Evolution of mollicutes: down a bumpy road with twists and turns

Research in Microbiology

Volumn 158, Issue 10, 2007, Pages 754-766

  Sirand Pugnet, Pascal ^a   Citti, Christine ^b   Barré, Aurélien ^a   Blanchard, Alain ^a  

^a UNIVERSITÉ DE BORDEAUX   (France)

^b IHAP   (France)

Author keywords

Genome evolution; Horizontal gene transfer; Low GC genomes; Mycoplasma

Indexed keywords

TRYPTOPHAN;

ARTICLE; BACTERIAL GENE; BODY GROWTH; CELL CYCLE; GENE CLUSTER; GENE STRUCTURE; GENE TRANSFER; MOLLICUTES; NONHUMAN; PRIORITY JOURNAL; RNA TRANSLATION;

MOLLICUTES; MYCOPLASMA;

EID: 36849045236     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2007.09.007     Document Type: Article

References (62)

1. Bai X., Zhang J., Ewing A., et al. Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J. Bacteriol. 188 (2006) 3682-3696
2. Bai X., Zhang J., Holford I.R., and Hogenhout S.A. Comparative genomics identifies genes shared by distantly related insect-transmitted plant pathogenic mollicutes. FEMS Microbiol. Lett. 235 (2004) 249-258
3. Baumann P., Baumann L., Lai C.Y., Rouhbakhsh D., Moran N.A., and Clark M.A. Genetics, physiology, and evolutionary relationships of the genus Buchnera: intracellular symbionts of aphids. Annu. Rev. Microbiol. 49 (1995) 55-94
4. Beaman K.D., and Pollack J.D. Synthesis of adenylate nucleotides by Mollicutes (mycoplasmas). J. Gen. Microbiol. 129 (1983) 3103-3110
5. Brown D.R., Zacher L.A., and Farmerie W.G. Spreading factors of Mycoplasma alligatoris, a flesh-eating mycoplasma. J. Bacteriol. 186 (2004) 3922-3927
6. Chambaud I., Heilig R., Ferris S., et al. The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res. 29 (2001) 2145-2153
7. Chopra-Dewasthaly R., Marenda M., Rosengarten R., Jechlinger W., and Citti C. Construction of the first shuttle vectors for gene cloning and homologous recombination in Mycoplasma agalactiae. FEMS Microbiol. Lett. 253 (2005) 89-94
8. Ciccarelli F.D., Doerks T., von Mering C., Creevey C.J., Snel B., and Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 311 (2006) 1283-1287
9. Citti C., Browning G.F., and Rosengarten R. Phenotypic diversity and cell invasion in host subversion by pathogenic mycoplasmas. In: Blanchard A., and Browning G.F. (Eds). Mycoplasmas: Molecular Biology, Pathogenicity and Strategies for Control (2005), Horizon Scientific Press, Norwich, UK 439-483
10. Clements M.O., Eriksson S., Thompson A., Lucchini S., Hinton J.C., Normark S., and Rhen M. Polynucleotide phosphorylase is a global regulator of virulence and persistency in Salmonella enterica. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 8784-8789
11. Cordova C.M., Lartigue C., Sirand-Pugnet P., Renaudin J., Cunha R.A., and Blanchard A. Identification of the origin of replication of the Mycoplasma pulmonis chromosome and its use in oriC replicative plasmids. J. Bacteriol. 184 (2002) 5426-5435
12. Dagan T., and Martin W. Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 870-875
13. Dandekar T., Snel B., Schmidt S., Lathe W., Suyama M., Huynen M., and Bork P. Comparative genome analysis of the mollicutes. In: Razin S., and Herrmann R. (Eds). Molecular Biology and Pathogenity of Mycoplasmas (2002), Kluwer Academic/Plenum Publisher, New York 255-278
14. Enright A.J., Kunin V., and Ouzounis C.A. Protein families and TRIBES in genome sequence space. Nucleic Acids Res. 31 (2003) 4632-4638
15. Fraser C.M., Gocayne J.D., White O., et al. The minimal gene complement of Mycoplasma genitalium. Science 270 (1995) 397-403
16. Gil R., Silva F.J., Pereto J., and Moya A. Determination of the core of a minimal bacterial gene set. Microbiol. Mol. Biol. Rev. 68 (2004) 518-537
17. Glass J.I., Assad-Garcia N., Alperovich N., Yooseph S., Lewis M.R., Maruf M., Hutchison III C.A., Smith H.O., and Venter J.C. Essential genes of a minimal bacterium. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 425-430
18. Glass J.I., Lefkowitz E.J., Glass J.S., Heiner C.R., Chen E.Y., and Cassell G.H. The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature 407 (2000) 757-762
19. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B.C., and Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24 (1996) 4420-4449
20. Jaffe J.D., Stange-Thomann N., Smith C., et al. The complete genome and proteome of Mycoplasma mobile. Genome Res. 14 (2004) 1447-1461
21. Janis C., Lartigue C., Frey J., Wroblewski H., Thiaucourt F., Blanchard A., and Sirand-Pugnet P. Versatile use of oriC plasmids for functional genomics of Mycoplasma capricolum subsp. capricolum. Appl. Environ. Microbiol. 71 (2005) 2888-2893
22. Johansson K.E., and Pettersson B. In: Razin S., and Herrmann R. (Eds). Molecular Biology and Pathogenicity of Mycoplasmas (2002), Kluwer Academic/Plenum Publisher, New York 1-30
23. Kobayashi K., Ehrlich S.D., Albertini A., et al. Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 4678-4683
24. Koonin E.V. Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 39 (2005) 309-338
25. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5 (2004) 150-163
26. Lartigue C., Blanchard A., Renaudin J., Thiaucourt F., and Sirand-Pugnet P. Host specificity of mollicutes oriC plasmids: functional analysis of replication origin. Nucleic Acids Res. 31 (2003) 6610-6618
