The emergence and early evolution of eukaryotes, with many complex and unique features already present in the Last Eukaryotic Common Ancestor (LECA), are challenging biological questions. The nature of LECA’s precursors that progressively accumulated these specific traits (i.e., proto-eukaryotes), as well as the mechanisms that led to modern eukaryotes, are enigmatic, and the roles that viruses could have played understudied. Yet, the NCLDVs (Nucleocytoviricota) could have significantly influenced eukaryogenesis. This viral phylum comprises diverse large and giant DNA viruses, widespread and collectively infecting the entire eukaryotic domain, and presumably already diversified before LECA. This suggests long-lasting interactions with their hosts, including gene transfers that seem particularly important between NCLDVs and eukaryotes. Homologs of eukaryotic proteins related to critical informational processes have already been detected in NCLDVs, with phylogenies supporting ancestral transfers from virus to cell. In the VirEukaGen project, we hypothesize that NCLDVs initially infected proto-eukaryotes, substantially participating in eukaryogenesis, notably through the transfers of genes that diverged or emerged in viral genomes. The objectives are to decipher the origin and early evolution of NCLDVs and Eukaryotes, respectively, and to assess their co-evolution over time. The VirEukaGen project will benefit from two recent large resources of environmental genomes of planktonic eukaryotes and NCLDVs, including new groups, and will notably combine extensive phylogenomic, phylogenetic, and gene cluster analyses. It is organized into 3 tasks: (1) the vertical evolution of marine eukaryotes and NCLDVs, (2) the horizontal transfers between them, and (3) the production of new genomic resources for informative clades and environments. Through the exploration of the (co)evolution of NCLDVs and eukaryotes, this project will clarify the roles that viruses have played in cellular evolution.

Metagenomics has revealed a tremendous number of uncultivated bacterial clades referred as the ‘microbial dark matter’, including a large group of nano-sized bacteria forming the candidate phyla radiation (CPR) accounting >15% of bacterial diversity. CPR are mainly composed of symbiotic organisms with key roles in ecosystem formation and nutrient cycling. In recent years, several studies have described the ecology, diversity and functioning of some CPR bacteria classified as predatory bacteria, but observations are not easy, remain random and only few hosts have been identified. Recently, our consortium reproducibly observed and identified different magnetotactic bacteria (MTB) populations inhabiting microoxic-anoxic habitats hosting nano-sized CPR bacteria. CPR cells are associated partially inside its magnetotactic host, which seems to modify its external membrane in response to the CPR contact. Thus, our observations rather suggest that MTB-CPR symbioses last over time without host disintegration and could also rely on a mutualistic interaction. The magnetism of MTB represents an advantage to characterize the functional bases of the interaction. In this project, we will tackle low risk/high gain reachable challenges with the study of the biodiversity of MTB-CPR interaction and the functional basis of the physical interaction and cooperation, but also propose to take on the culturing of a model which seems particularly rewarding. This project is based on a multidisciplinary consortium coupling environmental microbiology, single-cell genomics, microscopy and phylogenomics, and combining recognized expertise in all models and disciplines involved.

The MIRUS project aims at studying the ecological and evolutionary prominence of a major clade of marine eukaryotic DNA viruses (the mirusviruses) that were recently discovered using the metagenomic legacy of Tara Oceans. The mirusviruses are diverse and abundant in the sunlit ocean where they actively infect unicellular eukaryotes. Moreover, their remarkable gene content links for the first-time herpesviruses and all the giant viruses (phylum Nucleocytoviricota). Thus, the mirusviruses provide a new genomic window of opportunities to study the diversity, functioning and evolution of eukaryotic DNA viruses. Our main hypothesis is that the complex functional lifestyle of mirusviruses had a long-lasting influence on the ecology of marine ecosystems that led to the emergence of (i) animal herpesviruses by means of reductive evolution and (ii) all giant Nucleocytoviricota through a cross-realm transfer of hallmark informational genes. The MIRUS project aims at testing this hypothesis by exploring the ecology and evolution of marine mirusviruses. We will assess how mirusviruses influence the ecology of plankton by characterizing their functional potential, biogeography, and in situ activity during infection of unicellular eukaryotes. In parallel, we will also assess how mirusviruses have influenced the evolution of herpesviruses and Nucleocytoviricota by identifying and characterizing the evolution of hallmark mirusvirus genes. In doing so, we will determine the extent of quantifiable shared evolutionary history between mirusviruses, herpesviruses and Nucleocytoviricota. Our overarching goal is to bolster the current understanding of virus-eukaryote interactions in the oceans while proposing a refined model of evolution for eukaryotic DNA viruses.

