Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Thiaucourt, Francois ^a,e,f   Manso Silvan, Lucia ^a   Salah, Woubit ^a,e   Barbe, Valérie ^b   Vacherie, Benoit ^b   Jacob, Daniel ^c   Breton, Marc ^c,d   Dupuy, Virginie ^a   Lomenech, Anne M ^c   Blanchard, Alain ^c,d   Sirand Pugnet, Pascal ^c,d  

^a UMR ASTRE   (France)

^b DIF   (France)

^c UNIVERSITÉ DE BORDEAUX   (France)

^d Univ Bordeaux   (France)

^e TUSKEGEE UNIVERSITY   (United States)

^f CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; MEMBRANE PROTEIN; POLYSACCHARIDE; BACTERIAL DNA; BACTERIAL PROTEIN; LIPOPROTEIN;

ARTICLE; BACTERIAL GENOME; CARBOHYDRATE METABOLISM; CONTROLLED STUDY; GENE DUPLICATION; GENE INSERTION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC CODE; GENETIC VARIABILITY; MOLECULAR EVOLUTION; MULTIGENE FAMILY; MYCOPLASMA MYCOIDES; NONHUMAN; PLASTICITY; PROTEIN DEGRADATION; PSEUDOGENE; STRAIN DIFFERENCE; ANIMAL; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; DNA SEQUENCE; FEMALE; GENETICS; GOAT; MICROBIOLOGY; MOLECULAR GENETICS; PLASMID; PROTEOMICS; SEGMENTAL DUPLICATION; TRANSPOSON;

BOVINAE; ENTOMOPLASMATACEAE; MYCOPLASMA; MYCOPLASMA MYCOIDES; MYCOPLASMA MYCOIDES SUBSP. CAPRI; MYCOPLASMATALES;

ANIMALS; BACTERIAL PROTEINS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; EVOLUTION, MOLECULAR; FEMALE; GENETIC VARIATION; GENOME, BACTERIAL; GOATS; LIPOPROTEINS; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; MYCOPLASMA MYCOIDES; PLASMIDS; PROTEOMICS; SEGMENTAL DUPLICATIONS, GENOMIC; SEQUENCE ANALYSIS, DNA;

EID: 79952453160     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-114     Document Type: Article

References (71)

