In silico modelling of the function of disease-related CAZymes

Metagenomic mining unveils a novel GH130 enzyme with exclusive xylanase activity over a wide temperature and pH ranges

The equine gut harbors a diverse microbial community and represents a rich source of carbohydrate-active enzymes (CAZymes). To identify and characterize potentially novel CAZymes from a horse's hindgut metagenome, shotgun metagenomic sequencing was performed on DNA extracted from a stool sample of a male horse, followed by CAZyme annotation. Here, we report on the characterization of a novel enzyme (AH2) that was identified, synthesized, cloned, and characterized from the obtained CAZyme dataset. AH2 was identified as a GH130 family member and displayed exclusive xylanase activity, a trait hitherto unreported in prior characterization of GH130 CAZymes. AH2 displayed an optimal activity at a pH of 5.6 and a temperature of 50°C. AH2 maintained significant activity across a pH range of 4-10 (62-72%) and temperatures of 30-70°C (77-86%). The enzyme had remarkable stability, with minimal reductions in activity across a temperature range of 4-70°C and pH levels of 3, 7, and 9. Docking studies identified AH2's amino acids (Glu90 and Glu149) to be involved in substrate binding. Molecular dynamics simulation confirmed the structural stability of AH2 at pH 5.6 and 50°C, further supporting its resilience under these conditions. Our results expand on the known activities associated with the GH130 CAZyme family and demonstrate that the horse gut metagenome represents an unexplored source of novel CAZymes.

ONE-SENTENCE SUMMARY

A novel activity for members of the CAZyme family GH130.

Secretome Analysis of Thermothelomyces thermophilus LMBC 162 Cultivated with Tamarindus indica Seeds Reveals CAZymes for Degradation of Lignocellulosic Biomass

The analysis of the secretome allows us to identify the proteins, especially carbohydrate-active enzymes (CAZymes), secreted by different microorganisms cultivated under different conditions. The CAZymes are divided into five classes containing different protein families. Thermothelomyces thermophilus is a thermophilic ascomycete, a source of many glycoside hydrolases and oxidative enzymes that aid in the breakdown of lignocellulosic materials. The secretome analysis of T. thermophilus LMBC 162 cultivated with submerged fermentation using tamarind seeds as a carbon source revealed 79 proteins distributed between the five diverse classes of CAZymes: 5.55% auxiliary activity (AAs); 2.58% carbohydrate esterases (CEs); 20.58% polysaccharide lyases (PLs); and 71.29% glycoside hydrolases (GHs). In the identified GH families, 54.97% are cellulolytic, 16.27% are hemicellulolytic, and 0.05 are classified as other. Furthermore, 48.74% of CAZymes have carbohydrate-binding modules (CBMs). Observing the relative abundance, it is possible to state that only thirteen proteins comprise 92.19% of the identified proteins secreted and are probably the main proteins responsible for the efficient degradation of the bulk of the biomass: cellulose, hemicellulose, and pectin.

Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum

The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.