Biology subjects

Garcia-Romero, I.

Publications and source records attributed to Garcia-Romero, I..

3 recordsLinked to original sources

bioRxiv2025

Discovery of a stress-response integrative and conjugative element from Sphingopyxis granuli TFA broadly conserved across Sphingomonadales and Rhizobiales

Horizontal gene transfer is a pivotal element in the evolution of microbes, enabling them to acquire novel genes and phenotypes. Integrative and conjugative elements (ICEs) are a type of mobile genetic element that can integrate into the host genome and propagate during chromosome replication and cell division. The induction of ICE gene expression results in the excision of the ICE gene, the production of conserved conjugation machinery, a Type IV Secretion System, and the potential for DNA transfer to appropriate receptors. It has been observed that ICEs frequently contain cargo genes that do not typically align with the ICE life cycle. These genes often result in the manifestation of phenotypes that are of particular interest. The bacterium Sphingopyxis granuli strain TFA is being studied for its ability to degrade the contaminant tetralin present in crude oils. Genomic analysis identified eight possible integrative mobile elements in S. granuli TFA. Most of these regions exhibited a distribution pattern that was restricted to the species, and they lacked some functional modules that are characteristic of a complete ICE. This finding suggests the presence of degenerate structures or limited mobilization capacity. However, only two of the detected elements exhibited the capacity to retain all the modules necessary for transfer, integration, and maintenance. These elements also contained a cargo module that included genes associated with lipid metabolic pathways and resistance mechanisms. Among them, ICE3 was distinguished as the sole complete functional ICE that was also present in other species. Transcriptomic analysis under multiple stress conditions revealed differential and consistent activation of ICE3 genes, demonstrating their direct contribution to bacterial resilience and suggesting a key adaptive role in response to adverse environmental changes.

bioinformatics↗

bioRxiv2025

Uncovering the regulatory network of the small RNA SuhB and its contribution to stress resistance in Sphingopyxis granuli TFA

Post-transcriptional regulation by small RNAs (sRNAs) enables bacteria to fine-tune gene expression and rapidly adapt to fluctuating environmental conditions. In Sphingopyxis granuli TFA, SuhB, the only sRNA characterized to date in this strain, was previously shown to repress thnR translation to control tetralin degradation under carbon catabolite repression conditions. Here, we reveal additional regulatory roles of SuhB beyond carbon metabolism. Deletion of suhB increases sensitivity to diverse abiotic stresses, including osmotic, oxidative, desiccation, and copper stress. Label-free quantitative proteomic analysis indicates widespread alterations in the proteome in the absence of SuhB, affecting metabolic pathways and membrane-associated processes. Moreover, a LysR-type transcription factor mutant, identified as a direct activator of suhB, shows similar phenotypes. Together, these findings demonstrate that SuhB functions as a global post-transcriptional regulator, coordinating metabolic balance, membrane composition, and stress resistance in S. granuli TFA, highlighting the critical role of sRNA-mediated regulation in environmental bacteria.

microbiology↗

bioRxiv2020

Characterization of the exopolysaccharide biosynthesis pathway in Myxococcus xanthus

Myxococcus xanthus arranges into two morphologically distinct biofilms depending on its nutritional status, i.e. coordinately spreading colonies in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. A secreted polysaccharide referred to as exopolysaccharide (EPS) is a structural component of both biofilms and is also important for type IV pili-dependent motility and fruiting body formation. Here, we characterize the biosynthetic machinery responsible for EPS biosynthesis using bioinformatics, genetics, heterologous expression, and biochemical experiments. We show that this machinery constitutes a Wzx/Wzy-dependent pathway dedicated to EPS biosynthesis. Our data support that EpsZ (MXAN_7415) is the polyisoprenyl-phosphate hexose-1-phosphate transferase responsible for initiation of the repeat unit synthesis. Heterologous expression experiments support that EpsZ has galactose-1-P transferase activity. Moreover, MXAN_7416, renamed WzxEPS, and MXAN_7442, renamed WzyEPS, are the Wzx flippase and Wzy polymerase responsible for translocation and polymerization of the EPS repeat unit, respectively. Also, in this pathway, EpsV (MXAN_7421) is the polysaccharide co-polymerase and EpsY (MXAN_7417) the outer membrane polysaccharide export (OPX) protein. Mutants with single in-frame deletions in the five corresponding genes had defects in type IV pili-dependent motility and a conditional defect in fruiting body formation. Furthermore, all five mutants were deficient in type IV pili formation and genetic analyses suggest that EPS and/or the EPS biosynthetic machinery stimulates type IV pili extension. Additionally, we identify a polysaccharide biosynthesis gene cluster, which together with an orphan gene encoding an OPX protein make up a complete Wzx/Wzy-dependent pathway for synthesis of an unknown polysaccharide. ImportanceThe secreted polysaccharide referred to as exopolysaccharide (EPS) has important functions in the social life cycle of M. xanthus; however, little is known about how EPS is synthesized. Here, we characterized the EPS biosynthetic machinery and show that it makes up a Wzx/Wzy-dependent pathway for polysaccharide biosynthesis. Mutants lacking a component of this pathway had reduced type IV pili-dependent motility and a conditional defect in development. Also, these analysis suggest that EPS and/or the EPS biosynthetic machinery is important for type IV pili formation.

microbiology↗