Birth and death of genes linked to chromosomal inversion

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 4, 2011, Pages 1501-1506

  Furuta, Yoshikazu ^a   Kawai, Mikihiko ^a,b   Yahara, Koji ^c,d   Takahashi, Noriko ^a   Handa, Naofumi ^a   Tsuru, Takeshi ^a   Oshima, Kenshiro ^a   Yoshida, Masaru ^e   Azuma, Takeshi ^e   Hattori, Masahira ^a   Uchiyama, Ikuo ^b   Kobayashi, Ichizo ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^c KURUME UNIVERSITY   (Japan)

^d FUJITSU LABORATORIES LTD   (Japan)

^e KOBE UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

Author keywords

Gene duplication; Genome comparison; Genome rearrangement; Replicative inversion; Structural variation

Indexed keywords

OUTER MEMBRANE PROTEIN;

ARTICLE; CHROMOSOME DUPLICATION; CHROMOSOME INVERSION; DNA SEQUENCE; GENE LOCUS; GENE LOSS; GENETIC LINKAGE; HELICOBACTER PYLORI; HOMOLOGOUS RECOMBINATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SYNTENY;

BACTERIAL PROTEINS; BASE SEQUENCE; CHROMOSOME BREAKAGE; CHROMOSOME INVERSION; CHROMOSOMES, BACTERIAL; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, BACTERIAL; HELICOBACTER PYLORI; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; RECOMBINATION, GENETIC;

HELICOBACTER PYLORI;

EID: 79952129488     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1012579108     Document Type: Article

References (35)

1. Novick RP, Christie GE, Penadés JR (2010) The phage-related chromosomal islands of Gram-positive bacteria. Nat Rev Microbiol 8:541-551.
2. Ochman H, Davalos LM (2006) The nature and dynamics of bacterial genomes. Science 311:1730-1733.
3. Hastings PJ, Lupski JR, Rosenberg SM, Ira G (2009) Mechanisms of change in gene copy number. Nat Rev Genet 10:551-564.
4. Koonin EV, Wolf YI (2008) Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36:6688-6719.
5. Kuroda M, et al. (2001) Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357:1225-1240. (Pubitemid 32539050)
6. Tsuru T, Kobayashi I (2008) Multiple genome comparison within a bacterial species reveals a unit of evolution spanning two adjacent genes in a tandem paralog cluster. Mol Biol Evol 25:2457-2473.
7. Suerbaum S,Michetti P (2002) Helicobacter pylori infection. N Engl JMed 347:1175-1186.
8. Suerbaum S, Josenhans C (2007) Helicobacter pylori evolution and phenotypic diversification in a changing host. Nat Rev Microbiol 5:441-452. (Pubitemid 46780081)
9. Yamaoka Y, Alm RA (2008) Helicobacter pylori: Molecular Genetics and Cellular Biology, ed Yamaoka Y (Caister Academic, Hethersett. Norwich, UK), pp 37-60.
10. Yamaoka Y, Kwon DH, Graham DY (2000) A M(r) 34,000 proinflammatory outer membrane protein (oipA) of Helicobacter pylori. Proc Natl Acad Sci USA 97:7533-7538. (Pubitemid 30431498)
11. Alm RA, et al. (2000) Comparative genomics of Helicobacter pylori: Analysis of the outer membrane protein families. Infect Immun 68:4155-4168. (Pubitemid 30434570)
12. Shapiro JA (1979) Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc Natl Acad Sci USA 76: 1933-1937.
13. Kleckner N (1981) Transposable elements in prokaryotes. Annu Rev Genet 15: 341-404.
14. Oh JD, et al. (2006) The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression. Proc Natl Acad Sci USA 103:9999-10004. (Pubitemid 43993612)
15. Azuma T, et al. (2004) Distinct diversity of the cag pathogenicity island among Helicobacter pylori strains in Japan. J Clin Microbiol 42:2508-2517. (Pubitemid 38747498)
16. Schmid MB, Roth JR (1983) Genetic methods for analysis and manipulation of inversion mutations in bacteria. Genetics 105:517-537. (Pubitemid 14246273)
17. Fujitani Y, Kobayashi I (1999) Effect of DNA sequence divergence on homologous recombination as analyzed by a random-walk model. Genetics 153:1973-1988.
18. Alm RA, et al. (1999) Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176-180.
19. Tomb JF, et al. (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-547.
20. Kersulyte D, et al. (2009) Helicobacter pylori's plasticity zones are novel transposable elements. PLoS ONE 4:e6859.
21. Kersulyte D, Akopyants NS, Clifton SW, Roe BA, Berg DE (1998) Novel sequence organization and insertion specificity of IS605 and IS606: chimaeric transposable elements of Helicobacter pylori. Gene 223:175-186. (Pubitemid 29015926)
22. Nobusato A, Uchiyama I, Ohashi S, Kobayashi I (2000) Insertion with long target duplication: A mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene 259:99-108. (Pubitemid 32119241)
23. Furuta Y, Abe K, Kobayashi I (2010) Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements. Nucleic Acids Res 38:2428-2443.
24. Blanchette M, Kunisawa T, Sankoff D (1999) Gene order breakpoint evidence in animal mitochondrial phylogeny. J Mol Evol 49:193-203. (Pubitemid 29357862)
25. Kawai M, Nakao K, Uchiyama I, Kobayashi I (2006) How genomes rearrange: genome comparison within bacteria Neisseria suggests roles for mobile elements in formation of complex genome polymorphisms. Gene 383:52-63. (Pubitemid 44584586)
26. Iida S, Meyer J, Arber W (1981) Genesis and natural history of IS-mediated transposons. Cold Spring Harb Symp Quant Biol 45:27-43. (Pubitemid 11026001)
27. Dorer MS, Fero J, Salama NR (2010) DNA damage triggers genetic exchange in Helicobacter pylori. PLoS Pathog 6:e1001026.
28. Hastings PJ, Ira G, Lupski JR (2009) A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 5: e1000327.
29. Roberts RJ, et al. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31:1805-1812.
30. Hickman AB, et al. (2000) Unexpected structural diversity in DNA recombination: the restriction endonuclease connection. Mol Cell 5:1025-1034.
31. Uchiyama I, Higuchi T, Kobayashi I (2006) CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. BMC Bioinformatics 7:472.
32. Kawai M, Uchiyama I, Kobayashi I (2005) Genome comparison in silico in Neisseria suggests integration of filamentous bacteriophages by their own transposase. DNA Res 12:389-401. (Pubitemid 43843809)
33. Tsuru T, Kawai M, Mizutani-Ui Y, Uchiyama I, Kobayashi I (2006) Evolution of paralogous genes: Reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus. Mol Biol Evol 23:1269-1285. (Pubitemid 43781600)
34. Darling AC, Mau B, Blattner FR, Perna NT (2004) Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394-1403. (Pubitemid 39029237)
35. Bourque G, Pevzner PA (2002) Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res 12:26-36. (Pubitemid 34065587)