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An updated evolutionary classification of CRISPR–Cas systems

Makarova, Kira S., Wolf, Yuri I., Alkhnbashi, Omer S., Costa, Fabrizio, Shah, Shiraz A., Saunders, Sita J., Barrangou, Rodolphe, Brouns, Stan J. J., Charpentier, Emmanuelle, Haft, Daniel H., Horvath, Philippe, Moineau, Sylvain, Mojica, Francisco J. M., Terns, Rebecca M., Terns, Michael P., White, Malcolm F., Yakunin, Alexander F., Garrett, Roger A., van der Oost, John, Backofen, Rolf, Koonin, Eugene V.·2015·Nature Reviews Microbiology
DOI 10.1038/nrmicro3569PMC PMC5426118
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  • Recent studies suggest different classifications of CRISPR-Cas systems, with two classes and five or most recently six types having been described.

    “Recent studies suggest different classifications, with two classes and five [14] or most recently six types of CRISPR-Cas systems [15] having been described.”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [14]

    The citation [15] is attached to the claim that six types have been described. In “Classification of CRISPR–cas loci,” the cited paper instead says its classification has five types; its Conclusions likewise identify types IV and V as the two new putative types. (LLM, conf=0.90)

    Checked by a reasoning model — may be wrong.

    Experimental — accuracy not yet measured

  • Some type I, II and V systems also rely on Cas4 nuclease activity for the adaptation step.

    “Some type I, II and V systems also rely on Cas4 nuclease activity for the adaptation step [14,18].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [14]

    The adaptation-module passage (page not available in our copy) describes possible involvement of Cas4, an enzyme in the restriction endonuclease superfamily. The type II and putative type V sections say that subtype II-B and some putative type V loci encode Cas4; they do not establish that these systems rely on its nuclease activity for adaptation. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Type IV CRISPR systems are rare and do not carry the usual proteins needed for adaptation and cleavage such as Cas1, Cas2 and Cas4.

    “Type IV CRISPR systems are rare and do not carry the usual proteins CRISPR systems needed for the adaptation and cleavage such as Cas1, Cas2 and Cas4 [14].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [14]

    The ‘Putative type IV CRISPR–Cas systems’ section says that several bacterial genomes contain these systems and that the example lacks cas1 and cas2. The ‘Rare, unclassifiable CRISPR Cas systems’ section says Cas2 and Cas4 are uncharacteristic of type IV loci. But the paper identifies Cas1, Cas2 and Cas4 with adaptation, not target cleavage, and describes a predicted type IV effector complex; it does not establish that type IV systems lack proteins needed for cleavage. Page numbers were not supplied. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Class 2 CRISPR-Cas systems are the most widespread among the scientific community due to the simplicity of their mechanism.

    “Of both CRISPR-Cas classes, class 2 systems are the most widespread among the scientific community due to the simplicity of their mechanism.”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [14]

    The Class 2 section describes a single-subunit effector, and the Abstract says development of type II components into genome-editing tools triggered intensive research. The paper does not establish that class 2 systems are the most widespread in scientific use compared with class 1, or that their simplicity is the reason for that use. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Class 1 CRISPR-Cas systems require a convoluted multiprotein Cascade complex, whereas class 2 systems depend only on small RNA molecules, apart from the type's specific Cas protein.

    “Whereas class 1 systems require a convoluted multiprotein Cascade complex, class 2 systems depend only on small RNA molecules, apart from the type’s specific Cas protein [14].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [14]

    The Classification of CRISPR–cas loci section supports the central distinction: class 1 has multisubunit crRNA–effector complexes, while class 2 uses a single protein for effector-complex functions. But it names Cascade, Csm and Cmr as class 1 complexes, so not every class 1 system requires Cascade. The Type II section also identifies cas1 and cas2 in addition to cas9, so the claim that class 2 systems depend only on RNA and a type-specific Cas protein is too broad. (LLM, conf=0.89)

    Experimental — accuracy not yet measured

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Metadata

Authors
Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Terns, R. M., Terns, M. P., White, M. F., Yakunin, A. F., Garrett, R. A., van der Oost, J., Backofen, R., & Koonin, E. V.
Venue
Nature Reviews Microbiology
Publisher
Springer Science and Business Media LLC
Published
2015-09-28
Volume
13
Issue
11
Pages
722-736
ISSN
  • 1740-1526
  • 1740-1534
DOI
10.1038/nrmicro3569
PMC
PMC5426118
Cited by
2,480
References
7
Language
en
Licence
www.springer.com/tdm (tdm)

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 ›

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