Divergently overlapping cis-encoded antisense RNA regulating toxin-antitoxin systems from E. coli

References

• Mattick JS, Makunin IV. Small regulatory RNAs in mammals. Hum Mol Genet 2005; 14:Spec No 1 R121 - 32; http://dx.doi.org/10.1093/hmg/ddi101; PMID: 15809264
   PubMed Web of Science ®Google Scholar
• Storz G, Altuvia S, Wassarman KM. An abundance of RNA regulators. Annu Rev Biochem 2005; 74:199 - 217; http://dx.doi.org/10.1146/annurev.biochem.74.082803.133136; PMID: 15952886
   PubMed Web of Science ®Google Scholar
• Storz G, Gottesman S. Versatile roles of small RNA regulators in bacteria. The RNA world 3rd ed 2006; 567-94.
   Google Scholar
• Beisel CL, Storz G. Base pairing small RNAs and their roles in global regulatory networks. FEMS Microbiol Rev 2010; 34:866 - 82; PMID: 20662934
   PubMed Web of Science ®Google Scholar
• Aiba H. Mechanism of RNA silencing by Hfq-binding small RNAs. Curr Opin Microbiol 2007; 10:134 - 9; http://dx.doi.org/10.1016/j.mib.2007.03.010; PMID: 17383928
   PubMed Web of Science ®Google Scholar
• Gottesman S, Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011; 3:a003798; http://dx.doi.org/10.1101/cshperspect.a003798; PMID: 20980440
   PubMed Web of Science ®Google Scholar
• Wagner EG, Altuvia S, Romby P. Antisense RNAs in bacteria and their genetic elements. Adv Genet 2002; 46:361 - 98; http://dx.doi.org/10.1016/S0065-2660(02)46013-0; PMID: 11931231
   PubMed Web of Science ®Google Scholar
• Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 2007; 10:102 - 9; http://dx.doi.org/10.1016/j.mib.2007.03.012; PMID: 17387036
   PubMed Web of Science ®Google Scholar
• Tomizawa J, Itoh T, Selzer G, Som T. Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA. Proc Natl Acad Sci U S A 1981; 78:1421 - 5; http://dx.doi.org/10.1073/pnas.78.3.1421; PMID: 6165011
   PubMed Web of Science ®Google Scholar
• Gerdes K, Gultyaev AP, Franch T, Pedersen K, Mikkelsen ND. Antisense RNA-regulated programmed cell death. Annu Rev Genet 1997; 31:1 - 31; http://dx.doi.org/10.1146/annurev.genet.31.1.1; PMID: 9442888
   PubMed Web of Science ®Google Scholar
• Gerdes K, Rasmussen PB, Molin S. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc Natl Acad Sci U S A 1986; 83:3116 - 20; http://dx.doi.org/10.1073/pnas.83.10.3116; PMID: 3517851
   PubMed Web of Science ®Google Scholar
• Yarmolinsky MB. Programmed cell death in bacterial populations. Science 1995; 267:836 - 7; http://dx.doi.org/10.1126/science.7846528; PMID: 7846528
   PubMed Web of Science ®Google Scholar
• Pedersen K, Gerdes K. Multiple hok genes on the chromosome of Escherichia coli. Mol Microbiol 1999; 32:1090 - 102; http://dx.doi.org/10.1046/j.1365-2958.1999.01431.x; PMID: 10361310
   PubMed Web of Science ®Google Scholar
• Kawano M, Oshima T, Kasai H, Mori H. Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli. Mol Microbiol 2002; 45:333 - 49; http://dx.doi.org/10.1046/j.1365-2958.2002.03042.x; PMID: 12123448
   PubMed Web of Science ®Google Scholar
• Faridani OR, Nikravesh A, Pandey DP, Gerdes K, Good L. Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli. Nucleic Acids Res 2006; 34:5915 - 22; http://dx.doi.org/10.1093/nar/gkl750; PMID: 17065468
   PubMed Web of Science ®Google Scholar
• Gerdes K, Wagner EG. RNA antitoxins. Curr Opin Microbiol 2007; 10:117 - 24; http://dx.doi.org/10.1016/j.mib.2007.03.003; PMID: 17376733
   PubMed Web of Science ®Google Scholar