27. Lee I.M., Davis R.E., and Gundersen-Rindal D.E. Phytoplasma: phytopathogenic mollicutes. Annu. Rev. Microbiol. 54 (2000) 221-255
28. Lobry J.R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13 (1996) 660-665
29. Lowe T.M., and Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (1997) 955-964
30. Maniloff J. Phylogeny and evolution. In: Razin S., and Herrmann R. (Eds). Molecular Biology and Pathogenicity of Mycoplasmas (2002), Kluwer Academic/Plenum Publisher, New York 31-43
31. Minion F.C., Lefkowitz E.J., Madsen M.L., Cleary B.J., Swartzell S.M., and Mahairas G.G. The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J. Bacteriol. 186 (2004) 7123-7133
32. Mirkin B.G., Fenner T.I., Galperin M.Y., and Koonin E.V. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 3 (2003) 2
33. Morowitz H.J. The completeness of molecular biology. Isr. J. Med. Sci. 20 (1984) 750-753
34. Notredame C., Higgins D.G., and Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302 (2000) 205-217
35. Oba T., Andachi Y., Muto A., and Osawa S. CGG: an unassigned or nonsense codon in Mycoplasma capricolum. Proc. Natl. Acad. Sci. U.S.A. 88 (1991) 921-925
36. Oshima K., Kakizawa S., Nishigawa H., et al. Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat. Genet. 36 (2004) 27-29
37. Papazisi L., Gorton T.S., Kutish G., et al. The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain R(low). Microbiology 149 (2003) 2307-2316
38. Peterson S.N., and Fraser C.M. The complexity of simplicity. Genome Biol. 2 (2001) COMMENT2002
39. Ranea J.A., Buchan D.W., Thornton J.M., and Orengo C.A. Evolution of protein superfamilies and bacterial genome size. J. Mol. Biol. 336 (2004) 871-887
40. Razin S., Yogev D., and Naot Y. Molecular biology and pathogenicity of mycoplasmas. Microbiol. Mol. Biol. Rev. 62 (1998) 1094-1156
41. Rocha E.P. Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res. 14 (2004) 2279-2286
42. Rocha E.P., Cornet E., and Michel B. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet. 1 (2005) e15
43. Rocha E.P., Danchin A., and Viari A. Universal replication biases in bacteria. Mol. Microbiol. 32 (1999) 11-16
44. Rocha E.P., Sirand-Pugnet P., and Blanchard A. In: Blanchard A., and Browning G.F. (Eds). Mycoplasmas: Molecular Biology, Pathogenicity and Strategies for Control (2005), Horizon Scientific Press, Norwich, UK 31-73
45. Sasaki Y., Ishikawa J., Yamashita A., et al. The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans. Nucleic Acids Res. 30 (2002) 5293-5300
46. Selengut J.D., Haft D.H., Davidsen T., Ganapathy A., Gwinn-Giglio M., Nelson W.C., Richter A.R., and White O. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 35 (2007) D260-D264
47. Siguier P., Filee J., and Chandler M. Insertion sequences in prokaryotic genomes. Curr. Opin. Microbiol. 9 (2006) 526-531
48. Sirand-Pugnet P., Lartigue C., Marenda M., et al. Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet. 3 (2007) e75
49. Skamrov A., Feoktistova E., Goldman M., and Beabealashvilli R. Mycoplasma gallisepticum rpoA gene cluster. FEMS Microbiol. Lett. 208 (2002) 281-285
50. Snel B., Bork P., and Huynen M.A. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 12 (2002) 17-25
51. Tatusov R.L., Natale D.A., Garkavtsev I.V., et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29 (2001) 22-28
52. Touchon M., and Rocha E.P. Causes of insertion sequences abundance in prokaryotic genomes. Mol. Biol. Evol. 24 (2007) 969-981
53. Uchiyama I. MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucleic Acids Res. 35 (2007) D343-D346
54. Ussery D.W., and Hallin P.F. Genome Update: AT content in sequenced prokaryotic genomes. Microbiology 150 (2004) 749-752
55. Vasconcelos A.T., Ferreira H.B., Bizarro C.V., et al. Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. J. Bacteriol. 187 (2005) 5568-5577
56. Wagner A. Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes. Mol. Biol. Evol. 23 (2006) 723-733
57. Westberg J., Persson A., Holmberg A., Goesmann A., Lundeberg J., Johansson K.E., Pettersson B., and Uhlen M. The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res. 14 (2004) 221-227
58. Wise K.S., Foecking M.F., Roske K., Lee Y.J., Lee Y.M., Madan A., and Calcutt M.J. Distinctive repertoire of contingency genes conferring mutation-based phase variation and combinatorial expression of surface lipoproteins in Mycoplasma capricolum subsp. capricolum of the Mycoplasma mycoides phylogenetic cluster. J. Bacteriol. 188 (2006) 4926-4941
59. Woese C.R., Stackebrandt E., and Ludwig W. What are mycoplasmas: the relationship of tempo and mode in bacterial evolution. J. Mol. Evol. 21 (1984) 305-316
60. Ye F., Renaudin J., Bové J.M., and Laigret F. Cloning and sequencing of the replication origin (oriC) of the Spiroplasma citri chromosome and construction of autonomously replicating artificial plasmids. Curr. Microbiol. 29 (1994) 23-29
61. Zheng Y., Anton B.P., Roberts R.J., and Kasif S. Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics 6 (2005) 243
62. Zuo Y., and Deutscher M.P. Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res. 29 (2001) 1017-1026