1. Clay AL, Lloyd LC. The eradication of CBPP from Australia. Bull Off Int Epizoot 1974, 91:533-546.
2. Regalla J, Caporale V, Giovannini A, Santini F, Martel JL, Goncalves AP. Manifestation and epidemiology of contagious bovine pleuropneumonia in Europe. Rev Sci Tech 1996, 15(4):1309-1329.
3. Cottew GS, Breard A, DaMassa AJ, Erno H, Leach RH, Lefevre PC, Rodwell AW, Smith GR. Taxonomy of the Mycoplasma mycoides cluster. Isr J Med Sci 1987, 23(6):632-635.
4. Manso-Silvan L, Vilei EM, Sachse K, Djordjevic SP, Thiaucourt F, Frey J. Proposal to assign Mycoplasma leachii sp. nov. as a new species designation for Mycoplasma sp. bovine group 7 of Leach, and to reclassify Mycoplasma mycoides subsp. mycoides LC as a serovar of Mycoplasma mycoides subsp. capri. Int J Syst Evol Microbiol 2009, 59(6):1353-1358. 10.1099/ijs.0.005546-0, 19502315.
5. Thiaucourt F, Bolske G. Contagious caprine pleuropneumonia and other pulmonary mycoplasmoses of sheep and goats. Rev Sci Tech 1996, 15(4):1397-1414.
6. DaMassa AJ, Brooks DL. The external ear canal of goats and other animals as a mycoplasma habitat. Small Rum Res 1991, 4:85-93.
7. Costas M, Leach RH, Mitchelmore DL. Numerical analysis of PAGE protein patterns and the taxonomic relationships within the 'Mycoplasma mycoides cluster'. J Gen Microbiol 1987, 133(12):3319-3329.
8. Bashiruddin JB, Taylor TK, Gould AR. A PCR-based test for the specific identification of Mycoplasma mycoides subspecies mycoides SC. J Vet Diagn Invest 1994, 6(4):428-434.
9. Dedieu L, Mady V, Lefevre PC. Development of a selective polymerase chain reaction assay for the detection of Mycoplasma mycoides subsp. mycoides S.C. (contagious bovine pleuropneumonia agent). Vet Microbiol 1994, 42(4):327-339. 10.1016/0378-1135(94)90064-7, 9133058.
10. Fitzmaurice J, Sewell M, Manso-Silvan L, Thiaucourt F, McDonald WL, O'Keefe JS. Real-time polymerase chain reaction assays for the detection of members of the Mycoplasma mycoides cluster. N Z Vet J 2008, 56(1):40-47. 10.1080/00480169.2008.36803, 18322559.
11. Gorton TS, Barnett MM, Gull T, French RA, Lu Z, Kutish GF, Adams LG, Geary SJ. Development of real-time diagnostic assays specific for Mycoplasma mycoides subspecies mycoides Small Colony. Vet Microbiol 2005, 111(1-2):51-58. 10.1016/j.vetmic.2005.09.013, 16257143.
12. Le Goff C, Thiaucourt F. A competitive ELISA for the specific diagnosis of contagious bovine pleuropneumonia (CBPP). Vet Microbiol 1998, 60(2-4):179-191. 10.1016/S0378-1135(98)00156-4, 9646449.
13. Lorenzon S, Manso-Silván L, Thiaucourt F. Specific real-time PCR assays for the detection and quantification of Mycoplasma mycoides subsp. mycoides SC and Mycoplasma capricolum subsp. capripneumoniae. Mol Cell Probes 2008, 22:324-328. 10.1016/j.mcp.2008.07.003, 18678244.
14. Westberg J, Persson A, Holmberg A, Goesmann A, Lundeberg J, Johansson KE, Pettersson B, Uhlen M. The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res 2004, 14(2):221-227. 10.1101/gr.1673304, 327097, 14762060.
15. Nouvel L, Sirand-Pugnet P, Marenda M, Sagne E, Barbe V, Mangenot S, Schenowitz C, Jacob D, Barre A, Claverol S, et al. Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity. BMC Genomics 2010, 11(1):86.. 10.1186/1471-2164-11-86, 2824730, 20122262.
16. Sirand-Pugnet P, Lartigue C, Marenda M, Jacob D, Barre A, Barbe V, Schenowitz C, Mangenot S, Couloux A, Segurens B, et al. Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet 2007, 3(5):e75.. 10.1371/journal.pgen.0030075, 1868952, 17511520.
17. del Solar G, Moscoso M, Espinosa M. Rolling circle-replicating plasmids from gram-positive and gram-negative bacteria: a wall falls. Mol Microbiol 1993, 8(5):789-796. 10.1111/j.1365-2958.1993.tb01625.x, 8355606.
