In silico studies on structural, functional, and evolutionary analysis of bacterial chromate reductase family responsible for high chromate bioremediation efficiency

Paul, Manish; Pranjaya, Payel Puthal; Thatoi, Hrudayanath

doi:10.1007/s42452-020-03830-8

Cited by 8 publications

(8 citation statements)

References 60 publications

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“…[ 45 ] In another study, it has been reported that Tyrosine51, Proline82, Tyrosine84, Asparagine101, and Proline119 help to generate hydrophobic contacts with the ligand FMN. [ 18 ] Both reports validated the functionality of the FMN domain in specific amino acid sites in the genes OXR3 and OXR8 used for the study.…”

Section: Discussionmentioning

confidence: 89%

“…An earlier study that used an in silico approach to investigate the sequence and structural aspects of five bacterial chromate reductase‐related enzymes discovered that comparative multiple sequence alignment of different chromate reductase revealed that Ser13 in E. coli quinone reductase remains conserved among most homologous proteins. [ 18 ] The phylogenetic tree of OXR protein sequences inferred the similarity with the NCBI database chromate reductase protein sequences. The phylogenetic tree also revealed that OXR3 was discovered to be closely related to NADH‐dependent flavin oxidoreductase ( Desulfomicrobium sp.)…”

Section: Discussionmentioning

confidence: 99%

“…[ 17 ] A few microbial enzyme homologs with Cr‐reducing activity are NemA, YieF, and NfsA from Escherichia coli ; Frm2 and Ycp4 from Wickerhamomyces anomalus M10; NfrA from Bacillus subtilis; and ChrR from B. methylotrophicus . [ 18 ]…”

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: Discussionmentioning

confidence: 89%

Section: Discussionmentioning

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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“…This prevented arsenic buildup by expelling it out of the cytoplasm ( Yang et al, 2012 ). Notably, the quinone reductase gene ( chrR ) contributes to chromate bioremediation by decreasing chromate ( Paul et al, 2020 ). In addition to the cus ABCFRS operon, which is involved in the silver efflux system, gene systems or gene clusters were encoded for copper hemeostasis, such as copA, pcoE, cutC, cueO , and R ( Gudipaty et al, 2012 ).…”

Section: Discussionmentioning

confidence: 99%

Draft genome analysis for Enterobacter kobei, a promising lead bioremediation bacterium

El-Beltagi,

Halema,

Almutairi

et al. 2024

Front. Bioeng. Biotechnol.

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Lead pollution of the environment poses a major global threat to the ecosystem. Bacterial bioremediation offers a promising alternative to traditional methods for removing these pollutants, that are often hindered by various limitations. Our research focused on isolating lead-resistant bacteria from industrial wastewater generated by heavily lead-containing industries. Eight lead-resistant strains were successfully isolated, and subsequently identified through molecular analysis. Among these, Enterobacter kobei FACU6 emerged as a particularly promising candidate, demonstrating an efficient lead removal rate of 83.4% and a remarkable lead absorption capacity of 571.9 mg/g dry weight. Furthermore, E. kobei FACU6 displayed a remarkable a maximum tolerance concentration (MTC) for lead reaching 3,000 mg/L. To further investigate the morphological changes in E. kobei FACU6 in response to lead exposure, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed. These analyses revealed significant lead adsorption and intracellular accumulation in treated bacteria in contrast to the control bacterium. Whole-genome sequencing was performed to gain deeper insights into E. kobei’s lead resistance mechanisms. Structural annotation revealed a genome size of 4,856,454 bp, with a G + C content of 55.06%. The genome encodes 4,655 coding sequences (CDS), 75 tRNA genes, and 4 rRNA genes. Notably, genes associated with heavy metal resistance and their corresponding regulatory elements were identified within the genome. Furthermore, the expression levels of four specific heavy metal resistance genes were evaluated. Our findings revealed a statistically significant upregulation in gene expression under specific environmental conditions, including pH 7, temperature of 30°C, and high concentrations of heavy metals. The outstanding potential of E. kobei FACU6 as a source of diverse genes related to heavy metal resistance and plant growth promotion makes it a valuable candidate for developing safe and effective strategies for heavy metal disposal.

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“…R. planticola FACU 3 harbors ars RDABC operon and arsH which was encoded for arsenic resistance (Carlin et al 1995 ; Vorontsov et al 2007 ; Yang et al 2012 ). It is worth noting that the presence of quinone reductase gene ( chrR ) helps in reducing of chromate thus in chromate bioremediation (Eswaramoorthy et al 2012 ; Paul et al 2020 ). There are gene systems/gene cluster encoded for copper hemostasis like cop operon, cutC, cue O and cue R in addition to cus operon and pco/sil operon which participates in silver efflux system (Franke et al 2003 ; Gudipaty et al 2012 ) and found on the chromosome as several studies reported that these genes are regularly be located on the chromosome of Enterobacteriaceae species not restricted to plasmid (Baya et al 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Draft genome of Raoultella planticola, a high lead resistance bacterium from industrial wastewater

et al. 2023

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Isolation of heavy metals-resistant bacteria from their original habitat is a crucial step in bioremediation. Six lead (Pb) resistant bacterial strains were isolated and identified utilizing 16S rRNA to be Enterobacter ludwigii FACU 4, Shigella flexneri FACU, Microbacterium paraoxydans FACU, Klebsiella pneumoniae subsp. pneumonia FACU, Raoultella planticola FACU 3 and Staphylococcus xylosus FACU. It was determined that all these strains had their Minimum inhibitory concentration (MIC) to be 2500 ppm except R. planticola FACU 3 has a higher maximum tolerance concentration (MTC) up to 2700 ppm. We evaluated the survival of all six strains on lead stress, the efficiency of biosorption and lead uptake. It was found that R. planticola FACU 3 is the highest MTC and S. xylosus FACU was the lowest MTC in this evaluation. Therefore, transmission electron microscopy (TEM) confirmed the difference between the morphological responses of these two strains to lead stress. These findings led to explore more about the genome of R. planticola FACU 3 using illumine Miseq technology. Draft genome sequence analysis revealed the genome size of 5,648,460 bp and G + C content 55.8% and identified 5526 CDS, 75 tRNA and 4 rRNA. Sequencing technology facilitated the identification of about 47 genes related to resistance to many heavy metals including lead, arsenic, zinc, mercury, nickel, silver and chromium of R. planticola FACU 3 strain. Moreover, genome sequencing identified plant growth-promoting genes (PGPGs) including indole acetic acid (IAA) production, phosphate solubilization, phenazine production, trehalose metabolism and 4-hydroxybenzoate production genes and a lot of antibiotic-resistant genes.

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In silico studies on structural, functional, and evolutionary analysis of bacterial chromate reductase family responsible for high chromate bioremediation efficiency

Cited by 8 publications

References 60 publications

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

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

Draft genome analysis for Enterobacter kobei, a promising lead bioremediation bacterium

Draft genome of Raoultella planticola, a high lead resistance bacterium from industrial wastewater

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