Biology subjects

Gonzalez-Toro, F.

Publications and source records attributed to Gonzalez-Toro, F..

3 recordsLinked to original sources

bioRxiv2025

Clade-wide proteome analysis shows widespread non-canonical Dcr proteins in fungi.

Dicers (Dcrs) are central proteins involved in the biogenesis of small RNAs (sRNAs) in eukaryotes. Most of the knowledge on Dcr structure, function and evolution comes from studies conducted in animal and plant species. Comparatively, much less is known in fungi, which are a genetically and ecologically diverse group with important roles in ecosystems, agriculture, medicine, and biotechnology. While canonical Dcrs in plants and animals contain a well-defined domain architecture, most fungal Dcrs with experimentally validated functions lack one or more identifiable canonical domains, raising questions about how RNA-binding and precise sRNA processing is retained. Here, we conducted the most extensive survey of fungal Dcr proteins, analyzing 1,593 proteomes across eight phyla. We found a diversity of Dcr domain architectures, with some of them lacking an identifiable PAZ, Helicase, and/or double-stranded RNA binding domains. Phylogenetic analyses showed that different Dcr classes are distributed across distinct clades that often align with fungal taxonomic groups. Despite the lack of canonical domain architectures, we found that fungal Dcrs fold into a characteristic L-shaped structure and show PAZ-like folds, even in proteins without detectable PAZ sequences. Molecular docking and electrostatic analyses further indicate that these divergent Dcrs maintain key RNA-binding surfaces for proper sRNA processing. Our results indicate a remarkable evolutionary plasticity of Dcr in fungi, showing that essential sRNA processing functions can be retained through structural conservation, and highlighting fungi as models to study the modular evolution of the RNAi machinery in eukaryotes. Significance statementDicer (Dcr) proteins are central to RNA interference (RNAi), a gene regulatory mechanism conserved across eukaryotes. However, current models of Dcr structure, function, and evolution are largely based on studies in animals and plants. Here, we present the most comprehensive analysis to date of Dcr proteins in fungi, a diverse eukaryotic group including many societally important pathogens and symbiotes which are reliant on RNAi. Our findings reveal that despite widespread divergence from canonical Dcr architecture, fungal Dcrs conserve critical folds and RNA-binding features, further suggesting that core RNAi functions are maintained. This work establishes fungi as key models for studying the evolution and functional robustness of the RNAi machinery, offering broader insight into the diversity and plasticity of sRNA biogenesis pathways across eukaryotes.

genomics↗

bioRxiv2025

Class-agnostic annotation of small RNAs balances sensitivity and specificity in diverse organisms

Small RNAs (sRNAs) are important regulatory elements in eukaryotic organisms and comprise the functional elements of RNAi. Numerous classes of sRNAs have been annotated, however they vary greatly in their ease of annotation and compatibility with most annotators. Significant challenges exist for the annotation process, including variation in sRNA library quality, alignment depth, and poorly defined loci, collectively making this process difficult. Additionally, few annotators are fully agnostic to sRNA classes and may struggle identifying loci in less explored organisms (exceptional organisms, fungi). To address these problems, we present an integrated sRNA annotation suite, YASMA, which is specifically suited to finding reliable thresholds for locus annotation which balance sensitivity with specificity. By comparing YASMA with other annotators, we show that pipelines based on coverage-normalization methods have great advantages in balancing many metrics to produce a more reproducible annotation. We also demonstrate that YASMA produces more contiguous and representative loci, through the aggressive merging of similar adjacent expressed regions. Finally, we also show that the tool produces much more descriptive locus dimensions, a major advantage in species where sRNAs may be distinct or unique. Overall, we demonstrate substantial improvements in annotation accuracy, reproducibility, and description, particularly in non-model organisms and less-explored clades.

genomics↗

bioRxiv2024

Aniline Dioxygenase in Rhodococcus ruber R1: Insights into Skatole Degradation

Skatole is an aromatic heterocyclic compound with a strong offensive odor, produced by microorganisms during the anaerobic breakdown of tryptophan. Skatole accumulation is linked to environmental and health issues. Despite its persistence and harmful effects, skatoles biodegradation by microorganisms is poorly understood. We have recently isolated a gram-positive bacterium, Rhodococcus ruber R1, which uses skatole as its sole carbon and energy source. Here we report an operon consisting of 14 genes encoding aromatic oxygenase systems involved in skatole degradation in Rhodococcus ruber R1. Cells growing on skatole accumulate aniline transiently, indicating its role as an intermediate in the degradation pathway. We characterize six genes in this cluster that encode for an aniline dioxygenase, which converts aniline to catechol and is only activated in the presence of skatole. This gene cluster was successfully introduced into a heterologous strain enabling the full degradation of aniline and its derivatives. Phylogenetic analysis of aniline dioxygenase present in R1 strain reveals a widespread distribution of this system among bacteria, in contrast to the full skatole cluster, which is restricted to a few genera. These findings advance our understanding of the skatole degradation pathway and highlight R1s potential for bioremediation of skatole, aniline, and related contaminants.

microbiology↗