The hok mRNA family

RNA Biology

Volumn 9, Issue 12, 2012, Pages 1399-1404

  Steif, Adi ^a   Meyer, Irmtraud M ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Co transcriptional RNA folding; Hok sok; Mutually exclusive RNA structures; Post segregational killing; RNA structures regulating gene expression; Toxin antitoxin system; Transient RNA structures

Indexed keywords

BACTERIAL RNA; COMPLEMENTARY RNA; HOK PROTEIN; MEMBRANE PROTEIN; MESSENGER RNA; SHORT HAIRPIN RNA; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL CELL; BACTERIAL GENOME; BACTERIAL MEMBRANE; CELL DEATH; CELL GROWTH; CONTROLLED STUDY; ESCHERICHIA COLI; GENE EXPRESSION; GENE LOCUS; GENE REARRANGEMENT; GENETIC SUSCEPTIBILITY; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; RIBOSOME; RNA BINDING; RNA DEGRADATION; RNA TRANSLATION;

EID: 84875188868     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.22746     Document Type: Article

References (29)

1. Gerdes K, Larsen JE, Molin S. Stable inheritance of plasmid R1 requires two different loci. J Bacteriol 1985; 161:292-8; PMID:2981804. (Pubitemid 15157342)
2. Gerdes K, Rasmussen PB, Molin S. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc Natl Acad Sci USA 1986; 83:3116-20; PMID:3517851; http://dx.doi. org/10.1073/pnas.83.10.3116. (Pubitemid 16042987)
3. Thisted T, Gerdes K. Mechanism of post-segrega-tional 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; PMID:1370544; http://dx.doi.org/10.1016/0022-2836(92)90714-U.
4. Gerdes K, Bech F W, Jørgensen ST, Løbner-Olesen A, Rasmussen PB, Atlung T, et al. Mechanism of post-segregational 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.
5. Gerdes K, Wagner EG. RNA antitoxins. Curr Opin Microbiol 2007; 10:117-24; PMID:17376733; http://dx.doi.org/10.1016/j.mib.2007.03.003. (Pubitemid 46590043)
6. 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; PMID:1707122; http://dx.doi.org/10.1111/j.1365- 2958.1990.tb02029.x.
7. 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; PMID:1380562; http://dx.doi.org/10.1016/0022-2836(92)90621-P.
8. Franch T, Gerdes K. Programmed cell death in bacteria: translational repression by mRNA end-pairing. Mol Microbiol 1996; 21:1049-60; PMID:8885274; http://dx.doi.org/10.1046/j.1365-2958.1996.771431.x. (Pubitemid 26297770)
9. 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; PMID:9367744; http://dx.doi.org/10.1006/jmbi.1997.1294. (Pubitemid 27460212)
10. 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; PMID:9367743; http://dx.doi. org/10.1006/jmbi.1997.1295. (Pubitemid 27460211)
11. Møller-Jensen J, Franch T, Gerdes K. Temporal trans-lational control by a metastable RNA structure. J Biol Chem 2001; 276:35707-13; PMID:11461923; http://dx.doi.org/10.1074/jbc.M105347200.
12. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003; 31:3406-15; PMID:12824337; http://dx.doi. org/10.1093/nar/gkg595. (Pubitemid 37442169)
13. 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; PMID:7536849; http://dx.doi. org/10.1006/jmbi.1995.0186.
14. 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.
15. 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; PMID:3049248; http://dx.doi. org/10.1016/0378-1119(88)90362-9.
16. Nielsen AK, Thorsted P, Thisted T, Wagner EG, Gerdes K. The rifampicin-inducible genes srnB from F and pnd from R483 are regulated by anti-sense RNAs and mediate plasmid maintenance by killing of plasmid-free segregants. Mol Microbiol 1991; 5:1961-73; PMID:1722558; http://dx.doi. o r g/10.1111/j.1 3 65-29 5 8.19 91.t b 0 0 818. x. (Pubitemid 21896226)
17. Pedersen K, Gerdes K. Multiple hok genes on the chromosome of Escherichia coli. Mol Microbiol 1999; 32:1090-102; PMID:10361310; http://dx.doi. org/10.1046/j.1365-2958.1999.01431.x. (Pubitemid 29255774)
18. Faridani OR, Nikravesh A, Pandey DP, Gerdes K, Good L. Competitive inhibition of natural anti-sense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli. Nucleic Acids Res 2006; 34:5915-22; PMID:17065468; http://dx.doi. org/10.1093/nar/gkl750. (Pubitemid 44941170)
19. 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; PMID:15608160; http://dx.doi.org/10.1093/nar/gki081. (Pubitemid 40207843)
20. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009; 25:1335-7; PMID:19307242; http://dx.doi. org/10.1093/bioinformatics/btp157.
21. 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; PMID:18927115; http://dx.doi.org/10.1093/nar/gkn721.
22. 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; PMID:17101042; http://dx.doi.org/10.1186/1471-2105- 7-498.
23. Merino E, Yanofsky C. Transcription attenuation: a highly conserved regulatory strategy used by bacteria. Trends Genet 2005; 21:260-4; PMID:15851059; http://dx.doi.org/10.1016/j.tig.2005.03.002. (Pubitemid 40558929)
24. Mandal M, Breaker RR. Gene regulation by ribo-switches. Nat Rev Mol Cell Biol 2004; 5:451-63; PMID:15173824; http://dx.doi.org/10.1038/nrm1403.
25. 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; PMID:17956974; http://dx.doi. org/10.1261/rna.778107. (Pubitemid 350127560)
26. Wong TN, Sosnick TR, Pan T. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci USA 2007; 104:17995-8000; PMID:17986617; http://dx.doi.org/10.1073/ pnas.0705038104. (Pubitemid 350210809)
27. Micura R, Höbartner C. On secondary structure rearrangements and equilibria of small RNAs. Chembiochem 2003; 4:984-90; PMID:14523915; http://dx.doi.org/10.1002/cbic.200300664. (Pubitemid 37267586)
28. 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; PMID:19920124; http://dx.doi. org/10.1093/nar/gkp985.
29. 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; PMID:22434875; http://dx.doi.org/10.1093/nar/gks241.