The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis

Nucleic Acids Research

Volumn 29, Issue 10, 2001, Pages 2145-2153

  Chambaud, Isabelle ^a,b   Heilig, Roland ^c   Ferris, Stéphane ^b   Barbe, Valérie ^c   Samson, Delphine ^c   Galisson, Frédérique ^b   Moszer, Ivan ^b   Dybvig, Kevin ^d   Wróblewski, Henri ^e   Viari, Alain ^f   Rocha, Eduardo P C ^b,g   Blanchard, Alain ^a  

^a UNIVERSITÉ DE BORDEAUX   (France)

^b INSTITUT PASTEUR   (France)

^c CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^d UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^e UNIVERSITÉ DE RENNES 1   (France)

^f INRIA RHÔNE ALPES   (France)

^g Atelier de BioInformatique   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN; CYTOSINE; GUANINE; HEMOLYSIN; MEMBRANE ANTIGEN; NUCLEASE; NUCLEOTIDE; PROTEIN; PROTEINASE; RECOMBINASE; RIBOSOME RNA; VIRULENCE FACTOR;

ARTICLE; BACTERIAL CELL WALL; BACTERIAL CHROMOSOME; BACTERIAL GENE; CATALYSIS; CHROMOSOME INVERSION; CONTROLLED STUDY; DATA BASE; EUBACTERIUM; GENE SEQUENCE; GENETIC POLYMORPHISM; HYPOTHESIS; MOLLICUTES; MYCOPLASMA PULMONIS; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RESPIRATORY TRACT DISEASE; RNA REPLICATION; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS; TECHNIQUE; UREAPLASMA UREALYTICUM;

BACTERIA (MICROORGANISMS); MOLLICUTES; MURINAE; MYCOPLASMA; MYCOPLASMA PULMONIS; MYCOPLASMATALES; NEGIBACTERIA; PROKARYOTA; UREAPLASMA UREALYTICUM;

EID: 0035872855     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.10.2145     Document Type: Article

References (65)