18. del Solar G, Acebo P, Espinosa M. Replication control of plasmid pLS1: efficient regulation of plasmid copy number is exerted by the combined action of two plasmid components, CopG and RNA II. Mol Microbiol 1995, 18(5):913-924. 10.1111/j.1365-2958.1995.18050913.x, 8825095.
19. King KW, Woodard A, Dybvig K. Cloning and characterization of the recA genes from Mycoplasma pulmonis and M. mycoides subsp. mycoides. Gene 1994, 139(1):111-115. 10.1016/0378-1119(94)90532-0, 8112579.
20. Bergemann AD, Whitley JC, Finch LR. Homology of mycoplasma plasmid pADB201 and staphylococcal plasmid pE194. J Bacteriol 1989, 171(1):593-595. 209630, 2644210.
21. Djordjevic SP, Forbes WA, Forbes-Faulkner J, Kuhnert P, Hum S, Hornitzky MA, Vilei EM, Frey J. Genetic diversity among Mycoplasma species bovine group 7: Clonal isolates from an outbreak of polyarthritis, mastitis, and abortion in dairy cattle. Electrophoresis 2001, 22(16):3551-3561. 10.1002/1522-2683(200109)22:16<3551::AID-ELPS3551>3.0.CO;2-#, 11669541.
22. Schönert S, Seitz S, Krafft H, Feuerbaum E-A, Andernach I, Witz G, Dahl MK. Maltose and Maltodextrin Utilization by Bacillus subtilis. J Bacteriol 2006, 188(11):3911-3922. 1482931, 16707683.
23. Persson A, Jacobsson K, Frykberg L, Johansson K-E, Poumarat F. Variable Surface Protein Vmm of Mycoplasma mycoides subsp. mycoides Small Colony Type. J Bacteriol 2002, 184(13):3712-3722. 10.1128/JB.184.13.3712-3722.2002, 135138, 12057968.
24. Churchward G. Back to the future: the new ICE age. Mol Microbiol 2008, 70(3):554-556. 10.1111/j.1365-2958.2008.06415.x, 18761693.
25. Burrus V, Pavlovic G, Decaris B, Guédon G. Conjugative transposons: the tip of the iceberg. Mol Microbiol 2002, 46(3):601-610. 10.1046/j.1365-2958.2002.03191.x, 12410819.
26. Calcutt MJ, Lewis MS, Wise KS. Molecular Genetic Analysis of ICEF, an Integrative Conjugal Element That Is Present as a Repetitive Sequence in the Chromosome of Mycoplasma fermentans PG18. J Bacteriol 2002, 184(24):6929-6941. 10.1128/JB.184.24.6929-6941.2002, 135467, 12446643.
27. Marenda M, Barbe V, Gourgues G, Mangenot S, Sagne E, Citti C. A New Integrative Conjugative Element Occurs in Mycoplasma agalactiae as Chromosomal and Free Circular Forms. J Bacteriol 2006, 188(11):4137-4141. 10.1128/JB.00114-06, 1482908, 16707706.
28. Cho N-H, Kim H-R, Lee J-H, Kim S-Y, Kim J, Cha S, Kim S-Y, Darby AC, Fuxelius H-H, Yin J, et al. The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc Natl Acad Sci USA 2007, 104(19):7981-7986. 10.1073/pnas.0611553104, 1876558, 17483455.
29. Nakayama K, Yamashita A, Kurokawa K, Morimoto T, Ogawa M, Fukuhara M, Urakami H, Ohnishi M, Uchiyama I, Ogura Y, et al. The Whole-genome Sequencing of the Obligate Intracellular Bacterium Orientia tsutsugamushi Revealed Massive Gene Amplification During Reductive Genome Evolution. DNA Res 2008, 15(4):185-199. 10.1093/dnares/dsn011, 2575882, 18508905.
30. Auchtung JM, Lee CA, Monson RE, Lehman AP, Grossman AD. Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci USA 2005, 102(35):12554-12559. 10.1073/pnas.0505835102, 1194945, 16105942.
31. Marrero J, Waldor MK. Determinants of Entry Exclusion within Eex and TraG Are Cytoplasmic. J Bacteriol 2007, 189(17):6469-6473. 10.1128/JB.00522-07, 1951900, 17573467.
32. Siguier P, Filée J, Chandler M. Insertion sequences in prokaryotic genomes. Curr Opin Microbiol 2006, 9(5):526-531. 10.1016/j.mib.2006.08.005, 16935554.
33. Thomas A, Linden A, Mainil J, Bischof DF, Frey J, Vilei EM. Mycoplasma bovis shares insertion sequences with Mycoplasma agalactiae and Mycoplasma mycoides subsp. mycoides SC: Evolutionary and developmental aspects. FEMS Microbiol Lett 2005, 245(2):249-255. 10.1016/j.femsle.2005.03.013, 15837379.
