The hok mRNA family

References

• 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
• 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
• 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, 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, 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
• 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
• 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
• Franch T, Gerdes K. Programmed cell death in bacteria: translational repression by mRNA end-pairing. Mol Microbiol 1996; 21:1049 - 60; http://dx.doi.org/10.1046/j.1365-2958.1996.771431.x; PMID: 8885274
   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
• Gultyaev AP, Franch T, Gerdes K. Programmed cell death by hok/sok of plasmid R1: coupled nucleotide covariations reveal a phylogenetically conserved folding pathway in the hok family of mRNAs. J Mol Biol 1997; 273:26 - 37; http://dx.doi.org/10.1006/jmbi.1997.1295; PMID: 9367743
   PubMed Web of Science ®Google Scholar
• Møller-Jensen J, Franch T, Gerdes K. Temporal translational control by a metastable RNA structure. J Biol Chem 2001; 276:35707 - 13; http://dx.doi.org/10.1074/jbc.M105347200; PMID: 11461923
   PubMed Web of Science ®Google Scholar
• Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003; 31:3406 - 15; http://dx.doi.org/10.1093/nar/gkg595; PMID: 12824337
   PubMed Web of Science ®Google Scholar
• Thisted T, Sørensen NS, 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 1995; 247:859 - 73; http://dx.doi.org/10.1006/jmbi.1995.0186; PMID: 7536849
   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
• 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
• 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
• 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
• 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
• Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005; 33:Database issue D121 - 4; http://dx.doi.org/10.1093/nar/gki081; PMID: 15608160
   PubMed Web of Science ®Google Scholar
• Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009; 25:1335 - 7; http://dx.doi.org/10.1093/bioinformatics/btp157; PMID: 19307242
   PubMed Web of Science ®Google Scholar
• Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 2009; 37:Database issue D32 - 6; http://dx.doi.org/10.1093/nar/gkn721; PMID: 18927115
   PubMed Web of Science ®Google Scholar
• Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M. 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 2006; 7:498; http://dx.doi.org/10.1186/1471-2105-7-498; PMID: 17101042
   PubMed Web of Science ®Google Scholar
• Merino E, Yanofsky C. Transcription attenuation: a highly conserved regulatory strategy used by bacteria. Trends Genet 2005; 21:260 - 4; http://dx.doi.org/10.1016/j.tig.2005.03.002; PMID: 15851059
   PubMed Web of Science ®Google Scholar
• Mandal M, Breaker RR. Gene regulation by riboswitches. Nat Rev Mol Cell Biol 2004; 5:451 - 63; http://dx.doi.org/10.1038/nrm1403; PMID: 15173824
   PubMed Web of Science ®Google Scholar
• Chadalavada DM, Cerrone-Szakal AL, Bevilacqua PC. Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions. RNA 2007; 13:2189 - 201; http://dx.doi.org/10.1261/rna.778107; PMID: 17956974
   PubMed Web of Science ®Google Scholar
• Wong TN, Sosnick TR, Pan T. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A 2007; 104:17995 - 8000; http://dx.doi.org/10.1073/pnas.0705038104; PMID: 17986617
   PubMed Web of Science ®Google Scholar
• Micura R, Höbartner C. On secondary structure rearrangements and equilibria of small RNAs. Chembiochem 2003; 4:984 - 90; http://dx.doi.org/10.1002/cbic.200300664; PMID: 14523915
   PubMed Web of Science ®Google Scholar
• Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, et al. The Pfam protein families database. Nucleic Acids Res 2010; 38:Database issue D211 - 22; http://dx.doi.org/10.1093/nar/gkp985; PMID: 19920124
   PubMed Web of Science ®Google Scholar
• Lai D, Proctor JR, Zhu JY, Meyer IM. R-CHIE: a web server and R package for visualizing RNA secondary structures. Nucleic Acids Res 2012; 40:e95; http://dx.doi.org/10.1093/nar/gks241; PMID: 22434875
   PubMed Web of Science ®Google Scholar