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

@article{File2001EvolutionOD,
  title={Evolution of DNA Polymerase Families: Evidences for Multiple Gene Exchange Between Cellular and Viral Proteins},
  author={Jonathan Fil{\'e}e and Patrick Forterre and Tang Sen-lin and Jacqueline Laurent},
  journal={Journal of Molecular Evolution},
  year={2001},
  volume={54},
  pages={763-773}
}
Abstract. A phylogenetic analysis of the five major families of DNA polymerase is presented. Viral and plasmid sequences are included in this compilation along with cellular enzymes. The classification by Ito and Braithwaite (Ito and Braithwaite 1991) of the A, B, C, D, and X families has been extended to accommodate the ``Y family'' of DNA polymerases that are related to the eukaryotic RAD30 and the bacterial UmuC gene products. After analysis, our data suggest that no DNA polymerase family… 

Figures, Tables, and Topics from this paper

Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.
TLDR
An analysis of two full-length homologues of DNA polymerase γ, which were found in the genomes of two bacteriophages, which infect the chlorophyll-d containing cyanobacterium Acaryochloris marina, provides data that may assist in reconstructing the evolution of mitochondria.
Evolution of Eukaryotic DNA Polymerases via Interaction Between Cells and Large DNA Viruses
TLDR
Molecular phylogenetic analyses of the B-family DNA polymerases from nucleo-cytoplasmic large DNA viruses, eukaryotes, and archaea suggest that different NCLDV lineages such as Poxviridae and Mimiviridae were involved in the evolution of different DNA polymerase genes in archaeal–eukaryotic cell lineages, putatively through horizontal gene transfer.
Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain.
  • P. Forterre
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 2006
TLDR
This work explores the possibility that three such independent transfers were at the origin of Archaea, Bacteria, and Eukarya, respectively, and explains why each domain has its specific DNA replication apparatus.
The role played by viruses in the evolution of their hosts: a view based on informational protein phylogenies.
TLDR
It is suggested that lateral gene transfers from viruses to cells and nonorthologous gene replacements of cellular genes by viral ones are an important source of "genetic novelties" in the evolution of cellular lineages.
Diversity and evolution of B-family DNA polymerases
TLDR
A new, widespread group of bacterial PolBs are identified that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEPSilonN) than to Escherichia coli Pol II.
Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes
TLDR
The analysis of ∼2000 bacterial genomes revealed that they all, without a single exception, encode one or more DNA polymerase III α-subunit (PolIIIα) homologs, suggesting a specific evolutionary pathway leading to PolC and DnaE from the last common ancestor and reveals important differences between extant polymerase groups.
Phylogenetic analysis and evolutionary origins of DNA polymerase X-family members.
TLDR
A phylogenetic analysis is performed to understand the relationship between mammalian DNA polymerase β and other members of the X-family of DNA polymerases, which originated from an ancient common ancestor characterized in two Bacillus species.
Viral proteins functioning in organelles: a cryptic origin?
TLDR
It is proposed that a prophage related to T3/T7 was present in the ancestral alpha-proteobacterium at the origin of mitochondria and that RNA polymerase, DNA polymerase and DNA primase encoded by this prophages replaced the original bacterial enzymes to function in mitochondria.
Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases
  • E. Koonin
  • Biology, Medicine
    Biology Direct
  • 2006
TLDR
Comparative analysis of the diversity of genomic strategies and organizations of viruses and cellular life forms has the potential to open windows into the deep past of life's evolution, especially, with the regard to the origin of genome replication systems.
Origin and Evolution of DNA and DNA Replication Machineries
TLDR
Proposed hypotheses, including independent invention of DNA and DNA replication proteins, ancient gene transfer and gene loss, and/or nonorthologous replacement are reviewed, with more emphasis on recent proposals suggesting that viruses have played a major role in the origin and evolution of theDNA replication proteins and possibly of DNA itself.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 35 REFERENCES
A Hypothesis for DNA Viruses as the Origin of Eukaryotic Replication Proteins
TLDR
The hypothesis that DNA virus replication proteins gave rise to those of eukaryotes during evolution is examined and the DNA polymerase from phycodnavirus is chosen as the basis of this analysis, showing significant similarity with replicative DNA polymerases of eUKaryotes and certain of their large DNA viruses.
A Novel DNA Polymerase Family Found inArchaea
TLDR
A novel DNA polymerase family is proposed which is entirely different from other hitherto-described DNA polymerases and expressed in Escherichia coli had both DNA polymerizing and 3'-->5' exonuclease activities.
Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins
  • P. Forterre
  • Biology, Medicine
    Molecular microbiology
  • 1999
TLDR
It is suggested here that the original cellular DNA informational proteins have often been replaced by proteins of viral or plasmid origin, a phenomenon known as non‐orthologous gene displacement, which would explain the puzzling phylogenies and distribution of manyDNA informational proteins between the three domains of life.
Family A and family B DNA polymerases are structurally related: evolutionary implications.
TLDR
It is concluded that family A and B DNA polymerases, at least in the 3'-->5' exonuclease domain, are structurally as well as evolutionarily related.
DNA Polymerase C of the Thermophilic Bacterium Thermus aquaticus: Classification and Phylogenetic Analysis of the Family C DNA Polymerases
TLDR
A phylogenetic tree based on the class I family C DNA pols is still in the provisional stage, but some important conclusion can be drawn, including that the high-G+C and the low-G-C Gram-positive bacteria are not monophyletic.
DNA Polymerases: Structural Diversity and Common Mechanisms*
  • T. Steitz
  • Chemistry, Medicine
    The Journal of Biological Chemistry
  • 1999
TLDR
Of particular interest are the role of editing in the fidelity of copying, the common enzymatic mechanism of polymerases, and the manners in which different domain structures function in the polymerase reaction in analogous ways.
Compilation, alignment, and phylogenetic relationships of DNA polymerases.
TLDR
This is an update of an earlier compilation and alignment of DNA polymerase sequences (Ito and Braithwaite, 1991) that attempted to compile complete sequences, to facilitate the identification of conserved and viable regions of the DNA polymerases.
A possible functional role for a new class of eukaryotic DNA polymerases
TLDR
This report describes the characterization of the Drosophila DNA repair gene mus308, a gene involved in DNA cross-link repair with homology to prokaryotic DNA polymerase I genes, which is the first reported gene encoding both helicase and polymerase motifs in a single polypeptide.
Archaeal DNA replication: identifying the pieces to solve a puzzle.
TLDR
This review summarizes the present knowledge about archaeal DNA polymerases and their relationship with those accessory proteins, which were predicted from the genome sequences.
Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
TLDR
Phylogenetic analysis of eukaryotic and archaeal paralogs suggests that the gene duplications that gave rise to the three replicative par analogs occurred before the divergence of the earliest eukARYotic lineages, and that all eukariotes are likely to possess theseParalogs.
...
1
2
3
4
...