Morgan Gaïa

Les virophages sont des petits virus à ADN possédant une capside icosaédrique de 50-60 nm et un génome de 17 à 26 Kb codant potentiellement pour une vingtaine de gènes. Ils ont été découverts associés à des grands virus à ADN appartenant à l’ordre des Megavirales, pour lesquels leur présence serait délétère.Le premier projet du travail de thèse a été de faire le bilan des propriétés connues des virophages au travers d’une revue. La deuxième partie correspond à un bilan des avancées en matière d’isolement de virus géants dans les amibes – hôtes naturels des Mimiviridae –, pouvant être associés aux virophages. La troisième section se focalise sur la réplication des virophages Sputnik avec différents virus parmi les Mimiviridae, ainsi que sur l’isolement d’une nouvelle souche de Sputnik sans son hôte natif par l’utilisation d’un Mimiviridae en tant que virus rapporteur. La dernière partie est enfin basée sur l’identification d’un nouveau virophage – Zamilon – isolé en association avec un Mimiviridae du groupe C, et présentant une spécificité d'hôtes restreinte. Celle-ci est d'ailleurs étudiée.Les résultats présentés dans cette thèse démontrent une certaine complexité des interactions entre les virophages et leurs hôtes. Au sein d’une même famille d’hôtes, certains virophages possèdent un large spectre de spécificité, alors que d’autres ne peuvent se multiplier qu’avec certains d’entre eux, comme cela a déjà été observé chez les bactériophages. Compte-tenu de leur impact potentiel sur les virus géants, ces résultats soutiennent l’hypothèse d’une régulation des populations virales environnementales par les virophages.

Mirusviruses infect unicellular eukaryotes and are related to tailed bacteriophages and herpesviruses. Here we expand the known diversity of mirusviruses by screening diverse metagenomic assemblies and characterizing 1,202 non-redundant environmental genomes. Mirusviricota comprises a highly diversified phylum of large and giant eukaryotic viruses that rivals the evolutionary scope and functional complexity of nucleocytoviruses. Critically, major Mirusviricota lineages lack essential genes encoding components of the replication and transcription machineries and, concomitantly, encompass numerous spliceosomal introns that are enriched in virion morphogenesis genes. These features point to multiple transitions from cytoplasmic to nuclear reproduction during mirusvirus evolution. Many mirusvirus introns encode diverse homing endonucleases, suggestive of a previously undescribed mechanism promoting the horizontal mobility of spliceosomal introns. Available metatranscriptomes reveal long-range trans-splicing in a virion morphogenesis gene. Collectively, our data strongly suggest that nuclei of unicellular eukaryotes across marine and freshwater ecosystems worldwide are a major niche for replication of intron-rich mirusviruses.

Aminoacyl-tRNA synthetases (aaRSs), also known as tRNA ligases, are essential enzymes in translation. Owing to their functional essentiality, these enzymes are conserved in all domains of life and used as informative markers to trace the evolutionary history of cellular organisms. Unlike cellular organisms, viruses generally lack aaRSs because of their obligate parasitic nature, but several large and giant DNA viruses in the phylum Nucleocytoviricota encode aaRSs in their genomes. The discovery of viral aaRSs led to the idea that the phylogenetic analysis of aaRSs can shed light on ancient viral evolution. However, conflicting results have been reported from previous phylogenetic studies: one posited that nucleocytoviruses recently acquired their aaRSs from their host eukaryotes, while another hypothesized that the viral aaRSs have ancient origins. Here, we investigated 4,168 nucleocytovirus genomes, including metagenome-assembled genomes (MAGs) derived from large-scale metagenomic studies. In total, we identified 780 viral aaRS sequences in 273 viral genomes. We generated and examined phylogenetic trees of these aaRSs with a large set of cellular sequences to trace evolutionary relationships between viral and cellular aaRSs. The analyses suggest that the origins of some viral aaRSs predate the last common eukaryotic ancestor. Inside viral aaRS clades, we identify intricate evolutionary trajectories of viral aaRSs with horizontal transfers, losses, and displacements. Overall, these results suggest that ancestral nucleocytoviruses already developed complex genomes with an expanded set of aaRSs in the proto-eukaryotic era.

The phylum Nucleocytoviricota comprises a diverse group of double-stranded DNA viruses that display a wide range of gene repertoires. Although these gene repertoires determine the characteristics of individual viruses, the evolutionary processes that have shaped the gene repertoires of extant viruses since their common ancestor are poorly characterized. In this study, we aimed to address this gap in knowledge by using amalgamated likelihood estimation (ALE), a probabilistic tree reconciliation method that infers evolutionary scenarios by distinguishing origination, gene duplications, virus-to-virus horizontal gene transfer (vHGT), and gene losses. We analyzed over 4,700 gene families from 195 genomes spanning all known viral orders. The evolutionary reconstruction suggests a history of extensive gene gains and losses during the evolution of these viruses, notably with vHGT contributing to gene gains at a comparable level to duplications and originations. The vHGT frequently occurred between phylogenetically closely related viruses, as well as between distantly related viruses with an overlapping host range. We observed a pattern of massive gene duplications that followed vHGTs for gene families that was potentially related to host range control and virus-host arms race. These results suggest that vHGT represents a previously overlooked, yet important, evolutionary force that integrates the evolutionary paths of multiple viruses and affects shaping of Nucleocytoviricota virus gene repertoires.