1. Jacobs, E. (1997) Mycoplasma infections of the human respiratory tract. Wien. Klin. Wochensch., 109, 574-577.
2. Taylor-Robinson, D. and Furr, P.M. (1998) Update on sexually transmitted mycoplasmas. Lancet, 351, 12-15.
3. Frey, J. and Nicolet, J. (1997) Molecular identification and epidemiology of animal mycoplasmas. Wien. Klin. Wochensch., 109, 600-603.
4. Mushegian, A.R. and Koonin, E.V. (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl Acad. Sci. USA, 93, 10268-10273.
5. Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B.C. and Herrmann, R. (1996) Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res., 24, 4420-4449.
6. Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., Fleischmann, R. D., Bult, C.J., Kerlavage, A.R., Sutton, G., Kelley, J.M. et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science, 270, 397-403.
7. Glass, J.I., Lefkowitz, E.J., Glass, J.S., Heiner, C.R., Chen, E.Y. and Cassell, G.H. (2000) The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature, 407, 757-762.
8. Mansel, J.K., Rosenow, E.C.D., Smith, T.F. and Martin, J.W., Jr (1989) Mycoplasma pneumoniae pneumonia. Chest, 95, 639-646.
9. Cartner, S.C., Lindsey, J.R., Gibbs-Erwin, J., Cassell, G.H. and Simecka, J. W. (1998) Roles of innate and adaptive immunity in respiratory mycoplasmosis. Infect. Immun., 66, 3485-3491.
10. Citti, C. and Rosengarten, R. (1997) Mycoplasma genetic variation and its implication for pathogenesis. Wien. Klin. Wochensch., 109, 562-568.
11. Chambaud, I., Wroblewski, H. and Blanchard, A. (1999) Interactions between mycoplasma lipoproteins and the host immune system. Trends Microbiol., 7, 493-499.
12. Shen, X., Gumulak, J., Yu, H., French, C.T., Zou, N. and Dybvig, K.(2000) Gene rearrangements in the vsa locus of Mycoplasma pulmonis. J. Bacteriol., 182, 2900-2908.
13. Ewing, B., Hillier, L., Wendl, M.C. and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res., 8, 175-185.
14. Medigue, C., Rechenmann, F., Danchin, A. and Viari, A. (1999) Imagene: an integrated computer environment for sequence annotation and analysis. Bioinformatics, 15, 2-15.
15. Salzberg, S.L., Delcher, A.L., Kasif, S. and White, O. (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res., 26, 544-548.
16. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
17. Pearson, W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 183, 63-98.
18. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Howe, K.L. and Sonnhammer, E.L. (2000) The Pfam protein families database. Nucleic Acids Res., 28, 263-266.
19. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Finn, R.D. and Sonnhammer, E.L. (1999) Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res., 27, 260-262.
20. Sonnhammer, E.L., Eddy, S.R., Birney, E., Bateman, A. and Durbin, R. (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res., 26, 320-322.
21. Hofmann, K. and Stoffel, W. (1993) TMbase - a database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler, 347, 166.
22. Henikoff, S. and Henikoff, J.G. (1993) Performance evaluation of amino acid substitution matrices. Proteins, 17, 49-61.
23. Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
24. d'Aubenton Carafa, Y., Brody, E. and Thermes, C. (1990) Prediction of p-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol., 216, 835-858.
25. el-Mabrouk, N. and Lisacek, F. (1996) Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome. J. Mol. Biol., 264, 46-55.
26. Moszer, I., Rocha, E.P. and Danchin, A. (1999) Codon usage and lateral gene transfer in Bacillus subtilis. Curr. Opin. Microbiol., 2, 524-528.
27. Rocha, E.P., Danchin, A. and Viari, A. (1999) Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes. Mol. Biol. Evol., 16, 1219-1230.
28. Sonnhammer, E.L. and Durbin, R. (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene, 167, GC1-10.
29. Moszer, I. (1998) The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis. FEBS Lett., 430, 28-36.
30. Riley, M. (1993) Functions of the gene products of Escherichia coli. Microbiol. Rev., 57, 862-952.
31. Rocha, E.P., Danchin, A. and Viari, A. (1999) Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis. Nucleic Acids Res., 27, 3567-3576.
32. Stemke, G.W., Huang, Y., Laigret, F. and Bove, J.M. (1994) Cloning the ribosomal RNA operons of Mycoplasma flocculare and comparison with those of Mycoplasma hyopneumoniae. Microbiology, 140, 857-860.
33. Ermolaeva, M.D., Khalak, H.G., White, O., Smith, H.O. and Salzberg, S.L. (2000) Prediction of transcription terminators in bacterial genomes. J. Mol. Biol., 301, 27-33.
34. Ye, F., Renaudin, J., Bove, J.M. and Laigret, F. (1994) Cloning and sequencing of the replication origin (oriC) of the Spiroplasma citri chromosome and construction of autonomously replicating artificial plasmids. Curr. Microbiol., 29, 23-29.
35. Fujita, M.Q., Yoshikawa, H. and Ogasawara, N. (1992) Structure of the dnaA and DnaA-box region in the Mycoplasma capricolum chromosome: conservation and variations in the course of evolution. Gene, 110, 17-23.
36. Lobry, I.R. (1996) Asymmetric distribution patterns in the two DNA strands of bacteria. Mol. Biol. Evol., 13, 660-665.
37. Rocha, E.P., Danchin, A. and Viari, A. (1999) Universal replication biases in bacteria. Mol. Microbiol., 32, 11-16.
