. Induced mRNA stability in Bacillus subtilis. Proc Natl Acad Sci USA 84 (1987) 498-502
42. Woo W., and Lin-Chao S. Processing of the rne transcript by an RNase E-independent amino acid-dependent mechanism. J Biol Chem 272 (1997) 15516-15520
43. Garcia-Dominguez M., Muro-Pastor M.I., Reyes J.C., and Florencio F.J. Light-dependent regulation of cyanobacterial phytochrome expression. J Bacteriol 182 (2000) 38-44
44. Agrawal G.K., Kato H., Asayama M., and Shirai M. An AU-box motif upstream of the SD sequence of light-dependent psbA transcripts confers mRNA instability in darkness in cyanobacteria. Nucleic Acids Res 29 (2001) 1835-1843
45. Kulkarni R.D., and Golden S.S. mRNA stability is regulated by a coding-region element and the unique 5′ untranslated leader sequences of the three Synechococcus psbA transcripts. Mol Microbiol 24 (1997) 1131-1142
46. Georgellis D., Barlow T., Arvidson S., and von Gabain A. Retarded RNA turnover in Escherichia coli: A means of maintening gene expression during anaerobiosis. Mol Microbiol 9 (1993) 375-381
47. Klug G. Endonucleolytic degradation of puf mRNA in Rhodobacter capsulatus is influenced by oxygen. Proc Natl Acad Sci USA 88 (1991) 1765-1769
48. Jager S., Hebermehl M., Schiltz E., and Klug G. Composition and activity of the Rhodobacter capsulatus degradosome vary under different oxygen concentrations. J Mol Microbiol Biotechnol 7 (2004) 148-154
49. Mathy N., Jarrige A., Robert-Le Meur M., and Portier C. Increased expression of Escherichia coli polynucleotide phosphorylase at low temperatures is linked to a decrease in the efficiency of autocontrol. J Bacteriol 183 (2001) 3848-3854
50. Zangrossi S., Briani F., Ghisotti D., Regonesi M.E., Tortora P., and Dehò G. Transcriptional and posttranscriptional control of polynucleotide phosphorylase during cold acclimation in Escherichia coli. Mol Microbiol 36 (2000) 1470-1480
51. Goldenberg D., Azar I., and Oppenheim A.B. Differential mRNA stability of the cspA gene in the cold-shock response of Escherichia coli. Mol Microbiol 19 (1996) 241-248
52. Brandi A., Pietroni P., Gualerzi C.O., and Pon C.L. Posttranscriptional regulation of CspA expression in Escherichia coli. Mol Microbiol 19 (1996) 231-240
53. Cairrao F., Cruz A., Mori H., and Arraiano C.M. Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA. Mol Microbiol 50 (2003) 1349-1360
54. Sakamoto T., and Bryant D.A. Temperature-regulated mRNA accumulation and stabilization for fatty acid desaturase genes in the cyanobacterium Synechococcus sp. strain PCC 7002. Mol Microbiol 23 (1997) 1281-1292
55. Chamot D., and Owttrim G.W. Regulation of cold shock-induced RNA helicase gene expression in the Cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol 182 (2000) 1251-1256
56. Sato N., and Nakamura A. Involvement of the 5′-untranslated region in cold-regulated expression of the rbpA1 gene in the cyanobacterium Anabaena variabilis M3. Nucleic Acids Res 26 (1998) 2192-2199
57. Nickel M., Homuth G., Bohnisch C., Mader U., and Schweder T. Cold induction of the Bacillus subtilis bkd operon is mediated by increased mRNA stability. Mol Genet Genomics 272 (2004) 98-107
58. Repoila F., and Gottesman S. Signal transduction cascade for regulation of RpoS: Temperature regulation of DsrA. J Bacteriol 183 (2001) 4012-4023
59. Prud'homme-Genereux A., Beran R.K., Iost I., Ramey C.S., Mackie G.A., and Simons R.W. Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: Evidence for a "cold shock degradosome.". Mol Microbiol 54 (2004) 1409-1421
60. Khemici V., Toesca I., Poljak L., Vanzo N.F., and Carpousis A.J. The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: Functional replacement of RhlB by RhlE. Mol Microbiol 54 (2004) 1422-1430
61. Le Derout J., Regnier P., and Hajnsdorf E. Both temperature and medium composition regulate RNase E processing efficiency of the rpsO mRNA coding for ribosomal protein S15 of Escherichia coli. J Mol Biol 319 (2002) 341-349
62. Rasouly A., Shenhar Y., and Ron E.Z. Thermoregulation of Escherichia coli hchA transcript stability. J Bacteriol 189 (2007) 5779-5781
63. Afonyushkin T., Moll I., Blasi U., and Kaberdin V.R. Temperature-dependent stability and translation of Escherichia coli ompA mRNA. Biochem Biophys Res Commun 311 (2003) 604-609
64. Hasegawa H., Chatterjee A., Cui Y., and Chatterjee A.K. Elevated temperature enhances virulence of Erwinia carotovora subsp. carotovora strain EC153 to plants and stimulates production of the quorum sensing signal, N-acyl homoserine lactone, and extracellular proteins. Appl Environ Microbiol 71 (2005) 4655-4663
65. Yamauchi S., Okuyama H., Nishiyama Y., and Hayashi H. The rpoH gene encoding heat shock sigma factor sigma32 of psychrophilic bacterium Colwellia maris. Extremophiles 10 (2006) 149-158
66. Beltramo C., Grandvalet C., Pierre F., and Guzzo J. Evidence for multiple levels of regulation of Oenococcus oeni clpP-clpL locus expression in response to stress. J Bacteriol 186 (2004) 2200-2205
