Abstract
The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life (Eukarya, Bacteria and Archaea) and to generate controversial phylogenomic trees congruent with that of ribosomal genes, branching Mimivirus at its root. Here we used sequences from metagenomic databases, Marseillevirus and three new viruses extending the Mimiviridae family to generate the phylogenetic trees of eight proteins involved in different steps of DNA processing. Compared to the three ribosomal defined domains, we report a single common origin for Nucleocytoplasmic Large DNA Viruses (NCLDV), DNA processing genes rooted between Archaea and Eukarya, with a topology congruent with that of the ribosomal tree. As for translation, we found in our new viruses, together with Mimivirus, five proteins rooted deeply in the eukaryotic clade. In addition, comparison of informational genes repertoire based on phyletic pattern analysis supports existence of a clade containing NCLDVs clearly distinct from that of Eukarya, Bacteria and Archaea. We hypothesize that the core genome of NCLDV is as ancient as the three currently accepted domains of life.
Highlights
Molecular sequence analyses have allowed to partially identify the origins of genes
Reduction of RNA precursors into dNTP is catalyzed by ribonucleotide reductase (RNR), deoxythymidine 59-monophosphate is produced from deoxyuridine 59-monophosphate by thymidylate synthase
These two key enzymes are thought to have been involved in the transition from ancient RNA to the DNA world [9]. They have been identified in cells and in nucleocytoplasmic large DNA viruses (NCLDVs) and used for phylogenetic reconstructions
Summary
Molecular sequence analyses have allowed to partially identify the origins of genes. A putative tree of life based on ribosomal analysis was postulated that includes three domains: Eukarya, Bacteria and Archaea. Viruses are excluded from this classification system due to a lack of evidence that they possess a core of genes and because they lack ribosomes [1]. The double jelly-roll motif that can be found in the capsids of viruses infecting Archaea, Eukarya, or Bacteria, is proposed as evidence for an ancestry of some viruses [2,3]. We identify a common set of proteins present in all forms of life including cellular organisms and viruses, giant viruses, and we used this set of viral and cellular proteins to perform phylogenetic reconstructions
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