The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes

Overview

Journal J Mol Evol

Specialty Biochemistry

Date 2006 Apr 14

PMID 16612537

Citations 159

Authors

James S Godde

Amanda Bickerton

Affiliations

Soon will be listed here.

Abstract

We have found direct DNA repeats 21-47 bp in length interspersed with nonrepetitive sequences of similar length, or clustered regularly interspaced short palindromic repeats (CRISPRs) in a wide range of diverse prokaryotes, including many Archaeal and Eubacterial species. A number of cas, CRISPR-associated genes have also been characterized in many of the same organisms. Phylogenetic analysis of these cas genes suggests that the CRISPR loci have been propagated via HGT, horizontal gene transfer. We suggest a mechanism by which this HGT has occurred, namely, that the CRISPR loci can be carried between cells on megaplasmids > or = 40 kb in length.

Citing Articles

Determination of Technological Properties and CRISPR Profiles of Isolates Obtained from Local Yogurt Samples.

Coban H, Olgun D, Temur I, Durak M Microorganisms. 2025; 12(12.

PMID: 39770631 PMC: 11679738. DOI: 10.3390/microorganisms12122428.

Recent progress in prompt molecular detection of liquid biopsy using Cas enzymes: innovative approaches for cancer diagnosis and analysis.

Yazdi Z, Roshannezhad S, Sharif S, Abbaszadegan M J Transl Med. 2024; 22(1):1173.

PMID: 39741289 PMC: 11686959. DOI: 10.1186/s12967-024-05908-y.

Comprehensive Analysis of CRISPR-Cas Systems and Their Influence on Antibiotic Resistance in Strains.

Fallah T, Shafiei M Bioinform Biol Insights. 2024; 18:11779322241307984.

PMID: 39703747 PMC: 11656426. DOI: 10.1177/11779322241307984.

CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range.

Androsiuk L, Maane S, Tal S Microbiol Spectr. 2024; :e0010424.

PMID: 39508585 PMC: 11619364. DOI: 10.1128/spectrum.00104-24.

Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.

Chopra A, Bhuvanagiri G, Natu K, Chopra A Mol Oral Microbiol. 2024; 40(1):1-16.

PMID: 39224035 PMC: 11701197. DOI: 10.1111/omi.12483.

References

Venter J, Remington K, Heidelberg J, Halpern A, Rusch D, Eisen J . Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004; 304(5667):66-74. DOI: 10.1126/science.1093857. View

Jansen R, van Embden J, Gaastra W, Schouls L . Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002; 43(6):1565-75. DOI: 10.1046/j.1365-2958.2002.02839.x. View

She Q, Phan H, Garrett R, Albers S, Stedman K, Zillig W . Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon. Extremophiles. 1998; 2(4):417-25. DOI: 10.1007/s007920050087. View

Pourcel C, Salvignol G, Vergnaud G . CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology (Reading). 2005; 151(Pt 3):653-663. DOI: 10.1099/mic.0.27437-0. View

Heidelberg J, Seshadri R, Haveman S, Hemme C, Paulsen I, Kolonay J . The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol. 2004; 22(5):554-9. DOI: 10.1038/nbt959. View

Scott J, Churchward G . Conjugative transposition. Annu Rev Microbiol. 1995; 49:367-97. DOI: 10.1146/annurev.mi.49.100195.002055. View

Jansen R, van Embden J, Gaastra W, Schouls L . Identification of a novel family of sequence repeats among prokaryotes. OMICS. 2002; 6(1):23-33. DOI: 10.1089/15362310252780816. View

Mojica F, Diez-Villasenor C, Garcia-Martinez J, Soria E . Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. 2005; 60(2):174-82. DOI: 10.1007/s00239-004-0046-3. View

Bolotin A, Quinquis B, Sorokin A, Ehrlich S . Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology (Reading). 2005; 151(Pt 8):2551-2561. DOI: 10.1099/mic.0.28048-0. View

10.

Ussery D, Binnewies T, Gouveia-Oliveira R, Jarmer H, Hallin P . Genome update: DNA repeats in bacterial genomes. Microbiology (Reading). 2004; 150(Pt 11):3519-3521. DOI: 10.1099/mic.0.27628-0. View

11.

Mojica F, Diez-Villasenor C, Soria E, Juez G . Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol. 2000; 36(1):244-6. DOI: 10.1046/j.1365-2958.2000.01838.x. View

12.

Murray A, Lies D, Li G, Nealson K, Zhou J, Tiedje J . DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc Natl Acad Sci U S A. 2001; 98(17):9853-8. PMC: 55542. DOI: 10.1073/pnas.171178898. View

13.

Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H . The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol. 2004; 22(5):547-53. DOI: 10.1038/nbt956. View

14.

Makarova K, Aravind L, Grishin N, Rogozin I, Koonin E . A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res. 2002; 30(2):482-96. PMC: 99818. DOI: 10.1093/nar/30.2.482. View

15.

Haft D, Selengut J, Mongodin E, Nelson K . A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol. 2005; 1(6):e60. PMC: 1282333. DOI: 10.1371/journal.pcbi.0010060. View