Damien P Devos | Search PubMed

PubMed2025

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

MOTIVATION: Liquid-liquid phase separation (LLPS) is a key process underlying the formation of biomolecular condensates, such as membrane-less organelles, 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. RESULTS: 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 5000 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 IMPLEMENTATION: BAV-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.

Databases, Protein↗

PubMed2025

A century of research on the Planctomycetota bacterial phylum, previously known as Planctomycetes.

One hundred years after planctomycetes were discovered and 50 years since the first isolate was successfully cultured, this bacterial phylum remains enigmatic in many ways. In the last few decades, a significant effort to characterize new isolates has resulted in >150 described species, allowing a more comprehensive analysis of their features. However, metagenomic studies reveal that a diverse group of planctomycetes has yet to be cultured and characterized, and that many biological surprises are yet to be revealed. This is the case for the recently discovered phagotrophic Candidatus Uabimicrobium, which challenges our understanding of the distinction between prokaryotes and eukaryotes. The unique biology of planctomycete cells, such as their ability to divide without the FtsZ protein, their complex structure and characteristic morphology, their relatively large genomes containing many genes with unknown function, and their variable metabolic capabilities, imposes significant barriers for researchers. Although ubiquitous, the precise ecological roles of planctomycetes in various environments are still not fully understood. However, their distinctive metabolism opens the door to a large number of potential biotechnological applications, which are beginning to be unveiled. In this article, we first review the historical milestones in planctomycetes research and describe the pioneers of the field. We then describe the controversies and their resolutions, we highlight the past discoveries and current interrogations related to planctomycetes, and discuss the ongoing challenges that hinder a comprehensive understanding of their biology. We end up with directions for exploring the biology and ecological roles of these fascinating organisms.

Bacteria↗