• Kawano M, Aravind L, Storz G. An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol 2007; 64:738 - 54; http://dx.doi.org/10.1111/j.1365-2958.2007.05688.x; PMID: 17462020
   PubMed Web of Science ®Google Scholar
• Yamaguchi Y, Park JH, Inouye M. Toxin-antitoxin systems in bacteria and archaea. Annu Rev Genet 2011; 45:61 - 79; http://dx.doi.org/10.1146/annurev-genet-110410-132412; PMID: 22060041
   PubMed Web of Science ®Google Scholar
• Hayes F, Van Melderen L. Toxins-antitoxins: diversity, evolution and function. Crit Rev Biochem Mol Biol 2011; 46:386 - 408; http://dx.doi.org/10.3109/10409238.2011.600437; PMID: 21819231
   PubMed Web of Science ®Google Scholar
• Gerdes K, Larsen JE, Molin S. Stable inheritance of plasmid R1 requires two different loci. J Bacteriol 1985; 161:292 - 8; PMID: 2981804
   PubMed Web of Science ®Google Scholar
• Loh SM, Cram DS, Skurray RA. Nucleotide sequence and transcriptional analysis of a third function (Flm) involved in F-plasmid maintenance. Gene 1988; 66:259 - 68; http://dx.doi.org/10.1016/0378-1119(88)90362-9; PMID: 3049248
   PubMed Web of Science ®Google Scholar
• Golub EI, Panzer HA. The F factor of Escherichia coli carries a locus of stable plasmid inheritance stm, similar to the parB locus of plasmid RI. Mol Gen Genet 1988; 214:353 - 7; http://dx.doi.org/10.1007/BF00337735; PMID: 3070354
   PubMedGoogle Scholar
• Onishi Y. F factor promotes turnover of stable RNA in escherichia coli. Science 1975; 187:257 - 8; http://dx.doi.org/10.1126/science.1089310; PMID: 1089310
   PubMed Web of Science ®Google Scholar
• Ohnishi Y, Iguma H, Ono T, Nagaishi H, Clark AJ. Genetic mapping of the F plasmid gene that promotes degradation of stable ribonucleic acid in Escherichia coli. J Bacteriol 1977; 132:784 - 9; PMID: 336605
   PubMed Web of Science ®Google Scholar
• Ohnishi Y, Akimoto S. I-like R plasmids promote degradation of stable ribonucleic acid in Escherichia coli. J Bacteriol 1980; 144:833 - 5; PMID: 6159347
   PubMed Web of Science ®Google Scholar
• Nielsen AK, Thorsted P, Thisted T, Wagner EG, 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 1991; 5:1961 - 73; http://dx.doi.org/10.1111/j.1365-2958.1991.tb00818.x; PMID: 1722558
   PubMed Web of Science ®Google Scholar
• Gerdes K, Poulsen LK, Thisted T, Nielsen AK, Martinussen J, Andreasen PH. The hok killer gene family in gram-negative bacteria. New Biol 1990; 2:946 - 56; PMID: 2101633
   PubMedGoogle Scholar
• Gerdes K, Bech FW, Jørgensen ST, Løbner-Olesen A, Rasmussen PB, Atlung T, et al. Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon. EMBO J 1986; 5:2023 - 9; PMID: 3019679
   PubMed Web of Science ®Google Scholar
• Gerdes K, Rasmussen PB, Molin S. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc Natl Acad Sci U S A 1986; 83:3116 - 20; http://dx.doi.org/10.1073/pnas.83.10.3116; PMID: 3517851
   PubMed Web of Science ®Google Scholar
• Loh SM, Cram DS, Skurray RA. Nucleotide sequence and transcriptional analysis of a third function (Flm) involved in F-plasmid maintenance. Gene 1988; 66:259 - 68; http://dx.doi.org/10.1016/0378-1119(88)90362-9; PMID: 3049248
   PubMed Web of Science ®Google Scholar
• 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 1992; 223:41 - 54; http://dx.doi.org/10.1016/0022-2836(92)90714-U; PMID: 1370544
   PubMed Web of Science ®Google Scholar
