Biology subjects

De Castro, C.

Publications and source records attributed to De Castro, C..

4 recordsLinked to original sources

bioRxiv2026

A hierarchical orthology framework reveals viral carbohydrate-active genes across the global virosphere

Carbohydrate-active enzymes (CAZymes) shape virus-host interactions by modifying virion structures, host surfaces and extracellular glycans. However, the diversity and evolutionary origins of viral carbohydrate-active enzymes remain poorly understood, partly due to limited viral protein annotations. To address this, we present VirGenes, a database of viral orthologous groups constructed from the KEGG viral gene dataset. VirGenes uses a hierarchical framework that integrates sequence similarity, remote homology, and structural similarity to support evolutionary and functional analyses of viral proteins. By screening the sequence space of VirGenes, we identified 558 CAZyme-associated gene clusters spanning 102 CAZyme families, revealing particularly enriched repertoires in dsDNA viral lineages. Two bacteriophage families, Kleczkowskaviridae and Pootjesviridae, encoded more than 10 CAZymes per genome, followed by Mimiviridae, a representative family of eukaryotic giant viruses. Phylogenetic analyses systematically revealed divergent evolutionary histories of viral carbohydrate-active genes, including frequent horizontal transfer of endolysin genes from bacteria, which likely represents a viral strategy in the ongoing evolutionary arms race with their cellular hosts. Within the structural space of VirGenes, a large number of viral genes were found to contain CAZyme-like folds despite more than 85% of them lacking detectable sequence similarity to annotated CAZyme sequences. Notably, numerous hypothetical sequences from giant viruses exhibited glycoside hydrolase-like five-bladed {beta}-propeller folds. Overall, by integrating sequence, structural and functional evidence, we show that viral carbohydrate-active systems exemplify how distributed innovations, constrained by ancient folds, collectively build the functional complexity of the global virosphere. VirGenes is publicly accessible at https://www.genome.jp/vogdb/.

bioinformatics↗

bioRxiv2025

Cysteine-rich receptor-like kinases mediate Wall Teichoic Acid perception in Arabidopsis

Plants and animals detect microbe-associated molecular patterns (MAMPs) to initiate defense responses. Both lineages employ pattern recognition receptors (PRRs), yet plant mechanisms for sensing Gram-positive bacterial MAMPs remain poorly understood. Wall teichoic acids (WTAs), anionic glycopolymers unique to Gram-positive bacteria, are shown here to activate salicylic acid signaling, defense priming, and a non-canonical programmed cell death in Arabidopsis. We demonstrate that glycosylated WTAs from diverse Gram-positive species elicit these responses and provide genetic evidence that their recognition depends on two members of the plant-specific CYSTEINE-RICH RECEPTOR-LIKE KINASE (CRK) gene family, which is absent in animals and whose function remains elusive. These findings reveal WTAs as a novel class of MAMPs in plants and highlight CRKs as key components in their perception.

plant biology↗

bioRxiv2023

Wall teichoic acid substitution with glucose governs phage susceptibility of Staphylococcus epidermidis

The species- and clone-specific susceptibility of Staphylococcus cells for bacteriophages is governed by the structures and glycosylation patterns of wall teichoic acid (WTA) glycopolymers. The glycocodes of phage-WTA interaction in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) have remained unknown. We report a new S. epidermidis WTA glycosyltransferase TagE whose deletion confers resistance to siphoviruses such as {Phi}E72 but enables binding of otherwise unbound podoviruses. S. epidermidis glycerolphosphate WTA was found to be modified with glucose in a tagE-dependent manner. TagE is encoded together with the enzymes PgcA and GtaB providing uridine diphosphate-activated glucose. {Phi}E72 transduced several other CoNS species encoding TagE homologs suggesting that WTA glycosylation via TagE is a frequent trait among CoNS that permits inter-species horizontal gene transfer. Our study unravels a crucial mechanism of phage-Staphylococcus interaction and of horizontal gene transfer and it will help in the design of anti-staphylococcal phage therapies. ImportancePhages are highly specific for certain bacterial hosts, and some can transduce DNA even across species boundaries. How phages recognize cognate host cells remains incompletely understood. Phages infecting members of the genus Staphylococcus bind to wall teichoic acid (WTA) glycopolymers with highly variable structures and glycosylation patterns. How WTA is glycosylated in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative Staphylococcus (CoNS) species has remained unknown. We describe that S. epidermidis glycosylates its WTA backbone with glucose and we identify a cluster of three genes, responsible for glucose activation and transfer to WTA. Their inactivation strongly alters phage susceptibility patterns, yielding resistance to siphoviruses but susceptibility to podoviruses. Many different CoNS species with related glycosylation genes can exchange DNA via siphovirus {Phi}E72 suggesting that glucose-modified WTA is crucial for interspecies horizontal gene transfer. Our finding will help to develop antibacterial phage therapies and unravel routes of genetic exchange.

microbiology↗

bioRxiv2023

Knockout of GMC-oxidoreductase genes reveals functional redundancy in mimivirus

The mimivirus 1.2Mb genome was shown to be organized into a nucleocapsid-like genomic fiber encased in the nucleoid compartment inside the icosahedral capsid (1). The genomic fiber protein shell is composed of a mixture of two GMC-oxidoreductase paralogs, one of them being the main component of the glycosylated layer of fibrils at the surface of the virion (2). In this study, we determined the effect of the deletion of each of the corresponding genes on the genomic fiber and the layer of surface fibrils. First, we deleted the GMC-oxidoreductase the most abundant in the genomic fiber, and determined its structure and composition in the mutant. As expected, it was composed of the second GMC-oxidoreductase and contained 5- and 6-start helices similar to the wild-type fiber. This result led us to propose a model explaining their coexistence. Then, we deleted the GMC-oxidoreductase the most abundant in the layer of fibrils to analyze its protein composition in the mutant. Second, we showed that the fitness of single mutants and the double mutant were not decreased compared to the wild-type viruses in laboratory conditions. Third, we determined that deleting the GMC-oxidoreductase genes did not impact the glycosylation or the glycan composition of the layer of surface fibrils, despite modifying their protein composition. Since the glycosylation machinery and glycan composition of members of different clades are different (3, 4), we expanded the analysis of the protein composition of the layer of fibrils to members of the B and C clades and showed that it was different among the three clades and even among isolates within the same clade. Taken together, the results obtained on two distinct central processes (genome packaging and virion coating) illustrate an unexpected functional redundancy in members of the family Mimiviridae, suggesting this may be the major evolutionary force behind their giant genomes. One-Sentence SummaryFunctional redundancy preserves mimivirus genomic fiber and layer of fibrils formation.

microbiology↗