Biology subjects

Da Cunha, V.

Publications and source records attributed to Da Cunha, V..

7 recordsLinked to original sources

bioRxiv2026

Thermococcales pangenome uncovers new genera and modular evolution.

The order Thermococcales is unusual among Archaea in being known primarily from hundreds of lab-cultured isolates rather than metagenome-assembled genomes. Such cultivation is powerful for comparative genomics, allowing access to complete closed genomes rather than fragmented assemblies. We analysed 122 complete genomes, comprising all publicly available type species plus 67 new isolates, as a single pangenome. A combination of genome-scale metrics resolved 70 species across five genus-level clades, two proposed here as the new genera Oleococcus and Piezococcus, in addition to the canonical Pyrococcus, Palaeococcus, and Thermococcus. Only 6.1% of the 21,490 gene families are persistent, yet these contribute over half the genes in any genome. We observe that accessory functions, such as amino-acid biosynthesis, often behave modularly, being gained and lost as intact cassettes from genus-specific chromosomal loci. Combined with 114 mobile genetic elements, 72 of which are integrated in the chromosome at conserved tRNA genes, we find that Thermococcales genomes accommodate rapid horizontal turnover through a constrained chromosomal architecture.

genomics↗

bioRxiv2026

Insertions in universal proteins confirm that Nanohaloarchaea belong to DPANN-Archaea and suggest several new major archaeal clades.

The phylogenetic position of Nanohaloarchaea has been debated, these nanosized archaea being alternatively proposed as sister group to Haloarchaea, members of the DPANN-Archaea, or sister group to Methanocellales. Screening a set of universal proteins, we identified four insertions located at critical locations in three ribosomal proteins and one RNA polymerase subunit that support the branching of Nanohaloarchaea as sister group to Aenigmarchaea within DPANN cluster II (sensu Dombrowski et al., 2020). Insertion analyses and phylogeny of the monomeric primase specific to DPANN-Archaea confirm the existence of a robust clade grouping Undinarchaea, Naiadarchaea and DPANN cluster II, that we propose to call Nanostetteria. Our insertion analysis also supports including Altiarchaea within DPANN-Archaea and suggest a new clades that has not been recovered in phylogenetic analyses, one grouping DPANN-Archaea with Stygia (Hadarchaea and relative) and an even large one grouping these lineages with Acherontia (Thermococci and relatives). The insertion defining this larger clade, present in the ribosomal protein uS7, is also present at the same position in Thaumarchaea, Korarchaea and a subgroup of Asgardarchaea. Whereas the insertion in Thaumarchaea is certainly due to an independent event, we discuss alternative hypotheses that can explain those present in Korarchaea and Asgardarchaea. Finally, we noticed several cases of MAGs misannotations, indicating that insertion analysis can be useful to identify protein with misleading affiliations. The existence of insertions in otherwise highly conserved universal proteins involved in translation or transcription could partly explain the high rate of protein evolution in some archaeal lineage, especially in DPANN-Archaea.

evolutionary biology↗

bioRxiv2026

Permuted 23S rRNA is integrated in 50S ribosome particles in Thermococcus barophilus

In Archaea, a prevalent class of circular RNAs corresponds to 16S and 23S ribosomal RNA intermediates (circ-pre-rRNAs). A conserved bulge-helix-bulge (BHB) motif within the 16S and 23S rRNAs processing stems and adjacent to the circularization site in Euryarchaeota and TACK superphylum suggests that pre-rRNAs circularization is widely conserved across Archaea. Using genome-wide transcriptomic data obtained on total RNAs of wild-type Thermococcus barophilus cells, we recovered the canonical circularization junctions of the 16S and 23S circ-pre-rRNAs at the predicted BHB motifs. We also identified three alternatives 23S circular junctions introducing variability at the 3 end of the mature rRNA. We investigated the different forms of 16S and 23S by performing primer extension and RACE experiments. We showed that while the 16S rRNA has standard 5 and 3 extremities, the main form of 23S rRNA is circularly permuted, with helix H99 now at its 5 end. This permutation most probably emerged from the deletion of helix H98 from the 23S circ-pre-rRNA. Interestingly, we showed that the permuted 23S rRNA is incorporated into ribosome subunits and 70S monosomes. The significance of this event in generating functional 50S particles remains to be determined.