• Gerdes K, Helin K, Christensen OW, Løbner-Olesen A. Translational control and differential RNA decay are key elements regulating postsegregational expression of the killer protein encoded by the parB locus of plasmid R1. J Mol Biol 1988; 203:119 - 29; http://dx.doi.org/10.1016/0022-2836(88)90096-4; PMID: 2460630
   PubMed Web of Science ®Google Scholar
• Gerdes K, Thisted T, Martinussen J. Mechanism of post-segregational killing by the hok/sok system of plasmid R1: sok antisense RNA regulates formation of a hok mRNA species correlated with killing of plasmid-free cells. Mol Microbiol 1990; 4:1807 - 18; http://dx.doi.org/10.1111/j.1365-2958.1990.tb02029.x; PMID: 1707122
   PubMed Web of Science ®Google Scholar
• Franch T, Gultyaev AP, 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 1997; 273:38 - 51; http://dx.doi.org/10.1006/jmbi.1997.1294; PMID: 9367744
   PubMed Web of Science ®Google Scholar
• 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 1992; 223:41 - 54; http://dx.doi.org/10.1016/0022-2836(92)90714-U; PMID: 1370544
   PubMed Web of Science ®Google Scholar
• Gerdes K, Nielsen A, Thorsted P, Wagner EG. 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 1992; 226:637 - 49; http://dx.doi.org/10.1016/0022-2836(92)90621-P; PMID: 1380562
   PubMed Web of Science ®Google Scholar
• Thisted T, Nielsen AK, Gerdes K. Mechanism of post-segregational killing: translation of Hok, SrnB and Pnd mRNAs of plasmids R1, F and R483 is activated by 3′-end processing. EMBO J 1994; 13:1950 - 9; PMID: 8168492
   PubMed Web of Science ®Google Scholar
• Cohen SN. Surprises at the 3′ end of prokaryotic RNA. Cell 1995; 80:829 - 32; http://dx.doi.org/10.1016/0092-8674(95)90284-8; PMID: 7535193
   PubMed Web of Science ®Google Scholar
• Donovan WP, Kushner SR. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc Natl Acad Sci U S A 1986; 83:120 - 4; http://dx.doi.org/10.1073/pnas.83.1.120; PMID: 2417233
   PubMed Web of Science ®Google Scholar
• McLaren RS, Newbury SF, Dance GS, Causton HC, Higgins CF. mRNA degradation by processive 3′-5′ exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J Mol Biol 1991; 221:81 - 95; PMID: 1920421
   PubMed Web of Science ®Google Scholar
• Kawano M, Reynolds AA, Miranda-Rios J, Storz G. Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res 2005; 33:1040 - 50; http://dx.doi.org/10.1093/nar/gki256; PMID: 15718303
   PubMed Web of Science ®Google Scholar
• Oshima T, Aiba H, Baba T, Fujita K, Hayashi K, Honjo A, et al. A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map (supplement). DNA Res 1996; 3:211 - 23; http://dx.doi.org/10.1093/dnares/3.3.211; PMID: 8905239
   PubMedGoogle Scholar
• Yoshida T, Obata N, Oosawa K. Color-coding reveals tandem repeats in the Escherichia coli genome. J Mol Biol 2000; 298:343 - 9; http://dx.doi.org/10.1006/jmbi.2000.3667; PMID: 10772854
   PubMed Web of Science ®Google Scholar
• Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, et al. The complete genome sequence of Escherichia coli K-12. Science 1997; 277:1453 - 62; http://dx.doi.org/10.1126/science.277.5331.1453; PMID: 9278503
   PubMed Web of Science ®Google Scholar
• Kawano M, Kanaya S, Oshima T, Masuda Y, Ara T, Mori H. Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome: comparative study of Long Direct Repeat (LDR) sequences. DNA Res 2002; 9:1 - 10; http://dx.doi.org/10.1093/dnares/9.1.1; PMID: 11939563
   PubMed Web of Science ®Google Scholar
• Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G. Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res 2010; 38:3743 - 59; http://dx.doi.org/10.1093/nar/gkq054; PMID: 20156992
