Identification of a novel family of sequence repeats among prokaryotes

OMICS A Journal of Integrative Biology

Volumn 6, Issue 1, 2002, Pages 23-33

  Jansen, Rund ^a   Van Embden, Jam D A ^b   Gaastra, Wim ^a   Schouls, Leo M ^b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

PALINDROMIC DNA; SPACER DNA;

ALGORITHM; AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CAMPYLOBACTER; COMPARATIVE GENOMIC HYBRIDIZATION; CONSENSUS SEQUENCE; DNA FLANKING REGION; EUKARYOTE; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENOME; METHANOCOCCUS JANNASCHII; MYCOBACTERIUM TUBERCULOSIS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PASTEURELLA; PRIORITY JOURNAL; PROKARYOTE; SALMONELLA; SPECIES CONSERVATION; SPECIES DIFFERENCE; STRAIN DIFFERENCE; STRAIN IDENTIFICATION; TRANSPOSON; UNINDEXED SEQUENCE;

ARCHAEA; BACTERIA; BASE SEQUENCE; DNA, BACTERIAL; REPETITIVE SEQUENCES, NUCLEIC ACID; SOFTWARE;

ARCHAEA; BACTERIA (MICROORGANISMS); CAMPYLOBACTER; EUKARYOTA; METHANOCALDOCOCCUS JANNASCHII; METHANOCOCCUS; MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS; PASTEURELLA; PROKARYOTA; SALMONELLA; TRANSPOSONS;

EID: 0036408356     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/15362310252780816     Document Type: Article

References (24)

1. Bachellier, S., Perrin, D., Hofnung, M., et al. (1993). Bacterial interspersed mosaic elements (BIMEs) are present in the genome of Klebsiella. Mol Microbiol 7, 537-544.
2. Bachellier, S., Clement, J.M., Hofnung, M., et al. (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, 551-562.
3. Belland, R.J., Morrison, S.G., Carlson, J.H., et al. (1997). Promoter strength influences phase variation of neisserial opa genes. Mol Microbiol 23, 123-135.
4. Bult, C.J., White, O., Olsen, G.J., et al. (1996). Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073.
5. Correia, F.F., Inouye, S., and Inouye, M. (1988). A family of small repeated elements with some transposon-like properties in the genome of Neisseria gonorrhoeae. J Biol Chem 263, 12194-12198.
6. Dybvig, K. (1993). Dna rearrangements and phenotypic switching in prokaryotes. Mol Microbiol 10, 465-471.
7. Fang, Z., Morrison, N., Watt, B., et al. (1998). Is6110 transposition and evolutionary scenario of the direct repeat locus in a group of closely related Mycobacterium tuberculosis strains. J Bacteriol 180, 2102-2109.
8. Fleischmann, R.D., Adams, M.D., White, O., et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512.
9. Gilson, E., Clement, J.M., Brutlag, D., et al. (1984). A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J 3, 1417-1421.
10. Groenen, P.M., Bunschoten, A.E., Van Soolingen, D., et al. (1993). Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol Microbiol 10, 1057-1065.
11. Hoe, N., Nakashima, K., Grigsby, D., et al. (1999). Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains. Emerg Infect Dis 5, 254-263.
12. Hulton, C.S., Higgins, C.F., and Sharp, P.M. (1991). Eric sequences: A novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol 5, 825-834.
13. Ishino, Y., Shinagawa, H., Makino, K., et al. (1987). Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169, 5429-5433.
14. Kamerbeek, J., Schouls, L., Kolk, A., et al. (1997). Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35, 907-914.
15. Klenk, H.P., Clayton, R.A., Tomb, J.F., et al. (1997). The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobusfulgidus. Nature 390, 364-370.
16. Martin, B., Humbert, O., Camara, M., et al. (1992). A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Res 20, 3479-3483.
17. Masepohl, B., Gorlitz, K., and Bohme, H. (1996). Long tandemly repeated repetitive (LTRR) sequences in the filamentous cyanobacterium Anabaena sp. PCC 7120. Biochim Biophys Acta 1307, 26-30.
18. Mojica, F.J., Ferrer, C., Juez, G., et al. (1995). Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol Microbiol 17, 85-93.
19. Mojica, F.J., Diez-Villasenor, C., Soria, E., et al. (2000). Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol 36, 244-246.
20. Nakata, A., Amemura, M., and Makino, K. (1989). Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. J Bacteriol 171, 3553-3556.
21. Nelson, K.E., Clayton, R.A., Gill, S.R., et al. (1999). Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329.
22. Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., et al. (1997). Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics. J Bacteriol 179, 7135-7155.
23. Van Belkum, A., Scherer, S., Van Alphen, L., et al. (1998). Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62, 275-293.
24. Van Embden, J.D., Van Gorkom, T., Kremer, K., et al. (2000). Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J Bacteriol 182, 2393-2401.