Characterization of Mollivirus kamchatka , the First Modern Representative of the Proposed Molliviridae Family of Giant Viruses

Abstract

Microbes trapped in permanently frozen paleosoils (permafrost) are the focus of increasing research in the context of global warming. Our previous investigations led to the discovery and reactivation of two Acanthamoeba-infecting giant viruses, Mollivirus sibericum and Pithovirus sibericum, from a 30,000-year old permafrost layer. While several modern pithovirus strains have since been isolated, no contemporary mollivirus relative was found. We now describe Mollivirus kamchatka, a close relative to M. sibericum, isolated from surface soil sampled on the bank of the Kronotsky River in Kamchatka, Russian Federation. This discovery confirms that molliviruses have not gone extinct and are at least present in a distant subarctic continental location. This modern isolate exhibits a nucleocytoplasmic replication cycle identical to that of M. sibericum. Its spherical particle (0.6 μm in diameter) encloses a 648-kb GC-rich double-stranded DNA genome coding for 480 proteins, of which 61% are unique to these two molliviruses. The 461 homologous proteins are highly conserved (92% identical residues, on average), despite the presumed stasis of M. sibericum for the last 30,000 years. Selection pressure analyses show that most of these proteins contribute to virus fitness. The comparison of these first two molliviruses clarify their evolutionary relationship with the pandoraviruses, supporting their provisional classification in a distinct family, the Molliviridae, pending the eventual discovery of intermediary missing links better demonstrating their common ancestry. IMPORTANCE Virology has long been viewed through the prism of human, cattle, or plant diseases, leading to a largely incomplete picture of the viral world. The serendipitous discovery of the first giant virus visible under a light microscope (i.e., >0.3 μm in diameter), mimivirus, opened a new era of environmental virology, now incorporating protozoan-infecting viruses. Planet-wide isolation studies and metagenome analyses have shown the presence of giant viruses in most terrestrial and aquatic environments, including upper Pleistocene frozen soils. Those systematic surveys have led authors to propose several new distinct families, including the Mimiviridae, Marseilleviridae, Faustoviridae, Pandoraviridae, and Pithoviridae. We now propose to introduce one additional family, the Molliviridae, following the description of M. kamchatka, the first modern relative of M. sibericum, previously isolated from 30,000-year-old arctic permafrost.

Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes

“…For instance, the viruses with the largest known genomes so far, the pandoraviruses, exhibit a regionalized enrichment of core genes in the first half of their genomes [51]. A similar dichotomous distribution was revealed in the distantly related molliviruses, where genes shared between molliviruses and pandoraviruses are also co-localized in half of their genomes [52]. Likewise, in faustoviruses, sequence conservation is not uniformly distributed, although it displays a different pattern with greater sequence divergence in the middle of the genome and at the extremities [39].…”

The DNA methylation landscape of giant viruses

“…In prokaryotes, the analysis of the co-occurrence of R-M systems and genetic fluxes between bacteria revealed that genetic exchanges are favored between genomes that share the same R-M systems, regardless of their evolutionary distance 53 . A similar phenomenon might be at play between molliviruses and pandoraviruses, and partially explains their shared gene content 52 . Previous analyses have also suggested that amoeba act as a genetic melting pot between intracellular bacteria 54 , a concept that should now be extended to include amoeba-infecting viruses.…”

“…If we previously noticed that some genes might be swapped between strains of pandoraviruses 38 , the present case involves an exchange between viruses from totally different families only sharing the Acanthamoeba host. In the recently discovered mollivirus kamchatka 52 , a MTase without ortholog in Mollivirus sibericum was probably acquired from a pandoravirus. In prokaryotes, the analysis of the co-occurrence of R-M systems and genetic fluxes between bacteria revealed that genetic exchanges are favored between genomes that share the same R-M systems, regardless of their evolutionary distance 53 .…”

Host Range and Coding Potential of Eukaryotic Giant Viruses

“…Similar to cellular genomes, giant virus genomes undergo both expansive and reductive genome evolution. The increased genome size in giant viruses can be attributed to gene duplications, de novo gene origination, and lateral gene transfers (LGTs, or horizontal gene transfers [HGTs]) from cellular organisms or other viruses [ 13 , 55 , 56 , 135 , 136 , 137 ]. Among these sources, LGTs generally bring in more innovative functions to viral genomes.…”