Biology subjects

Silme, R. S.

Publications and source records attributed to Silme, R. S..

5 recordsLinked to original sources

bioRxiv2026

Integrative Genomic and Metabolomic Analysis of Terribacillus aidigensis KB25 Highlights Its Antifungal Activity against Phytophthora infestans and Adaptive Responses to Salt Stress

This study characterizes Terribacillus aidigensis strain KB25, a novel halotolerant isolate from a thermal spring, exhibiting potent antifungal activity against the late blight pathogen Phytophthora infestans. Whole-genome sequencing and electron microscopy revealed significant physiological adaptations to salt stress and a rich genomic repertoire encoding secondary metabolites. Metabolomic profiling of the bacteria-fungus interaction demonstrated upregulated cofactor biosynthesis and energy metabolism, specifically identifying antimicrobial terpene derivatives as key inhibitory agents. Complementary molecular docking studies provided mechanistic insights, predicting high-affinity binding between bacterial sporulenol and the P. infestans RxLR effector. Notably, the analysis indicated a strong structural interaction between the bacterial ABC-type proline/glycine betaine permease and the glutamate receptor, suggesting a mechanism for mediating plant stress tolerance. These findings validate the dual efficacy of KB25 which indicates direct pathogen suppression via bioactive metabolite secretion and the potential modulation of host stress signalling. Integrated genomic-metabolomic analysis was also proved our findings. Consequently, T. aidigensis KB25 represents a promising, sustainable biocontrol agent for managing late blight, particularly within saline agro-ecosystems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/704535v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@fc50d6org.highwire.dtl.DTLVardef@11f3a1dorg.highwire.dtl.DTLVardef@12051c7org.highwire.dtl.DTLVardef@d8e16b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

The Specific Genetic Markers to Diagnose Xanthomonads Infecting Pepper and Tomato Plants

We have improved a marker system to examine the genetic diversity in Xanthomonads species by using whole genome sequence analysis and repetitive regions in the bacterial genome. Specifically, we amplified microsatellite regions using PCR, and the resulting fragments were digested with specific enzymes. These fragment profiles served as molecular markers. Consequently, a more precise marker for bacterial identification was developed by combining the microsatellite and RFLP methods to differentiate Xanthomonads species. In Addition, we analysed the ancestral ordering of various Xanthomonas species genomes available in NCBI using Progressive Mauve Alignment. The data revealed unique collinear regions characteristic of Xanthomonas species. These regions were also associated with cut genomic fragments used as markers, enabling the discrimination of Xanthomonas species infecting tomato and pepper. We propose that these findings contribute to understanding the genetic diversity of Xanthomonas and rapidly diagnosis.

molecular biology↗

bioRxiv2024

Pesticide degradation capacity of a novel strain belonging to Serratia sarumanii (GBS19) with its genomic profile

The use of pesticides in agricultural pest control and the potential for biological degradation of these chemicals are significant factors in environmental conservation. Sustainable pest control strategies should prioritize the preservation of non-target organisms and the maintenance of soil ecosystem dynamics. Initiation from this point, this study aimed to identify microorganisms capable of pesticide biodegradation commonly used in our regions intensive agricultural fields. The microorganism with the broadest degradation spectrum was identified in vitro studies, and whole-genome sequence analyses indicated that some genomic regions were able to degrade pesticides, which was also confirmed with LC-MS analysis. Detailed genomic analyses linked to allele sequence definitions for ribosomal MLST have classified this strain as Serratia sarumanii under the Serratia genus. Moreover, our findings showed that the introduction of this microorganism can stimulate the degradation of certain pesticides in the environment while, interestingly, simultaneously enhancing the potency of low concentrations of some other pesticides through a synergistic effect. To validate of GBS19 biodegradation capacity, additional studies carried out on 25 pesticide active chemicals using LC-MS chromatographic analysis revealed that the Serratia sarumanii GBS19 strain is able to biodegrade some active compounds of various pesticides (fludioxonil, fenhexamid, pyrimethanil, and spirodiclofen) by up to 54%, 52%, 46%, and 23%, respectively. These results highlight the degrative properties of our prominent original strain as a gene pool which can be put into practice by transforming into competent strain using recombinant DNA technology.

