12 Antisense RNAs in bacteria and their genetic elements

Advances in Genetics

Volumn 46, Issue , 2002, Pages 361-398

  Wagner, E Gerhart H ^a   Altuvia, Shoshy ^b   Romby, Pascale ^c  

^a UPPSALA UNIVERSITY   (Sweden)

^b HEBREW UNIVERSITY   (Israel)

^c INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; COMPLEMENTARY RNA;

BACTERIAL CHROMOSOME; BACTERIOPHAGE; BACTERIUM; BACTERIUM CONJUGATION; BIOLOGICAL MODEL; DNA REPLICATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MUTATION; PLASMID; REVIEW; TRANSPOSON;

BACTERIA; BACTERIOPHAGES; CHROMOSOMES, BACTERIAL; CONJUGATION, GENETIC; DNA REPLICATION; DNA TRANSPOSABLE ELEMENTS; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, GENETIC; MUTATION; PLASMIDS; RNA, ANTISENSE; RNA, BACTERIAL;

EID: 0036371843     PISSN: 00652660     EISSN: None     Source Type: Book Series    
DOI: 10.1016/s0065-2660(02)46013-0     Document Type: Review

References (214)

1. Aiba H. Matsuyama S. Mizuno T. 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
2. Altuvia S. Wagner E.G.H. Switching on and off with RNA Proc. Natl. Acad. Sci. USA 97 2000 9824 9826
3. Altuvia S. Weinstein-Fischer D. Zhang A. Postow L. Storz G. A small, stable RNA induced by oxidative stress: Role as a pleiotropic regulator and antimutator Cell 90 1997 43 53
4. Altuvia S. Zhang A. Argaman L. Tiwari A. Storz G. The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding EMBO J. 17 1998 6069 6075
5. Andersen J. Delihas N. micF RNA binds to the 5′ end of ompF mRNA and to a protein from Escherichia coli Biochemistry 29 1990 9249 9256
6. Andersen J. Forst S.A. Zhao K. Inouye M. Delihas N. The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli J. Biol. Chem. 264 1989 17961 17970
7. Argaman L. Altuvia S. fhlA repression by OxyS RNA: Kissing complex formation at two sites results in a stable antisense-target RNA complex J. Mol. Biol. 300 2000 1101 1112
8. Argaman L. Hershberg R. Vogel J. Bejerano G. Wagner E.G.H. Margalit H. Altuvia S. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli Curr. Biol. 11 2001 941 950
9. Arini A. Keller M.P. Arber W. An antisense RNA in IS30 regulates the translational expression of the transposase Biol. Chem. 378 1997 1421 1431
10. Asano K. Kato A. Moriwaki H. Hama C. Shiba K. Mizobuchi K. Positive and negative regulations of plasmid CoLIb-P9 repZ gene expression at the translational level J. Biol. Chem. 266 1991 3774 3781
11. Asano K. Mizobuchi K. Copy number control of IncIα plasmid ColIb-P9 by competition between pseudoknot formation and antisense RNA binding at a specific RNA site EMBO J. 17 1998 5201 5213
12. Asano K. Mizobuchi K. An RNA pseudoknot as the molecular switch for translation of the repZ gene encoding the replication initiator of IncIα plasmid ColIb-P9 J. Biol. Chem. 273 1998 11815 11825
13. Asano K. Mizobuchi K. Structural analysis of late intermediate complex formed between plasmid ColIb-P9 Inc RNA and its target RNA. How does a single antisense RNA repress translation of two genes at different rates? J. Biol. Chem. 275 2000 1269 1274
14. Asano K. Moriwaki H. Mizobuchi K. An induced mRNA secondary structure enhances repZ translation in plasmid ColIb-P9 J. Biol. Chem. 266 1991 24549 24556
15. Benito Y. Kolb F.A. Romby P. Lina G. Etienne J. Vandenesch F. Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression RNA 6 2000 668 679
16. Biere A.L. Citron M. Schuster H. Transcriptional control via translational repression by c4 antisense RNA of bacteriophages P1 and P7 Genes Dev. 6 1992 2409 2416
17. Bingle L.E. Thomas C.M. Regulatory circuits for plasmid survival Curr. Opin. Microbiol. 4 2001 194 200
18. Blomberg P. Engdahl H.M. Malmgren C. Romby P. Wagner E.G.H. Replication control of plasmid R1: Disruption of an inhibitory RNA structure that sequesters the repA ribosome-binding site permits tap -independent RepA synthesis Mol. Microbiol. 12 1994 49 60
19. Blomberg P. Nordström K. Wagner E.G.H. Replication control of plasmid R1: RepA synthesis is regulated by CopA RNA through inhibition of leader peptide translation EMBO J. 11 1992 2675 2683
20. Blomberg P. Wagner E.G.H. Nordström K. Control of replication of plasmid R1: The duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III EMBO J. 9 1990 2331 2340
21. Brady G. Frey J. Danbara H. Timmis K.N. Replication control mutations of plasmid R6-5 and their effects on interactions of the RNA-I control element with its target J. Bacteriol. 154 1983 429 436
22. Brantl S. Birch-Hirschfeld E. Behnke D. RepR protein expression on plasmid pIP501 is controlled by an antisense RNA-mediated transcription attenuation mechanism J. Bacteriol. 175 1993 4052 4061
