A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/cas subtypes exist in prokaryotic genomes

PLoS Computational Biology

Volumn 1, Issue 6, 2005, Pages 0474-0483

  Haft, Daniel H ^a   Selengut, Jeremy ^a   Mongodin, Emmanuel F ^a   Nelson, Karen E ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; HIDDEN MARKOV MODELS;

CAS GENES; GENETIC ELEMENTS; HIDDEN-MARKOV MODELS; HIGH SELECTIVITY; HIGH SENSITIVITY; MULTIPLE SEQUENCE ALIGNMENTS; PALINDROMIC; PROKARYOTIC GENOMES; PROKARYOTIC SPECIES; PROTEIN FAMILY;

PROTEINS;

PROTEIN;

ARCHAEAL GENE; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; CLASSIFICATION; DNA MICROARRAY; FUNGAL GENE; GENETICS; GENOME; HALOARCULA MARISMORTUI; METABOLISM; MULTIGENE FAMILY; NUCLEOTIDE REPEAT; PHYLOGENY; PROBABILITY; PROKARYOTIC CELL; YERSINIA PESTIS;

GENES, ARCHAEAL; GENES, BACTERIAL; GENES, FUNGAL; GENOME; GENOME, BACTERIAL; HALOARCULA MARISMORTUI; MARKOV CHAINS; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; PROKARYOTIC CELLS; PROTEINS; REPETITIVE SEQUENCES, NUCLEIC ACID; YERSINIA PESTIS;

EID: 34248400310     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010060     Document Type: Article

References (32)

1. Mojica FJ, Ferrer C, Juez G, Rodriguez-Valera F (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.
2. Mojica FJ, Diez-Villasenor C, Soria E, Juez G (2000) Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol 36: 244-246.
3. Jansen R, Embden JD, Gaastra W, Schouls LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43: 1565-1575.
4. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A (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.
5. Jansen R, van Embden JD, Gaastra W, Schouls LM (2002) Identification of a novel family of sequence repeats among prokaryotes. OMICS 6: 23-33.
6. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, et al. (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 98: 7835-7840.
7. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058-1073.
8. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, et al. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399: 323-329.
9. Greve B, Jensen S, Brugger K, Zillig W, Garrett RA (2004) Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1: 231-239.
10. Peng X, Brugger K, Shen B, Chen L, She Q, et al. (2003) Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes. J Bacteriol 185: 2410-2417.
11. Tang TH, Bachelle rie JP, Rozhdestvensky T, Bortolin ML, Huber H, et al. (2002) Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc Natl Acad Sci U S A 99: 7536-7541.
12. Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Soria E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60: 174-182.
13. Pourcel C, Salvignol G, Vergnaud G (2005) CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151: 653-663.
14. Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV (2002) A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res 30: 482-496.
15. Mongodin EF, Hance IR, DeBoy RT, Gill SR, Daugherty S, et al. (2005) Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species. J Bacteriol 187: 4935-4944.
16. Rogozin IB, Makarova KS, Murvai J, Czabarka E, Wolf YI, et al. (2002) Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res 30: 2212-2223.
17. Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, et al. (2000) The Pfam protein families database. Nucleic Acids Res 28: 263-266.
18. Ellehauge E, Norregaard-Madsen M, Sogaard-Andersen L (1998) The FruA signal transduction protein provides a checkpoint for the temporal coordination of intercellular signals in Myxococcus xanthus development. Mol Microbiol 30: 807-817.
19. Boysen A, Ellehauge E, Julien B, Sogaard-Andersen L (2002) The DevT protein stimulates synthesis of FruA, a signal transduction protein required for fruiting body morphogenesis in Myxococcus xanthus. J Bacteriol 184: 1540-1546.
20. Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O (2001) The Comprehensive Microbial Resource. Nucleic Acids Res 29: 123-125.
21. Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, et al. (2005) Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii. J Proteome Res 4: 464-472.
22. Thony-Meyer L, Kaiser D (1993) devRS, an autoregulated and essential genetic locus for fruiting body development in Myxococcus xanthus. J Bacteriol 175: 7450-7462.
23. Schouls LM, Reulen S, Duim B, Wagenaar JA, Willems RJ, et al. (2003) Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: Strain diversity, host range, and recombination. J Clin Microbiol 41: 15-26.
24. Methe BA, Webster J, Nevin K, Butler J, Lovley DR (2005) DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens. Appl Environ Microbiol 71: 2530-2538.
25. Stragier P, Ablordey A, Meyers WM, Portaels F (2005) Genotyping Mycobacterium ulcerans and Mycobacterium marinum by using mycobacterial interspersed repetitive units. J Bacteriol 187: 1639-1647.
26. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, et al. (1997) Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35: 907-914.
27. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et al. (2001) REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29: 4633-4642.
28. Kurtz S, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2000) Computation and visualization of degenerate repeats in complete genomes. Proc Int Conf Intell Syst Mol Biol 8: 228-238.
29. Kurtz S, Schleiermacher C (1999) REPuter: Fast computation of maximal repeats in complete genomes. Bioinformatics 15: 426-427.
30. Sonnhammer EL, Durbin R (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: GC1-GC10.
31. Haft DH, Selengut JD, White O (2003) The TIGRFAMs database of protein families. Nucleic Acids Res 31: 371-373.
32. Haft DH, Selengut JD, Brinkac LM, Zafar N, White O (2005) Genome Properties: A system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics 21: 293-306.