Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets

Nucleic Acids Research

Volumn 35, Issue 3, 2007, Pages 962-974

  Mandin, Pierre ^a,b,c   Geissmann, Thomas ^d   Cossart, Pascale ^a,b,c   Repoila, Francis ^a,b,c   Vergassola, Massimo ^a  

^a INSTITUT PASTEUR   (France)

^b INSERM   (France)

^c USC 2020   (France)

^d UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; NUCLEOTIDE; SPACER DNA; UNTRANSLATED RNA;

ARTICLE; BACTERIAL GENETICS; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIAL VIRULENCE; COMPUTER MODEL; CONTROLLED STUDY; GENE EXPRESSION; GENE TARGETING; GENETIC IDENTIFICATION; GENUS; LISTERIA INNOCUA; LISTERIA MONOCYTOGENES; NONHUMAN; OPEN READING FRAME; PREDICTION; PRIORITY JOURNAL; RNA BINDING; RNA TRANSCRIPTION; THERMODYNAMICS;

5' FLANKING REGION; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA, INTERGENIC; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENES, BACTERIAL; GENOMICS; LISTERIA MONOCYTOGENES; MOLECULAR SEQUENCE DATA; RNA, MESSENGER; RNA, UNTRANSLATED;

BACTERIA (MICROORGANISMS); LISTERIA; LISTERIA INNOCUA; LISTERIA MONOCYTOGENES;

EID: 33847371621     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1096     Document Type: Article

References (56)