23. Brantl S. Wagner E.G.H. Antisense RNA-mediated transcriptional attenuation occurs faster than stable antisense/target RNA pairing: An in vitro study of plasmid pIP501 EMBO J. 13 1994 3599 3607
24. Brantl S. Wagner E.G.H. An unusually long-lived antisense RNA in plasmid copy number control: In vivo RNAs encoded by the streptococcal plasmid pIP501 J. Mol. Biol. 255 1996 275 288
25. Brantl S. Wagner E.G.H. Dual function of the copR gene product of plasmid pIP501 J. Bacteriol. 179 1997 7016 7024
26. Brantl S. Wagner E.G.H. Antisense RNA-mediated transcriptional attenuation: An in vitro study of plasmid pT181 Mol. Microbiol. 35 2000 1469 1482
27. Brendel V. Perelson A.S. Quantitative model of ColE1 plasmid copy number control J. Mol. Biol. 229 1993 860 872
28. Brenner M. Tomizawa J. Quantitation of ColE1-encoded replication elements Proc. Natl. Acad. Sci. USA 88 1991 405 409
29. Briani F. Ghisotti D. Dehó G. Antisense RNA-dependent transcription termination sites that modulate lysogenic development of satellite phage P4 Mol. Microbiol. 36 2000 1124 1134
30. Case C.C. Roels S.M. Jensen P.D. Lee J. Kleckner N. Simons R.W. The unusual stability of the IS 10 anti-sense RNA is critical for its function and is determined by the structure of its stem-domain EMBO J. 8 1989 4297 4305
31. Case C.C. Simons E.L. Simons R.W. The IS 10 transposase mRNA is destabilized during antisense RNA control EMBO J. 9 1990 1259 1266
32. Chattoraj D.K. Control of plasmid DNA replication by iterons: No longer paradoxical Mol. Microbiol. 37 2000 467 476
33. Chen Q. Crosa J.H. Antisense RNA, fur , iron, and the regulation of iron transport genes in Vibrio anguillarum J. Biol. Chem. 271 1996 18885 18891
34. Chou J.H. Greenberg J.T. Demple B. Posttranscriptional repression of Escherichia coli OmpF protein in response to redox stress: Positive control of the micF antisense RNA by the soxRS locus J. Bacteriol. 175 1993 1026 1031
35. Citron M. Schuster H. The c4 repressors of bacteriophages P1 and P7 are antisense RNAs Cell 62 1990 591 598
36. Citron M. Schuster H. The c4 repressor of bacteriophage P1 is a processed 77 base antisense RNA Nucleic Acids Res. 20 1992 3085 3090
37. Condon C. Putzer H. Grunberg-Manago M. Processing of the leader mRNA plays a major role in the induction of thrS expression following threonine starvation in Bacillus subtilis Proc. Natl. Acad. Sci. USA 93 1996 6992 6997
38. Craig M.E. Crothers D.M. Doty P. Relaxation kinetics of dimer formation by self complementary oligonucleotides J. Mol. Biol. 62 1971 383 401
39. Csiszàr K. Houmard J. Damerval T. Tandeau de Marsac N. Transcriptional analysis of the cyanobacterial gvpABC operon in differentiated cells: Occurrence of an antisense RNA complementary to three overlapping transcripts Gene 60 1987 29 37
40. Dam Mikkelsen N. 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
41. del Solar G. Espinosa M. The copy number of plasmid pLS1 is regulated by two trans -acting plasmid products: The antisense RNA II and the repressor protein, RepA Mol. Microbiol. 6 1992 83 94
42. del Solar G. Espinosa M. Plasamid copy number control: An ever-growing story Mol. Microbiol. 37 2000 492 500
43. Delihas N. Regulation of gene expression by trans -encoded antisense RNAs Mol. Microbiol. 15 1995 411 414
44. Delihas N. Antisense micF RNA and 5′-UTR of the target ompF RNA: Phylogenetic conservation of primary and secondary structures Nucleic Acids Symp. Ser. 1997 33 35
45. Dong X. Womble D.D. Luckow V.A. Rownd R.H. Regulation of transcription of the repA1 gene in the replication control region of IncFII plasmid NR1 by gene dosage of the repA2 transcription repressor protein J. Bacteriol. 161 1985 544 551
46. Eguchi Y. Tomizawa J. Complex formed by complementary RNA stem-loops and its stabilization by a protein: Function of CoIE1 Rom protein Cell 60 1990 199 209
47. Eguchi Y. Tomizawa J. Complexes formed by complementary RNA stem-loops. Their formations, structures and interaction with ColE1 Rom protein J. Mol. Biol. 220 1991 831 842
48. Ehrenberg M. Hypothesis: Hypersensitive plasmid copy number control for ColE1 Biophys. J. 70 1996 135 145
49. Ehrenberg M. Sverredal A. A model for copy number control of the plasmid R1 J. Mol. Biol. 246 1995 472 485
50. Ferrario M. Ernsting B.R. Borst D.W. Wiese D.E.n. Blumenthal R.M. Matthews R.G. The leucine-responsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF J. Bacteriol. 177 1995 103 113
