Multifaceted roles of plant glycosyl hydrolases during pathogen infections: more to discover.

MAIN CONCLUSION: Carbohydrates are hydrolyzed by a family of carbohydrate-active enzymes (CAZymes) called glycosidases or glycosyl hydrolases. Here, we have summarized the roles of various plant defense glycosidases that possess different substrate specificities. We have also highlighted the open questions in this research field. Glycosidases or glycosyl hydrolases (GHs) are a family of carbohydrate-active enzymes (CAZymes) that hydrolyze glycosidic bonds in carbohydrates and glycoconjugates. Compared to those of all other sequenced organisms, plant genomes contain a remarkable diversity of glycosidases. Plant glycosidases exhibit activities on various substrates and have been shown to play important roles during pathogen infections. Plant glycosidases from different GH families have been shown to act upon pathogen components, host cell walls, host apoplastic sugars, host secondary metabolites, and host N-glycans to mediate immunity against invading pathogens. We could classify the activities of these plant defense GHs under eleven different mechanisms through which they operate during pathogen infections. Here, we have provided comprehensive information on the catalytic activities, GH family classification, subcellular localization, domain structure, functional roles, and microbial strategies to regulate the activities of defense-related plant GHs. We have also emphasized the research gaps and potential investigations needed to advance this topic of research.

Enterococcus faecalis thrives in dual-species biofilm models under iron-rich conditions.

Escherichia coli (E. coli) and Enterococcus faecalis (E. faecalis) are pathogenic strains that often coexist in intestinal flora of humans and are prone to cause biofilm-associated infections, such as gastrointestinal tract and urinary tract infections. Earlier studies have demonstrated that E. faecalis biofilm can metabolize ferrous ions in iron-rich environments and promote biofilm growth under in-vivo conditions. However, the influence of iron transporters on dual-species biofilm growth and the nature of molecular-level interactions between iron transporter proteins and Fe2+ remains unknown. Therefore, in this work, co-culture studies were performed and the study indicates that Fe2+ at concentrations of 50-150 µM promotes the colonization of E. coli, and Fe2+ concentrations of 50-200 µM promote the growth of E. faecalis and dual-species colonies. Atomic absorption spectroscopy results reveal that Fe2+ ion augmentation in bacterial cells was increased to 4 folds in the single-species model and 11 folds in the dual-species model under iron-supplemented conditions. Furthermore, Fe2+ augmentation increased the antibiotic resistance of E. faecalis in both single- and dual-species bacterial cultures. In addition, in-silico docking were performed to determine a three-dimensional (3D) structure of ferrous iron-transporter proteins FeoB of E. faecalis and its affinity to extracellular Fe2+. Our model suggests that the FeoB facilitates the Fe2+ uptake in E. faecalis cells in the absence of iron chelator, 2,2-bipyridyl.

Nanotechnology based solutions to combat zoonotic viruses with special attention to SARS, MERS, and COVID 19: Detection, protection and medication.

Zoonotic viruses originate from birds or animal sources and responsible for disease transmission from animals to people through zoonotic spill over and presents a significant global health concern due to lack of rapid diagnostics and therapeutics. The Corona viruses (CoV) were known to be transmitted in mammals. Early this year, SARS-CoV-2, a novel strain of corona virus, was identified as the causative pathogen of an outbreak of viral pneumonia in Wuhan, China. The disease later named corona virus disease 2019 (COVID-19), subsequently spread across the globe rapidly. Nano-particles and viruses are comparable in size, which serves to be a major advantage of using nano-material in clinical strategy to combat viruses. Nanotechnology provides novel solutions against zoonotic viruses by providing cheap and efficient detection methods, novel, and new effective rapid diagnostics and therapeutics. The prospective of nanotechnology in COVID 19 is exceptionally high due to their small size, large surface-to-volume ratio, susceptibility to modification, intrinsic viricidal activity. The nano-based strategies address the COVID 19 by extending their role in i) designing nano-materials for drug/vaccine delivery, ii) developing nano-based diagnostic approaches like nano-sensors iii) novel nano-based personal protection equipment to be used in prevention strategies.This review aims to bring attention to the significant contribution of nanotechnology to mitigate against zoonotic viral pandemics by prevention, faster diagnosis and medication point of view.

Structural and functional insights of sortases and their interactions with antivirulence compounds.

Sortase proteins play a crucial role as integral membrane proteins in anchoring bacterial surface proteins by recognizing them through a Cell-Wall Sorting (CWS) motif and cleaving them at specific sites before initiating pilus assembly. Both sortases and their substrate proteins are major virulence factors in numerous Gram-positive pathogens, making them attractive targets for antimicrobial intervention. Recognizing the significance of virulence proteins, a comprehensive exploration of their structural and functional characteristics is essential to enhance our understanding of pilus assembly in diverse Gram-positive bacteria. Therefore, this review article discusses the structural features of different classes of sortases and pilin proteins, primarily serving as substrates for sortase-assembled pili. Moreover, it thoroughly examines the molecular-level interactions between sortases and their inhibitors, providing insights from both structural and functional perspectives. In essence, this review article will provide a contemporary and complete understanding of both sortase pathways and various strategies to target them effectively to counteract the virulence.