1. Storz,G., Altuvia,S. and Wassarman,K.M. (2005) An abundance of RNA regulators. Annu. Rev. Biochem., 74, 199-217.
2. Repoila,F., Majdalani,N. and Gottesman,S. (2003) Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: The RpoS paradigm. Mol. Microbiol., 48, 855-861.
3. Wassarman,K.M. (2002) Small RNAs in bacteria: Diverse regulators of gene expression in response to environmental changes. Cell, 109, 141-144.
4. Johansson,J. and Cossart,P. (2003) RNA-mediated control of virulence gene expression in bacterial pathogens. Trends Microbiol., 11, 280-285.
5. Romby,P., Vandenesch,F. and Wagner,E.G. (2006) The role of RNAs in the regulation of virulence-gene expression. Curr. Opin. Microbiol., 9, 229-236.
6. Vazquez-Boland,J.A., Kuhn,M., Berche,P., Chakraborty,T., Dominguez-Bernal,G., Goebel,W., Gonzalez-Zorn,B., Wehland,J. and Kreft,J. (2001) Listeria pathogenesis and molecular virulence determinants. Clin. Microbiol. Rev., 14, 584-640.
7. Pizarro-Cerda,J. and Cossart,P. (2006) Subversion of cellular functions by Listeria monocytogenes. J. Pathol., 208, 215-223.
8. Dussurget,O., Pizarro-Cerda,J. and Cossart,P. (2004) Molecular determinants of Listeria monocytogenes virulence. Annu. Rev. Microbiol., 58, 587-610.
9. Johansson,J., Mandin,P., Renzoni,A., Chiaruttini,C., Springer,M. and Cossart,P. (2002) An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell, 110, 551-561.
10. Kim,H., Marquis,H. and Boor,K.J. (2005) SigmaB contributes to Listeria monocytogenes invasion by controlling expression of inlA and inlB. Microbiology, 151, 3215-3222.
11. Mandin,P., Fsihi,H., Dussurget,O., Vergassola,M., Milohanic,E., Toledo-Arana,A., Lasa,I., Johansson,J. and Cossart,P. (2005) VirR, a response regulator critical for Listeria monocytogenes virulence. Mol. Microbiol., 57, 1367-1380.
12. Williams,T., Bauer,S., Beier,D. and Kuhn,M, (2005) Construction and characterization of Listeria monocytogenes mutants with in-frame deletions in the response regulator genes identified in the genome sequence. Infect. Immun., 73, 3152-3159.
13. Christiansen,J.K., Larsen,M.H., Ingmer,H., Sogaard-Andersen,L. and Kalslipolitis,B.H. (2004) The RNA-binding protein Hfq of Listeria monocytogenes: Role in stress tolerance and virulence. J. Bacteriol., 186, 3355-3362.
14. Valentin-Hansen,P., Eriksen,M. and Udesen,C. (2004) The bacterial Sm-like protein Hfq: A key player in RNA transactions. Mol. Microbiol., 51, 1525-1533.
15. Christiansen,J.K., Nielsen,J.S., Ebersbach,T., Valentin-Hansen,P., Sogaard-Andersen,L. and Kallipolitis,B.H., (2006) Identification of small Hfq-binding RNAs in Listeria monocytogenes. Rna., 12, 1383-1396
16. Gottesman,S. (2004) The small RNA regulators of Escherichia coli: Roles and mechanisms*. Annu. Rev. Microbiol., 58, 303-328.
17. Huntzinger,E., Boisset,S., Saveanu C., Benito,Y., Geissmann,T., Namane,A., Lina,G., EtienneJ., Ehresmann,B., Ehresmann,C. et al. (2005) Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression. EMBO J., 24, 824-835.
18. Tjaden,B., Goodwin,S.S., Opdyke,J.A., Guillier,M., Fu,D.X., Gottesman,S. and Storz,G. (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res., 34, 2791-2802.
19. Glaser,P., Frangeul,L., Buchrieser,C., Rusniok,C., Amend,A., Baquero,F., Berche,P., Bloecker,H., Brandt,P., Chakraborty,T. et al. (2001) Comparative genomics of Listeria species. Science, 294, 849-852.
20. Vogel,J. and Sharma,C.M. (2005) How to find small non-coding RNAs in bacteria. Biol. Chem., 386, 1219-1238.
21. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
22. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
23. d'Aubenton Carafa,Y., Brody,E. and Thermes,C. (1990) Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol., 216, 835-858.
24. Griffiths-Jones,S., Moxon,S., Marshall,M., Khanna,A., Eddy,S.R. and Bateman,A. (2005) Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-124.
25. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G., (1998) Biological Sequence Analysis, Probabilistic Models of Proteins and Nucleic acids., Cambridge, UK: Cambridge University Press.
26. Arnaud,M., Chastanet,A. and Debarbouille,M., (2004) New vector for efficient allelic replacement in naturally nontransformable, low-GC-content, gram-positive bacteria. Appl. Environ. Microbiol., 70, 6887-6891.
27. Trieu-Cuot,P., Carlier,C., Poyart-Salmeron,C. and Courvalin,P. (1990) A pair of mobilizable shuttle vectors conferring resistance to spectinomycin for molecular cloning in Escherichia coli and in gram-positive bacteria. Nucleic Acids Res., 18, 4296.
