Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome

Revealing microbial functionalities and ecological roles in Rajpardi lignite mine: insights from metagenomics analysis

The present study employs a metagenomics approach to evaluate microbial communities' ecological functions and potential within the Rajpardi lignite mine of Gujarat, India. Through whole genome shotgun sequencing on the Illumina Miseq platform, we obtained 10 071 318 sequences, which unveiled a diverse and abundant microbial community primarily composed of Proteobacteria, Acidobacteria, and Nitrospirae. Comprehensive taxonomic profiling and gene prediction was carried out using the SqueezeMeta pipline, which highlighted significant contributions to carbohydrate, amino acid, and energy metabolism. The detection of antimicrobial resistance and stress resistance genes, such as blaTEM and merA, suggests that these microbes possess the ability to adapt to harsh environmental conditions. Genome binning revealed species such as Acidiphilum sp. 20-67-58, emphasizing the nature of these communities as they adapted to an acidic environment. This finding highlights the crucial role of microbes in biogeochemical cycles, emphasizing their potential in bioremediation, pollutant degradation, and ecosystem restoration.

Cloning, bioinformatics analysis, and expression of the ubiquitin 2 (ubq-2) gene from the dog roundworm Toxocara canis

Toxocariasis, caused by the dog roundworm Toxocara canis, is a globally distributed zoonotic parasitic disease that poses a significant threat to veterinary and public health. The ubiquitin plus an L40 ribosomal protein (UBQ-2) in parasites plays a crucial role in protein degradation and meiotic divisions, thereby affecting parasite development, survival, and parasite-host interactions. In this study, we identified for the first time a full-length cDNA encoding the UBQ-2 protein from the T. canis-omic dataset, called Tcubq-2. After cloning and sequencing, we conducted sequence analysis and structural modeling of TcUBQ-2 using online bioinformatics tools. The recombinant TcUBQ-2 protein (rTcUBQ-2) was prokaryotically expressed and subjected to Western blot analysis to assess its antigenicity and immunoreactivity. Additionally, we performed immunolocalization of the endogenous protein in adult T. canis and evaluated its serodiagnostic potential using sera from naïve and infected mice and dogs. Our results showed that the complete cDNA sequence of Tcubq-2 was 387 bp in length and encoded a polypeptide of 128 amino acids, lacking both an N-terminal signal sequence and a transmembrane domain. Sequence and phylogenetic analyses showed that TcUBQ-2 shared the closest genetic distance with its homologs in Parascaris univalens and Ascaris suum. Real-time quantitative PCR and Western blotting revealed an expression peak of TcUBQ-2 in the intestine-hatched second-stage (L3) larvae compared to other developmental stages of T. canis. Tissue localization of endogenous TcUBQ-2 revealed its broad distributions in the body wall, muscle, gut epithelium, and microvilli of adult T. canis, with gender-specific expression in the uterus, ovary, and non-embryonated eggs of females. Based on its strong immunogenic properties, a recombinant TcUBQ-2 (rTcUBQ-2)-based ELISA was established and exhibited a sensitivity of 100% and a specificity of 95.8% to detect anti-T. canis mouse sera and a sensitivity of 79.2% and a specificity of 83.3% to detect anti-T. canis dog sera, respectively. This study presents a comprehensive bioinformatics analysis of the dog roundworm TcUBQ-2, and its strong serodiagnostic performance suggests that rTcUBQ-2 has the potential to be developed into an ELISA-based serological test for detecting toxocariasis in dogs and other accidental hosts, including humans.

Insights into the dynamic interactions of RNase a and osmolytes through computational approaches

Osmolytes are small organic molecules that are known to stabilize proteins and other biological macromolecules under various stressful conditions. They belong to various categories such as amino acids, methylamines, and polyols. These substances are commonly known as 'compatible solutes' because they do not disrupt cellular processes and help regulate the osmotic balance within cells. In the case of ribonuclease A (RNase A), which is prone to aggregation, the presence of osmolytes can help to maintain its structural stability and prevent unwanted interactions leading to protein aggregation. In this study, we investigated the interaction between RNase A and several osmolytes using molecular docking and molecular dynamics (MD) simulations. We performed molecular docking to predict the binding mode and binding affinity of each osmolyte with RNase A. MD simulations were then carried out to investigate the dynamics and stability of the RNase A-osmolyte complexes. Our results show that two osmolytes, glucosylglycerol and sucrose have favorable binding affinities with RNase A. The possible role of these osmolytes in stabilizing the RNase A and prevention of aggregation is also explored. By providing computational insights into the interaction between RNase A and osmolytes, the study offers valuable information that could aid in comprehending the mechanisms by which osmolytes protect proteins and help in designing therapeutics for protein-related disorders based on osmolytes. These findings may have significant implications for the development of novel strategies aimed at preventing protein misfolding and aggregation in diverse disease conditions.Communicated by Ramaswamy H. Sarma.

A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice

Lhx3 is a LIM-homeodomain transcription factor that affects body size in mammals by regulating the secretion of pituitary hormones. Akita, Shiba Inu, and Mame Shiba Inu dogs are Japanese native dog breeds that have different body sizes. To determine whether Lhx3 plays a role in the differing body sizes of these three dog breeds, we sequenced the Lhx3 gene in the three breeds, which led to the identification of an SNP in codon 280 (S280N) associated with body size. The allele frequency at this SNP differed significantly between the large Akita and the two kinds of smaller Shiba dogs. To validate the function of this SNP on body size, we introduced this change into the Lhx3 gene of mice. Homozygous mutant mice (S279N+/+) were found to have significantly increased body lengths and weights compared to heterozygous mutant (S279N+/-) and wild-type (S279N-/-) mice several weeks after weaning. These results demonstrate that a nonsynonymous substitution in Lhx3 plays an important role in regulating body size in mammals.

The Impact of Metagenomics on Biocatalysis

In the ever-growing demand for sustainable ways to produce high-value small molecules, biocatalysis has come to the forefront of greener routes to these chemicals. As such, the need to constantly find and optimise suitable biocatalysts for specific transformations has never been greater. Metagenome mining has been shown to rapidly expand the toolkit of promiscuous enzymes needed for new transformations, without requiring protein engineering steps. If protein engineering is needed, the metagenomic candidate can often provide a better starting point for engineering than a previously discovered enzyme on the open database or from literature, for instance. In this review, we highlight where metagenomics has made substantial impact on the area of biocatalysis in recent years. We review the discovery of enzymes in previously unexplored or 'hidden' sequence space, leading to the characterisation of enzymes with enhanced properties that originate from natural selection pressures in native environments.