One of the aims of the VIREVOL project was to elucidate the genome organization of giant viruses in order to compare it with what is found in the cellular world and eventually get some insights on the role they may have played for the evolution of the cells. We addressed the genome organization on two families of viruses. We studied the Mimiviridae and the Marseilleviridae which are giant and large DNA viruses infecting unicellular eukaryotes from the Acanthamoeba genus. Surprisingly, they use opposite genome organization while it results in both cases to the efficient compaction of the genomes in their icosahedral capsids. We used Cryo-EM in both cases to analyze this organization.
Mimivirus genomic fibre:
For Mimivirus, after capsid opening, we managed to purify the 30 nm rod-shaped structure expelled from the capsids and analyzed them using Cryo-EM and proteomics to determine its structure and composition. The 1.2Mb genome is encased into a ~30 nm wide helical and flexible protein shell where the dsDNA is compacted with 5 to 6 DNA strands lining the interior of the protein shell. The shell is surprisingly made of an enzyme also composing the glycosylated fibrils surrounding the capsids. Additional proteins, including the viral RNA can fit in the central channel, revealing a remarkable evolutionary strategy for packaging and protecting the viral genome, in a state ready for immediate transcription upon delivery in the host cytoplasm (doi :10.1101/2022.02.17.480895).
Marseilleviridae genome compaction:
While organization of genomic DNA into nucleosomes was considered a hallmark of eukaryotes, Marseilleviridae, encoding fused remote homologs of the four eukaryotic histones, are also able to form nucleosomes, resembling cell nucleosomes, to compact their genomes. Our results further expand the range of ‘organisms’ that have nucleosomes and suggest a specialized function of histones in the biology of these unusual viruses. We also developed the genetics of this virus and were able to demonstrate that histone doublets are essential for infectivity (doi : 10.1016/j.cell.2021.06.032).
Another aim of the VIREVOL project was to understand the processes at work in giant virus co-evolution with their host.
Autonomous glycosylation machinery of Mimiviridae:
A specific study on members of the Mimiviridae family revealed they are making complex glycans using their virally encoded glycosylation machinery, thus expanding glycosylation to the viral world. For instance, Mimivirus makes two huge polysaccharides of 70kDa and 25 kDa, made of rare capsular sugars which are branched on the fibrils surrounding the capsids (doi: 10.1002/anie.202106671). The sugar composition also appears to be clade specific suggesting giant virus built a versatile, constantly evolving toolbox, most likely to cope with other viruses and bacteria competing for a same host (microLife, doi.org/10.1093/femsml/uqac002)
Epigenetics in giant viruses:
DNA methylation is an important epigenetic mark that contributes to various regulations in all domains of life. Giant viruses are widespread dsDNA viruses with gene contents overlapping the cellular world that also encode DNA methyltransferases. Yet, virtually nothing is known about the methylation of their DNA. We used single-molecule real-time sequencing to study the complete methylome of a large spectrum of giant viruses. We show that DNA methylation is widespread, affecting 2/3 of the tested families and identified the corresponding viral methyltransferases and show that they are subject to intricate gene transfers between bacteria, viruses and their eukaryotic host. Most methyltransferases are conserved, functional and under purifying selection, suggesting that they increase the viruses' fitness. Some virally encoded methyltransferases are also paired with restriction endonucleases forming Restriction-Modification systems. Our data suggest that giant viruses' methyltransferases are involved in diverse forms of virus-pathogens interactions during coinfections (doi:10.1038/s41467-020-16414-2 )