67. Anderson K.L., Roberts C., Disz T., Vonstein V., Hwang K., Overbeek R., et al. Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. J Bacteriol 188 (2006) 6739-6756
68. Edmonds M. A history of polyA sequences: From formation to factors to function. Prog Nucleic Acid Res Mol Biol 71 (2002) 285-389
69. Briani F., Del Vecchio E., Migliorini D., Hajnsdorf E., Regnier P., Ghisotti D., et al. RNase E and polyadenyl polymerase I are involved in maturation of CI RNA, the P4 phage immunity factor. J Mol Biol 318 (2002) 321-331
70. Hajnsdorf E., Braun F., Haugel-Nielsen J., and Regnier P. Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli. Proc Natl Acad Sci USA 92 (1995) 3973-3977
71. Le Derout J., Folichon M., Briani F., Dehò G., Régnier P., and Hajnsdorf E. Hfq affects the length and the frequency of short oligo(A) tails at the 3′ end of Escherichia coli rpsO mRNAs. Nucleic Acids Res 31 (2003) 4017-4023
72. Li Z., Pandit S., and Deutscher M.P. Polyadenylation of stable RNA precursors in vivo. Proc Natl Acad Sci USA 95 (1998) 12158-12162
73. van Meerten D., Zelwer M., Regnier P., and Duin J. In vivo oligo(A) insertions in phage MS2: Role of Escherichia coli poly(A) polymerase. Nucleic Acids Res 27 (1999) 3891-3898
74. Xu F., Lin-Chao S., and 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 USA 90 (1993) 6756-6760
75. Anderson J.T. RNA turnover: Unexpected consequences of being tailed. Curr Biol 15 (2005) R635-638
76. Sarkar N. Polyadenylation of mRNA in bacteria. Microbiology 142 (1996) 3125-3133
77. Sarkar N. Polyadenylation of mRNA in prokaryotes. Annu Rev Biochem 66 (1997) 173-197
78. Nakazato H., Venkatesan S., and Edmonds M. Polyadenylic acid sequences in E. coli messenger RNA. Nature 256 (1975) 144 16
79. Srinivasan P.R., Ramanarayanan M., and Rabbani E. Presence of polyriboadenylate sequences in pulse-labeled RNA of Escherichia coli. Proc Natl Acad Sci USA 72 (1975) 2910-2914
80. Sarkar N., Langley D., and Paulus H. Isolation and characterization of polyadenylate-containing RNA from Bacillus brevis. Biochemistry 17 (1978) 3468-3474
81. Kramer R.A., Rosenberg M., and Steitz J.A. Nucleotide sequences of the 5′ and 3′ termini of bacteriophage T7 early messenger RNAs synthesized in vivo: Evidence for sequence specificity in RNA processing. J Mol Biol 89 (1974) 767-776
82. Marujo P.E., Hajnsdorf E., Le Derout J., Andrade R., Arraiano C.M., and Régnier P. RNase II removes the oligo(A) tails that destabilize the rpsO mRNA of Escherichia coli. RNA 6 (2000) 1185-1193
83. O'Hara E.B., Chekanova J.A., Ingle C.A., Kushner Z.R., Peters E., and Kushner S.R. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc Natl Acad Sci USA 92 (1995) 1807-1811
84. Goodrich A.F., and Steege D.A. Roles of polyadenylation and nucleolytic cleavage in the filamentous phage mRNA processing and decay pathways in Escherichia coli. RNA 5 (1999) 972-985
85. Karnik P., Taljanidisz J., Sasvari-Szekely M., and Sarkar N. 3′-terminal polyadenylate sequenses of Escherichia coli tryptophan synthetase α-subunit messenger RNA. J Mol Biol 196 (1987) 347-354
86. Taljanidisz J., Karnik P., and Sarkar N. Messenger ribonucleic acid for lipoprotein of the Escherichia coliouter membrane is polyadenylated. J Mol Biol 193 (1987) 507-515
87. Mohanty B.K., and 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 34 (1999) 1109-1119
88. Johnson M.D., Popowski J., Cao G., Shen P., and Sarkar N. Bacteriophage T7 mRNA is polyadenylated. Mol Microbiol 27 (1998) 23-30
89. Campos-Guillén J., Bralley P., Jones G.H., Bechhofer D.H., and Olmedo-Alvarez G. Addition of poly(A) and heteropoymeric 3′ ends in Bacillus subtilis wild-type and polynucleotide phosphorylase-deficient strains. J Bacteriol 187 (2005) 4698-4706
90. Cao G., and Sarkar N. Stationary phase-specific mRNAs in Escherichia coli are polyadenylated. Biochem Biophys Res Commun 239 (1997) 46-50
91. Mohanty B.K., and Kushner S.R. The majority of Escherichia coli mRNAs undergo posttranscriptional modification in exponentially growing cells. Nucleic Acids Res 34 (2006) 5695-5704
92. Szalewska-Palasz A., Wrobel B., and Wegrzyn G. Rapid degradation of polyadenylated oop RNA. FEBS Lett 432 (1998) 70-72
93. Mikkelsen N.D., and Gerdes K. Sok antisense RNA from plasmid R1 is functionally inactivated by RNase E and polyadenylated by poly(A)polymerase I. Mol Microbiol 26 (1997) 311-320
94. Reichenbach B., Maes A., Kalamorz F., Hajnsdorf E., and Görke B. The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli. Nucleic Acids Res 36 (2008) 2570-2580
95. Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner E., Margalit H., et al. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Current Biol 11 (2001) 941-950
96. Bralley P.J. Overexpresion of the polynucleotide phosphorylase gene (pnp) of Streptomyces antibioticus affects mRNA stability and poly(A) tail length but not ppGpp levels. Microbiology 149 (2003) 2173-2182 GH.
