CoChat
Sign Up
Cited by 1,558

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

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

Bolotin, Alexander, Quinquis, Benoit, Sorokin, Alexei, Ehrlich, S. Dusko·2005·Microbiology
DOI 10.1099/mic.0.28048-0
Open this paper in CoChat — free account

Abstract

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.

Overview

Integrity signals

Registry

Crossref · 10.1099/mic.0.28048-0

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Two other laboratories independently reached conclusions similar to Mojica's about CRISPR as an immune system in the same year.

    “In the same year as Mojica, two other laboratories independently reached similar conclusions [6, 7], announcing the beginning of an era of active research into this extraordinary natural phenomenon.”

    From CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing (2022) · cites this paper as [6]

  • Bolotin et al. discovered a specific pattern in the nucleotide sequences on one side of the described spacers of the CRISPR arrays, later understood as PAMs.

    “Another important observation made by Bolotin et al. was the discovery of a specific pattern in the nucleotide sequences on one side of the described spacers of the CRISPR arrays, but the understanding of the role for this phenomenon was only revealed in later studies.”

    From CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing (2022) · cites this paper as [6]

  • Cas9 was first described in association with CRISPR repeats by Bolotin et al., originally named Cas5.

    “This protein was first described in connection with its association with CRISPR repeats in an article by Bolotin et al. [6], where it was originally named Cas5 (other alternative names are Csn1 and Csx12).”

    From CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing (2022) · cites this paper as [6]

  • Bolotin et al. identified the presence of the HNH motif (His-Asn-His) in Cas9.

    “In addition, the authors identified the presence of the HNH motif (His-Asn-His), which is also found in other nucleases.”

    From CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing (2022) · cites this paper as [6]

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 29

  1. Bolotin, 2004, Complete genome sequence and comparative analysis of the dairy bacterium Streptococcus thermophilus, Nat Biotechnol, 22, 1554, 10.1038/nbt1034 · DOI
  2. Brussow, 2002, Phage genomics, small is beautiful, Cell, 108, 13, 10.1016/S0092-8674(01)00637-7 · DOI
  3. Coffey, 2002, Bacteriophage-resistance systems in dairy starter strains, molecular analysis to application, Antonie van Leeuwenhoek, 82, 303, 10.1023/A:1020639717181 · DOI
  4. Desiere, 2002, Comparative genomics of phages and prophages in lactic acid bacteria, Antonie van Leeuwenhoek, 82, 73, 10.1023/A:1020676825358 · DOI
  5. Dryden, 2001, Nucleoside triphosphate-dependent restriction enzymes, Nucleic Acids Res, 29, 3728, 10.1093/nar/29.18.3728 · DOI
  6. Groenen, 1993, Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis, application for strain differentiation by a novel typing method, Mol Microbiol, 43, 1057, 10.1111/j.1365-2958.1993.tb00976.x · DOI · Paper page
  7. Higgins, 1989, Fast and sensitive multiple sequence alignments on a microcomputer, Comput Appl Biosci, 43, 151
  8. Hoe, 1999, Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains, Emerg Infect Dis, 43, 254, 10.3201/eid0502.990210 · DOI · Paper page
  9. Jansen, 2002, Identification of genes that are associated with DNA repeats in prokaryotes, Mol Microbiol, 43, 1565, 10.1046/j.1365-2958.2002.02839.x · DOI · Paper page
  10. Kamerbeek, 1997, Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology, J Clin Microbiol, 43, 907, 10.1128/JCM.35.4.907-914.1997 · DOI
  11. Le Marrec, 1997, Two groups of bacteriophages infecting Streptococcus thermophilus can be distinguished on the basis of mode of packaging and genetic determinants for major structural proteins, Appl Environ Microbiol, 63, 3246, 10.1128/AEM.63.8.3246-3253.1997 · DOI
  12. Makarova, 2002, A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis, Nucleic Acids Res, 30, 482, 10.1093/nar/30.2.482 · DOI · Paper page
  13. Maté,, 2004, Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases, J Biol Chem, 279, 34763, 10.1074/jbc.M403719200 · DOI
  14. Mojica, 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, 43, 85, 10.1111/j.1365-2958.1995.mmi_17010085.x · DOI
  15. Mojica, 2000, Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria, Mol Microbiol, 43, 244, 10.1046/j.1365-2958.2000.01838.x · DOI
  16. Peng, 2003, Genus-specific protein binding to the large clusters of DNA repeats (Short Regularly Spaced Repeats) present in Sulfolobus genomes, J Bacteriol, 185, 2410, 10.1128/JB.185.8.2410-2417.2003 · DOI
  17. Pourcel, 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, 10.1099/mic.0.27437-0 · DOI · Paper page
  18. Saravanan, 2004, Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily, Nucleic Acids Res, 32, 6129, 10.1093/nar/gkh951 · DOI
  19. Schouls, 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, 10.1128/JCM.41.1.15-26.2003 · DOI
  20. She, 1998, Genetic profile of pNOB8 from Sulfolobus, the first conjugative plasmid from an archaeon, Extremophiles, 2, 417, 10.1007/s007920050087 · DOI
  21. Simpson, 1993, A method for the isolation of RNA from Streptococcus salivarius and its application to the transcriptional analysis of the gtfJK locus, FEMS Microbiol Lett, 108, 93, 10.1111/j.1574-6968.1993.tb06079.x · DOI
  22. Singleton, 2004, Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks, Nature, 432, 187, 10.1038/nature02988 · DOI
  23. Stanley, 1999, Characterisation of Streptococcus thermophilus CNRZ1205 and its cured and re-lysogenised derivatives, FEMS Microbiol Lett, 176, 503, 10.1111/j.1574-6968.1999.tb13704.x · DOI
  24. Sturino, 2002, Expression of antisense RNA targeted against Streptococcus thermophilus bacteriophages, Appl Environ Microbiol, 68, 588, 10.1128/AEM.68.2.588-596.2002 · DOI
  25. Sturino, 2004, Antisense RNA targeting of primase interferes with bacteriophage replication in Streptococcus thermophilus, Appl Environ Microbiol, 70, 1735, 10.1128/AEM.70.3.1735-1743.2004 · DOI
  26. Tang, 2002, Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus, Proc Natl Acad Sci U S A, 99, 7536, 10.1073/pnas.112047299 · DOI
  27. Tang, 2005, Identification of novel non-coding RNAs as potential anti-sense regulators in the archaeon Sulfolobus solfataricus, Mol Microbiol, 55, 469, 10.1111/j.1365-2958.2004.04428.x · DOI
  28. Terzaghi, 1975, Improved medium for lactic streptococci and their bacteriophages, Appl Microbiol, 29, 807, 10.1128/AEM.29.6.807-813.1975 · DOI · Paper page
  29. Walker, 2002, Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes & apoptotic endonucleases, Nucleic Acids Res, 30, 3225, 10.1093/nar/gkf420 · DOI

Cited by

Sorted by citations

Metadata

Authors
Bolotin, A., Quinquis, B., Sorokin, A., & Ehrlich, S. D.
Affiliations
Génétique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy en Josas CEDEX, France
Venue
Microbiology
Publisher
Microbiology Society
Published
2005-08-01
Volume
151
Issue
8
Pages
2551-2561
ISSN
  • 1350-0872
  • 1465-2080
DOI
10.1099/mic.0.28048-0
Cited by
1,558
References
1
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review