Genomics of Megavirus and the elusive fourth domain of Life

Abstract

We recently described Megavirus chilensis, a giant virus isolated off the coast of Chile, also replicating in fresh water acanthamoeba. Its 1,259,197-bp genome encodes 1,120 proteins and is the largest known viral genome. Megavirus and its closest relative Mimivirus only share 594 orthologous genes, themselves sharing only 50% of identical residues in average. Despite this divergence, comparable to the maximal divergence exhibited by bacteria within the same division (e.g., gamma proteobacteria), Megavirus retained all of the genomic features unique to Mimivirus, in particular its genes encoding key-elements of the translation apparatus, a trademark of cellular organisms. Besides homologs to the four aminoacyl-tRNA synthetases (aaRS) encoded by Mimivirus, Megavirus added three additional ones, raising the total of known virus-encoded aaRS to seven: IleRS, TrpRS, AsnRS, ArgRS, CysRS, MetRS, TyrRS. This finding strongly suggests that large DNA viruses derived from an ancestral cellular genome by reductive evolution. The nature of this cellular ancestor remains hotly debated.

Potassium Ion Channels: Could They Have Evolved from Viruses?

“…An alternative explanation is that K + channels evolved from viruses. This view is consistent with the fact that some large DNA viruses might predate the separation of the three main branches of cellular life, namely bacteria, archea, and eukarya (Boyer et al, 2010;Legendre et al, 2012;Nasir et al, 2012). In this context, it is interesting to note that the aforementioned bioinformatics analysis of multiple chloroviruses (Jeanniard et al, 2013) provides evidence that some genes are transferred from the virus to the host.…”

“…With their small size, their functional simplicity, and their selfassembly into tetramers, these Kcv proteins have all the hallmarks expected for such a pore precursor unit . In addition, the fact that these large DNA viruses might predate the separation of the three main branches of cellular life, namely bacteria, archaea, and eukarya (Raoult et al, 2004;Boyer et al, 2010;Legendre et al, 2012;Nasir et al, 2012), is consistent with the idea that viral Kcv channels could be the common ancestor of more complex K + channels.…”

“…Some of these giant viruses encode more genes than many bacteria. The size of these viruses and their genetic complexity has fostered the idea that these large DNA viruses might even represent a fourth domain of life (Raoult et al, 2004;Boyer et al, 2010;Legendre et al, 2012;Nasir et al, 2012). One version of this hypothesis is that these viruses were descendants of more complex, autonomous organisms that lost the capacity to replicate by themselves and consequently became parasitic (Raoult et al, 2004;Legendre et al, 2012).…”

Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes?

“…As mentioned above, the first attempt was done using seven mimivirus genes and resulted in a phylogenetic tree where this virus branched as a deeply diverging lineage sister to the eukaryotes [21]. Thus, it appeared that the elusive fourth domain of life had been found and that it was composed of a variety of giant viruses [28][29][30][31].…”

The Megavirus Chilensis Cu,Zn-Superoxide Dismutase: the First Viral Structure of a Typical Cellular Copper Chaperone-Independent Hyperstable Dimeric Enzyme

“…The virion consists of an icosahedral capsid of 400 nm in diameter enclosed in a layer of fibrils. It shares ϳ600 genes with the single species of the genus Mimivirus, with an average of 50% of residues being identical at the protein sequence level (8,10). Mimivirus penetrates A. castellanii cells by phagocytosis.…”