51. Fierro-Monti I.P. Reid S.J. Woods D.R. Differential expression of a Clostridium acetobutylicum antisense RNA: Implications for regulation of glutamine synthetase J. Bacteriol. 174 1992 7642 7647
52. Firth N. Ippen-Ihler K. Skurray R.A. Structure and function of the F factor and mechanism of conjugation Neidhard F.C. Curtiss R. III Ingraham J.L. Lin E.C.C. Low K.B. Magasanik B. Reznikoff W.S. Schaechter M. Umbarger H.E. Escherichia coli and Salmonella vol. 2 1996 ASM Press Washington, DC 2377 2401
53. Forti F. Sabbattini P. Sironi G. Zangrossi S. Dehò G. Ghisotti D. Immunity determinant of phage-plasmid P4 is a short processed RNA J. Mol. Biol. 249 1995 869 878
54. Franch T. Gerdes K. Programmed cell death in bacteria: Translational repression by mRNA end-pairing Mol. Microbiol. 21 1996 1049 1060
55. Franch T. Gerdes K. U-turns and regulatory RNAs Curr. Opin. Microbiol. 3 2000 159 164
56. Franch T. Gultyaev A.P. Gerdes K. Programmed cell death by hok/sok of plasmid R1: Processing at the hok mRNA 3′-end triggers structural rearrangements that allow translation and antisense RNA binding J. Mol. Biol. 273 1997 38 51
57. Franch T. Petersen M. Wagner E.G.H. Jacobsen J.P. Gerdes K. Antisense RNA regulation in prokaryotes: Rapid RNA/RNA interaction facilitated by a general U-turn loop structure J. Mol. Biol. 294 1999 1115 1125
58. Frost L. Lee S. Yanchar N. Paranchych W. finP and fisO mutations in FinP anti-sense RNA suggest a model for FinOP action in the repression of bacterial conjugation by the Flac plasmid JCFL0 Mol. Gen. Genet. 218 1989 152 160
59. Galli D.M. Leblanc D.J. Transcriptional analysis of rolling circle replicating plasmid pVT736-1: Evidence for replication control by antisense RNA J. Bacteriol. 177 1995 4474 4480
60. Gerdes K. Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress J. Bacteriol. 182 2000 561 572
61. Gerdes K. Gultyaev A.P. Franch T. Pedersen K. Mikkelsen N.D. Antisense RNA-regulated programmed cell death Annu. Rev. Genet. 31 1997 1 331
62. Gerdes K. Rasmussen P.B. Molin S. Unique type of plasmid maintenance function: Postsegregational killing of plasmid-free cells Proc. Natl. Acad. Sci. USA 83 1986 3116 3120
63. Ghetu A.F. Gubbins M.J. Oikawa K. Kay C.M. Frost L.S. Glover J.N. The FinO repressor of bacterial conjugation contains two RNA binding regions Biochemistry 38 1999 14036 14044
64. Gidrol X. Farr S. Interaction of a redox-sensitive DNA-binding factor with the 5′-flanking region of the micF gene in Escherichia coli Mol. Microbiol. 10 1993 877 884
65. Givskov M. Molin S. Copy mutants of plasmid R1: Effects of base pair substitutions in the copA gene on the replication control system Mol. Gen. Genet. 194 1984 286 292
66. Greenfield T.J. Weaver K.E. Antisense RNA regulation of the pAD1 par post-segregational killing system requires interaction at the 5′ and 3′ ends of the RNAs Mol. Microbiol. 37 2000 661 670
67. Grosjean H. Soll D.G. Crothers D.M. Studies of the complex between transfer RNAs with complementary anticodons. I. Origins of enhanced affinity between complementary triplets J. Mol. Biol. 103 1976 499 519
68. Grundy F.J. Henkin T.M. Conservation of a transcription antitermination mechanism in aminoacyl-tRNA synthetase and amino acid biosynthesis genes in gram-positive bacteria J. Mol. Biol. 235 1994 798 804
69. Hama C. Takizawa T. Moriwaki H. Mizobuchi K. Role of leader peptide synthesis in repZ gene expression of the ColIb-P9 plasmid J. Biol. Chem. 265 1990 10666 10673
70. Henkin T.M. tRNA-directed transcription antitermination Mol. Microbiol. 13 1994 381 387
71. Hildebrandt M. Nellen W. Differential antisense transcription from the Dictyostelium EB4 gene locus: Implications on antisense-mediated regulation of mRNA stability Cell 69 1992 197 204
72. Hiraga S. Chromosome and plasmid partition in Escherichia coli Annu. Rev. Biochem. 61 1992 283 306
73. Hjalt T. Wagner E.G.H. The effect of loop size in antisense and target RNAs on the efficiency of antisense RNA control Nucleic Acids Res. 20 1992 6723 6732
74. Hjalt T.A. Wagner E.G.H. Bulged-out nucleotides in an antisense RNA are required for rapid target RNA binding in vitro and inhibition in vivo Nucleic Acids Res. 23 1995 580 587
75. Itoh T. Tomizawa J. Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H Proc. Natl. Acad. Sci. USA 77 1980 2450 2454
76. Itoh T. Tomizawa J. Purification of ribonuclease H as a factor required for initiation of in vitro Co1E1 DNA replication Nucleic Acids Res. 10 1982 5949 5965
77. Jacques J.P. Susskind M.M. Use of electrophoretic mobility to determine the secondary structure of a small antisense RNA Nucleic Acids Res. 19 1991 2971 2977