97. Bralley P., Gust B., Chang S., Chater K.F., and Jones G.H. RNA 3′-tail synthesis in Streptomyces: In vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase. Microbiology 152 (2006) 627-636
98. Mohanty B.K., and Kushner S.R. Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism. Mol Microbiol 34 (1999) 1094-1108
99. Haugel-Nielsen J., Hajnsdorf E., and Regnier P. The rpsO mRNA of Escherichia coli is polyadenylated at multiple sites resulting from endonucleolytic processing and exonucleolytic degradation. EMBO J 15 (1996) 3144-3152
100. Söderbom F., Binnie U., Masters M., and Wagner E. Regulation of plasmid R1 replication: PcnB and RNase E expedite the decay of the antisense RNA, copA. Mol Microbiol 26 (1997) 493-504
101. Khemici V., and Carpousis A.J. The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers. Mol Microbiol 51 (2004) 777-790
102. Cheng Z., and Deutscher M.P. An important role for RNase R in mRNA decay. Mol Cell 17 (2005) 313-318
103. Coburn G.A., and Mackie G.A. Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes. J Mol Biol 279 (1998) 1061-1074
104. Lopilato J., Bortner S., and 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 205 (1986) 285-290
105. Liu J., and Parkinson J.S. Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control. J Bacteriol 171 (1989) 1254-1261
106. Cao G., and Sarkar N. Identification of the gene for an Escherichia coli poly(A) polymerase. Proc Natl Acad Sci USA 89 (1992) 10380-10384
107. Cohen S.N. Surprises at the 3′ end of prokaryotic RNA. Cell 80 (1995) 829-832
108. Andrade J.M., and Arraiano C.M. PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins. RNA 14 (2008) 543-551
109. Viegas S.C., Pfeiffer V., Sittka A., Silva I.J., Vogel J., and Arraiano C.M. Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res 15 (2007) 7651-7664
110. Ghisotti D., Chiaramonte R., Forti F., Zangrossi S., Sironi G., and Deho G. Genetic analysis of the immunity region of phage-plasmid P4. Mol Microbiol 6 (1992) 3405-3413
111. Hajnsdorf E., and 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 286 (1999) 1033-1043
112. Mackie G.A. Stabilization of the 3′ one third of Escherichia coli ribosomal protein S20 mRNA in mutants lacking polynucleotide phosphorylase. J Bacteriol 171 (1989) 4112-4120
113. Coburn G.A., and 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 271 (1996) 15776-15781
114. Hajnsdorf E., Braun F., Haugel-Nielsen J., Le Derout J., and Regnier P. Multiple degradation pathways of the rpsO mRNA of E. coli. RNase E interacts with the 5′ and 3′ extremities of the primary transcript. Biochimie 78 (1996) 416-424
115. Blum E., Carpousis A.J., and Higgins C.F. Polyadenylation promotes degradation of 3′-structured RNA by the Escherichia coli mRNA degradosome in vitro. J Biol Chem 274 (1999) 4009-4016
116. Xu F., and Cohen S.N. RNA degradation in Escherichia coli regulated by 3′ adenylation and 5′ phosphorylation. Nature 374 (1995) 180-183
117. Coburn G.A., Miao X., Briant D.J., and Mackie G.A. Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEAD-box RNA helicase. Genes Dev 13 (1999) 2594-2603
118. Mackie G.A., and Genereaux J.L. 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 (1993) 998-1012
119. Plamann M.D., and Stauffer G.V. E.coli glyA mRNA decay: The role of 3′ secondary structure and the effects of the pnp and rnb mutations. Mol Gen Genet 220 (1990) 301-306
120. McLaren R.S., Newbury S.F., Dance G.S.C., Causton H.C., and Higgins C.F. mRNA degradation by processive 3′-5′ exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J Mol Biol 221 (1991) 81-95
121. Mohanty B.K., and 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 36 (2000) 982-994
122. Masters M., Colloms M.D., Oliver I.R., He L., Macnaughton E.J., and Charters Y. The pcnB gene of Escherichia coli, which is required for ColE1 copy number maintenance, is dispensable. J Bacteriol 175 (1993) 4405-4413
123. Raynal L.C., Krisch H.M., and Carpousis A.J. The Bacillus subtilis nucleotidyltransferase is a tRNA CCA-adding enzyme. J Bacteriol 180 (1998) 6276-6282
124. Yue D., Maizels N., and 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 archael hyperthermophile Sulfolobus shibatae. RNA 2 (1996) 895-908
125. Betat H., Rammelt C., Martin G., and Mörl M. Exchange of regions between bacterial poly(A)polymerase and the CCA-adding enzyme generates altered specificiies. Mol Cell 15 (2004) 389-398
126. Binns N., and Masters M. Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: A second chromosomal example of translation initiated at AUU. Mol Microbiol 44 (2002) 1287-1298
127. August J.T., Ortiz P.J., and Hurwitz J. Ribonucleic acid-dependent ribonucleotide incorporation. I. Purification and properties of the enzyme. J Biol Chem 237 (1962) 3786-3793
128. Sippel A.E. Purification and characterization of adenosine triphosphate: Ribonucleic acid adenyltransferase from Escherichia coli. Eur J Biochem 37 (1973) 31-40
129. Yehudai-Resheff S., and Schuster G. Characterization of the E. coli poly(A) polymerase: Nucleotide specificity, RNA binding affinities and RNA structure dependence. Nucleic Acids Res 28 (2000) 1139-1144
130. Folichon M., Allemand F., Regnier P., and Hajnsdorf E. Stimulation of poly(A) synthesis by E. coli poly(A)polymerase I is correlated with Hfq binding to poly(A) tails. FEBS J 272 (2005) 454-463
131. Mohanty B.K., and Kushner S.R. Polynucleotide phosphorylase functions both as a 3′-5′ exonuclease and a poly(A) polymerase in Escherichia coli. Proc Natl Acad Sci USA 97 (2000) 11966-11971
132. Feng Y., and Cohen S.N. Unpaired terminal nucleotides and 5′ monoposphorylation govern 3′ polyadenylation by Escherichia coli poly(A) polymerase I. Proc Natl Acad Sci USA 97 (2000) 6415-6420
133. Hajnsdorf E., and Régnier P. Host factor HFq of Escherichia coli stimulates elongation of poly(A) tails by poly(A)polymerase I. Proc Natl Acad Sci USA 97 (2000) 1501-1505
134. Sano H., and Feix G. Terminal riboadenylate transferase from Escherichia coli. Eur J Biochem 71 (1976) 577-583
135. Zuo Y., and Deutscher M.P. Exoribonuclease superfamilies: Structural analysis and phylogenetic distribution. Nucleic Acids Res 29 (2001) 1017-1026