28. Janabi,N. (2002) Selective inhibition of cyclooxygenase-2 expression by 15-deoxy-delta(12,14)(12,14)-prostaglandin J(2) in activated human astrocytes, but not in human brain macrophages. J. Immunol., 168, 4747-4755.
29. Wassarman,K.M., Repoila,F., Rosenow,C., Storz,G. and Gottesman,S. (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev., 15, 1637-1651.
30. Argaman,L., Hershberg,R., Vogel,J., Bejerano,G., Wagner,E.G., Margalit,H. and Altuvia,S. (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr. Biol., 11, 941-950.
31. Axmann,I.M., Kensche,P., Vogel,J., Kohl,S., Herzel,H. and Hess,W.R. (2005) Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol., 6, R73.
32. Pichon,C. and Felden,B. (2005) Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc. Natl. Acad. Sci. U.S.A., 102, 14249-14254.
33. Brown,J.W. (1999) The Ribonuclease P Database. Nucleic Acids Res., 27, 314.
34. Withey,J.H. and Friedman,D.I. (2003) A salvage pathway for protein structures: TmRNA and trans-translation. Annu. Rev. Microbiol., 57, 101-123.
35. Trotochaud,A.E. and Wassarman,K.M. (2004) 6S RNA function enhances long-term cell survival. J. Bacteriol., 186, 4978-4985.
36. Wassarman,K.M. and Storz,G. (2000) 6S RNA regulates E. coli RNA polymerase activity. Cell, 101, 613-623.
37. Lenz,D.H., Mok,K.C., Lilley,B.N., Kulkarni,R.V., Wingreen,N.S. and Bassler,B.L. (2004) The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell, 118, 69-82.
38. Nelson,K.E., Fouts,D.E., Mongodin,E.F., Ravel,J., DeBoy,R.T., Kolonay,J.F., Rasko,D.A., Angiuoli,S.V., Gill,S.R., Paulsen,I.T. et al. (2004) Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res., 32, 2386-2395.
39. Campos-Guillen,J., Bralley,P., Jones,G.H., Bechhofer,D.H. and Olmedo-Alvarez,G. (2005) Addition of poly(A) and heteropolymeric 3′ ends in Bacillus subtilis wild-type and polynucleotide phosphorylase-deficient strains. J. Bacteriol., 187, 4698-4706.
40. Chen,I. and Dubnau,D. (2004) DNA uptake during bacterial transformation. Nat. Rev. Microbiol., 2, 241-249.
41. Bobik,T.A., Ailion,M. and Roth,J.R. (1992) A single regulatory gene integrates control of vitamin B12 synthesis and propanediol degradation. J. Bacteriol., 174, 2253-2266.
42. Masse,E., Escorcia,F.E. and Gottesman,S. (2003) Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev., 17, 2374-2383.
43. Majdalani,N., Cunning,C., Sledjeski,D., Elliott,T. and Gottesman,S. (1998) 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. U.S.A., 95, 12462-12467.
44. Moller,T., Franch,T., Udesen,C., Gerdes,K. and Valentin-Hansen,P. (2002) Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Dev., 16, 1696-1706.
45. Wagner,E.G. and Flardh,K. (2002) Antisense RNAs everywhere? Trends Genet., 18, 223-226.
46. Argaman,L. and Altuvia,S. (2000) fh1A repression by OxyS RNA: Kissing complex formation at two sites results in a stable antisense-target RNA complex. J. Mol. Biol., 300, 1101-1112.
47. Lease,R.A. and Belfort,M. (2000) A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc. Natl. Acad. Sci. U.S.A., 97, 9919-9924.
48. Opdyke,J.A., Kang,J.G. and Storz,G. (2004) GadY, a small-RNA regulator of acid response genes in Escherichia coli. J. Bacteriol., 186, 6698-6705.
49. Storz,G., Opdyke,J.A. and Zhang,A. (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol., 7, 140-144.
50. Morita,T., Mochizuki,Y. and Aiba,H. (2006) Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction. Proc. Natl. Acad. Sci. U.S.A., 103, 4858-4863.
51. Godde,J.S. and Bickerton,A. (2006) The repetitive DNA elements called CRISPRs and their associated genes: Evidence of horizontal transfer among prokaryotes. J. Mol. Evol., 62, 718-729.
52. Haft,D.H., Selengut,J., Mongodin,E.F. and Nelson,K.E. (2005) A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol., 1, e60.
53. Makarova,K.S., Grishin,N.V., Shabalina,S.A., Wolf,Y.I. and Koonin,E.V. (2006) A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with, eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct., 1, 7.
54. Majdalani,N., Vanderpool,C.K. and Gottesman,S. (2005) Bacterial small RNA regulators. Crit. Rev. Biochem. Mol. Biol., 40, 93-113.
55. Borezee,E., Msadek,T., Durant,L. and Berche,P. (2000) Identification in Listeria monocytogenes of MecA, a homologue of the Bacillus subtilis competence regulatory protein. J. Bacteriol., 182, 5931-5934.
56. Hamoen,L.W., Venema,G. and Kuipers,O.P. (2003) Controlling competence in Bacillus subtilis: Shared use of regulators. Microbiology, 149, 9-17.