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Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements

Abstract

Prokaryotes contain short DNA repeats known as CRISPR, recognizable by the regular spacing existing between the recurring units. They represent the most widely distributed family of repeats among prokaryotic genomes, suggesting a biological function. The origin of the intervening sequences, at present unknown, could provide clues about their biological activities. Here we show that CRISPR spacers derive from preexisting sequences, either chromosomal or within transmissible genetic elements such as bacteriophages and conjugative plasmids. Remarkably, these extrachromosomal elements fail to infect the specific spacer-carrier strain, implying a relationship between CRISPR and immunity against targeted DNA. Bacteriophages and conjugative plasmids are involved in prokaryotic population control, evolution, and pathogenicity. All these biological traits could be influenced by the presence of specific spacers. CRISPR loci can be visualized as mosaics of a repeated unit, separated by sequences at some time present elsewhere in the cell.

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Acknowledgments

This work was financed by research grants from the Conselleria de Cultura, Educació i Ciència, Generalitat Valenciana (CTIDIB/2002/155 and gv04B-457). C.D. is supported by a graduate fellowship from the Ministerio de Educación, Cultura y Deporte. We are indebted to Kathy Hernández for assistance and to J. Antón for critical reading of the manuscript.

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Correspondence to Francisco J.M. Mojica.

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Reviewing Editor: Dr. John Huelsenbeck

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Mojica, F.J., Díez-Villaseñor, C., García-Martínez, J. et al. Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements. J Mol Evol 60, 174–182 (2005). https://doi.org/10.1007/s00239-004-0046-3

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Keywords

  • CRISPR
  • DNA repeats
  • Conjugative plasmids
  • Bacteriophages
  • Lateral gene transfer
  • Prokaryotic evolution
  • Pathogenicity