34. Darling AE, Miklós I, Ragan MA. Dynamics of Genome Rearrangement in Bacterial Populations. PLoS Genet 2008, 4(7):e1000128.. 10.1371/journal.pgen.1000128, 2483231, 18650965.
35. Fournier PE, Kardouri KE, Leroy Q, Robert C, Giumelli B, Renesto P, Socolovoschi C, Parola P, Audic S, Raoult D. Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction. BMC Genomics 2009, 10:166. 10.1186/1471-2164-10-166, 2694212, 19379498.
36. Hjerde E, Lorentzen M, Holden M, Seeger K, Paulsen S, Bason N, Churcher C, Harris D, Norbertczak H, Quail M, et al. The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay. BMC Genomics 2008, 9(1):616.. 10.1186/1471-2164-9-616, 2627896, 19099551.
37. Thomas A, Linden A, Mainil J, Dizier I, Baseman JB, Kannan TR, Fleury B, Frey J, Vilei EM. The p40 adhesin pseudogene of Mycoplasma bovis. Vet Microbiol 2004, 104(3-4):213-217. 10.1016/j.vetmic.2004.09.009, 15564030.
38. Manso-Silván L, Perrier X, Thiaucourt F. Phylogeny of the Mycoplasma mycoides cluster based on analysis of five conserved protein-coding sequences: consequences in taxonomy. Int J Syst Evol Microbiol 2007, 57:2247-2258.
39. Abu-Groun EA, Taylor RR, Varsani H, Wadher BJ, Leach RH, Miles RJ. Biochemical diversity within the "Mycoplasma mycoides" cluster. Microbiology 1994, 140(8):2033-2042. 10.1099/13500872-140-8-2033, 7921253.
40. Rice P, Houshaymi BM, Nicholas RA, Miles RJ. A rapid biochemical test to aid identification of Mycoplasma mycoides subsp. mycoides small colony (SC) strains. Lett Appl Microbiol 2000, 30(1):70-74. 10.1046/j.1472-765x.2000.00674.x, 10728565.
41. Vilei E, Correia I, Ferronha MH, Bischof D, Frey J. beta-D-Glucoside utilization by Mycoplasma mycoides subsp. mycoides SC: possible involvement in the control of cytotoxicity towards bovine lung cells. BMC Microbiology 2007, 7(1):31.. 10.1186/1471-2180-7-31, 1855930, 17439646.
42. Moussa A, Nir-Paz R, Rottem S. Binding of IgA by Mycoplasma penetrans. Curr Microbiol 2009, 58(4):360-365. 10.1007/s00284-009-9359-1, 19189179.
43. Citti C, Rosengarten R. Mycoplasma genetic variation and its implication for pathogenesis. Wien Klin Wochenschr 1997, 109(14-15):562-568.
44. Harada K, Tanaka H, Komori S, Tsuji Y, Nagata K, Tsutsui H, Koyama K. Vaginal infection with Ureaplasma urealyticum accounts for preterm delivery via induction of inflammatory responses. Microbiol Immunol 2008, 52(6):297-304. 10.1111/j.1348-0421.2008.00039.x, 18577163.
45. Dedieu L, Totte P, Rodrigues V, Vilei EM, Frey J. Comparative analysis of four lipoproteins from Mycoplasma mycoides subsp. mycoides Small Colony identifies LppA as a major T-cell antigen. Comp Immunol Microbiol Inf Dis 2009, Corrected Proof.
46. Hallamaa K, Tang S-L, Ficorilli N, Browning G. Differential expression of lipoprotein genes in Mycoplasma pneumoniae after contact with human lung epithelial cells, and under oxidative and acidic stress. BMC Microbiology 2008, 8(1):124.. 10.1186/1471-2180-8-124, 2515320, 18647421.
47. Riehle MM, Bennett AF, Long AD. Genetic architecture of thermal adaptation in Escherichia coli. Proc Natl Acad Sci USA 2001, 98(2):525-530. 10.1073/pnas.021448998, 14620, 11149947.
48. Mira A, Klasson L, Andersson SGE. Microbial genome evolution: sources of variability. Curr Opin Microbiol 2002, 5(5):506-512. 10.1016/S1369-5274(02)00358-2, 12354559.
49. Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucl Acids Res 2008, 36(21):6688-6719. 10.1093/nar/gkn668, 2588523, 18948295.
50. Lynch M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA 2007, 104(Suppl 1):8597-8604. 10.1073/pnas.0702207104, 1876435, 17494740.
51. Janis C, Lartigue C, Frey J, Wroblewski H, Thiaucourt F, Blanchard A, Sirand-Pugnet P. Versatile Use of oriC Plasmids for Functional Genomics of Mycoplasma capricolum subsp. capricolum. Appl Environ Microbiol 2005, 71(6):2888-2893. 10.1128/AEM.71.6.2888-2893.2005, 1151838, 15932982.