78. Jain C. IS 10 antisense control in vivo is affected by mutations throughout the region of complementarity between the interacting RNAs J. Mol. Biol. 246 1995 585 594
79. Janssen P.J. Jones D.T. Woods D.R. Studies on Clostridium acetobutylicum glnA promoters and antisense RNA Mol. Microbiol. 4 1990 1575 1583
80. Jensen R.B. Gerdes K. Programmed cell death in bacteria: Proteic plasmid stabilization systems Mol. Microbiol. 17 1995 205 210
81. Jerome L.J. van Biesen T. Frost L.S. Degradation of FinP antisense RNA from F-like plasmids: The RNA-binding protein, FinO, protects FinP from ribonuclease E J. Mol. Biol. 285 1999 1457 1473
82. Kim K. Meyer R.J. Copy-number of broad host-range plasmid R1162 is regulated by a small RNA Nucleic Acids Res. 14 1986 8027 8046
83. Kittle J.D. Simons R.W. Lee J. Kleckner N. Insertion sequence IS 10 anti-sense pairing initiates by an interaction between the 5′ end of the target RNA and a loop in the anti-sense RNA J. Mol. Biol. 210 1989 561 572
84. Kolb F.A. Engdahl H.M. Slagter-Jäger J.G. Ehresmann B. Ehresmann C. Westhof E. Wagner E.G.H. Romby P. Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA EMBO J. 19 2000 5905 5915
85. Kolb F.A. Malmgren C. Westhof E. Ehresmann C. Ehresmann B. Wagner E.G.H. Romby P. An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment RNA 6 2000 311 324
86. Kolb F.A. Westhof E. Ehresmann B. Ehresmann C. Wagner E.G.H. Romby P. Four-way junctions in antisense RNA-mRNA complexes involved in plasmid replication control: A common theme? J. Mol. Biol. 309 2001 605 614
87. Koraimann G. Koraimann C. Koronakis V. Schlager S. Högenauer G. Repression and derepression of conjugation of plasmid R1 by wild-type and mutated finP antisense RNA Mol. Microbiol. 5 1991 77 87
88. Koraimann G. Teferle K. Markolin G. Woger W. Högenauer G. The FinOP repressor system of plasmid R1: Analysis of the antisense RNA control of traJ expression and conjugative DNA transfer Mol. Microbiol. 21 1996 811 821
89. Krinke L. Mahoney M. Wulff D.L. The role of the OOP antisense RNA in coliphage lambda development Mol. Microbiol. 5 1991 1265 1272
90. Krinke L. 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
91. Krinke L. Wulff D.L. RNase III-dependent hydrolysis of lambda cII-O gene mRNA mediated by lambda OOP antisense RNA Genes Dev. 4 1990 2223 2233
92. Lacatena R.M. Cesareni G. Base pairing of RNA I with its complementary sequence in the primer precursor inhibits ColE1 replication Nature 294 1981 623 626
93. Lacatena R.M. Cesareni G. Interaction between RNA1 and the primer precursor in the regulation of Co1E1 replication J. Mol. Biol. 170 1983 635 650
94. Le Chatelier E. Ehrlich S.D. Janniere L. Countertranscript-driven attenuation system of the pAMβ1 repE gene Mol. Microbiol. 20 1996 1099 1112
95. Lease R.A. 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
96. Lease R.A. Belfort M. Riboregulation by DsrA RNA: trans -actions for global economy Mol. Microbiol. 38 2000 667 672
97. Lease R.A. Cusick M.E. Belfort M. Riboregulation in Escherichia coli : DsrA RNA acts by RNA:RNA interactions at multiple loci Proc. Natl. Acad. Sci. USA 95 1998 12456 12461
98. Lee A.J. Crothers D.M. The solution structure of an RNA loop-loop complex: The ColE1 inverted loop sequence Structure 6 1998 993 1005
99. Liao S.M. Wu T.H. Chiang C.H. Susskind M.M. McClure W.R. Control of gene expression in bacteriophage P22 by a small antisense RNA. I. Characterization in vitro of the Psar promoter and the sar RNA transcript Genes Dev. 1 1987 197 203
100. Light J. Molin S. The sites of action of the two copy number control functions of plasmid R1 Mol. Gen. Genet. 187 1982 486 493
101. Lin-Chao S. Cohen S.N. The rate of processing and degradation of antisense RNAI regulates the replication of ColE1-type plasmids in vivo Cell 65 1991 1233 1242
102. Ma C. Simons R.W. The IS 10 antisense RNA blocks ribosome binding at the transposase translation initiation site EMBO J. 9 1990 1267 1274
103. Majdalani N. Cunning C. Sledjeski D. Elliott T. 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
104. Malmgren C. Engdahl H.M. Romby P. Wagner E.G.H. An antisense/target RNA duplex or a strong intramolecular RNA structure 5′ of a translation initiation signal blocks ribosome binding: The case of plasmid R1 RNA 2 1996 1022 1032
105. Malmgren C. Wagner E.G.H. Ehresmann C. Ehresmann B. Romby P. Antisense RNA control of plasmid R1 replication. The dominant product of the antisense RNA-mRNA binding is not a full RNA duplex J. Biol. Chem. 272 1997 12508 12512