136. Ezraty B., Dahlgren B., and Deutscher M.P. The RNase Z homologue encoded by Escherichia coli elaC gene is RNase BN. J Biol Chem 280 (2005) 16542-16545
137. Cao G., and 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 USA 89 (1992) 7546-7550
138. Saira M.I. Comparative sequence analysis of ribonucleases HII, III, II, PH and D. Nucleic Acids Res 25 (1997) 3187-3195
139. Spahr P.F., and Schlessinger D. Breakdown of messenger ribonucleic acid by a potassium-activated phosphodiesterase from Escherichia coli. J Biol Chem 238 (1963) 2251-2253
140. Shen V., and Schlessinger D. In: Boyer P. (Ed). The Enzymes vol. XV Part B (1982), Academic Press, New York 501-515
141. Deutscher M.P., and Reuven N.B. Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci USA 88 (1991) 3277-3280
142. Folichon M., Marujo P.E., Arluison V., Le Derout J., Pellegrini O., Hajnsdorf E., et al. Fate of mRNA extremities generated by intrinsic termination: Detailed analysis of reactions catalyzed by ribonuclease II and poly(A) polymerase. Biochimie 87 (2005) 819-826
143. Coburn G.A., and Mackie G.A. Overexpression, purification and properties of Escherichia coli ribonuclease II. J Biol Chem 271 (1996) 1048-1053
144. Spickler C., and Mackie G.A. Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure. J Bacteriol 182 (2000) 2422-2427
145. Gupta R.S., Kasai T., and Schlessinger D. Purification and some novel properties of Escherichia coli RNase II. J Biol Chem 252 (1977) 8945-8949
146. Braun F., Hajnsdorf E., and 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 19 (1996) 997-1005
147. Cheng Z., and Deutscher M.P. Purification and characterization of the Escherichia coli exoribonuclease RNase R. J Biol Chem 277 (2002) 21624-21629
148. Amblar M., and Arraiano C.M. A single mutation in Escherichia coli ribonuclease II inactivates the enzyme without affecting RNA binding. FEBS J 272 (2005) 2345
149. Mott J.E., Galloway J.L., and Platt T. Maturation of Escherichia coli tryptophan operon mRNA: Evidence for 3′ exonucleolytic processing after rho-dependent termination. EMBO J 4 (1985) 1887-1891
150. Newbury S.F., Smith N.H., Robinson E.C., Hiles I.D., and Higgins C.F. Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell 48 (1987) 297-310
151. Pepe C.M., Maslesa-Galic S., and Simons R.W. Decay of the IS10 antisense RNA by 3′ exoribonucleases: Evidence that RNase II stabilizes RNA-OUT against PNPase attack. Mol Microbiol 13 (1994) 1133-1142
152. Zuo Y., Vincent H.A., Zhang J., Wang Y., Deutscher M.P., and Malhotra A. Structural basis for processivity and single-strand specificity of RNase II. Mol Cell 24 (2006) 149-156
153. Frazao C., McVey C.E., Amblar M., Barbas A., Vonrhein C., Arraiano C.M., et al. Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex. Nature 443 (2006) 110-114
154. Barbas A., Matos R.G., Amblar M., Lopez-Vinas E., Gomez-Puertas P., and Arraiano C.M. New insights into the mechanism of RNA degradation by ribonuclease II: Identification of the residue responsible for setting the RNase II end product. J Biol Chem 283 (2008) 13070-13076
155. Deutscher M.P. Degradation of stable RNA in bacteria. J Biol Chem 278 (2003) 45041-45044
156. Amblar M., Barbas A., Fialho A.M., and Arraiano C.M. Characterization of the functional domains of Escherichia coli RNase II. J Mol Biol 360 (2006) 921-933
157. Grunberg-Manago M. In: Cohn W. (Ed). Progress in nucleic acids research (1963), Academic Press, New York 93-133
158. Donovan W.P., and Kushner S.R. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K12. Proc Natl Acad Sci USA 83 (1986) 120-124
159. Miczak A., Kaberdin V.R., Wei C., and Lin-Chao S. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc Natl Acad Sci USA 93 (1996) 3865-3969
160. Py B., Higgins C.H., Krisch H.M., and Carpousis A.J. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381 (1996) 169-172
161. Carpousis A.J. The RNA degradosome of Escherichia coli: An mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 61 (2007) 71-87
162. Symmons M.F., Jones G.H., and Luisi B.F. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity and regulation. Structure 8 (2000) 1215-1226
163. Symmons M.F., Williams M.G., Luisi B.F., Jones G.H., and Carpousis A.J. Running rings around RNA: A superfamily of phosphate-dependent RNases. TiBS 27 (2002) 11-18
164. Thang M.N., Guschlbauer W., Zachau H.G., and Grunberg-Manago M. Degradation of transfer nucleic acid by polynucleotide phosphorylase. J Mol Biol 26 (1967) 403-421
165. Kasai T., Gupta R.S., and Schlessinger D. Exoribonucleasesin wild-type Escherichia coli and RNase II-deficient mutants. J Biol Chem 252 (1977) 8950-8956
166. Vincent H.A., and Deutscher M.P. Substrate recognition and catalysis by the exoribonuclease RNase R. J Biol Chem 281 (2006) 29769-29775
167. Cheng Z.F., and Deutscher M.P. Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R. Proc Natl Acad Sci USA 100 (2003) 6388-6393
168. Hajnsdorf E., Steier O., Coscoy L., Teysset L., and 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-rnb-pnp mutant. EMBO J 13 (1994) 3368-3377
169. Régnier P., and Arraiano C.M. Degradation of mRNA in bacteria: Emergence of ubiquitous features. Bioessays 22 (2000) 235-244
170. Cheng Z., Zuo Y., Li Z., Rudd K.E., and Deutscher M.P. The vacB gene required for virulence in Shigella flexneri encodes the exoribonuclease RNase R. J Biol Chem 273 (1998) 14077-14080
171. Coburn G.A., and Mackie G.A. Degradation of mRNA in Escherichia coli: An old problem with some new twists. Prog Nucl Acid Res Mol Biol 62 (1999) 55-108
172. Li Z., and Deutscher M.P. RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA 8 (2002) 97-109
173. Soderbom F., Svard S.G., and Kirsebom L.A. RNase E cleavage in the 5′ leader of a tRNA precursor. J Mol Biol 352 (2005) 22-27
174. Ow M.C., and Kushner S.R. Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes Dev 16 (2002) 1102-1115
175. Vanzo N., Li Y.S., Py B., Blum E., Higgins C.F., Raynal L.C., et al. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev 12 (1998) 2770-2781
176. Mackie G.A. Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395 (1998) 720-723
177. Huang H., Liao J., and Cohen S.N. Poly(A) and poly(U)-specific RNA 3′ tail shortening by E. coli ribonuclease E. Nature 391 (1998) 99-102
