Characterization of species-specific repeats in 613 prokaryotic species

DNA Research

Volumn 19, Issue 3, 2012, Pages 219-230

  Koressaar, Triinu ^a   Remm, Maido ^a  

^a UNIVERSITY OF TARTU   (Estonia)

Author keywords

identification; pathogen; prokaryote; repeat; species specific

Indexed keywords

RIBOSOME RNA; TRANSFER RNA;

ARTICLE; GENE DUPLICATION; GENE FREQUENCY; GENE SEQUENCE; GENETIC ANALYSIS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PROKARYOTE;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, RIBOSOMAL; RNA, TRANSFER; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 84863604154     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dss006     Document Type: Article

References (41)

1. Koonin, E. V. and Wolf, Y. I. 2008, Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world, Nucleic Acids Res., 36, 6688-719.
2. Nakabachi, A., Yamashita, A., Toh, H., et al. 2006, The 160-kilobase genome of the bacterial endosymbiont Carsonella, Science, 314, 267. (Pubitemid 44571965)
3. Schneiker, S., Perlova, O., Kaiser, O., et al. 2007, Complete genome sequence of the myxobacterium Sorangium cellulosum, Nat. Biotechnol., 25, 1281-9. (Pubitemid 350076516)
4. Delihas, N. 2008, Small mobile sequences in bacteria display diverse structure/function motifs, Mol. Microbiol., 67, 475-81.
5. Achaz, G., Rocha, E. P., Netter, P. and Coissac, E. 2002, Origin and fate of repeats in bacteria, Nucleic Acids Res., 30, 2987-94. (Pubitemid 34778159)
6. Wu, M., Sun, L. V., Vamathevan, J., et al. 2004, Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements, PLoS Biol., 2, E69.
7. Rocha, E. P. C., Danchin, A. and Viari, A. 1999, Functional and evolutionary roles of long repeats in prokaryotes, Res. Microbiol., 150, 725-33. (Pubitemid 30035892)
8. 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, 1219-30. (Pubitemid 29409866)
9. Smillie, C., Garcillan-Barcia, M. P., Francia, M. V., Rocha, E. P. and de la Cruz, F. 2010, Mobility of plasmids, Microbiol. Mol. Biol. Rev., 74, 434-52.
10. Mavrodi, D. V., Loper, J. E., Paulsen, I. T. and Thomashow, L. S. 2009, Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5, BMC Microbiol., 9, 8.
11. Toleman, M. A., Bennett, P. M. and Walsh, T. R. 2006, ISCR elements: novel gene-capturing systems of the 21st century? Microbiol. Mol. Biol. Rev., 70, 296-316. (Pubitemid 43898667)
12. Nesmelova, I. V. and Hackett, P. B. 2010, DDE transposases: Structural similarity and diversity, Adv. Drug Deliv. Rev., 62, 1187-1195.
13. Brochet, M., Da Cunha, V., Couve, E., Rusniok, C., Trieu- Cuot, P. and Glaser, P. 2009, Atypical association of DDE transposition with conjugation specifies a new family of mobile elements, Mol. Microbiol., 71, 948-59.
14. Wozniak, R. A. and Waldor, M. K. 2010, Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nat. Rev. Microbiol., 8, 552-63.
15. Tobes, R. and Pareja, E. 2006, Bacterial repetitive extragenic palindromic sequences are DNA targets for insertion sequence elements, BMC Genomics, 7, 62.
16. Mes, T. H. and Doeleman, M. 2006, Positive selection on transposase genes of insertion sequences in the Crocosphaera watsonii genome, J. Bacteriol., 188, 7176-85. (Pubitemid 44547622)
17. Nunvar, J., Huckova, T. and Licha, I. 2010, Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes, BMC Genomics, 11, 44.
18. Cortez, D., Forterre, P. and Gribaldo, S. 2009, A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes, Genome Biol., 10, R65.
19. Gogarten, J. P. and Townsend, J. P. 2005, Horizontal gene transfer, genome innovation and evolution, Nat. Rev. Microbiol., 3, 679-87.
