Biology subjects

Devos, D. P.

Publications and source records attributed to Devos, D. P..

5 recordsLinked to original sources

bioRxiv2025

Domain-combination based pan-genomic Tree of Life

Reconstructing the Tree of Life (ToL) remains a central challenge in evolutionary biology. While sequence-based methods have resolved much of lifes diversity, deep evolutionary relationships often remain elusive, particularly across the three superkingdoms of life. Here, we present a complementary approach using genome-wide occurrence of protein domain combinations as phylogenetic signal. We analyzed 5,343 complete proteomes spanning Bacteria, Archaea, and Eukaryota, and inferred a pan-genomic ToL from [~]77,000 domain combinations, including isolated domains and domain pairs. Our reconstruction recovers major clades and captures both vertical inheritance and signals from non-vertical processes such as lateral gene transfer, endosymbiosis, and genome reduction. Ancestral reconstructions reveal functional innovations that mark key evolutionary transitions--such as the emergence of vesicle trafficking in Eukaryota or methanogenesis in Archaea. We found that organisms with reduced genomes, like Chlamydiota, tend to be misplaced in domain combination-based phylogenies due to sparse combinatorial data. Our results demonstrate that domain combinations carry a strong, evolutionary signal that is both biologically and functionally informative. While not a substitute for sequence-based phylogenetics, domain combination-based trees offer an alternative perspective, capable of integrating both vertical and lateral processes into a unified evolutionary framework. Author SummaryTraditional evolutionary trees are typically built from sequences, but this approach struggles to resolve deep branches in the Tree of Life. Here, we use combinations of protein domains--the functional modules that make up proteins to resolve major relationships in the tree. By analyzing over 5,000 complete proteomes from Bacteria, Archaea, and Eukaryotes, we reconstruct a Tree of Life that reflects both vertical inheritance and key evolutionary processes like endosymbiosis and gene transfer. This domain-based approach not only recovers known relationships but also reveals how major biological innovations emerged. Our results show that domain combinations provide a powerful and interpretable signal for studying evolution at a genomic scale.

evolutionary biology↗

bioRxiv2025

BAV-LLPS: A database of bacterial, archaea and virus liquid-liquid phase separation proteins

Liquid-liquid phase separation (LLPS) is a key process underlying the formation of biomolecular condensates (BMCs), such as membrane-less organelles (MLOs), that compartmentalize biochemical processes inside the cells. While LLPS has been extensively studied in eukaryotes, its role in bacteria, archaea, and viruses remains far less characterized. Recent studies in bacteria have revealed that LLPS-driven condensates play critical roles in RNA processing, stress response, and pathogenicity. Similarly, many viruses exploit LLPS to facilitate crucial steps in their infection cycles, including viral entry, genome replication, assembly, and host immune evasion. In this work, we introduce a hand-curated database of LLPS proteins from bacteria, archaea, and viruses (BAV-LLPS Database). This resource, extended through sequence similarity searches, comprises over 5,000 proteins and integrates diverse data including biological annotations, sequence features, predicted disordered regions, LLPS per site probability, and AlphaFold2-based structural models. Additionally, our web server enables users to explore both the curated and homologous derived datasets, providing a platform to uncover evolutionary relationships and intrinsic and differential properties of LLPS proteins across various taxonomic groups. This work seeks to deepen our understanding of LLPS mechanisms beyond eukaryotic organisms, emphasizing their significance across diverse life forms. It also aims to foster the development of specialized predictive tools that will facilitate the exploration and characterization of LLPS processes in a wide array of living organisms, thereby contributing to advancements in both fundamental biological research and applied biomedical sciences. Availability and ImplementationBAV-LLPS DB is freely accessible at https://bav-llps-db.bioinformatica.org/. The data can be retrieved from the website. The source code of the database can be downloaded from https://bav-llps-db.bioinformatica.org/download Contactgusparisi@gmail.com and gboccaccio@leloir.org.ar

bioinformatics↗

bioRxiv2024

Specificities and commonalities of the Planctomycetes plasmidome

Although plasmids play a crucial role in antibiotic resistance and contemporary biotechnology, our comprehension of their natural ecological dynamics remains restricted to a few bacterial groups. Planctomycetes is a bacterial phylum with unusual molecular and cellular biology for which little is known about its plasmidome. This study provides the first comprehensive description of the diversity of the endogenous plasmids found in Planctomycetes, which may be used as starting points to generate different genetic tools for research on this phylum. Plasmids from Planctomycetes encode a wide variety of biological functions, although for a large portion of the encoded genes a function cannot be assigned, which is usual in Planctomycetes. They seemed to have largely coevolved with the genome of their hosts, with which they share many homologs. We also detected recent transfer events of insertion sequences between co-habiting chromosomes and plasmids. 60% of the plasmid genes are distantly related to chromosomally-encoded genes and 40% have homologs in plasmids from other bacterial groups, while 36% of the proteins composing the planctomycetal plasmidome are exclusive. Most planctomycetal plasmids encode a replication initiation protein of the RPA family in the proximity of a putative iteron-containing replication origin, as well as active type I partition systems. One conjugative and three mobilizable plasmids were identified, suggesting horizontal gene transfer via conjugation in this phylum.

microbiology↗

bioRxiv2021

The 'squalene route' to carotenoid biosynthesis is widespread in Bacteria.

Squalene is mostly associated with the biosynthesis of polycyclic triterpenes. Although there have been suggestions that squalene could be involved in the biosynthesis of carotenoids, functionally and evolutionarily related to polycyclic triterpenes, evidence of this squalene route in nature was lacking. We demonstrate that planctomycetes synthesize C30 carotenoids via squalene and that this squalene route is widely distributed in Bacteria. We also investigated the functional roles of hopanoids and carotenoids in Planctomycetes and show that their protective functions under stress conditions are complementary. Our evolutionary analyses suggest that the C30 carotenoid biosynthetic pathway is the most ancestral, with a potential origin in Firmicutes or Planctomycetes. In addition, we propose an evolutionary scenario to explain the diversification of the different carotenoid and squalene pathways. Together, these results improve the evolutionary contextualization of these molecules. Likewise, the widespread occurrence of the squalene route in bacteria increases the functional repertoire of squalene.

microbiology↗

bioRxiv2020

Pex24 and Pex32 tether peroxisomes to the ER for organelle biogenesis, positioning and segregation

We analyzed all four Pex23 family proteins of the yeast Hansenula polymorpha, which localize to the ER. Of these Pex24 and Pex32, but not Pex23 and Pex29, accumulate at peroxisome-ER contacts, where they are important for normal peroxisome biogenesis and proliferation and contribute to organelle positioning and segregation. Upon deletion of PEX24 and PEX32 - and to a lesser extent of PEX23 and PEX29 - peroxisome-ER contacts are disrupted, concomitant with peroxisomal defects. These defects are suppressed upon introduction of an artificial peroxisome-ER tether. Accumulation of Pex32 at peroxisomes-ER contacts is lost in the absence of the peroxisomal membrane protein Pex11. At the same time peroxisome-ER contacts are disrupted, indicating that Pex11 contributes to Pex32-dependent peroxisome-ER contact formation. Summarizing, our data indicate that H. polymorpha Pex24 and Pex32 are tethers at peroxisome-ER contacts that are important for normal peroxisome biogenesis and dynamics. SummaryTwo Hansenula polymorpha ER proteins, Pex24 and Pex32, are tethers at peroxisome-ER contacts and function together with the peroxisomal protein Pex11. Their absence disturbs these contacts leading to multiple peroxisomal defects, which can be restored by an artificial tether.

cell biology↗