Discovering cutting-edge methods for the synthesis of chiral amines is essential since many pharmaceutical molecules contain this motif. Moreover, to meet the challenges of sustainability, it is imperative to develop green, chemo-, regio- and stereo-selective processes. Biocatalysis meets its expectations but the known enzymatic methods to obtain amines suffer from an equilibrium shift requirement, or the need to recycle cofactors. On the contrary, enzymes forming C-C bonds do not have these drawbacks and would allow, in a single thermodynamically favored and highly selective step, to build the carbon backbone of target molecules while providing access to the amino moiety. Moreover, they display a broad spectrum of electrophilic carbonyl substrates. Thus, we assume that they will also be able to accept imines. With this in mind, we will explore two families of enzymes: aldolases and synthases which should allow to catalyze a reaction between a nucleophile and an imine as electrophile. The 4-amino-3,4-dideoxy-D-arabino-heptulosonate 7-phosphate (ADAHP) synthases have already shown their ability to use an imine as an electrophile. However, this weakly documented activity has never been exploited in synthesis. We propose to perform the first large-scale exploration of the biodiversity of the ADAHP synthases family to evaluate their catalytic capacities for chiral amines synthesis. In the case of aldolases, whose electrophilic substrate is an aldehyde, the aim is to identify a promiscuous activity towards imines, on the basis of our recent studies which have demonstrated the great plasticity of their active site. This would reveal a new activity called "aldaminase" which will bring a major advance in the well-known asymmetric Mannich reaction by allowing the use of enolizable aldehydes. The enzymes will be searched in the genomic biodiversity thanks to a bioinformatic approach, to build a collection of several hundreds of synthases and aldolases with a special focus on extremophilic microorganisms and from metagenomes (Tara project). Molecular probes will be synthetized to perform a high throughput screening in the retroaldamination direction using spectrophotometric assays. Indeed, as aldaminase activity was never described within the aldolase family, and considering the problem of imine instability in water, we hypothesize that a first detection of the retro-Mannich reaction is a more achievable goal. On emerging hits, modifications will then be undertaken by rational mutagenesis approaches, with the support of molecular modeling, to both increase their activities towards imines and reduce their natural abilities to convert the corresponding carbonyl into aldol. The best biocatalysts will be tested in deep eutectic solvents, allowing to increase water sensitive imines concentration. In the presence of efficient "aldaminases", the synthesis of essential synthons for the preparation of various pharmaceutical products will be considered. This highly interdisciplinary project brings together two partners whose collaboration has already been fruitful. Partner 1 (ICCF) brings a strong expertise in the field of biocatalytic processes and particularly in the study and exploitation of carboligases. Physical chemists specialized in the study of eutectic solvents are also members of the partner’s 1 team. Partner 2 (CEA/Genoscope), brings a unique expertise in the fields of exploration of catalytic capacities in the biodiversity on a large scale, which combines bioinformatics methods for the analysis of (meta)genomes, cloning and high throughput screening. This project will allow the development of the largest collection of carboligases existing to date. The ALDAMINASE project promises remarkable innovations in the field of biocatalysis and should constitute a major advance in sustainable synthesis of active pharmaceutical ingredients.

In the ARCHANE project, we propose to use archaeal model organisms as chassis to study the biochemical properties of eukaryotic signature proteins found in archaea and their impact on cellular physiology. The aim of this project is to experimentally reconstruct the cellular complexification leading to the emergence of the Asgard archaeal ancestor of eukaryotes by successive introduction of functional eukaryote signature proteins from the TACK (Thaumarchaeota–Aigarchaeota–Crenarchaeota–Korarchaeota) superphylum and Asgardarchaeota into cultivable and genetically tractable archaea, an ambitious task never attempted before. This program should shed light on the pathway of eukaryogenesis from an ancestral archaeon towards the increased cellular complexity of Eukaryotes.