Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (234K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (63)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Rocha, E. P. C.
Right arrow Articles by Blanchard, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rocha, E. P. C.
Right arrow Articles by Blanchard, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2002, Vol. 30, No. 9 2031-2042
© 2002 Oxford University Press

Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution

Eduardo P. C. Rocha1,2,* and Alain Blanchard3

1Atelier de Bioinformatique, 12 Rue Cuvier, 75005 Paris, France, 2Unité GGB, URA2171, Institut Pasteur, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France and 3INRA–Université de Bordeaux 2, Institut de Biologie Végétale Moléculaire, 71 Avenue Edouard Bourleaux, BP 81, 33883 Villenave d‘Ornon Cedex, France

Mycoplasmas evolved by a drastic reduction in genome size, but their genomes contain numerous repeated sequences with important roles in their evolution. We have established a bioinformatic strategy to detect the major recombination hot-spots in the genomes of Mycoplasma pneumoniae, Mycoplasma genitalium, Ureaplasma urealyticum and Mycoplasma pulmonis. This allowed the identification of large numbers of potentially variable regions, as well as a comparison of the relative recombination potentials of different genomic regions. Different trends are perceptible among mycoplasmas, probably due to different functional and structural constraints. The largest potential for illegitimate recombination in M.pulmonis is found at the vsa locus and its comparison in two different strains reveals numerous changes since divergence. On the other hand, the main M.pneumoniae and M.genitalium adhesins rely on large distant repeats and, hence, homologous recombination for variation. However, the relation between the existence of repeats and antigenic variation is not necessarily straightforward, since repeats of P1 adhesin were found to be anti-correlated with epitopes recognized by patient antibodies. These different strategies have important consequences for the structures of genomes, since large distant repeats correlate well with the major chromosomal rearrangements. Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in comparison to co-oriented repeats.

* To whom correspondence should be addressed at: Atelier de Bioinformatique, 12 Rue Cuvier, 75005 Paris, France. Tel: +33 1 44 27 65 36; Fax: +33 1 44 27 63 12; Email: erocha{at}abi.snv.jussieu.fr


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 MicrobiologyHome page
E. B. M. Spuesens, M. Oduber, T. Hoogenboezem, M. Sluijter, N. G. Hartwig, A. M. C. van Rossum, and C. Vink
Sequence variations in RepMP2/3 and RepMP4 elements reveal intragenomic homologous DNA recombination events in Mycoplasma pneumoniae
Microbiology, July 1, 2009; 155(7): 2182 - 2196.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J.-Q. Chen, Y. Wu, H. Yang, J. Bergelson, M. Kreitman, and D. Tian
Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria
Mol. Biol. Evol., July 1, 2009; 26(7): 1523 - 1531.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
S. Degrange, C. Cazanave, A. Charron, H. Renaudin, C. Bebear, and C. M. Bebear
Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Molecular Typing of Mycoplasma pneumoniae
J. Clin. Microbiol., April 1, 2009; 47(4): 914 - 923.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
K. Dybvig, C. Zuhua, P. Lao, D. S. Jordan, C. T. French, A.-H. T. Tu, and A. E. Loraine
Genome of Mycoplasma arthritidis
Infect. Immun., September 1, 2008; 76(9): 4000 - 4008.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
L. T. T. Tran-Nguyen, M. Kube, B. Schneider, R. Reinhardt, and K. S. Gibb
Comparative Genome Analysis of "Candidatus Phytoplasma australiense" (Subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains OY-M and AY-WB
J. Bacteriol., June 1, 2008; 190(11): 3979 - 3991.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
O. Musatovova, T. R. Kannan, and J. B. Baseman
Genomic Analysis Reveals Mycoplasma pneumoniae Repetitive Element 1-Mediated Recombination in a Clinical Isolate
Infect. Immun., April 1, 2008; 76(4): 1639 - 1648.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Mrazek, X. Guo, and A. Shah
Simple sequence repeats in prokaryotic genomes
PNAS, May 15, 2007; 104(20): 8472 - 8477.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
K. Dybvig, Z. Cao, C. T. French, and H. Yu
Evidence for Type III Restriction and Modification Systems in Mycoplasma pulmonis
J. Bacteriol., March 15, 2007; 189(6): 2197 - 2202.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
S. L. Iverson-Cabral, S. G. Astete, C. R. Cohen, E. P. C. Rocha, and P. A. Totten
Intrastrain Heterogeneity of the mgpB Gene in Mycoplasma genitalium Is Extensive In Vitro and In Vivo and Suggests that Variation Is Generated via Recombination with Repetitive Chromosomal Sequences
Infect. Immun., July 1, 2006; 74(7): 3715 - 3726.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. Mrazek
Analysis of Distribution Indicates Diverse Functions of Simple Sequence Repeats in Mycoplasma Genomes
Mol. Biol. Evol., July 1, 2006; 23(7): 1370 - 1385.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
T. Tsuru, M. Kawai, Y. Mizutani-Ui, I. Uchiyama, and I. Kobayashi
Evolution of Paralogous Genes: Reconstruction of Genome Rearrangements Through Comparison of Multiple Genomes Within Staphylococcus aureus
Mol. Biol. Evol., June 1, 2006; 23(6): 1269 - 1285.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
X. Bai, J. Zhang, A. Ewing, S. A. Miller, A. Jancso Radek, D. V. Shevchenko, K. Tsukerman, T. Walunas, A. Lapidus, J. W. Campbell, et al.
Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts.
J. Bacteriol., May 1, 2006; 188(10): 3682 - 3696.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
O. Musatovova, C. Herrera, and J. B. Baseman
Proximal Region of the Gene Encoding Cytadherence-Related Protein Permits Molecular Typing of Mycoplasma genitalium Clinical Strains by PCR-Restriction Fragment Length Polymorphism
J. Clin. Microbiol., February 1, 2006; 44(2): 598 - 603.
[Abstract] [Full Text] [PDF]

