Bacterial chromate reduction: A review of important genomic, proteomic, and bioinformatic analysis

ABSTRACT

Toxic hexavalent chromium (Cr⁶⁺) released during various industrial and mining processes leads to serious environmental problems and health hazards. Cr⁶⁺ compounds are known to be highly toxic, mutagenic, teratogenic, and carcinogenic. Microorganisms such as bacteria employ various resistance mechanisms such as ion transport (efflux), reduction, DNA repair, and so on to overcome chromate toxicity. The genes responsible for such activity are either located in chromosome or in the plasmid of bacteria. In total of 2557 chromate resistance genes found in bacteria (2,368), eukarya (171), and archea (18) have been retrieved from the National Center for Biotechnology Information (NCBI) gene database obtained from both culture-dependent and -independent methods and were analyzed for their function, location, and diversification. Further proteomic analysis revealed a hydrophobic membrane protein such as ChrA belong to the chromate ion transporter (CHR) superfamily found to be involved in efflux of chromate ion from the cell cytoplasm conferring chromate resistance in bacteria were retrieved from the NCBI database and categorized in two groups of monodomain proteins with a sequence length of 123–234 amino acids, called bacterial short-chain CHR (bacterial SCHR), and bidomain proteins with a sequence length of 345–495 amino acids, called bacterial long-chain CHR (bacterial LCHR). Phylogenetic divergence study of 237 LCHR and 121 SCHR proteins was conducted using the neighbor-joining method in MEGA6.0 and found to be clustered into four and six clusters, respectively. Apart from CHR superfamily, various groups of oxidoreductase enzymes such as chromate reductase, nitroreductase, iron reductase, quinone reductase, hydrogenase, flavin reductase, and nicotinamide adenine dinucleotide phosphate (NADPH)–dependent reductase showing potential toward reduction of chromate have also been identified in different microorganisms. Comparative structural analyses of seven well-studied enzymes involved in chromate reduction from Protein Data Bank database were categorized either NADPH-dependent flavin mononucleotide (FMN) reductase or FMN-dependent nitroreductase. In spite of structural diversity (e.g., tetramer/dimer, arrangements of helices/sheets/coils) all are found to be involved in chromate reduction. Chromate reductions mediated by transfer of electron from nicotinamide adenine dinucleotide to various substrates (electron acceptor such as chromate) through FMN cofactor. The anchoring amino acid residues such as Glu, Tyr, Ser, Asn, Phe and Arg interact with FMN in NADPH-dependent FMN reductases but Gly, Arg, and Ser are the interacting residues in FMN-dependent nitroreductase. Enzyme-specific domains such as PF00724, PF03358, and PF00881 are present in these enzymes. The enzymes with known structures and functions can be easily manipulated through protein engineering approach for potential applications.

KEYWORDS:

• Bioinformatics analysis
• CHR family
• chromate detoxification
• chromate efflux
• hexavalent chromium

Acknowledgments

All authors have equally contributed to this article. The authors report no declarations of interest.