106. Mamat U. Rietschel E.T. Schmidt G. Repression of lipopolysaccharide biosynthesis in Escherichia coli by an antisense RNA of Acetobacter methanolicus phage Acm1 Mol. Microbiol. 15 1995 1115 1125
107. Marino J.P. Gregorian R.S.J. Csankovszki G. Crothers D.M. Bent helix formation between RNA hairpins with complementary loops Science 268 1995 1448 1454
108. Masukata H. Tomizawa J. Effects of point mutations on formation and structure of the RNA primer for ColE1 DNA replication Cell 36 1984 513 522
109. Masukata H. Tomizawa J. Control of primer formation for ColE1 plasmid replication: Conformational change of the primer transcript Cell 44 1986 125 136
110. Masukata H. Tomizawa J. A mechanism of formation of a persistent hybrid between elongating RNA and template DNA Cell 62 1990 331 338
111. Morfeldt E. Taylor D. von Gabain A. Arvidson S. Activation of alpha-toxin translation in Staphylococcus aureus by the trans -encoded antisense RNA, RNAIII EMBO J. 14 1995 4569 4577
112. Muesing M. Tamm J. Shepard H.M. Polisky B. A single base-pair alteration is responsible for the DNA overproduction phenotype of a plasmid copy-number mutant Cell 24 1981 235 242
113. Nielsen A.K. Thorsted P. Thisted T. Wagner E.G.H. Gerdes K. The rifampicin-inducible genes srnB from F and pnd from R483 are regulated by antisense RNAs and mediate plasmid maintenance by killing of plasmid-free segregants Mol. Microbiol. 5 1991 1961 1973
114. Nordgren S. Slagter-Jäger J.G. Wagner E.G.H. Real time kinetic studies of interaction between folded antisense and target RNAs using surface plasmon resonance J. Mol. Biol. 310 2001 1125 1134
115. Nordström K. Aagaard-Hansen H. Maintenance of bacterial plasmids: Comparison of theoretical calculations and experiments with plasmid R1 in Escherichia coli Mol. Gen. Genet. 197 1984 1 7
116. Nordström K. Wagner E.G.H. Kinetic aspects of control of plasmid replication by antisense RNA Trends Biochem. Sci. 19 1994 294 300
117. Novick R.P. Iordanescu S. Projan S.J. Kornblum J. Edelman I. pT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator Cell 59 1989 395 404
118. Novick R.P. Ross H.F. Projan S.J. Kornblum J. Kreiswirth B. Moghazeh S. Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule EMBO J. 12 1993 3967 3975
119. Öhman M. Wagner E.G.H. Secondary structure analysis of the RepA mRNA leader transcript involved in control of replication of plasmid R1 Nucleic Acids Res. 17 1989 2557 2579
120. Patient M.E. Summers D.K. ColE1 multimer formation triggers inhibition of Escherichia coli cell division Mol. Microbiol. 9 1993 1089 1095
121. Paulsson J. Berg O.G. Ehrenberg M. Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation Proc. Natl. Acad. Sci. USA 97 2000 7148 7153
122. Paulsson J. Ehrenberg M. Trade-off between segregational stability and metabolic burden: A mathematical model of plasmid ColE1 replication control J. Mol. Biol. 279 1998 73 88
123. Paulsson J. Ehrenberg M. Molecular clocks reduce plasmid loss rates: The R1 case J. Mol. Biol. 297 2000 179 192
124. Pedersen K. Gerdes K. Multiple hok genes on the chromosome of Escherichia coli Mol. Microbiol. 32 1999 1090 1102
125. Pepe C.M. Maslesa-Galic S. Simons R.W. Decay of the IS 10 antisense RNA by 3′ exoribonucleases: evidence that RNase II stabilizes RNA-OUT against PNPase attack Mol. Microbiol. 13 1994 1133 1142
126. Persson C. Wagner E.G.H. Nordström K. Control of replication of plasmid R1: Kinetics of in vitro interaction between the antisense RNA, CopA, and its target, CopT EMBO J. 7 1988 3279 3288
127. Persson C. Wagner E.G.H. Nordström K. Control of replication of plasmid R1: Formation of an initial transient complex is rate-limiting for antisense RNA-target RNA pairing EMBO J. 9 1990 3777 3785
128. Persson C. Wagner E.G.H. Nordström K. Control of replication of plasmid R1: Structures and sequences of the antisense RNA, CopA, required for its binding to the target RNA, CopT EMBO J. 9 1990 3767 3775
129. Piazza F. Zappone M. Sana M. Briani F. Deho G. Polynucleotide phosphorylase of Escherichia coli is required for the establishment of bacteriophage P4 immunity J. Bacteriol. 178 1996 5513 5521
130. Polisky B. Tamm J. Fitzwater T. Construction of Co1E1 RNA1 mutants and analysis of their function in vivo Basic Life Sci. 30 1985 321 333
131. Polisky B. Zhang X.Y. Fitzwater T. Mutations affecting primer RNA interaction with the replication repressor RNA I in plasmid CoIE1: Potential RNA folding pathway mutants EMBO J. 9 1990 295 304
132. Pörschke D. Eigen M. Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic-oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH J. Mol. Biol. 62 1971 361 381
