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Modeling colicin operons as genetic arms in plasmid-genome conflicts

View ORCID ProfilePavithra Anantharaman Sudhakari, View ORCID ProfileBhaskar Chandra Mohan Ramisetty
doi: https://doi.org/10.1101/2021.05.15.444200
Pavithra Anantharaman Sudhakari
Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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  • ORCID record for Pavithra Anantharaman Sudhakari
Bhaskar Chandra Mohan Ramisetty
Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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  • For correspondence: ramisettybcm@biotech.sastra.edu bcmr25@gmail.com
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Abstract

Plasmids are acellular propagating entities that depend, as molecular parasites, on bacteria for propagation. The conflict between the bacterial genome and the parasitic plasmids allows the emergence of ‘genetic arms’ such as Colicin (Col) operons. Endonuclease Col operons encode three proteins; an endonuclease colicin (cleaves nucleic acids), an immunity protein (inactivates its cognate colicin), and lysis protein (aids in colicin release via host cell lysis). Col operons are efficient plasmid-maintenance systems; (i) the plasmid cured cells are killed by the colicins; (ii) damaged cells lyse and release the colicins that eliminate the competitors; and (iii) the released plasmids invade new bacteria. Surprisingly, some bacterial genomes have Col operons. The eco-evolutionary drive and physiological relevance of genomic Col operons are unknown. We investigated plasmidic and genomic Col operons using sequence analyses from an eco-evolutionary perspective. We found 1,248 genomic and plasmidic colicins across 30 bacterial genera. Although 51% of the genomes harbor colicins, the majority of the genomic colicins lacked a functional lysis gene, suggesting the negative selection of lethal genes. The immunity gene of the Col operon protects the cured host, thereby eliminating the metabolic burden due to plasmid. We show mutual exclusivity of Col operons on genomes and plasmids. We propose an ‘anti-addiction’ hypothesis for genomic colicins. Using a stochastic agent-based model, we show that the genomic colicins confer an advantage to the host genome in terms of immunity to the toxin and elimination of plasmid burden. Col operons are ‘genetic arms’ that regulate the ecological interplay of bacterial genomes and plasmids.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 17, 2021.
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Modeling colicin operons as genetic arms in plasmid-genome conflicts
Pavithra Anantharaman Sudhakari, Bhaskar Chandra Mohan Ramisetty
bioRxiv 2021.05.15.444200; doi: https://doi.org/10.1101/2021.05.15.444200
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Modeling colicin operons as genetic arms in plasmid-genome conflicts
Pavithra Anantharaman Sudhakari, Bhaskar Chandra Mohan Ramisetty
bioRxiv 2021.05.15.444200; doi: https://doi.org/10.1101/2021.05.15.444200

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