Biology subjects

Baysal, O.

Publications and source records attributed to Baysal, O..

10 recordsLinked to original sources

bioRxiv2026

Genomic and Kinetic Modeling Involving Nanoparticle-Mediated Delivery of a Novel Chitinase Enzyme to Outpace Tuta absoluta Damage

The tomato leafminer, Tuta absoluta, poses a severe global agricultural threat due to its rapid leaf-mining behavior and swift development of resistance to conventional chemical pesticides. While microbial chitinases are potent biopesticides, their field efficacy is limited by environmental degradation and the short exposure window before larvae penetrate leaf tissues. This study evaluates a stimuli-responsive, controlled-release nanobiopesticide system utilizing a novel chitinase from newly characterized Serratia marcescens GBS19. A 61.1 kDa chitinase (GBS19_ChiA) was heterologously expressed in Escherichia coli and purified to a specific activity of 215.01 U/mg. The enzyme was immobilized onto starch-coated silica nanoparticles designed for target-triggered release via host alpha-amylase. Genomic profiling and R-based kinetic modeling were integrated to evaluate the efficacy of purified and immobilized forms against T. absoluta. Immobilization enhanced thermal and pH stability, with the nanocarrier maintaining 85% activity over 10 weeks. In larval bioassays, immobilization increased mortality from 21.9% to 59.4% (5000 U/mL) by day 3, reaching 62.5% by day 6. Genomic analysis identified an expansive secretome and a Type VI Secretion System (T6SS), characterizing GBS19 as a multi-pronged pathogen. Kinetic modeling established that while immobilized enzymes are effective, the 2.5-hour exposure time on T. absoluta requires the synergistic action of chitinases (ChiA/B/C) to reach the lethal desiccation threshold before larvae establish protective mines. Starch-coated silica nanoparticles significantly improve chitinase stability and delivery. However, overcoming the rapid penetration of T. absoluta necessitates a whole-cell or multi-enzyme synergistic approach to outpace larval behavioural defences.

biochemistry↗

bioRxiv2026

Multidimensional Characterization of Novel Phage UCB24 Targeting Erwinia amylovora

This study evaluates the novel bacteriophage UCB24 as an eco-friendly biocontrol agent against Erwinia amylovora, the bacterial pathogen responsible for fire blight. Following purification, UCB24 was characterized for its optimal multiplicity of infection (MOI), infection kinetics, and environmental stability across diverse pH and temperature ranges. Microtitration assays and scanning electron microscopy (SEM) confirmed distinct morphology of the phage and its potent capacity to disrupt E. amylovora biofilms. Whole-genome sequencing and phylogenetic profiling identified UCB24 as a genetically distinct relative of four known phages. Furthermore, protein-protein interaction analyses revealed a strong binding affinity between the phage lysin and the hosts N-acetylmuramic-acid 6-phosphate etherase, uncovering the precise molecular mechanism driving targeted host destruction. In vivo plant trials demonstrated exceptional protective efficacy in Apple cv. Gala (88.61%) and Quince cv. Esme (81.37%), significantly outperforming traditional copper treatments under severe baseline pathogen pressure. Consequently, UCB24 represents a highly effective and sustainable biopesticide for managing fire blight in susceptible orchard ecosystems.

microbiology↗

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

Bacillus velezensis EU07 suppresses Fusarium graminearum via transcriptomic reprogramming

Fusarium graminearum, the causal agent of Fusarium head blight, is a devastating pathogen of cereals worldwide. Biological control using Bacillus species has emerged as a sustainable strategy to suppress this pathogen, but the molecular basis of antagonism remains poorly understood. Here, we investigated the interaction between Bacillus velezensis EU07 and F. graminearum strain K1-4 through morphological assays and RNA-seq profiling. Microscopy revealed severe hyphal distortions including swelling and branching abnormalities, following exposure to EU07 cell pellets. Transcriptomic analysis after 6 h of treatment identified 1,264 differentially expressed genes (DEGs), with 732 downregulated and 532 upregulated. Genes encoding secondary metabolite biosynthesis enzymes, including trichothecene (TRI) cluster genes, cytochrome P450s, and transporters, were strongly repressed. Key metabolic pathways, such as amino acid catabolism and mitochondrial transporters (e.g., 2-oxoglutarate/malate carrier protein), also showed reduced expression. Conversely, genes associated with oxidative stress responses, detoxification, and membrane transport were induced, reflecting a compensatory survival strategy. These results demonstrate that EU07 disrupts F. graminearum both morphologically and at the transcriptional level, suppressing virulence-associated pathways while triggering stress adaptation. This dual impact highlights B. velezensis EU07 as a promising biocontrol agent and provides candidate fungal genes for targeted RNAi-based crop protection strategies.

plant biology↗

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↗

bioRxiv2025

Pea-Saving Partners: Bacillus and Pseudomonas combat downy mildew in pea crops

Downy mildew (DM) is a destructive disease that significantly reduces the yield and quality of important pulses (legumes) and horticultural crops, particularly during humid and cool seasons. This disease is caused by obligate and host-specific oomycete pathogens. Controlling the pathogen is challenging due to its long-term survival as spores and its rapid mutation. Use of chemical pesticides has been the most effective method to control DM pathogens, but their environmental hazards are a global concern. Current research is focused on exploring the potential of microbial biological control agents (MBCA), particularly rhizobacteria strains of the genera Bacillus and Pseudomonas, which have shown suppression of plant pathogens. However, to date, no MBCA has been reported to be effective against DM pathogens in pulses. We investigated the effectiveness of Bacillus and Pseudomonas strains as potential biopesticides against the pea downy mildew pathogen Peronospora viciae f. sp. pisi (Pvp). In our study, in vitro bioassays showed 100% inhibition of Pvp spore germination compared to the control. In planta antagonism assays further demonstrated significant suppression (>80%) of Pvp sporulation in pea plants sprayed with strains of Bacillus velezensis or P. fluorescens or their filtrates. The drench application also showed significant effects where either a Pseudomonas or cold-adapted Bacillus strain was used. We observed a synergistic effect for the dual foliar application of the microbes compared to individual application (27.6 to 46.7% suppression). Furthermore, the results from the molecular biomass analysis were consistent with the results of the sporulation assays. This demonstrates the strong interactive and promotive benefits of using Bacillus and Pseudomonas as biocontrol agents Based on these results, we conclude that these MBCAs could be effective in combatting Pvp infections in the field.

plant 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

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↗