Biology subjects

Reyes-Ramirez, F.

Publications and source records attributed to Reyes-Ramirez, F..

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↗

bioRxiv2021

The functional differences between paralogous regulators define the control of the General Stress Response in Sphingopyxis granuli TFA

Sphingopyxis granuli TFA is a contaminant degrading alphaproteobacterium that responds to adverse conditions by inducing the General Stress Response (GSR), an adaptive response that controls the transcription of a variety of genes to overcome adverse conditions. The GSR triggered by TFA is driven by two extracytoplasmic function {sigma} factors (ECFs), EcfG1 and EcfG2, whose functional differences have been addressed previously, being EcfG2 the main activator. Upstream in this cascade, NepR anti-{sigma} factors directly inhibit EcfG activity under non-stress conditions, whereas PhyR response regulators sequester the NepR elements upon stress sensing to relieve EcfG inhibition. These elements, which are essential mediators of the GSR regulation, are duplicated in TFA, being NepR1 and NepR2, and PhyR1 and PhyR2. Here, based on multiple genetic, phenotypical and biochemical evidences including in vitro transcription assays, we have assigned distinct functional features to each of these paralogs and assessed their contribution to the GSR regulation, dictating its timing and the intensity. We show that different stress signals are differentially integrated into the GSR by PhyR1 and PhyR2, therefore producing different levels of GSR activation. We demonstrate in vitro that both NepR1 and NepR2 bind EcfG1 and EcfG2, although NepR1 produces a more stable interaction than NepR2. Conversely, NepR2 interacts with phosphorylated PhyR1 and PhyR2 more efficiently than NepR1. We propose an integrative model where NepR2 would play a dual negative role: it would directly inhibit the {sigma} factors upon activation of the GSR and it would modulate the GSR activity indirectly by titrating the PhyR regulators. IMPORTANCEIn Alphaproteobacteria, the General Stress Response (GSR) aims at protecting against a variety of stresses. Needing to integrate different signals, its modulation is capital to produce a proportionate response according to the environmental conditions. Individual alphaproteobacterial species have evolved distinct GSR cascades in which the information flow is usually straightforward to ascertain due to the presence of a single copy of at least one of its main regulators (PhyR, NepR and EcfG), restricting the regulatory possibilities. However, Sphingopyxis granuli TFA encodes two paralogs of each regulator, multiplying the possible regulatory interplays. We demonstrate that functional differences between paralogous GSR regulators allow an intrinsic feedback regulation in this pathway. We provide evidence of a NepR anti-{sigma} factor that exerts a dual negative feedback regulation on the GSR by interacting with the EcfG {sigma} factors and with the PhyR regulators. This would attune its output to the actual needs of the cell.

microbiology↗