genomics↗

bioRxiv2024

Exploring the genome-wide expression level of the bacterial strain belonging to Bacillus safensis (MM19) against Phomopsis viticola

IntroductionRhizobacteria has the suppression ability to compete with pathogenic microorganisms and help for plant immunity and defense mechanism. Their growth and survival in rhizosphere ensure biological balance in favor of the host plant. MethodsIn our study, with agar diffusion assays, we found a rhizobacterium species belonging to Bacillus safensis, which can significantly suppress Phomopsis viticola. To elucidate the antagonistic mechanism, genome-wide gene expression profiling of B. safensis (strain MM19) was performed in the presence and absence of P. viticola. We used RNA-seq analysis to obtain a comprehensive overview of the responsive B. safensis whole gene expression classified according to biological and metabolic process to P. viticola concomitant growth in liquid culture. ResultsThe differential gene expression profiles of B. safensis (MM19) revealed significantly increased expression of prominent genes related to thiamine biosynthesis involving various metabolites and enzymes that play role in the suppression of mycelium growth and pathogen inhibition. Correspondingly, the expression of three major genes (HOG1, FUS3, SGI) involving in the virulence of P. viticola was followed using qPCR analysis. HOG1 was the highest expressed gene in the pathogen when it co-cultivated with MM19. Based on these findings, we performed molecular docking and dynamics analysis to explore the interaction between HOG1 and thiamine, besides expression of network analysis constructed using Cytoscape. DiscussionThe results proved that the functional genomic data related to thiamine biosynthesis and corresponding pathways ensure a priming role in the antagonistic behavior of B. safensis (MM19) against P. viticola as a supporter for plant immunity.

microbiology↗

bioRxiv2021

Phomoarcherin B as a novel HIV-1 reverse transcriptase RNase H activity inhibitor: conclusions from comprehensive computational analysis

The HIV epidemic has claimed more than 32.7 million live since its emergence in 1981, while many ART and HAART therapies are available and provide relief and control for patients, most of these therapeutics come with long-term side effects, resistance, socio-economical barriers, and other obstacles. In this study, genomic analysis was performed on 98 HIV-1 genomes to determine the most coherent target that could be utilized to restrict and cease the viral replication, the reverse transcriptase enzyme. Following the identification of the target protein, the RNase H activity of the reverse transcriptase was nominated as the potent target given the limited research associated with it. A library of 94 thousand small molecule inhibitors was generated and virtual screening was performed to identify hits, based on the reproducibility of the screening results, 4 compounds with the best scores were considered and their interaction within the active site was analyzed. Subsequently, all-atom molecular dynamics simulations and MM-PBSA was performed to validate the stability and binding free energy of the hits within the RNase H active. In silico ADMET assays were performed on the hit compounds to analyze their drug-likeness, physicochemical and pharmacological properties. Phomoarcherin B, a pentacyclic aromatic sesquiterpene naturally found in the endophytic fungus Phomopsis archeri, known for its anticancer properties scored the best in all the experiments and was nominated as a potential inhibitor of the HIV-1 reverse transcriptase RNase H activity. Author SummaryThe Human immunodeficiency virus 1 (HIV-1) has remained a global public health issue for the past 4 decades with millions of patients around the globe affected. Long years of research in the field of anti-viral therapies had introduced several drugs to combat the viral infection, however, most of these drugs come with their shortcomings. In this study, computational drug discovery approaches were utilized to research novel drugs that could be used as anti-viral agents against the former virus, the results had revealed Phomoarcherin B, a natural compound from an endophytic fungus to hold promising therapeutic potentials.

bioinformatics↗