Biology subjects

Baysal, O.

Publications and source records attributed to Baysal, O..

3 recordsLinked to original sources

bioRxiv2024

Unveiling Novel Biocontrol Strategies: Serratia marcescens chiA Gene Against Myzus persicae

BackgroundMicroorganisms produce a diverse array of enzymes with potential applications in biological control and pest management. Among these enzymes, chitinase stands out due to its safety for non-target organisms and the environment. Chitinase enzymes play a crucial role in breaking down chitin, which serves as a critical component in insect exoskeletons and fungal cell walls. As a result, they emerge as valuable tools for managing both agricultural pests and pathogens. ResultsThe chiA gene region of Serratia marcescens GBS19 was successfully amplified via PCR and cloned into expression vectors. The resulting chiA protein was expressed and purified through His-tag affinity chromatography. The purified chiA enzyme exhibited optimal activity at 40 {degrees}C and pH 5. The insecticidal properties of the purified chiA enzyme were tested against the agricultural pest Myzus persicae, revealing an LD50 value of 15,804 ppm. Comparative analysis with ref_seq chiA enzymes demonstrated that our purified enzyme shows 98.93% similarity, indicating a high degree of conservation and likely functional similarity. Bioinformatics modelling highlighted a strong binding affinity (-4.10 kcal/mol) between the enzyme and chitin, which was also confirmed with modelled chitin layer and enzyme interaction. ConclusionThe study underscores the potential of S. marcescens GBS19 chitinase as an effective and environmentally safe biocontrol agent. The chiA enzyme exhibits promising insecticidal properties, specifically against M. persicae, and its strong binding affinity to chitin supports its effectiveness. Given its safety for non-target organisms and the environment, S. marcescens GBS19 chitinase holds significant promise as a tool for integrated pest management, contributing to sustainable agricultural practices using directed recombinant DNA technology.

molecular biology↗

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↗