Evolution of Type IV CRISPR-Cas Systems: Insights from CRISPR Loci in Integrative Conjugative Elements of Acidithiobacillia

Ana Moya-Beltrán, Kira S. Makarova, Lillian G. Acuña, Yuri I. Wolf, Paulo C. Covarrubias, Sergey A. Shmakov, Cristian Silva, Igor Tolstoy, D. Barrie Johnson, Eugene V. Koonin, Raquel Quatrini

    Research output: Contribution to journalArticlepeer-review

    18 Citations (Scopus)

    Abstract

    Type IV CRISPR-Cas are a distinct variety of highly derived CRISPR-Cas systems that appear to have evolved from type III systems through the loss of the target-cleaving nuclease and partial deterioration of the large subunit of the effector complex. All known type IV CRISPR-Cas systems are encoded on plasmids, integrative and conjugative elements (ICEs), or prophages, and are thought to contribute to competition between these elements, although the mechanistic details of their function remain unknown. There is a clear parallel between the compositions and likely origin of type IV and type I systems recruited by Tn7-like transposons and mediating RNA-guided transposition. We investigated the diversity and evolutionary relationships of type IV systems, with a focus on those in Acidithiobacillia, where this variety of CRISPR is particularly abundant and always found on ICEs. Our analysis revealed remarkable evolutionary plasticity of type IV CRISPR-Cas systems, with adaptation and ancillary genes originating from different ancestral CRISPR-Cas varieties, and extensive gene shuffling within the type IV loci. The adaptation module and the CRISPR array apparently were lost in the type IV ancestor but were subsequently recaptured by type IV systems on several independent occasions. We demonstrate a high level of heterogeneity among the repeats with type IV CRISPR arrays, which far exceed the heterogeneity of any other known CRISPR repeats and suggest a unique adaptation mechanism. The spacers in the type IV arrays, for which protospacers could be identified, match plasmid genes, in particular those encoding the conjugation apparatus components. Both the biochemical mechanism of type IV CRISPR-Cas function and their role in the competition among mobile genetic elements remain to be investigated.
    Original languageEnglish
    Pages (from-to)656-672
    Number of pages17
    JournalThe CRISPR Journal
    Volume4
    Issue number5
    Early online date28 Sept 2021
    DOIs
    Publication statusPublished - 15 Oct 2021

    Bibliographical note

    Funding Information:
    K.S.M., Y.I.W., S.A.S., I.T., and E.V.K. are supported by the Intramural Research Program of the National Institutes of Health of the USA (National Library of Medicine). This work was supported the Agencia Nacional de Investigación y Desarrollo (ANID, Chile) under Grants FONDECYT 1181251 (R.Q.), FONDECYT 11201070 (L.G.A.), Programa de Apoyo a Centros con Financia-miento Basal AFB170004 (R.Q.), CONICYT-PFCHA/ Doctorado Nacional/20171049 (A.M.-B.), CONICYT-PFCHA/Doctorado Nacional/21090398 (L.G.A.), CONICYT-PFCHA/Doctorado Nacional/21120305 (P.C.C.), CONICYT/FONDAP Grant No. 15110027 (L.G.A.), and the ANID—Millennium Science Initiative Programme—NCN17_093, granted by the Ministry of Economy, Development and Tourism from Chile (R.Q.).

    Publisher Copyright:
    © Copyright 2021, Mary Ann Liebert, Inc., publishers 2021.

    Keywords

    • Genetics
    • Biotechnology

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