Chromium is a toxic heavy metal abundantly present in the environment, specifically in groundwater. The groundwater in Saudi Arabia was assessed for heavy metal presence; chromium was detected at a high concentration in Madinah. Many researchers have used various bioprocesses over the last few decades to mitigate Cr(VI) toxicity. The genus Pseudomonas member Pseudomonas putida is widely dispersed in the natural environment. P. putida is chromate-resistant and has a high chromate reduction rate. Bioremediation procedures can eradicate the most potently toxic metal, Cr(VI), in water, air, and soil. Chromate reductase (ChrR) is a bacterial enzyme from P. putida that can be utilized in bioremediation to remove chromate from the environment in a cost-effective and environmentally safe approach. To comprehend the role of ChrR in reducing Cr(VI) to Cr(III), a thorough sequence analysis was followed by constructing models for wild-type and mutants by applying several homology modeling techniques. The protein structure quality of the generated models was evaluated, and the best model was adopted for further optimization by employing an energy minimization technique. Molecular docking studies investigated the intra-molecular interaction between wild-type and mutant ChrR and Cr(VI). Our study is a novel method for determining the 3D structure and interaction of ChrR with Cr(VI) to convert it to a less hazardous form (III). Additionally, it provides stable mutants: Arg83Trp, Gly124Ile, and His127Trp, with a high binding affinity for Cr(VI), which can be considered for protein engineering to produce stable and efficacious enzymes to reduce Cr(VI) to a less toxic form.

Microorganisms are ubiquitously present in the environment and exert significant influence on numerous natural phenomena. The soil and groundwater systems, precipitation, and effluent outfalls from factories, refineries, and waste treatment facilities are all sources of heavy metal contamination. For example, Madinah, Saudi Arabia, has alarmingly high levels of lead and cadmium. The non-essential minerals cadmium (Cd) and lead (Pb) have been linked to damage to vital organs. Bioremediation is an essential component in the process of cleaning up polluted soil and water where biological agents such as bacteria are used to remove the contaminants. It is demonstrated that Pseudomonas aeruginosa (P. aeruginosa) isolated from activated sludge was able to remove Cd and Pb from water. The protein sequence of metallothionein from P. aeruginosa was retrieved to explore it for physicoparameters, orthologs, domain, family, motifs, and conserved residues. The homology structure was generated, and models were validated. Docking of the best model with the heavy metals was carried out to inspect the intramolecular interactions. The target protein was found to belong to the “metallothionein_pro” family, containing six motifs, and showed a close orthologous relationship with other heavy metal-resistant bacteria. The best model was generated by Phyre2. In this study, three key residues of metallothionein were identified that participate in heavy metal (Pb and Cd) binding, viz., Ala33, Ser34, and Glu59. In addition, the study provides an essential basis to explore protein engineering for the optimum use of metallothionein protein to reduce/remove heavy metals from the environment.

Heavy metals, specifically cadmium (Cd) and lead (Pb), contaminating water bodies of Madinah (Saudi Arabia), is a significant environmental concern that necessitates prompt action. Madinah is exposed to toxic metals from multiple sources, such as tobacco, fresh and canned foods, and industrial activities. This influx of toxic metals presents potential hazards to both human health and the surrounding environment. The aim of this study is to explore the viability of utilizing metallothionein from Pseudomonas putida (P. putida) as a method of bioremediation to mitigate the deleterious effects of pollution attributable to Pb and Cd. The use of various computational approaches, such as physicochemical assessments, structural modeling, molecular docking, and protein–protein interaction investigations, has enabled us to successfully identify the exceptional metal-binding properties that metallothionein displays in P. putida. The identification of specific amino acid residues, namely GLU30 and GLN21, is crucial in understanding their pivotal role in facilitating the coordination of lead and cadmium. In addition, post-translational modifications present opportunities for augmenting the capacity to bind metals, thereby creating possibilities for focused engineering. The intricate web of interactions among proteins serves to emphasize the protein’s participation in essential cellular mechanisms, thereby emphasizing its potential contributions to detoxification pathways. The present study establishes a strong basis for forthcoming experimental inquiries, offering potential novel approaches in bioremediation to tackle the issue of heavy metal contamination. Metallothionein from P. putida presents a highly encouraging potential as a viable remedy for environmental remediation, as it is capable of proficiently alleviating the detrimental consequences related to heavy metal pollution.

In Saudi Arabia, seawater desalination is the primary source of acquiring freshwater, and groundwater contains a high concentration of toxic heavy metals. Chromium (Cr) is one of the heavy metals that is widely distributed in the environment, particularly in the groundwater of Madinah. Diverse techniques are employed to eliminate the toxicity of heavy metals from the environment, but, lately, the focus has shifted to biological remediation systems, due to their higher removal efficiencies, lower costs, and more ecologically benign characteristics than the conventional methods. Providencia bacteria engage in a variety of adsorption processes to interact with heavy metals. In this study, we aim to investigate the role of potential active site residues in the bioengineering of chromate reductase (ChrR) from Providencia alcalifaciens to reduce the Cr to a lesser toxic form by employing robust computational approaches. This study highlights Cr bioremediation by providing high-quality homology-modeled structures of wild type and mutants and key residues of ChrR for bioengineering to reduce the Cr toxicity in the environment. Glu79 is found to be a key residue for Cr binding. The mutant models of Arg82Cys, Gln126Trp, and Glu144Trp are observed to establish more metallic interactions within the binding pocket of ChrR. In addition, the wild type ChrR (P. alcalifaciens) has been found to be unstable. However, the mutations stabilized the structure by preserving the metallic contacts between the critical amino acid residues of the identified motifs and the Cr(VI). Therefore, the mutants discovered in the study can be taken into account for protein engineering to create reliable and effective enzymes to convert Cr(VI) into a lesser toxic form.

This study aimed to isolate and investigate a bacterium from an Egyptian adult's healthy oral cavity, focusing on its probiotic properties, especially its antagonistic activity against oral pathogens. The isolated bacterium NT04 using 16S rRNA gene sequencing, was identified as Enterococcus faecium. In this study, the whole genome of Enterococcus faecium NT04 was sequenced and annotated by bioinformatics analysis tools. Numerous genes encoding the production of diverse metabolic and probiotic properties, such as bacteriocin-like inhibitory substances (Enterocin A and B), cofactors, antioxidants, and vitamins, were confirmed by genomic analysis. There were no pathogenicity islands or plasmid insertions found. This strain is virulent for host colonization rather than invasion. Genomic characteristics of strain NT04 support its potentiality as an anti-oral pathogen probiotic candidate.