133. Poulsen L.K. Refn A. Molin S. Andersson P. The gef gene from Escherichia coli is regulated at the level of translation Mol. Microbiol. 5 1991 1639 1648
134. Praszkier J. Bird P. Nikoletti S. Pittard J. Role of countertranscript RNA in the copy number control system of an IncB miniplasmid J. Bacteriol. 171 1989 5056 5064
135. Praszkier J. Wei T. Siemering K. Pittard J. Comparative analysis of the replication regions of IncB, IncK, and IncZ plasmids J. Bacteriol. 173 1991 2393 2397
136. Praszkier J. Wilson I.W. Pittard A.J. Mutations affecting translational coupling between the rep genes of an IncB miniplasmid J. Bacteriol. 174 1992 2376 2383
137. Predki P.F. Nayak L.M. Gottlieb M.B. Regan L. Dissecting RNA-protein interactions: RNA-RNA recognition by Rop Cell 80 1995 41 50
138. Pritchard R.H. Barth P.T. Collins J. Control of DNA synthesis in bacteria Symp. Soc. Gen. Microbiol. 19 1969 263 297
139. Putzer H. Grunberg-Manago M. Springer M. Bacterial aminoacyl-tRNA synthetases: Genes and regulation of expression Söll D. RajBhandari U. tRNA: Structure, Biosynthesis and Function 1995 ASM Press Washington, DC 293 333
140. Ramani N. Hedeshian M. Freundlich M. micF antisense RNA has a major role in osmoregulation of OmpF in Escherichia coli J. Bacteriol. 176 1994 5005 5010
141. Ranade K. Poteete A.R. Superinfection exclusion ( sieB ) genes of bacteriophages P22 and lambda J. Bacteriol. 175 1993 4712 4718
142. Ranade K. Poteete A.R. A switch in translation mediated by an antisense RNA Genes Dev. 7 1993 1498 1507
143. Reinhart B.J. Slack F.J. Basson M. Pasquinelli A.E. Bettinger J.C. Rougvie A.E. Horvitz H.R. Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature 403 2000 901 906
144. Riedel H.D. Heinrich J. Schuster H. Cloning, expression, and characterization of the icd gene in the immI operon of bacteriophage P1 J. Bacteriol. 175 1993 2833 2838
145. Riise E. Stougaard P. Bindslev B. Nordström K. Molin S. Molecular cloning and functional characterization of a copy number control gene ( copB ) of plasmid R1 J. Bacteriol. 551 1982 1136 1145
146. Rosen J. Ryder T. Ohtsubo H. Ohtsubo E. Role of RNA transcripts in replication incompatibility and copy number control in antibiotic resistance plasmid derivatives Nature 290 1981 794 797
147. Sabbattini P. Forti F. Ghisotti D. Dehò G. Control of transcription termination by an RNA factor in bacteriophage P4 immunity: Identification of the target sites J. Bacteriol. 177 1995 1425 1434
148. Sabbattini P. Six E. Zangrossi S. Briani F. Ghisotti D. Dehò G. Immunity specificity determinants in the P4-like retronphage phi R73 Virology 216 1996 389 396
149. Salinas P.C. Waldbeser L.S. Crosa J.H. Regulation of the expression of bacterial iron transport genes: Possible role of an antisense RNA as a repressor Gene 123 1993 33 38
150. Schaefer K.L. McClure W.R. Antisense RNA control of gene expression in bacteriophage P22. I. Structures of sar RNA and its target, ant mRNA RNA 3 1997 141 156
151. Schaefer K.L. McClure W.R. Antisense RNA control of gene expression in bacteriophage P22. II. Kinetic mechanism and cation specificity of the pairing reaction RNA 3 1997 157 174
152. Schmidt M. Zheng P. Delihas N. Secondary structures of Escherichia coli antisense micF RNA, the 5′-end of the target ompF mRNA, and the RNA/RNA duplex Biochemistry 34 1995 3621 3631
153. Sharpe M.E. Chatwin H.M. Macpherson C. Withers H.L. Summers D.K. Analysis of the CoIE1 stability determinant Rcd Microbiology 145 1999 2135 2144
154. Shiba K. Mizobuchi K. Posttranscriptional control of plasmid ColIb-P9 repZ gene expression by a small RNA J. Bacteriol. 172 1990 1992 1997
155. Siemering K.R. Praszkier J. Pittard A.J. Interaction between the antisense and target RNAs involved in the regulation of IncB plasmid replication J. Bacteriol. 175 1993 2895 2906
156. Siemering K.R. Praszkier J. Pittard A.J. Mechanism of binding of the antisense and target RNAs involved in the regulation of IncB plasmid replication J. Bacteriol. 176 1994 2677 2688
157. Simons R.W. Kleckner N. Translational control of IS 10 transposition Cell 34 1983 683 691
158. Sledjeski D. Gottesman S. A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli Proc. Natl. Acad. Sci. USA 92 1995 2003 2007
159. Sledjeski D.D. Gupta A. Gottesman S. The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli EMBO J. 15 1996 3993 4000
160. Söderbom F. Binnie U. Masters M. Wagner E.G.H. Regulation of plasmid R1 replication: PcnB and RNase E expedite the decay of the antisense RNA, CopA Mol. Microbiol. 26 1997 493 504
