Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin.

Numerous prokaryote genomes contain structures known as clustered regularly interspaced short palindromic repeats (CRISPRs), composed of 25-50 bp repeats separated by unique sequence spacers of similar length. CRISPR structures are found in the vicinity of four genes named cas1 to cas4. In silico analysis revealed another cluster of three genes associated with CRISPR structures in many bacterial species, named here as cas1B, cas5 and cas6, and also revealed a certain number of spacers that have homology with extant genes, most frequently derived from phages, but also derived from other extrachromosomal elements. Sequence analysis of CRISPR structures from 24 strains of Streptococcus thermophilus and Streptococcus vestibularis confirmed the homology of spacers with extrachromosomal elements. Phage sensitivity of S. thermophilus strains appears to be correlated with the number of spacers in the CRISPR locus the strain carries. The authors suggest that the spacer elements are the traces of past invasions by extrachromosomal elements, and hypothesize that they provide the cell immunity against phage infection, and more generally foreign DNA expression, by coding an anti-sense RNA. The presence of gene fragments in CRISPR structures and the nuclease motifs in cas genes of both cluster types suggests that CRISPR formation involves a DNA degradation step.

[1]  A. Goffeau,et al.  Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus , 2004, Nature Biotechnology.

[2]  Alex van Belkum,et al.  Short-Sequence DNA Repeats in Prokaryotic Genomes , 1998, Microbiology and Molecular Biology Reviews.

[3]  P. Groenen,et al.  Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method , 1993, Molecular microbiology.

[4]  Dale B. Wigley,et al.  Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks , 2004, Nature.

[5]  Roger W. Hendrix,et al.  Phage Genomics Small Is Beautiful , 2002, Cell.

[6]  R. Garrett,et al.  Genus-Specific Protein Binding to the Large Clusters of DNA Repeats (Short Regularly Spaced Repeats) Present in Sulfolobus Genomes , 2003, Journal of bacteriology.

[7]  F. Rodríguez-Valera,et al.  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 , 1995, Molecular microbiology.

[8]  L. Walsh,et al.  Two groups of bacteriophages infecting Streptococcus thermophilus can be distinguished on the basis of mode of packaging and genetic determinants for major structural proteins , 1997, Applied and environmental microbiology.

[9]  Colin Kleanthous,et al.  Structure-based Analysis of the Metal-dependent Mechanism of H-N-H Endonucleases* , 2004, Journal of Biological Chemistry.

[10]  Desmond G. Higgins,et al.  Fast and sensitive multiple sequence alignments on a microcomputer , 1989, Comput. Appl. Biosci..

[11]  R. P. Ross,et al.  Bacteriophage-resistance systems in dairy starter strains: molecular analysis to application , 2002, Antonie van Leeuwenhoek.

[12]  D. van Sinderen,et al.  Characterisation of Streptococcus thermophilus CNRZ1205 and its cured and re-lysogenised derivatives. , 1999, FEMS microbiology letters.

[13]  G. Vergnaud,et al.  CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. , 2005, Microbiology.

[14]  W. Sandine,et al.  Improved Medium for Lactic Streptococci and Their Bacteriophages , 1975, Applied microbiology.

[15]  Janusz M Bujnicki,et al.  Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. , 2004, Nucleic acids research.

[16]  T. Klaenhammer,et al.  Antisense RNA Targeting of Primase Interferes with Bacteriophage Replication in Streptococcus thermophilus , 2004, Applied and Environmental Microbiology.

[17]  J. Musser,et al.  Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains. , 1999, Emerging infectious diseases.

[18]  R. Garrett,et al.  Identification of novel non‐coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus , 2004, Molecular microbiology.

[19]  R. Garrett,et al.  Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon , 1998, Extremophiles.

[20]  Rob J. L. Willems,et al.  Comparative Genotyping of Campylobacter jejuni by Amplified Fragment Length Polymorphism, Multilocus Sequence Typing, and Short Repeat Sequencing: Strain Diversity, Host Range, and Recombination , 2003, Journal of Clinical Microbiology.

[21]  L. Schouls,et al.  Identification of genes that are associated with DNA repeats in prokaryotes , 2002, Molecular microbiology.

[22]  A. Pommer,et al.  Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes and apoptotic endonucleases. , 2002, Nucleic acids research.

[23]  P. Giffard,et al.  A method for the isolation of RNA from Streptococcus salivarius and its application to the transcriptional analysis of the gtfJK locus. , 1993, FEMS microbiology letters.

[24]  F. J. Mojica,et al.  Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria , 2000, Molecular microbiology.

[25]  M. Ventura,et al.  Comparative genomics of phages and prophages in lactic acid bacteria , 2004, Antonie van Leeuwenhoek.

[26]  A. Hüttenhofer,et al.  Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[27]  D. Dryden,et al.  Nucleoside triphosphate-dependent restriction enzymes. , 2001, Nucleic acids research.

[28]  T. Klaenhammer,et al.  Expression of Antisense RNA Targeted against Streptococcus thermophilus Bacteriophages , 2002, Applied and Environmental Microbiology.

[29]  Nick V Grishin,et al.  A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. , 2002, Nucleic acids research.

[30]  D van Soolingen,et al.  Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology , 1997, Journal of clinical microbiology.