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Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses
Published on: December 29, 2015
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DNA polymerase swapping in Caudoviricetes bacteriophages
Natalya Yutin1, Igor Tolstoy1, Pascal Mutz1
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Virology Journal
|August 26, 2024
Summary
DNA polymerase (DNAP) swapping occurred frequently in tailed phages, leading to closely related phages with unrelated DNAPs. This evolution likely helps phages evade host defenses and replication conflicts.
Area of Science:
- Virology
- Molecular Biology
- Evolutionary Biology
Background:
- Viruses in the realm Duplodnaviria possess double-stranded DNA genomes and conserved gene modules but vary in DNA replication proteins.
- DNA polymerases (DNAPs) are crucial for DNA replication and are classified into four unrelated families (A-D).
- Previous work showed closely related viruses in the order Crassvirales can encode DNAPs from different families.
Purpose of the Study:
- To investigate the evolutionary dynamics of DNA polymerase (DNAP) gene families in tailed phages.
- To identify instances and patterns of DNAP gene swapping within the Caudoviricetes class.
Main Methods:
- Constructed comprehensive evolutionary trees of tailed bacteriophages, including those with different DNAP families.
- Validated DNAP swaps using constrained tree analysis of large terminase subunits and Mauve genome alignments.
- Predicted the structures of novel DNAPs using AlphaFold2.
Main Results:
- Identified four additional groups of tailed phages with multiple DNAP gene swaps between families A, B, and C.
- Observed DNAP swapping occurs "in situ" without altering surrounding gene organization.
- Discovered two new, highly divergent groups of family A DNAPs in some phage genomes.
Conclusions:
- DNAP gene replacement by different families occurred independently numerous times during tailed phage evolution.
- Phage DNAP swapping may be driven by the need to evade host antiphage mechanisms or avoid replicon incompatibility.
- This evolutionary process can result in very closely related phages encoding unrelated DNAPs.
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