161. Söderbom F. Wagner E.G.H. Degradation pathway of CopA, the antisense RNA that controls replication of plasmid R1 Microbiology 144 1998 1907 1917
162. Stolt P. Zillig W. Antisense RNA mediates transcriptional processing in an archaebacterium, indicating a novel kind of RNase activity Mol. Microbiol. 7 1993 875 882
163. Stolt P. Zillig W. Structure specific ds/ss-RNase activity in the extreme halophile Halobacterium salinarium Nucleic Acids Res. 21 1993 5595 5599
164. Stougaard P. Molin S. Nordström K. RNAs involved in copy-number control and incompatibility of plasmid R1 Proc. Natl. Acad. Sci. USA 78 1981 6008 6012
165. Sugiyama T. Itoh T. Control of ColE2 DNA replication: In vitro binding of the antisense RNA to the Rep mRNA Nucleic Acids Res. 21 1993 5972 5977
166. Summers D.K. Beton C.W. Withers H.L. Multicopy plasmid instability: The dimer catastrophe hypothesis Mol. Microbiol. 8 1993 1031 1038
167. Suzuki T. Ueguchi C. Mizuno T. H-NS regulates OmpF expression through micF antisense RNA in Escherichia coli J. Bacteriol. 178 1996 3650 3653
168. Takechi S. Yasueda H. Itoh T. Control of ColE2 plasmid replication: Regulation of Rep expression by a plasmid-coded antisense RNA Mol. Gen. Genet. 244 1994 49 56
169. Tamm J. Polisky B. Structural analysis of RNA molecules involved in plasmid copy number control Nucleic Acids Res. 11 1983 6381 6397
170. Tegmark K. Morfeldt E. Arvidson S. Regulation of agr -dependent virulence genes in Staphylococcus aureus by RNAIII from coagulase-negative staphylococci J. Bacteriol. 180 1998 3181 3186
171. Tetart F. Bouche J.P. Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules Mol. Microbiol. 6 1992 615 620
172. Thisted T. Gerdes K. Mechanism of post-segregational killing by the hok/sok system of plasmid R1. Sok antisense RNA regulates hok gene expression indirectly through the overlapping mok gene J. Mol. Biol. 223 1992 41 54
173. Thisted T. Sorensen N.S. Gerdes K. Mechanism of post-segregational killing: Secondary structure analysis of the entire Hok mRNA from plasmid R1 suggests a fold-back structure that prevents translation and antisense RNA binding J. Mol. Biol. 247 1995 859 873
174. Thisted T. Sørensen N.S. Wagner E.G.H. Gerdes K. Mechanism of post-segregational killing: Sok antisense RNA interacts with Hok mRNA via its 5′-end single-stranded leader and competes with the 3-end of Hok mRNA for binding to the mok translational initiation region EMBO J. 13 1994 1960 1968
175. Tomizawa J. Control of ColE1 plasmid replication: The process of binding of RNA I to the primer transcript Cell 38 1984 861 870
176. Tomizawa J. Control of ColE1 plasmid replication: Initial interaction of RNA I and the an unstable complex formed by RNA I and RNA II Cell 40 1985 527 535
177. Tomizawa J. Control of ColE1 plasmid replication: Binding of RNA I to RNA II and inhibition of primer formation Cell 47 1986 89 97
178. Tomizawa J. Control of ColE1 plasmid replication. Interaction of Rom protein with an unstable complex formed by RNA I and RNA II J. Mol. Biol. 212 1990 695 708
179. Tomizawa J. Control of ColE1 plasmid replication. Intermediates in the binding of RNA I and RNA II J. Mol. Biol. 212 1990 683 694
180. Tomizawa J. Itoh T. Plasmid ColE1 incompatibility determined by interaction of RNA I with primer transcript Proc. Natl. Acad. Sci. USA 78 1981 6096 6100
181. Tomizawa J. Itoh T. Selzer G. Som T. Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA Proc. Natl. Acad. Sci. USA 78 1981 1421 1425
182. Twigg A.J. Sherratt D. Trans-complementable copy-number mutants of plasmid ColE1 Nature 283 1980 216 218
183. Uhlin B.E. Nordström K. A runaway-replication mutant of plasmid R1drd-19: Temperature-dependent loss of copy number control Mol. Gen. Genet. 165 1978 167 179
184. van Biesen T. Frost L.S. The FinO protein of IncF plasmids binds FinP antisense RNA and its target, traJ mRNA, and promotes duplex formation Mol. Microbiol. 14 1994 427 436
185. van Biesen T. Söderbom F. Wagner E.G.H. Frost L.S. Structural and functional analyses of the FinP antisense RNA regulatory system of the F conjugative plasmid Mol. Microbiol. 10 1993 35 43
186. Wagner E.G.H. Blomberg P. Nordström K. Replication control in plasmid R1: Duplex formation between the antisense RNA, CopA, and its target, CopT, is not required for inhibition of RepA synthesis EMBO J. 11 1992 1195 1203
187. Wagner E.G.H. Brantl S. Kissing and RNA stability in antisense control of plasmid replication Trends Biochem. Sci. 23 1998 451 454
