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Large-scale computational discovery and analysis of virus-derived microbial nanocompartments

Author

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  • Michael P. Andreas

    (University of Michigan Medical School)

  • Tobias W. Giessen

    (University of Michigan Medical School
    University of Michigan Medical School)

Abstract

Encapsulins are a class of microbial protein compartments defined by the viral HK97-fold of their capsid protein, self-assembly into icosahedral shells, and dedicated cargo loading mechanism for sequestering specific enzymes. Encapsulins are often misannotated and traditional sequence-based searches yield many false positive hits in the form of phage capsids. Here, we develop an integrated search strategy to carry out a large-scale computational analysis of prokaryotic genomes with the goal of discovering an exhaustive and curated set of all HK97-fold encapsulin-like systems. We find over 6,000 encapsulin-like systems in 31 bacterial and four archaeal phyla, including two novel encapsulin families. We formulate hypotheses about their potential biological functions and biomedical relevance, which range from natural product biosynthesis and stress resistance to carbon metabolism and anaerobic hydrogen production. An evolutionary analysis of encapsulins and related HK97-type virus families shows that they share a common ancestor, and we conclude that encapsulins likely evolved from HK97-type bacteriophages.

Suggested Citation

  • Michael P. Andreas & Tobias W. Giessen, 2021. "Large-scale computational discovery and analysis of virus-derived microbial nanocompartments," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25071-y
    DOI: 10.1038/s41467-021-25071-y
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    Cited by:

    1. Jesse A. Jones & Michael P. Andreas & Tobias W. Giessen, 2024. "Structural basis for peroxidase encapsulation inside the encapsulin from the Gram-negative pathogen Klebsiella pneumoniae," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Michael P. Andreas & Tobias W. Giessen, 2024. "The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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