178. Walsh A.P., Tock M.H., Mallen M.H., Kaberdin V.R., von Gabain A., and McDowall K.J. Cleavage of poly(A) tails on the 3′-end of RNA by
179. Deutscher M.P., and Li Z. Exoribonucleases and their multiple roles in RNA metabolism. Prog Nucleic Acid Res Mol Biol 66 (2001) 67-105
180. Li Z., and Deutscher M.P. The tRNA processing enzyme RNase T is essential for maturation of 5S RNA. Proc Natl Acad Sci USA 92 (1995) 6883-6886
181. Li Z., Pandit S., and Deutscher M.P. 3′ exoribonucleolytic trimming is a common feature of the mauration of small, stable RNAs in Escherichia coli. Proc Natl Acad Sci USA 95 (1998) 2856-2861
182. Li Z., Pandit S., and Deutscher M.P. Maturation of 23S ribosomal RNA requires the exoribonuclease RNase T. RNA 5 (1999) 139-146
183. Zuo Y., and Deutscher M.P. The physiological role of RNase T can be explained by its unusual substrate specificity. J Biol Chem 277 (2002) 29654-29661
184. Li Z., Reimers S., Pandit S., and Deutscher M.P. RNA quality control: Degradation of defective transfer RNA. EMBO J 21 (2002) 1132-1138
185. Mohanty B.K., and Kushner S.R. Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Mol Microbiol 50 (2003) 645-658
186. Worrall J.A., Howe F.S., McKay A.R., Robinson C.V., and Luisi B.F. Allosteric activation of the ATPase activity of the Escherichia coli RhlB RNA helicase. J Biol Chem 283 (2008) 5567-5576
187. Jasiecki J., and Wegrzyn G. Growth-rate dependent RNA polyadenylation in Escherichia coli. EMBO Rep 4 (2003) 172-177
188. Mohanty B.K., Maples V.F., and Kushner S.R. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol Microbiol 54 (2004) 905-920
189. Raynal L.C., Krisch H.M., and Carpousis A.J. Bacterial poly(A)polymerase: An enzyme that modulates RNA stability. Biochimie 78 (1996) 390-398
190. Jones P.G., VanBogelen R.A., and Neidhardt F.C. Induction of proteins in response to low temperature in Escherichia coli. J Bacteriol 169 (1987) 2092-2095
191. Chen C., and Deutscher M.P. Elevation of RNase R in response to multiple stress conditions. J Biol Chem 280 (2005) 34393 286
192. Goverde R.L., Huis in't Veld J.H., Kusters J.G., and Mooi F.R. The psychrotrophic bacterium Yersinia enterocolitica requires expression of pnp, the gene for polynucleotide phosphorylase, for growth at low temperature (5 degrees C). Mol Microbiol 28 (1998) 555-569
193. Luttinger A., Hahn J., and Dubnau D. Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis. Mol Microbiol 19 (1996) 343-356
194. Jarrige A., Mathy N., and Portier C. PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader. EMBO J 20 (2001) 6845-6855
195. Portier C., Dondon L., Grunberg-Manago M., and 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 6 (1987) 2165-2170
196. Robert-Le Meur M., and Portier C. E. coli polynucleotide phosphorylase expression is autoregulated through an RNase III-dependent mechanism. EMBO J 11 (1992) 2633-2641
197. Cairrào F., Chora A., Zilhao R., Carpousis A.J., and Arraiano C.M. RNase II levels change according to the growth conditions: Characterization of gmr, a new Escherichia coli gene involved in the modulation of RNase II. Mol Microbiol 39 (2001) 1550-1561
198. Zilhao R., Cairrao F., Regnier P., and Arraiano C.M. PNPase modulates RNase II expression in Escherichia coli: Implications for mRNA decay and cell metabolism. Mol Microbiol 20 (1996) 1033-1042
199. Söderbom F., and Wagner E. Degradation pathway of CopA, the antisense RNA that controls replication of plasmid R1. Microbiology 144 (1998) 1907-1917
200. Raynal L.C., and 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 32 (1999) 765-775
201. Wahle E., and Keller W. The biochemistry of polyadenylation. Trends Biochem Sci 21 (1996) 247-250
202. Senear A.W., and Steitz J.A. Site-specific interaction of Qb host factor and ribosomal protein S1 with Qb and R17 bacteriophage RNAs. J Biol Chem 251 (1976) 1902-1912
203. Zhang A., Altuvia S., Tiwari A., Argaman L., Hengge-Aronis R., and Storz G. The oxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-1) protein. EMBO J 17 (1998) 6061-6068
204. de Haseth P.L., and Uhlenbeck O.C. Interaction of Escherichia coli host factor protein with oligoriboadenylates. Biochemistry 19 (1980) 6138-6146
205. Folichon M., Arluison V., Pellegrini O., Huntzinger E., Regnier P., and Hajnsdorf E. The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation. Nucleic Acids Res 31 (2003) 7302-7310
206. Valentin-Hansen P., Eriksen M., and Udesen C. The bacterial Sm-like protein Hfq: A key player in RNA transactions. Mol Microbiol 51 (2004) 1525-1533
207. Brennan R.G., and Link T.M. Hfq structure, function and ligand binding. Curr Opin Microbiol 10 (2007) 125-133
208. Gottesman S. Micros for microbes: Noncoding regulatory RNAs in bacteria. Trends Genet 21 (2005) 399-404
209. Storz G., Opdyke J.A., and Zhang A. Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 7 (2004) 140-144
210. Morita T., Maki K., and Aiba H. RNase E based-ribonucleoprotein complexes: Mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 19 (2005) 2176-2186
211. Jasiecki J., and Wegrzyn G. Localization of Escherichia coli poly(A) polymerase I in cellular membrane. Biochem Biophys Res Commun 329 (2005) 598-602
212. Liou G., Jane W., Cohen S.N., Lin N., and Lin-Chao S. RNA degradosomes exist in vivo in Escherichia coli as multicomponent complexes associated with the cytoplasmic membrane via the N-terminal region of ribonuclease E. Proc Natl Acad Sci USA 98 (2001) 63-68
213. Taghbalout A., and Rothfield L. RNase E and the other constituents of the RNA degradosome are components of the bacterial cytoskeleton. Proc Natl Acad Sci USA 104 (2007) 1667-1672
214. Liou G., Chan H., Lin C., and Lin-Chao S. DEAD box RhlB helicase physically associates with exoribonuclease PNPase to degrade double stranded RNA independent of the degradosome asssembling region of RNase E. J Biol Chem 277 (2002) 41157
215. Jasiecki J., and Wegrzyn G. Phosphorylation of Escherichia coli poly(A) polymerase I and effects of this modification on the enzyme activity. FEMS Microbiol Lett 261 (2006) 118-122