188. Wagner E.G.H. Nordström K. Structural analysis of an RNA molecule involved in replication control of plasmid R1 Nucleic Acids Res. 14 1986 2523 2538
189. Wagner E.G.H. Simons R.W. Antisense RNA control in bacteria, phages, and plasmids Annu. Rev. Microbiol. 48 1994 713 742
190. Waldbeser L.S. Chen Q. Crosa J.H. Antisense RNA regulation of the fatB iron transport protein gene in Vibrio anguillarum Mol. Microbiol. 17 1995 747 756
191. Warnecke J.M. Nitschke M. Moolenaar C.E. Rietschel E.T. Hartmann R.K. Mamat U. The 5′-proximal hairpin loop of lbi RNA is a key structural element in repression of D-galactan II biosynthesis in Klebsiella pneumoniae serotype O1 Mol. Microbiol. 36 2000 697 709
192. Wassarman K.M. Repoila F. Rosenow C. Storz G. Gottesman S. Identification of novel small RNAs using comparative genomics and microarrays Genes Dev. 15 2001 1637 1651
193. Wassarman K.M. Zhang A. Storz G. Small RNAs in Escherichia coli Trends Microbiol. 7 1999 37 45
194. Wightman B. Ha I. Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans Cell 75 1993 855 862
195. Wilson I.W. Praszkier J. Pittard A.J. Mutations affecting pseudoknot control of the replication of B group plasmids J. Bacteriol. 175 1993 6476 6483
196. Wilson I.W. Siemering K.R. Praszkier J. Pittard A.J. Importance of structural differences between complementary RNA molecules to control of replication of an IncB plasmid J. Bacteriol. 179 1997 742 753
197. Womble D.D. Dong X. Luckow V.A. Wu R.P. Rownd R.H. Analysis of the individual regulatory components of the IncFII plasmid replication control system J. Bacteriol. 161 1985 534 543
198. Wong E.M. Polisky B. Alternative conformations of the ColE1 replication primer modulate its interaction with RNA I Cell 42 1985 959 966
199. Wrobel B. Herman-Antosiewicz A. Szalewska-Palasz S. Wegrzyn G. Polyadenylation of oop RNA in the regulation of bacteriophage lambda development Gene 212 1998 57 65
200. Wu R. Wang X. Womble D.D. Rownd R.H. Expression of the repA1 gene of IncFII plasmid NR1 is translationally coupled to expression of an overlapping leader peptide J. Bacteriol. 174 1992 7620 7628
201. Wu R.P. Womble D.D. Rownd R.H. Incompatibility mutants of IncFII plasmid NR1 and their effect on replication control J. Bacteriol. 163 1985 973 982
202. Wu T.H. Liao S.M. McClure W.R. Susskind M.M. Control of gene expression in bacteriophage P22 by a small antisense RNA. II. Characterization of mutants defective in repression Genes Dev. 1 1987 204 212
203. Xu F. Lin-Chao S. Cohen S.N. The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates Proc. Natl. Acad. Sci. USA 90 1993 6756 6760
204. Zeiler B. Simons R.W. Antisense RNA structure and function Simons R.W. Grunberg-Manago M. RNA Structure and Function 1998 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY 437 464
205. Zhang A. Altuvia S. Storz G. The novel oxyS RNA regulates expression of the sigma S subunit of Escherichia coli RNA polymerase Nucleic Acids Symp. Ser. 1997 27 28
206. Zhang A. Altuvia S. Tiwari A. Argaman L. Hengge-Aronis R. Storz G. The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein EMBO J. 17 1998 6061 6068
207. Asano K. Niimi T. Yokoyama S. Mizobuchi K. Structural basis for binding of the plasmid ColIb-P9 antisense Inc RNA to its target RNA with the 5′-rUUGGCG-3′ motif in the loop sequence J. Biol. Chem. 273 1998 11826 11838
208. del Solar G. Acebo P. Espinosa M. Replication control of plasmid pLS1: Efficient regulation of plasmid copy number is exerted by the combined action of two plasmid components, CopG and RNA II Mol. Microbiol. 18 1995 913 924
209. Eguchi Y. Itoh T. Tomizawa J. Antisense RNA Annu. Rev. Biochem. 60 1991 631 652
210. Gerdes K. Moller-Jensen J. Bugge Jensen R. Plasmid and chromosome partitioning: Surprises from phylogeny Mol. Microbiol. 37 2000 455 466
211. Greenfield T.J. Ehli E. Kirshenmann T. Franch T. Gerdes K. Weaver K.E. The antisense RNA of the par locus of pAD1 regulates the expression of a 33-amino-acid toxic peptide by an unusual mechanism Mol. Microbiol. 37 2000 652 660
212. Hama C. Takizawa T. Moriwaki H. Urasaki Y. Mizobuchi K. Organization of the replication control region of plasmid ColIb-P9 J. Bacteriol. 172 1990 1983 1991
213. Nordström K. Molin S. Light J. Control of replication of bacterial plasmids: Genetics, molecular biology, and physiology of the plasmid R1 system Plasmid 12 1984 71 90
214. Paulsson J. Nordström K. Ehrenberg M. Requirements for rapid plasmid ColE1 copy number adjustments: A mathematical model of inhibition modes and RNA turnover rates Plasmid 39 1998 215 234