Home page
 Antimicrob. Agents Chemother.Home page
L. F. Fehri, P. Sirand-Pugnet, G. Gourgues, G. Jan, H. Wroblewski, and A. Blanchard
Resistance to Antimicrobial Peptides and Stress Response in Mycoplasma pulmonis
Antimicrob. Agents Chemother., October 1, 2005; 49(10): 4154 - 4165.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
A. T. R. Vasconcelos, H. B. Ferreira, C. V. Bizarro, S. L. Bonatto, M. O. Carvalho, P. M. Pinto, D. F. Almeida, L. G. P. Almeida, R. Almeida, L. Alves-Filho, et al.
Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae
J. Bacteriol., August 15, 2005; 187(16): 5568 - 5577.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
J. Kang, S. Huang, and M. J. Blaser
Structural and Functional Divergence of MutS2 from Bacterial MutS1 and Eukaryotic MSH4-MSH5 Homologs
J. Bacteriol., May 15, 2005; 187(10): 3528 - 3537.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
C. Foucault, B. La Scola, H. Lindroos, S. G. E. Andersson, and D. Raoult
Multispacer Typing Technique for Sequence-Based Typing of Bartonella quintana
J. Clin. Microbiol., January 1, 2005; 43(1): 41 - 48.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
I. Catrein, R. Dumke, J. Weiner III, E. Jacobs, and R. Herrmann
Cross-complementation between the products of the genes P1 and ORF6 of Mycoplasma pneumoniae subtypes 1 and 2
Microbiology, December 1, 2004; 150(12): 3989 - 4000.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
L. Gomez-Valero, A. Latorre, and F. J. Silva
The Evolutionary Fate of Nonfunctional DNA in the Bacterial Endosymbiont Buchnera aphidicola
Mol. Biol. Evol., November 1, 2004; 21(11): 2172 - 2181.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
F. Kong and G. L. Gilbert
Postgenomic taxonomy of human ureaplasmas - a case study based on multiple gene sequences
Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1815 - 1821.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
Y.-C. Li, A. B. Korol, T. Fahima, and E. Nevo
Microsatellites Within Genes: Structure, Function, and Evolution
Mol. Biol. Evol., June 1, 2004; 21(6): 991 - 1007.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. R. Denver, S. L. Swenson, and M. Lynch
An Evolutionary Analysis of the Helix-Hairpin-Helix Superfamily of DNA Repair Glycosylases
Mol. Biol. Evol., October 1, 2003; 20(10): 1603 - 1611.
[Abstract] [Full Text]

Home page
 GeneticsHome page
G. Achaz, E. Coissac, P. Netter, and E. P. C. Rocha
Associations Between Inverted Repeats and the Structural Evolution of Bacterial Genomes
Genetics, August 1, 2003; 164(4): 1279 - 1289.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
E. P.C. Rocha
An Appraisal of the Potential for Illegitimate Recombination in Bacterial Genomes and Its Consequences: From Duplications to Genome Reduction
Genome Res., June 1, 2003; 13(6): 1123 - 1132.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
V. Daubin and G. Perriere
G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes
Mol. Biol. Evol., April 1, 2003; 20(4): 471 - 483.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. P. C. Rocha, O. Pradillon, H. Bui, C. Sayada, and E. Denamur
A new family of highly variable proteins in the Chlamydophila pneumoniae genome
Nucleic Acids Res., October 15, 2002; 30(20): 4351 - 4360.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Achaz, E. P. C. Rocha, P. Netter, and E. Coissac
Origin and fate of repeats in bacteria
Nucleic Acids Res., July 1, 2002; 30(13): 2987 - 2994.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.