216. Feng Y., Huang H., Liao J., and Cohen S.N. Escherichia coli poly(A) binding proteins that interact with components of degradosomes or impede RNA decay mediated by polynucleotide phosphorylase and RNase E. J Biol Chem 276 (2001) 31651-31656
217. Houseley J., LaCava J., and Tollervey D. RNA-quality control by the exosome. Nat Rev Mol Cell Biol 7 (2006) 529-539
218. Vanacova S., Wolf J., Martin G., Blank D., Dettwiler S., Friedlein A., et al. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3 (2005) e189
219. Marujo P.E., Braun F., Haugel-Nielsen J., Le Derout J., Arraiano C.M., and Regnier P. Inactivation of the decay pathway initiated at an internal site by RNase E promotes poly(A)-dependent degradation of the rpsO mRNA in Escherichia coli. Mol Microbiol 50 (2003) 1283-1294
220. Mohanty B.K., and Kushner S.R. Polyadenylation of Escherichia coli transcripts plays an integral role in regulating intracellular levels of polynucleotide phosphorylase and RNase E. Mol Microbiol 45 (2002) 1315-1324
221. Joanny G., Le Derout J., Bréchemier-Baey D., Labas V., Vinh J., Régnier P., et al. Polyadenylation of a functional mRNA controls gene expression in E. coli. Nucleic Acids Res 35 (2007) 2494-2502
222. Urban J.H., and Vogel J. Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biol 6 (2008) e64
223. Lisitsky I., Klaff P., and Schuster G. Addition of destabilizing poly(A)-rich sequences to endonuclease cleavage sites during the degradation of chloroplast mRNA. Proc Natl Acad Sci USA 93 (1996) 13398-13403
224. Slomovic S., Portnoy V., Yehudai-Resheff S., Bronshtein E., and Schuster G. Polynucleotide phosphorylase and the archaeal exosome as poly(A)-polymerases. Biochim Biophys Acta 1779 (2008) 247-255
225. Rott R., Zipor G., Portnoy V., Liveanu V., and Schuster G. RNA polyadenylation and degradation in cyanobacteria are similar to the chloroplast but different from E. coli. J Biol Chem 278 (2003) 15771-15777
226. Portnoy V., and Schuster G. Mycoplasma gallisepticum as the first analyzed bacterium in which RNA is not polyadenylated. FEMS Microbiol Lett 283 (2008) 97-103
227. Bralley P., and Jones G.H. cDNA cloning confirms the polyadenylation of RNA decay intermedites in Streptomyces coelicolor. Microbiology 148 (2002) 1421-1425
228. Yehudai-Resheff S., Portnoy V., Yogev S., Adir N., and Schuster G. Domain analysis of the chloroplast polynucleotide phosphorylase reveals discrete functions in RNA degradation, polyadenylation, and sequence homology with exosome proteins. Plant Cell 15 (2003) 2003-2019
229. Wilusz C.J., and Wilusz J. New ways to meet your (3′) end oligouridylation as a step on the path to destruction. Genes Dev 22 (2008) 1-7
230. Lee K., Zhan X., Gao J., Qiu J., Feng Y., Meganathan R., et al. RraA. A protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli. Cell 114 (2003) 623-634
231. Gao J., Lee K., Zhao M., Qiu J., Zhan X., Saxena A., et al. Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Mol Microbiol 61 (2006) 394-406
232. Zhan X., Gao J., Jain C., Cieslewicz M.J., Swartz J.R., and Georgiou G. Genetic analysis of disulfide isomerization in Escherichia coli: Expression of DsbC is modulated by RNase E-dependent mRNA processing. J Bacteriol 186 (2004) 654-660
233. Zhao M., Zhou L., Kawarasaki Y., and Georgiou G. Regulation of RraA, a protein inhibitor of RNase E-mediated RNA decay. J Bacteriol 188 (2006) 3257-3263
234. Monzingo A.F., Gao J., Qiu J., Georgiou G., and Robertus J.D. The X-ray structure of Escherichia coli RraA (MenG), a protein inhibitor of RNA processing. J Mol Biol 332 (2003) 1015-1024
235. Kanesaki T., Hamada T., and Yonesaki T. Opposite roles of the dmd gene in the control of RNase E and RNase LS activities. Genes Genet Syst 80 (2005) 241-249
236. Ueno H., and Yonesaki T. Recognition and specific degradation of bacteriophage T4 mRNAs. Genetics 158 (2001) 7-17
237. Zilhao R., Regnier P., and Arraiano C.M. The role of endonucleases in the expression of ribonuclease II in Escherichia coli. FEMS Microbiol Lett 130 (1995) 237-244
238. Weber H., Pesavento C., Possling A., Tischendorf G., and Hengge R. Cyclic-di-GMP-mediated signaling within the sigma network of Escherichia coli. Mol Microbiol 62 (2006) 1014-1034
239. Wassarman K.M., Repoila F., Rosenow C., Storz G., and Gottesman S. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15 (2001) 1637-1651
240. Rivas E., Klein R.J., Jones T.A., and Eddy S.R. Computational identification of noncoding RNAs in E. coli by comparative genomics. Current Biol 11 (2001) 1369-1373
241. Chen S., Lesnik E.A., Hall T.A., Sampath R., Griffey R.H., Ecker D.J., et al. A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. BioSystems 65 (2002) 157-177
242. Hershberg R., Altuvia S., and Margalit H. A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res 31 (2003) 1813-1820
243. Aiba H., Matsuyama S., Mizuno T., and Mizushima S. Function of micF as an antisense RNA in osmoregulatory expression of the ompF gene in Escherichia coli. J Bacteriol 169 (1987) 3007-3012
244. Andersen J., and Delihas N. micF RNA binds to the 5′ end of ompF mRNA and to a protein from Escherichia coli. Biochemistry 29 (1990) 9249-9256
245. Altuvia S., Zhang A., Argaman L., Tiwari A., and Storz G. The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding. EMBO J 17 (1998) 6069-6075
246. s subunit of Escherichia coli RNA polymerase. Nucl Acids Symp Ser 36 (1997) 27-28
247. Moller T., Franch T., Hojrup P., Keene D., Bächinger H.P., Brennan R.G., et al. HFq: A bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell 9 (2002) 23-30
248. Majdalani N., Cunning C., Sledjeski D., Elliott T., and Gottesman S. DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. Proc Natl Acad Sci USA 95 (1998) 12462-12467
249. Lease R.A., and Belfort M. A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc Natl Acad Sci USA 97 (2000) 9919-9924
250. Braun F., Le Derout J., and Régnier P. Ribosomes inhibit an RNase E cleavage which induces the decay of the rpsO mRNA of Escherichia coli. EMBO J 17 (1998) 4790-4797
251. S subunit of RNA polymerase in Escherichia coli. J Bacteriol 179 (1997) 297-300
252. Takada A., Wachi M., and Nagai K. Negative regulatory role of the Escherichia coli hfq gene in cell division. Biochem Biophys Res Com 266 (1999) 579-583