Chemiluminescence-Based Assay to Monitor Early Oxidative Bursts in Soybean (Glycine max) Lateral Roots.

The reactive oxygen species (ROS) burst assay is a valuable tool for studying pattern-triggered immunity (PTI) in plants. During PTI, the interaction between pathogen recognition receptors (PRRs) and pathogen-associated molecular patterns (PAMPs) leads to the rapid production of ROS in the apoplastic space. The resultant ROS can be measured using a chemiluminescent approach that involves the usage of horseradish peroxidase and luminol. Although several methods and protocols are available to detect early ROS bursts in leaf tissues, no dedicated method is available for root tissues. Here, we have established a reliable method to measure the PAMP-triggered ROS burst response in soybean lateral roots. In plants, lateral roots are the potential entry and colonization sites for pathogens in the rhizosphere. We have used important PAMPs such as chitohexaose, flagellin 22 peptide fragment, and laminarin to validate our method. In addition, we provide a detailed methodology for the isolation and application of fungal cell wall components to monitor the oxidative burst in soybean lateral roots. Furthermore, we provide methodology for performing ROS burst assays in soybean leaf discs with laminarin and fungal cell walls. This approach could also be applied to leaf and root tissues of other plant species to study the PTI response upon elicitor treatment. © 2023 Wiley Periodicals LLC. Basic Protocol: Reactive oxygen species (ROS) burst assay in soybean lateral root tissues Alternate Protocol: ROS burst assay in soybean leaf discs Support Protocol: Isolating fungal cell wall fractions.

Predicting quorum sensing peptides using stacked generalization ensemble with gradient boosting based feature selection.

Bacteria exist in natural environments for most of their life as complex, heterogeneous, and multicellular aggregates. Under these circumstances, critical cell functions are controlled by several signaling molecules known as quorum sensing (QS) molecules. In Gram-positive bacteria, peptides are deployed as QS molecules. The development of antibodies against such QS molecules has been identified as a promising therapeutic intervention for bacterial control. Hence, the identification of QS peptides has received considerable attention. Availability of a fast and reliable predictive model to effectively identify QS peptides can help the existing high throughput experiments. In this study, a stacked generalization ensemble model with Gradient Boosting Machine (GBM)-based feature selection, namely EnsembleQS was developed to predict QS peptides with high accuracy. On selected GBM features (791D), the EnsembleQS outperformed finely tuned baseline classifiers and demonstrated robust performance, indicating the superiority of the model. The accuracy of EnsembleQS is 4% higher than those resulting from ensemble model on hybrid dataset. When evaluating an independent data set of 40 QS peptides, the EnsembleQS model showed an accuracy of 93.4% with Matthew's Correlation Coefficient (MCC) and area under the ROC curve (AUC) values of 0.91 and 0.951, respectively. These results suggest that EnsembleQS will be a useful computational framework for predicting QS peptides and will efficiently support proteomics research. The source code and all datasets used in this study are publicly available at https://github.com/proteinexplorers/EnsembleQS .

Improved laccase production from Pleurotus floridanus using deoiled microalgal biomass: statistical and hybrid swarm-based neural networks modeling approach.

Fungal laccases are versatile biocatalyst and occupy a prominent place in various industrial applications due to its broad substrate specificity. The simplest method to enhance the laccase production is by usage of cheap substrates in the fermentation processes incorporating modeling approaches for optimization. Integrated biorefinery concept is receiving wide popularity by making use of various products from microalgal biomass. The research aimed to identify the potential of deoiled microalgal biomass (DMB), a waste product from algal biorefinery as a nutrient supplement to enhance laccase production in Pleurotus floridanus by submerged fermentation. The maximum production was obtained in the presence of DMB as an additional nutrient supplement and copper sulfate as an inducer. The predictive capabilities of the two methodologies Response Surface Methodology (RSM) and hybrid Particle swarm optimization (PSO)-based Artificial Neural Network (ANN) were compared and validated. The results showed that ANN coupled with PSO predicted with more accuracy with an R 2 value of 0.99 than the RSM model with an R 2 value of 0.97. The optimized condition as predicted by superior model hybrid PSO-based ANN was glucose (3.51%), DMB (0.545%), pH (4.9), temperature (24.68 â„ƒ) and CuSO4 (1.35 mM). The experimental laccase activity was 80.45 ± 0.132 U/mL which was 1.3 fold higher than unoptimized condition. This study promotes the usage of DMB as a novel supplement for the improved production of Pleurotus floridanus laccase. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03404-y.

Modelling, docking and simulation analysis of Bisphenol A interaction with laccase from Trichoderma.

Fungal laccases are widely known for the degradation of recalcitrant xenobiotic compounds. Hence, it is of interest to study the interaction between laccase from Trichoderma laccase and Endocrine-Disrupting Chemical (EDC) named Bisphenol A. The molecular docking analysis of laccase from Trichoderma laccase with 23 xenobiotics and bisphenol A was completed. We show Bisphenol having optimal binding features (Glide score of -5.44 and the Glide energy -37.65 kcal/mol) with laccase from Trichoderma laccase.