38. Dandekar, T., Huynen, M., Regula, J.T., Ueberle, B., Zimmermann, C.U., Andrade, M.A., Doerks, T., Sanchez-Pulido, L., Snel, B., Suyama, M. et al. (2000) Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Res., 28, 3278-3288.
39. Lopez de Saro, F.J., Yoshikawa, N. and Helmann, J.D. (1999) Expression, abundance, and RNA polymerase binding properties of the δ factor of Bacillus subtilis. J. Biol. Chem., 274, 15953-15958.
40. Quentin, Y., Fichant, G. and Denizot, F. (1999) Inventory, assembly and analysis of Bacillus subtilis ABC transport systems. J. Mol. Biol., 287, 467-784.
41. Miles, R.J. (1992) Catabolism in mollicutes. J. Gen. Microbiol., 138, 1773-1783.
42. Himmelreich, R., Plagens, H., Hilbert, H., Reiner, B. and Herrmann, R. (1997) Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res., 24, 701-712.
43. Peterson, S.N. and Fraser, C.M. (2001) The complexity of simplicity. Genome Biol., 2, 2002.1-2002.7.
44. Hutchison, C.A., Peterson, S.N., Gill, S.R., Cline, R.T., White, O., Fraser, C.M., Smith, H.O. and Venter, J.C. (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science, 286, 2165-2169.
45. Gaurivaud, P., Laigret, F., Garnier, M. and Bové, J.M. (2000) Fructose utilization and pathogenicity of Spiroplasma citri: characterization of the fructose operon. Gene, 252, 61-69.
46. Wendrich, T.M. and Marahiel, M.A. (1997) Cloning and characterization of a relA/spoT homologue from Bacillus subtilis. Mol. Microbiol., 26, 65-79.
47. Scoarughi, G.L., Cimmino, C. and Donini, P. (1999) Helicobacter pylori: a eubacterium lacking the stringent response. J. Bacteriol., 181, 552-555.
48. Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R.L., Zhao, Q. et al. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science, 282, 754-759.
49. Dybvig, K., Sitaraman, R. and French, C.T. (1998) A family of phase-variable restriction enzymes with differing specificities generated by high-frequency gene rearrangements. Proc. Natl Acad. Sci. USA, 95, 13923-13928.
50. Muhlradt, P.F., Kiess, M., Meyer, H., Sussmuth, R. and Jung, G. (1997) Isolation, structure elucidation, and synthesis of a macrophage stimulatory lipopeptide from Mycoplasma fermentans acting at picomolar concentration. J. Exp. Med., 185, 1951-1958.
51. Piec, G., Mirkovitch, J., Palacio, S., Muhlradt, P.F. and Felix, R. (1999) Effect of MALP-2, a lipopeptide from Mycoplasma fermentans, on bone resorption in vitro. Infect. Immun., 67, 6281-6285.
52. Beermann, C., Lochnit, G., Geyer, R., Groscurth, P. and Filgueira, L. (2000) The lipid component of lipoproteins from Borrelia burgdorferi: structural analysis, antigenicity, and presentation via human dendritic cells. Biochem. Biophys. Res. Com., 267, 897-905.
53. Jarvill-Taylor, K.J. and Minion, F.C. (1995) The effect of thiol-active compounds and sterols on the membrane-associated hemolysin of Mycoplasma pulmonis. FEMS Microbiol. Lett., 128, 213-218.
54. Hyatt, D.R., ter Huurne, A.A., van der Zeijst, B.A. and Joens, L.A. (1994) Reduced virulence of Serpulina hyodysenteriae hemolysin-negative mutants in pigs and their potential to protect pigs against challenge with a virulent strain. Infect. Immun., 62, 2244-2248.
55. Wren, B.W., Stabler, R.A., Das, S.S., Butcher, P.D., Mangan, J.A., Clarke, J.D., Casali, N., Parish, T. and Stoker, N.G. (1998) Characterization of a haemolysin from Mycobacterium tuberculosis with homology to a virulence factor of Serpulina hyodysenteriae. Microbiology, 144, 1205-1211.
56. Bendjennat, M., Blanchard, A., Loutfi, M., Montagnier, L. and Bahraoui, E. (1997) Purification and characterization of Mycoplasma penetrans Ca2+/Mg2+-dependent endonuclease. J. Bacteriol., 179, 2210-2220.
57. Bendjennat, M., Blanchard, A., Loutfi, M., Montagnier, L. and Bahraoui, E. (1999) Role of Mycoplasma penetrans endonuclease P40 as a potential pathogenic determinant. Infect. Immun., 67, 4456-4462.
58. Brennan, P.C. and Feinstein, R.N. (1969) Relationship of hydrogen peroxide production by Mycoplasma pulmonis to virulence for catalase-deficient mice. J. Bacteriol., 98, 1036-1040.
59. Dybvig, K. and Cassell, G.H. (1987) Transposition of Gram-positive transposon Tn916 in Acholeplasma laidlawii and Mycoplasma pulmonis. Science, 235, 1392-1394.
60. Dybvig, K., French, C.T. and Voelker, L.L. (2000) Construction and use of derivatives of transposon Tn4001 that function in Mycoplasma pulmonis and Mycoplasma arthritidis. J. Bacteriol., 182, 4343-4347.
61. Wang, G., Humayun, M.Z. and Taylor, D.E. (1999) Mutation as an origin of genetic variability in Helicobacter pylori. Trends Microbiol., 7, 488-493.
62. Hood, D.W., Deadman, M.E., Jennings, M.P., Bisercic, M., Fleischmann, R.D., Venter, J.C. and Moxon, R. (1996) DNA repeats identify novel virulence genes in Haemophilus influenzae. Proc. Natl Acad. Sci. USA, 93, 11121-11125.
63. Cole, S., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S., Eiglmeier, K., Gas, S., Barry, C.R. et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature, 393, 537-544.
64. Parkhill, J., Achtman, M., James, K.D., Bentley, S.D., Churcher, C., Klee, S.R., Morelli, G., Basham, D., Brown, D., Chillingworth, T. et al. (2000) Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature, 404, 502-506.
65. Saunders, N.J., Jeffries, A.C., Peden, J.F., Hood, D.W., Tettelin, H., Rappuolli, R. and Moxon, E.R. (2000) Repeat-associated phase-variable genes in the complete genome sequence of Neisseria meningitidis strain MC58. Mol. Microbiol., 37, 207-215.