253. Tsui H., Leung H., and Winkler M.E. Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol Microbiol 13 (1994) 35-49
254. Ziolkowska K., Derreumaux P., Folichon M., Pellegrini O., Regnier P., Boni I.V., et al. Hfq variant with altered RNA binding functions. Nucleic Acids Res 34 (2006) 709-720
255. Vassilieva I.M., and Garber M.B. The regulatory role of the HFq protein in bacterial cells. Mol Biol 36 (2002) 785-791
256. Nogueira T., and Springer M. Posttranscriptional control by global regulators of gene expression in bacteria. Curr Opin Microbiol 3 (2000) 154-158
257. Zhang A., Wassarman K.M., Rosenow C., Tjaden B.C., Storz G., and Gottesman S. Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50 (2003) 1111-1124
258. Sledjeski D.D., Whitman C., and Zhang A. HFq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol 183 (2001) 1997-2005
259. Zhang A., Wassarman K.M., Ortega J., Steven A.C., and Storz G. The Sm-like HFq protein increases OxyS RNA interaction with target mRNAs. Mol Cell 9 (2002) 11-22
260. Vanderpool C.K., and Gottesman S. Involvement of a novel transcriptional activator and small RNA in posttranscriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol Microbiol 54 (2004) 1076-1089
261. Mikulecky P.J., Kaw M.K., Brescia C.C., Takach J.C., Sledjeski D.D., and Feig A.L. Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat Struct Mol Biol 11 (2004) 1206-1214
262. Vecerek B., Rajkowitsch L., Sonnleitner E., Schroeder R., and Blasi U. The C-terminal domain of Escherichia coli Hfq is required for regulation. Nucleic Acids Res 36 (2008) 133-143
263. Arluison V., Derreumaux P., Allemand F., Folichon M., Hajnsdorf E., and Regnier P. Structural modeling of the Sm-like protein Hfq from Escherichia coli. J Mol Biol 320 (2002) 705-712
264. Kawamoto H., Koide Y., Morita T., and Aiba H. Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Mol Microbiol 61 (2006) 1013-1022
265. Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 10 (2007) 102-109
266. Boisset S., Geissmann T., Huntzinger E., Fechter P., Bendridi N., Possedko M., et al. Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev 21 (2007) 1353-1366
267. Vytvytska O., Jakobsen J.S., Balcunate G., Andersen J.S., Baccarini M., and von Gabain A. Host-factor I, Hfq, binds to Escherichia coli ompA mRNA in a growth rate-dependent fashion and egulates its stability. Proc Natl Acad Sci USA 95 (1998) 14118-14123
268. Massé E., Escorcia F.E., and Gottesman S. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev 17 (2003) 2374-2383
269. Tsui H., Feng G., and Winkler M.E. Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12. J Bacteriol 179 (1997) 7476-7487
270. Moll I., Afonyushkin T., Vytvytska O., Kaberdin V.R., and Blasi U. Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 9 (2003) 1308-1314
271. Geissmann T.A., and Touati D. Hfq, a new chaperoning role: Binding to messenger RNA determines access for small RNA regulator. EMBO J 23 (2004) 396-405
272. Butland G., Peregrin-Alvarez J.M., Li J., Yang W., Yang X., Canadien V., et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 (2005) 531-537
273. Kajitani M., and Ishihama A. Identification and sequence determination of the host factor gene for bacteriophage Qb. Nucleic Acids Res 9 (1991) 1063-1066
274. Sukhodolets M.V., and Garges S. Interaction of Escherichia coli RNA polymerase with the ribosomal protein S1 and the Sm-like ATPase Hfq. Biochemistry 42 (2003) 8022-8034
275. Vecerek B., Moll I., Afonyushkin T., Kaberdin V., and Bläsi U. Interaction of the RNA chaperone Hfq with mRNAs: Direct and indirect roles in iron metabolism of Escherichia coli. Mol Microbiol 50 (2003) 897-910
276. Davis B.M., and Waldor M.K. RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA. Mol Microbiol 65 (2007) 373-385
277. Ueno H., and Yonesaki T. Role of Escherichia coli HFq in late-gene silencing of bacteriophage T4 dmd mutant. Genes Genet Syst 77 (2002) 301-308
278. Masse E., and Arguin M. Ironing out the problem: new mechanisms of iron homeostasis. Trends Biochem Sci 30 (2005) 462-468
279. Carpousis A.J. Degradation of targeted mRNAs in Escherichia coli: Regulation by a small antisense RNA. Genes Dev 17 (2003) 2351-2355
280. Afonyushkin T., Vecerek B., Moll I., Blasi U., and Kaberdin V.R. Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB. Nucleic Acids Res 33 (2005) 1678-1689
281. Prevost K., Salvail H., Desnoyers G., Jacques J.F., Phaneuf E., and Masse E. The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis. Mol Microbiol 64 (2007) 1260-1273
282. Kimata K., Tanaka Y., Inada T., and Aiba H. Expression of the glucose transporter gene, ptsG, is regulated at the mRNA degradation step in response to glycolytic flux in Escherichia coli. EMBO J 20 (2001) 3587-3595
283. Morita T., Mochizuki Y., and Aiba H. Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction. Proc Natl Acad Sci USA 103 (2006) 4858 3
284. Morita T., Kawamoto H., Mizota T., Inada T., and Aiba H. Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli. Mol Microbiol 54 (2004) 1063-1075
285. Opdyke J.A., Kang J.G., and Storz G. GadY, a small-RNA regulator of acid response genes in Escherichia coli. J Bacteriol 186 (2004) 6698-6705
286. Takada A., Umitsuki G., Nagai K., and Wachi M. RNase E is required for induction of the glutamate-dependent acid resistance system in Escherichia coli. Biosci Biotechnol Biochem 71 (2007) 158-164
287. Krinke L., and Wulff D.L. RNase III-dependent hydrolysis of lcII-O gene mRNA mediated by l OOP antisense RNA. Genes Dev 4 (1990) 2223-2233
288. Krinke L., and Wulff D.L. OOP RNA, produced from multicopy plasmids, inhibits lambda cII gene expression through an RNase III-dependent mechanism. Genes Dev 1 (1987) 1005-1013
289. Duhring U., Axmann I.M., Hess W.R., and Wilde A. An internal antisense RNA regulates expression of the photosynthesis gene isiA. Proc Natl Acad Sci USA 103 (2006) 7054-7058
290. Waldbeser L.S., Chen Q., and Crosa J.H. Antisense RNA regulation of the fatB iron transport protein gene in Vibrio anguillarum. Mol Microbiol 17 (1995) 747-756
