CRISPR elements in the Thermococcales: evidence for associated horizontal gene transfer in Pyrococcus furiosus

• Autorzy: Portillo M C , Gonzalez J M
• Języki publikacji: EN

Abstrakty

EN

The presence and distribution of CRISPR (clustered regularly interspaced short palindrome repeat) elements in the archaeal order Thermococcales were analyzed. Four complete genome sequences from the species Pyrococcas abyssi, P. furiosus, P. horikoshii, and Thermococcus kodakaraensis were studied. A fragment of the genome of P. furiosus was flanked by CRISPR elements upstream and by a single element downstream. The composition of the gene sequences contained in this genome fragment (positions 699013 to 855319) showed significant differences from the other genes in the P. furiosus genome. Differences were observed in the GC content at the third codon positions and the frequency of codon usage between the genes located in the analyzed fragment and the other genes in the P. furiosus genome. These results represent the first evidence suggesting that repeated CRISPR elements can be involved in horizontal gene transfer and genomic differentiation of hyperthermophilic Archaea.

Słowa kluczowe

EN

CRISPR zob.clustered regularly interspaced short palindromic repeat; clustered regularly interspaced short palindromic repeat; Thermococcales; horizontal gene transfer; Pyrococcus furiosus; genome

• Wydawca: -
• Czasopismo: Journal of Applied Genetics
• Rocznik: 2009
• Tom: 50
• Numer: 4
• Opis fizyczny: p.421-430,fig.,ref.

Twórcy

autor

Portillo M C

• Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012-Sevilla, Spain

autor

Gonzalez J M

• Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012-Sevilla, Spain

Bibliografia

• Andersson AF, Banfield JF, 2008. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320: 1047-1050.
• Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-1712.
• Bolotin A, Quinquis B, Sorokin A, Ehrlich SD, 2005. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extra- chromosomal origin. Microbiology 151: 2551-2561.
• Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH, Snijders APL, et al. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321: 960-964.
• DeBoy RT, Mongodin EF, Emerson JB, Nelson KE, 2006. Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. J Bacteriol 188: 2551-2561.
• Garcia-Vallvé S, Romeu A, Palau J, 2000. Horizontal gene transfer in bacterial and archaeal complete genomes. Gen Res 10: 1719-1725.
• Godde JS, Bickerton A, 2006. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal gene transfer among prokaryotes. J Mol Evol 62: 718-729.
• Jansen R, van Embden JDA, Gaastra W, Schouls LM, 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43: 1565-1575.
• Lillestol RK, Redder P, Garrett RA, Brugger K, 2006. A putative viral defence mechanism in archaeal cells. Archaea 2: 59-72.
• Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV, 2006. A putative RNA-interference- based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 1.7: 1-26.
• Marraffini LA, Sontheimer EJ, 2008. CRISPR interference limits horizontal gene transfer in Staphylococci by targeting DNA. Science 322: 1843-1845.
• Mojica FJM, Ferrer C, Juez G, Rodrigues-Valera F, 1995 Long stretches of short tandem repeats are present in largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol Microbiol 17: 85-93.
• 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.
• Sokal RR, Rohlf FJ, 1981. Biometry, 2nd edn. New York: Freeman WH & Co.
• Sorek R, Kunin V, Hugenholtz P, 2008. CRISPR - a widespread system that provides acquired resistance against phages in Bacteria and Archaea. Nat Rev Microbiol 6: 181-186.
• Tyson GW, Banfield JF, 2008. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10: 200-207.