   PubMed Web of Science ®Google Scholar
• Fozo EM, Hemm MR, Storz G. Small toxic proteins and the antisense RNAs that repress them. Microbiol Mol Biol Rev 2008; 72:579 - 89; http://dx.doi.org/10.1128/MMBR.00025-08; PMID: 19052321
   PubMed Web of Science ®Google Scholar
• Gerdes K, Bech FW, Jørgensen ST, Løbner-Olesen A, Rasmussen PB, Atlung T, et al. Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon. EMBO J 1986; 5:2023 - 9; PMID: 3019679
   PubMed Web of Science ®Google Scholar
• Van Melderen L. Toxin-antitoxin systems: why so many, what for?. Curr Opin Microbiol 2010; 13:781 - 5; http://dx.doi.org/10.1016/j.mib.2010.10.006; PMID: 21041110
   PubMed Web of Science ®Google Scholar
• Kobayashi I, Nobusato A, Kobayashi-Takahashi N, Uchiyama I. Shaping the genome--restriction-modification systems as mobile genetic elements. Curr Opin Genet Dev 1999; 9:649 - 56; http://dx.doi.org/10.1016/S0959-437X(99)00026-X; PMID: 10607611
   PubMed Web of Science ®Google Scholar
• Schmidt H, Hensel M. Pathogenicity islands in bacterial pathogenesis. Clin Microbiol Rev 2004; 17:14 - 56; http://dx.doi.org/10.1128/CMR.17.1.14-56.2004; PMID: 14726454
   PubMed Web of Science ®Google Scholar
• Lemos JA, Brown TA Jr., Abranches J, Burne RA. Characteristics of Streptococcus mutans strains lacking the MazEF and RelBE toxin-antitoxin modules. FEMS Microbiol Lett 2005; 253:251 - 7; http://dx.doi.org/10.1016/j.femsle.2005.09.045; PMID: 16243456
   PubMed Web of Science ®Google Scholar
• Fozo EM, Hemm MR, Storz G. Small toxic proteins and the antisense RNAs that repress them. Microbiol Mol Biol Rev 2008; 72:579 - 89; http://dx.doi.org/10.1128/MMBR.00025-08; PMID: 19052321
   PubMed Web of Science ®Google Scholar
• Hayes F, Van Melderen L. Toxins-antitoxins: diversity, evolution and function. Crit Rev Biochem Mol Biol 2011; 46:386 - 408; http://dx.doi.org/10.3109/10409238.2011.600437; PMID: 21819231
   PubMed Web of Science ®Google Scholar
• Pineda M, Gregory BD, Szczypinski B, Baxter KR, Hochschild A, Miller ES, et al. A family of anti-sigma70 proteins in T4-type phages and bacteria that are similar to AsiA, a Transcription inhibitor and co-activator of bacteriophage T4. J Mol Biol 2004; 344:1183 - 97; http://dx.doi.org/10.1016/j.jmb.2004.10.003; PMID: 15561138
   PubMed Web of Science ®Google Scholar
• Pecota DC, Wood TK. Exclusion of T4 phage by the hok/sok killer locus from plasmid R1. J Bacteriol 1996; 178:2044 - 50; PMID: 8606182
   PubMed Web of Science ®Google Scholar
• Pandey DP, Gerdes K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 2005; 33:966 - 76; http://dx.doi.org/10.1093/nar/gki201; PMID: 15718296
   PubMed Web of Science ®Google Scholar
• Magnuson RD. Hypothetical functions of toxin-antitoxin systems. J Bacteriol 2007; 189:6089 - 92; http://dx.doi.org/10.1128/JB.00958-07; PMID: 17616596
   PubMed Web of Science ®Google Scholar
• Shao Y, Harrison EM, Bi D, Tai C, He X, Ou HY, et al. TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea. Nucleic Acids Res 2011; 39:Database issue D606 - 11; http://dx.doi.org/10.1093/nar/gkq908; PMID: 20929871
   PubMedGoogle Scholar
• Maisonneuve E, Shakespeare LJ, Jørgensen MG, Gerdes K. Bacterial persistence by RNA endonucleases. Proc Natl Acad Sci U S A 2011; 108:13206 - 11; http://dx.doi.org/10.1073/pnas.1100186108; PMID: 21788497
   PubMed Web of Science ®Google Scholar