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Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families

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Abstract

CRISPR-Cas is a widespread anti-viral adaptive immune system in the microorganisms. Viruses living in bacteria or some phages carry anti-CRISPR proteins to evade immunity by CRISPR-Cas. The anti-CRISPR proteins are prevalent in phages capable of lying dormant in a CRISPR-carrying host, while their orthologs frequently found in virulent phages. Here, we propose a probabilistic strategy of ancestral sequence reconstruction (ASR) and Hidden Markov Model (HMM) profile search to fish out sequences of anti-CRISPR proteins from environmental metagenomic, human microbiome metagenomic, human microbiome reference genome, and NCBI’s non-redundant databases. Our results revealed that the metagenome database dark matter might contain anti-CRISPR encoding genes.

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Acknowledgements

We would like to thank Dr. Feng-Biao Guo and Dr. Chris M. Brown, who kindly provided us with mirror site of the anti-CRISPR database containing the anti-CRISPR protein sequences.

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Authors and Affiliations

  1. Department of Genomics and Bioinformatics, Aix-Marseille University, 13007, Marseille, France

    Sweta Nidhi

  2. Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, 211007, India

    Pooja Tripathi

  3. Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, 211007, India

    Vijay Tripathi

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SN contributed to conceptualization and methodology; SN, PT, and VT contributed to formal analysis and investigation and writing—original draft of the preparation.

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Correspondence to Vijay Tripathi.

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Nidhi, S., Tripathi, P. & Tripathi, V. Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families. Mol Biotechnol 65, 273–281 (2023). https://doi.org/10.1007/s12033-022-00558-1

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