291. Blomberg P., Wagner E., and Nordström K. Control of replication of plasmid R1: The duplex between the antisense RNA, Cop A, and its target, Cop T, is processed specifically in vivo and in vitro by RNase III. EMBO J 9 (1990) 2331-2340
292. Gerdes K., Nielsen A., Thorsted P., and Wagner E.G. Mechanism of killer gene activation. Antisense RNA-dependent RNase III cleavage ensures rapid turn-over of the stable hok, srnB and pndA effector messenger RNAs. J Mol Biol 226 (1992) 637-649
293. Case C.C., Simons E.L., and Simons R.W. The IS10 transposase mRNA is destabilized during antisense RNA control. EMBO J 9 (1990) 1259-1266
294. Romeo T., Gong M., Liu M.Y., and Brun-Zinkernagel A.M. Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties. J Bacteriol 175 (1993) 4744-4755
295. Sabnis N.A., Yang H., and Romeo T. Pleiotropic regulation of central carbohydrate metabolism in Escherichia coli via the gene csrA. J Biol Chem 270 (1995) 29096-29104
296. Liu M.Y., Yang H., and Romeo T. The product of the pleiotropic Escherichia coli gene csrA modulates glycogen biosynthesis via effects on mRNA stability. J Bacteriol 177 (1995) 2663-2672
297. Liu M.Y., and Romeo T. The global regulator CsrA of Escherichia coli is a specific mRNA-binding protein. J Bacteriol 179 (1997) 4639-4642
298. Liu M.Y., Gui G., Wei B., Preston III J.F., Oakford L., Yuksel U., et al. The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. J Biol Chem 272 (1997) 17502-17510
299. Weilbacher T., Suzuki K., Dubey A.K., Wang X., Gudapaty S., Morozov I., et al. A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol Microbiol 48 (2003) 657-670
300. Babitzke P., and Romeo T. CsrB sRNA family: Sequestration of RNA-binding regulatory proteins. Curr Opin Microbiol 10 (2007) 156-163
301. Wei B.L., Brun-Zinkernagel A.M., Simecka J.W., Pruss B.M., Babitzke P., and Romeo T. Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli. Mol Microbiol 40 (2001) 245-256
302. Suzuki K., Babitzke P., Kushner S., and Romeo T. Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes Dev 20 (2006) 2605-2617
303. Heeb S., Kuehne S.A., Bycroft M., Crivii S., Allen M.D., Haas D., et al. Functional analysis of the posttranscriptional regulator RsmA reveals a novel RNA-binding site. J Mol Biol 355 (2006) 1026-1036
304. Pessi G., Williams F., Hindle Z., Heurlier K., Holden M.T., Camara M., et al. The global posttranscriptional regulator RsmA modulates production of virulence determinants and N-acylhomoserine lactones in Pseudomonas aeruginosa. J Bacteriol 183 (2001) 6676-6683
305. Dulebohn D., Choy J., Sundermeier T., Okan N., and Karzai A.W. Trans-translation: The tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay. Biochemistry 46 (2007) 4681-4693
306. Yamamoto Y., Sunohara T., Jojima K., Inada T., and Aiba H. SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs. RNA 9 (2003) 408-418
307. Mehta P., Richards J., and Karzai A.W. tmRNA determinants required for facilitating nonstop mRNA decay. RNA 12 (2006) 2187-2198
308. Sunohara T., Jojima K., Tagami H., Inada T., and Aiba H. Ribosome stalling during translation elongation induces cleavage of mRNA being translated in Escherichia coli. J Biol Chem 279 (2004) 15368-15375
309. Sunohara T., Jojima K., Yamamoto Y., Inada T., and Aiba H. Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA. RNA 10 (2004) 378-386
310. Hayes C.S., and Sauer R.T. Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol Cell 12 (2003) 903-911
311. Pedersen K., Zavialov A.V., Pavlov M.Y., Elf J., Gerdes K., and Ehrenberg M. The bacterial toxin relE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell 112 (2003) 131-140
312. Christensen S.K., and Gerdes K. RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA. Mol Microbiol 48 (2003) 1389-1400
313. Christensen S.K., Pedersen K., Hansen F.G., and Gerdes K. Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA. J Mol Biol 332 (2003) 809-819
314. Ivanova N., Pavlov M.Y., Felden B., and Ehrenberg M. Ribosome rescue by tmRNA requires truncated mRNAs. J Mol Biol 338 (2004) 33-41
315. Karzai A.W., and Sauer R.T. Protein factors associated with the ssrA-smpB tagging and ribosome rescue complex. Proc Natl Acad Sci USA 98 (2001) 3040-3044
316. Hong S.J., Tran Q.A., and Keiler K.C. Cell cycle-regulated degradation of tmRNA is controlled by RNase R and SmpB. Mol Microbiol 57 (2005) 565-575
317. Richards J., Mehta P., and Karzai A.W. RNase R degrades non-stop mRNAs selectively in an SmpB-tmRNA-dependent manner. Mol Microbiol 62 (2006) 1700-1712
318. Winkler W.C., Nahvi A., Roth A., Collins J.A., and Breaker R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428 (2004) 281-286
319. Barrick J.E., and Breaker R.R. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8 (2007) R239
320. Tucker B.J., and Breaker R.R. Riboswitches as versatile gene control elements. Curr Opin Struct Biol 15 (2005) 342-348
321. Mandal M., Boese B., Barrick J.E., Winkler W.C., and Breaker R.R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113 (2003) 577-586
322. Barrick J.E., Corbino K.A., Winkler W.C., Nahvi A., Mandal M., Collins J., et al. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci USA 101 (2004) 6421-6426
323. Collins J.A., Irnov I., Baker S., and Winkler W.C. Mechanism of mRNA destabilization by the glmS ribozyme. Genes Dev 21 (2007) 3356-3368
324. Altman S., Wesolowski D., Guerrier-Takada C., and Li Y. RNase P cleaves transient structures in some riboswitches. Proc Natl Acad Sci USA 102 (2005) 11284-11289
325. Deutscher M.P. Degradation of RNA in bacteria: Comparison of mRNA and stable RNA. Nucleic Acids Res 34 (2006) 659-666
326. Marcaida M.J., DePristo M.A., Chandran V., Carpousis A.J., and Luisi B.F. The RNA degradosome: Life in the fast lane of adaptive molecular evolution. Trends Biochem Sci 31 (2006) 359-365
327. Condon C. Maturation and degradation of RNA in bacteria. Curr Opin Microbiol 10 (2007) 271-278
328. Sousa S., Marchand I., and Dreyfus M. Autoregulation allows Escherichia coli RNase E to continuously adjust its synthesis to that of its substrates. Mol Microbiol 42 (2001) 867-878
329. Bardwell J., Régnier P., Chen S.M., Nakamura Y., Grunberg-Manago M., and Court D.L. Autoregulation of RNase III operon by mRNA processing. EMBO J 8 (1989) 3401-3407