Summary: Large and giant double-stranded DNA viruses are diverse and highly prevalent in the environment where they substantially affect the ecology and evolution of eukaryotes ^1–4 . Until now, they were only sporadically found in the digestive system of vertebrates ^5–7 . Here, we present the discovery of a diversified group of DNA viruses with large linear genomes dubbed egoviruses that comprise a putative viral order most closely related to animal-infecting poxviruses. Egoviruses are found worldwide, almost exclusively in the digestive system of humans, livestock and wild animals. One egovirus is human-specific, evolutionarily constrained, and spread across continents, demonstrating a long-term association between egoviruses and the human population. Analysis of eukaryotic homologs of egovirus core genes suggests that these viruses primarily infect Trichostomatia (Ciliates), which play a central role in ruminant digestive processes ⁸ , and Parabasalia (Metamonada), which directly influence animal immunity and gut microbiome ecology ⁹ . Egoviruses also contributed to the genetic makeup of polintons, endogenous viruses that proliferated in genomes of Trichomonas vaginalis ¹⁰ and its close relatives among the Parabasalia . Unlike poxviruses that form brick-shaped virions, egoviruses are predicted to form multilayered icosahedral capsids resembling those of asfuviruses and likely representing the ancestral virion structure. Egoviruses currently are the only known clade of eukaryotic DNA viruses abundant in the animal digestive system. Phylogenomic analysis suggests an evolutionary scenario whereby egovirus-like ancestors of poxviruses infected anaerobic unicellular eukaryotes inside the gut of ancestral animals, before transitioning to animal cell infection which was accompanied by the virion metamorphosis.

Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phylaNucleocytoviricotaandMirusviricotaare groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus–host network at the polar–nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.

Our perception of viruses has been drastically evolving since the inception of the field of virology over a century ago. In particular, the discovery of giant viruses from the Nucleocytoviricota phylum marked a pivotal moment. Their previously concealed diversity and abundance unearthed an unprecedented complexity in the virus world, a complexity that called for new definitions and concepts. These giant viruses underscore the intricate interactions that unfold over time between viruses and their hosts, and are themselves suspected to have played a significant role as a driving force in the evolution of eukaryotes since the dawn of this cellular domain. Whether they possess exceptional relationships with their hosts or whether they unveil the actual depths of evolutionary connections between viruses and cells otherwise hidden in smaller viruses, the attraction giant viruses exert on the scientific community and beyond continues to grow. Yet, they still hold surprises. Indeed, the recent identification of mirusviruses connects giant viruses to herpesviruses, each belonging to distinct viral realms. This discovery substantially broadens the evolutionary landscape of Nucleocytoviricota. Undoubtedly, the years to come will reveal their share of surprises.

DNA viruses have a major influence on the ecology and evolution of cellular organisms^1–4, but their overall diversity and evolutionary trajectories remain elusive⁵. Here we carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota. The virion morphogenesis module of this large monophyletic clade is typical of viruses from the realm Duplodnaviria⁶, with multiple components strongly indicating a common ancestry with animal-infecting Herpesvirales. Yet, a substantial fraction of mirusvirus genes, including hallmark transcription machinery genes missing in herpesviruses, are closely related homologues of giant eukaryotic DNA viruses from another viral realm, Varidnaviria. These remarkable chimaeric attributes connecting Mirusviricota to herpesviruses and giant eukaryotic viruses are supported by more than 100 environmental mirusvirus genomes, including a near-complete contiguous genome of 432 kilobases. Moreover, mirusviruses are among the most abundant and active eukaryotic viruses characterized in the sunlit oceans, encoding a diverse array of functions used during the infection of microbial eukaryotes from pole to pole. The prevalence, functional activity, diversification and atypical chimaeric attributes of mirusviruses point to a lasting role of Mirusviricota in the ecology of marine ecosystems and in the evolution of eukaryotic DNA viruses.

Il est maintenant bien établi que les virus ont joué un rôle important dans l’évolution des eucaryotes modernes. Dans cette revue, nous commentons le rôle qu’ils ont pu jouer dans l’eucaryogenèse. Nous discutons les analyses phylogénétiques qui mettent en évidence l’origine virale de plusieurs protéines clés de la biologie moléculaire des eucaryotes et des observations récentes qui, par analogie, pourraient suggérer une origine virale du noyau cellulaire. Nous mettons en parallèle la complexité des eucaryotes avec l’unicité de leur virosphère et avançons l’hypothèse selon laquelle des mécanismes de la différenciation cellulaire auraient leur source dans ceux mis en œuvre par les virus pour transformer les cellules infectées en cellules virales.

Type II DNA topoisomerases of the family A (Topo IIA) are present in all bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologues and have no orthologues in Archaea. Interestingly, eukaryotic Topo IIA have close homologues in viruses of the phylum Nucleocytoviricota , an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses (NCLDV). Topo IIA are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses combining viral and cellular Topo IIA homologs. Topo IIA encoded by bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota , respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both bacteria and Caudoviricetes from the dataset, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long branch attraction artefact. The topology of our tree suggests that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes , before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.