microbiology↗

bioRxiv2022

A paralog of Pcc1 is the fifth core subunit of KEOPS complex in Archaea

In Archaea and Eukaryotes, the synthesis of a universal tRNA modification, t6A, is catalyzed by the KEOPS complex composed of Kae1, Bud32, Cgi121 and Pcc1. A fifth subunit, Gon7, is found only in Fungi and Metazoa. Mutations in all five genes encoding human KEOPS subunits leads to Galloway-Mowat syndrome, a severe genetic disease causing childhood lethality. Here, we describe the discovery and biochemical characterization of the archaeal fifth KEOPS subunit. This protein, dubbed Pcc2, is a paralog of Pcc1 and is widely conserved in Archaea. Pcc1 and Pcc2 form a heterodimer in solution, show modest sequence conservation but very high structural similarity. The 5-subunit KEOPS lost its capacity to form dimers but its tRNA binding and t6A synthetic activity remained robust. Pcc2 can substitute Pcc1 but the resulting KEOPS complex is inactive suggesting a distinct function for the two paralogs. Comparative sequence and structure analyses point to a possible evolutionary link between archaeal Pcc2 and eukaryotic Gon7 proteins. Our work thus reveals that Pcc2 has evolved to regulate the oligomeric state of KEOPS complex thus adding another layer of complexity to the biosynthesis of t6A that seems to be conserved from Archaea to Eukaryotes.

biochemistry↗

bioRxiv2022

Viral origin of eukaryotic type IIA DNA topoisomerases

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.

evolutionary biology↗

bioRxiv2020

Giant viruses encode novel types of actins possibly related to the origin of eukaryotic actin: the viractins

Actin is a major component of the eukaryotic cytoskeleton. Many related actin homologues can be found in eukaryotes1, some of them being present in most or all eukaryotic lineages. The gene repertoire of the Last Eukaryotic Common Ancestor (LECA) therefore would have harbored both actin and various actin-related proteins (ARPs). A current hypothesis is that the different ARPs originated by gene duplication in the proto-eukaryotic lineage from an actin gene that was inherited from Asgard archaea. Here, we report the first detection of actin-related genes in viruses (viractins), encoded by 19 genomes belonging to the Imitervirales, a viral order encompassing the giant Mimiviridae. Most viractins were closely related to the actin, contrasting with actin-related genes of Asgard archaea and Bathyarchaea (a newly discovered clade). Our phylogenetic analysis suggests viractins could have been acquired from proto-eukaryotes and possibly gave rise to the conventional eukaryotic actin after being reintroduced into the pre-LECA eukaryotic lineage.

evolutionary biology↗

bioRxiv2019

Evolution of the PRD1-adenovirus lineage: a viral tree of life incongruent with the cellular universal tree of life

Double-stranded DNA viruses of the PRD1-adenovirus lineage are characterized by homologous major capsid proteins containing one or two {beta}-barrel domains known as the jelly roll folds. Most of them also share homologous packaging ATPases of the FtsK/HerA superfamily P-loop ATPases. Remarkably, members of this lineage infect hosts from the three domains of life, suggesting that viruses from this lineage could be very ancient and share a common ancestor. Here we analyzed the evolutionary history of these cosmopolitan viruses by inferring phylogenies based on single or concatenated genes. These viruses can be divided into two supergroups infecting either eukaryotes or prokaryotes. The latter can be further divided into two groups of bacterioviruses and one group of archaeoviruses. This viral tree is thus incongruent with the cellular tree of life in which Archaea are closer to Eukarya and more divergent from Bacteria. We discuss various evolutionary scenarios that could explain this paradox.

evolutionary biology↗