Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

BMC Evolutionary Biology (Impact Factor: 3.37). 08/2012; 12(1):156. DOI: 10.1186/1471-2148-12-156
Source: PubMed


The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.

Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a ‘fourth supergroup’ along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity.

Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet’s biosphere.

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Available from: Arshan Nasir, Dec 18, 2013
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    • "Recently discovered giant viruses like Mimivirus or Megavirus (belonging to the Megaviridae), that possess genomes of a size comparable to the genomes of bacteria (containing few tRNA genes, translation initiation and elongation factors and even some simple repeats), blur the established frontiers between viruses and cellular organisms (Raoult et al., 2004). Giant viruses coexisted with the cellular ancestors (Nasir et al., 2012). Such findings support our view that various acellular forms deserve to be added to the existing broadly accepted six-kingdom system of life (Cavalier-Smith, 2004). "
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    • "Using two of them, which are universal and encode DNA-dependent RNA polymerase subunits, recent phylogenetic analyses with a comprehensive sequence set further supported the four branches of life hypothesis (Sharma et al., 2014). In addition, other research groups strengthened this hypothesis using different methodological approaches or datasets (Wu et al., 2011; Nasir et al., 2012). Eventually, the term " TRUC " (an acronym for Things Resisting Uncompleted Classifications) was introduced for a new classification of life that includes a fourth TRUC, consisting of Megavirales, standing out from the ribosome-based three domain classification (Raoult, 2013, 2014), and we recently described pandoraviruses as new members of a " Fourth TRUC " club (Sharma et al., 2015). "
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    • "phylogenetic analysis of these universal genes has suggested that the giant viruses did not fall into any of three domains of cellular life ( bacteria , archaea and eukaryote ) and prompted the hypothesis that these viruses evolved by reductive evolution from a hypothetical ( conceivably , extinct ) cellular domain ( Colson et al . , 2012 , 2011 ; Nasir et al . , 2012 ; Raoult et al . , 2004 ) . However , independent phylogenetic studies that employed representative sets of cellular life forms from the three domains and more advanced phylogenetic methods have effectively refuted the fourth domain hypothesis by showing that nearly all universal genes of the giant viruses were nested within the eukar -"
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