52. Janis C, Bischof D, Gourgues G, Frey J, Blanchard A, Sirand-Pugnet P. Unmarked insertional mutagenesis in the bovine pathogen Mycoplasma mycoides subsp. mycoides SC: characterization of a lppQ mutant. Microbiology 2008, 154(Pt 8):2427-2436. 10.1099/mic.0.2008/017640-0, 2628567, 18667575.
53. Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, Bataille E, Dossat C, Gas S, Kreimeyer A, Lenoble P, et al. Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles. PLoS ONE 2008, 3(3):e1805.. 10.1371/journal.pone.0001805, 2265553, 18350144.
54. Frangeul L, Glaser P, Rusniok C, Buchrieser C, Duchaud E, Dehoux P, Kunst F. CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projects. Bioinformatics 2004, 20(5):790-797. 10.1093/bioinformatics/btg490, 14752000.
55. Isono K, McIninch JD, Borodovsky M. Characteristic Features of the Nucleotide Sequences of Yeast Mitochondrial Ribosomal Protein Genes as Analyzed by Computer Program GeneMark. DNA Res 1994, 1(6):263-269. 10.1093/dnares/1.6.263, 7719921.
56. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
57. Barre A, de Daruvar A, Blanchard A. MolliGen, a database dedicated to the comparative genomics of Mollicutes. Nucl Acids Res 2004, 32(suppl_1):D307-310. 10.1093/nar/gkh114, 308848, 14681420.
58. Rice P, Longden I, Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
59. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, et al. New developments in the InterPro database. Nucl Acids Res 2007, 35(suppl_1):D224-228. 10.1093/nar/gkl841, 1899100, 17202162.
60. Hulo N, Sigrist CJA, Le Saux V, Langendijk-Genevaux PS, Bordoli L, Gattiker A, De Castro E, Bucher P, Bairoch A. Recent improvements to the PROSITE database. Nucl Acids Res 2004, 32(suppl_1):D134-137. 10.1093/nar/gkh044, 308778, 14681377.
61. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 2001, 305(3):567-580. 10.1006/jmbi.2000.4315, 11152613.
62. Lowe T, Eddy S. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 1997, 25(5):955-964. 10.1093/nar/25.5.955, 146525, 9023104.
63. Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J. 5 S Ribosomal RNA Database. Nucl Acids Res 2002, 30(1):176-178. 10.1093/nar/30.1.176, 99124, 11752286.
64. Wuyts J, Perriere G, Van de Peer Y. The European ribosomal RNA database. Nucl Acids Res 2004, 32(suppl_1):D101-103. 10.1093/nar/gkh065, 308799, 14681368.
65. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements. Genome Res 2004, 14(7):1394-1403. 10.1101/gr.2289704, 442156, 15231754.
66. Uchiyama I. MBGD: microbial genome database for comparative analysis. Nucl Acids Res 2003, 31(1):58-62. 10.1093/nar/gkg109, 165556, 12519947.
67. Uchiyama I. MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucl Acids Res 2007, 35(suppl_1):D343-346. 10.1093/nar/gkl978, 1751538, 17135196.
68. Bergemann AD, Whitley JC, Finch LR. Taxonomic significance of differences in DNA methylation within the Mycoplasma mycoides cluster detected with restriction endonucleases MboI and DpnI. Lett Appl Microbiol 1990, 11:48-51.
69. Smith GR, Oliphant JC. Some in-vitro characters of the subspecies of Mycoplasma mycoides. J Hyg (Lond) 1982, 89(3):521-527. 10.1017/S0022172400071096, 2134239, 6759579.
70. Nicholas RA, Bashiruddin JB. Mycoplasma mycoides subspecies mycoides (small colony variant): the agent of contagious bovine pleuropneumonia and member of the "Mycoplasma mycoides cluster". J Comp Pathol 1995, 113(1):1-27. 10.1016/S0021-9975(05)80065-9, 7490334.
71. Carver TJ, Rutherford KM, Berriman M, Rajandream M-A, Barrell BG, Parkhill J. ACT: the Artemis comparison tool. Bioinformatics 2005, 21(16):3422-3423. 10.1093/bioinformatics/bti553, 15976072.