20. Canchaya, C., Fournous, G., Chibani-Chennoufi, S., Dillmann, M. L. and Brussow, H. 2003, Phage as agents of lateral gene transfer, Curr. Opin. Microbiol., 6, 417-24. (Pubitemid 37075363)
21. Frost, L. S., Leplae, R., Summers, A. O. and Toussaint, A. 2005, Mobile genetic elements: the agents of open source evolution, Nat. Rev. Microbiol., 3, 722-32. (Pubitemid 41195088)
22. Ravin, N. V., Mardanov, A. V., Beletsky, A. V., et al. 2009, Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis, J. Bacteriol., 191, 2371-9.
23. Salzberg, S. L., Sommer, D. D., Schatz, M. C., et al. 2008, Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A, BMC Genomics, 9, 204.
24. Koressaar, T., Joers, K. and Remm, M. 2009, Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms, Bioinformatics, 25, 1349-55.
25. Fouts, D. E. 2006, Phage-Finder: automated identification and classification of prophage regions in complete bacterial genome sequences, Nucleic Acids Res., 34, 5839-51. (Pubitemid 44941163)
26. Varani, A. M., Siguier, P., Gourbeyre, E., Charneau, V. and Chandler, M. 2011, ISsaga is an ensemble of web-based methods for high throughput identification and semiautomatic annotation of insertion sequences in prokaryotic genomes, Genome Biol., 12, R30.
27. Grissa, I., Vergnaud, G. and Pourcel, C. 2007, CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Res., 35, W52-7.
28. Finn, R. D., Mistry, J., Tate, J., et al. 2010, The Pfam protein families database, Nucleic Acids Res., 38, D211-22.
29. Soda, S., Otsuki, H., Inoue, D., Tsutsui, H., Sei, K. and Ike, M. 2008, Transfer of antibiotic multiresistant plasmid RP4 from Escherichia coli to activated sludge bacteria, J. Biosci. Bioeng., 106, 292-6.
30. Zhao, F., Bai, J., Wu, J., et al. 2010, Sequencing and genetic variation of multidrug resistance plasmids in Klebsiella pneumoniae, PLoS One, 5, e10141.
31. Bachellier, S., Clement, J. M., Hofnung, M. and Gilson, E. 1997, Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence, Genetics, 145, 551-62. (Pubitemid 27108011)
32. Sharples, G. J. and Lloyd, R. G. 1990, A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes, Nucleic Acids Res., 18, 6503-8.
33. Chen, S. L. and Shapiro, L. 2003, Identification of long intergenic repeat sequences associated withDNAmethylation sites in Caulobacter crescentus and other alpha-proteobacteria, J. Bacteriol., 185, 4997-5002. (Pubitemid 36962308)
34. Doolittle, W. F. and Sapienza, C. 1980, Selfish genes, the phenotype paradigm and genome evolution, Nature, 284, 601-3.
35. Orgel, L. E. and Crick, F. H. 1980, Selfish DNA: the ultimate parasite, Nature, 284, 604-7. (Pubitemid 10070866)
36. Lynch, M., O'Hely, M., Walsh, B. and Force, A. 2001, The probability of preservation of a newly arisen gene duplicate, Genetics, 159, 1789-804. (Pubitemid 34087615)
37. Bolhuis, A. 2004, The archaeal Sec-dependent protein translocation pathway, Philos. Trans. R. Soc. Lond. B Biol. Sci., 359, 919-27. (Pubitemid 38784080)
38. Holland, K. A. and Holland, I. B. 2005, Adventures with ABC-proteins: highly conserved ATP-dependent transporters, Acta Microbiol. Immunol. Hung., 52, 309-22. (Pubitemid 41804777)
39. Lally, E. T., Hill, R. B., Kieba, I. R. and Korostoff, J. 1999, The interaction between RTX toxins and target cells, Trends Microbiol., 7, 356-61. (Pubitemid 29421660)
40. Achtman, M. and Wagner, M. 2008, Microbial diversity and the genetic nature of microbial species, Nat. Rev. Microbiol., 6, 431-40. (Pubitemid 351696437)
41. Belanger, S. D., Boissinot, M., Menard, C., Picard, F. J. and Bergeron, M. G. 2002, Rapid detection of Shiga toxinproducing bacteria in feces by multiplex PCR with molecular beacons on the smart cycler, J. Clin. Microbiol., 40, 1436-40. (Pubitemid 34279913)