Bioprospecting uncultivable microbial diversity in tannery effluent contaminated soil using shotgun sequencing and bio-reduction of chromium by indigenous chromate reductase genes

Singh, Ayushi; Varma, Ajit; Prasad, Ram; Porwal, Shalini

doi:10.1016/j.envres.2022.114338

Cited by 5 publications

(8 citation statements)

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“…The phylogenetic tree from the previous study helped to map six OXR genes based on diversity and map units. [ 27 ] The OXR genes were isolated from the metagenomic DNA shotgun sequencing of tannery effluent‐contaminated soil samples. The amplification of the mapped genes was done with the help of specific primers, that was further extracted and purified using the QIA quick Gel Extraction Kit (28704; QIAGEN, Delhi).…”

Section: Methodsmentioning

confidence: 99%

“…The purified gene was then cloned, and the purified clones were further expressed in the pEZY19 vector in E. coli (BL21). [ 27 ]…”

Section: Methodsmentioning

confidence: 99%

“…The shotgun sequencing of the metagenomic DNA isolated from tannery effluent‐contaminated soil, collected from Kanpur, India, [ 27 ] helped in mapping the DNA sequences of OXR genes. These DNA sequences were translated to protein sequences using the EXPASY resource.…”

Section: Methodsmentioning

confidence: 99%

“…It has considerably developed our knowledge regarding the microbial world in many cases. [27] The oxidoreductases are helpful in Cr reduction. Oxidoreductases catalyze oxidation and reduction reactions that occur within the cell.…”

Section: Introductionmentioning

confidence: 99%

“…The Cr(VI) reducing efficiency by OXR gene clones was studied, the reduction of Cr(VI) to Cr(III) was found to be maximum with the clone containing the OXR8 gene, and the minimum was found in the clone with OXR3 gene. [ 27 ] Structural and functional validation using bioinformatics approaches of OXR genes is evaluated in this study, and additionally, we have compared OXR8 and OXR3 sequences along with a plausible mechanism behind the Cr(VI) reduction. This study aimed to understand the likely mechanism of Cr(VI) reduction by the OXR gene clones and then in silico analysis was done to understand the structural characteristics.…”

Section: Introductionmentioning

confidence: 99%

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In silico analysis of chromium‐reducing OXR genes derived from tannery effluent‐contaminated soil metagenome

Singh,

Patel,

Varma

et al. 2024

CLEAN Soil Air Water

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Tannery effluent waste comprises various potentially toxic metals, including chromium (Cr) with varying acute or chronic toxicity. Cr(VI) is known to be a category‐A carcinogen. Reduction of toxic Cr(VI) to Cr(III), which has lesser bioavailability, is one of the mechanisms used by many microbes to withstand Cr(VI) toxicity in the contaminated effluents. Oxidoreductase (OXRs) reduces toxic Cr(VI) to Cr(III); hence a thorough understanding of the OXRs is important for developing a suitable strategy to minimize Cr(VI) toxicity. Therefore, the OXR‐encoding genes were sequenced using metagenomic DNA shotgun sequencing from the tannery effluent‐contaminated soil. Six OXR‐encoding genes were expressed in Escherichia coli, and OXR activity was confirmed by in situ quantitative assays. The six proteins were subjected to phylogenetic and evolutionary analysis. Further, detailed structural analysis of the two OXRs, namely, OXR3 and OXR8 with lowest and highest activity respectively, were investigated in silico for structural characteristics. The results revealed that both the proteins were soluble FMN‐linked oxidoreductases. Eight conserved active site residues (Pro24, Thr26, Ala59, Tyr139, His178, Tyr180, His219, Tyr221, Arg269, and Lys360) in the enzyme OXR3 were predicted. Similarly, nine conserved active site residues (Pro20, Thr22, Ala55, Glu97, His191, Tyr193, Arg241, Cys334, and Arg335) were predicted in OXR8. The tertiary structure of OXR8 was an aldolase TIM barrel structure, like Thermus scotoductus chromate reductase. Docking with FMN revealed the involvement of all the nine predicted active site residues in FMN binding with Pro20, Thr22, and Cys334 as the most important ones.

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Section: Methodsmentioning

confidence: 99%

“…The purified gene was then cloned, and the purified clones were further expressed in the pEZY19 vector in E. coli (BL21). [ 27 ]…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%