Evolution of DNA Polymerase Families: Evidences for Multiple Gene Exchange between Cellular and Viral Proteins

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 1993

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Dear Colleagues,

Phylogenetic evidence supports complex evolutionary scenarios for some DNA polymerases. The evolutionary history of some DNA polymerases appears to be complex with some domains conserved in viruses and cells. Conserved relationships exist for some DNA polymerases in Eukaryota, Archaea, viruses, and some bacteria. Some DNA polymerase genes appear to have evolved through horizontal gene transfers between viruses and host cells. Advances in DNA sequencing have enabled rapid expansion of available sequences for DNA polymerases for both viruses and host organisms. Molecular phylogenetic analysis of these expanded sets of available DNA polymerase sequences can provide new insights into the evolutionary history of these genes. You are invited to submit manuscripts to this Special Issue on the topic “Evolution of DNA polymerase families: evidences for multiple gene exchanges between cellular and viral proteins”.

Dr. Darrell O. Ricke
Guest Editor

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Keywords

  • DNA polymerase
  • virus
  • evolution
  • phylogeny

Published Papers (1 paper)

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Research

13 pages, 2849 KiB  
Article
Natural History of DNA-Dependent DNA Polymerases: Multiple Pathways to the Origins of DNA
by Sávio Torres de Farias, Ariadne Nobrega Marinho Furtado, Ariosvaldo Pereira dos Santos Junior and Marco V. José
Viruses 2023, 15(3), 749; https://0-doi-org.brum.beds.ac.uk/10.3390/v15030749 - 14 Mar 2023
Cited by 3 | Viewed by 1725
Abstract
One of the major evolutionary transitions that led to DNA replacing RNA as the primary informational molecule in biological systems is still the subject of an intense debate in the scientific community. DNA polymerases are currently split into various families. Families A, B, [...] Read more.
One of the major evolutionary transitions that led to DNA replacing RNA as the primary informational molecule in biological systems is still the subject of an intense debate in the scientific community. DNA polymerases are currently split into various families. Families A, B, and C are the most significant. In bacteria and some types of viruses, enzymes from families A and C predominate, whereas family B enzymes are more common in Archaea, Eukarya, and some types of viruses. A phylogenetic analysis of these three families of DNA polymerase was carried out. We assumed that reverse transcriptase was the ancestor of DNA polymerases. Our findings suggest that families A and C emerged and organized themselves when the earliest bacterial lineages had diverged, and that these earliest lineages had RNA genomes that were in transition—that is, the information was temporally stored in DNA molecules that were continuously being produced by reverse transcription. The origin of DNA and the apparatus for its replication in the mitochondrial ancestors may have occurred independently of DNA and the replication machinery of other bacterial lineages, according to these two alternate modes of genetic material replication. The family C enzymes emerged in a particular bacterial lineage before being passed to viral lineages, which must have functioned by disseminating this machinery to the other lineages of bacteria. Bacterial DNA viruses must have evolved at least twice independently, in addition to the requirement that DNA have arisen twice in bacterial lineages. We offer two possible scenarios based on what we know about bacterial DNA polymerases. One hypothesis contends that family A was initially produced and spread to the other lineages through viral lineages before being supplanted by the emergence of family C and acquisition at that position of the principal replicative polymerase. The evidence points to the independence of these events and suggests that the viral lineage’s acquisition of cellular replicative machinery was crucial for the establishment of a DNA genome in the other bacterial lineages, since these viral lineages may have served as a conduit for the machinery’s delivery to other bacterial lineages that diverged with the RNA genome. Our data suggest that family B initially established itself in viral lineages and was transferred to ancestral Archaea lineages before the group diversified; thus, the DNA genome must have emerged first in this cellular lineage. Our data point to multiple evolutionary steps in the origins of DNA polymerase, having started off at least twice in the bacterial lineage and once in the archaeal lineage. Given that viral lineages are implicated in a significant portion of the distribution of DNA replication equipment in both bacterial (families A and C) and Archaeal lineages (family A), our data point to a complex scenario. Full article
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