Multi-metal tolerance of von Willebrand factor type D domain isolated from metal contaminated site by metatranscriptomics approach

Thakur, Bharti; Yadav, Ravi; Vallon, Laurent; Marmeisse, Roland; Fraissinet‐Tachet, Laurence; Reddy, S. M.

doi:10.1016/j.scitotenv.2019.01.201

Cited by 9 publications

(8 citation statements)

References 60 publications

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“…Some of these genes were selected randomly and characterized to provide metal tolerance. These genes include ubiquitin fusion protein, von Willebrand factor type D domain, heat shock protein type I like protein, serine protease inhibitor, aldehyde dehydrogenase, and DHHC palmitoyl transferase-like protein (Thakur et al 2018(Thakur et al , 2019(Thakur et al , 2021Mukherjee et al 2019aMukherjee et al , 2019bMukherjee et al , 2020Mukherjee et al , 2021. These characterized cDNAs have shown high tolerance toward different heavy metals like Cd, Cu, Zn, and Co.…”

Section: Resultsmentioning

confidence: 99%

“…The sequences were compared for homologous sequences available in databases by using BLASTX. Few of the metaltolerant cDNAs were assessed for their tolerance mechanisms by transforming them into metalsensitive yeast mutants by functional complementation, and testing their abilities to tolerate high concentrations of metals such as Cd, Cu, Zn, and Co (Mukherjee et al 2019a(Mukherjee et al , b, 2021Thakur et al 2019Thakur et al , 2021.…”

Section: Identification Of Metal-tolerant Genesmentioning

confidence: 99%

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Metagenomic analysis of heavy metal-contaminated soils reveals distinct clades with adaptive features

Thakur

Yadav

Marmeisse

et al. 2022

Int. J. Environ. Sci. Technol.

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Heavy metal pollution poses a serious threat to soil, water, and the atmospheric environment. Many microbes sustain and respond to the metal stress, and the mechanisms involved in these processes remain unclear. The metagenomics and metatranscriptomics approaches were applied to study the structure and function of eukaryotic microbial communities in heavy metal-contaminated soils of two geographic locations situated in different climatic regions. To achieve this, amplicons of the hypervariable V4 region of 18S rDNA and cDNA synthesized from 18S rRNA extracted from these soils were generated and sequenced through paired-end sequencing chemistry on the Illumina-MiSeq platform. The NGS dataset processed by the Mothur pipeline and analyzed by Parallel-Meta 3 pipeline illustrated the presence of all the major eukaryotic phyla. Taxa diversity and community structure of micro-eukaryotes within and between the samples from two locations were compared. Clustering, heatmap, and PCA analysis supported the variation in taxonomic diversity and community structure in the datasets of these two sites. Analysis of taxa abundance in both sites identified marker organisms for the further characterization of such types of environments. A functional metatranscriptomics study revealed the identification of various expressed eukaryotic genes, which are involved in metal tolerance. These metal-tolerant gene families were phylogenetically related to the different eukaryotic lineages reported in the metagenomic analysis. Hence, this approach could be widely applied in microbial ecology to understand the role of active microbes in such specific environmental conditions.

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Section: Resultsmentioning

confidence: 99%

Section: Identification Of Metal-tolerant Genesmentioning

confidence: 99%

Metagenomic analysis of heavy metal-contaminated soils reveals distinct clades with adaptive features

Thakur

Yadav

Marmeisse

et al. 2022

Int. J. Environ. Sci. Technol.

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“…Twenty soil cores were collected, mixed in equal volumes to make a composite sample, sieved through 2.0-mm mesh, and preserved in dry ice and then stored at − 70 °C until further experiments. The physicochemical properties of the soil were determined as described in Thakur et al (2019) and were as follows: pH 7.15; total phosphorus 291 mg/kg; available phosphorus 14.2 mg/kg; organic carbon 1.6%; and total nitrogen 0.12%. The metal contents (mg/kg) of the soil samples were as follows: Cd 2.5, Zn 385 and Cu 64.…”

Section: Soil Sampling and Analysismentioning

confidence: 99%

“…This approach is a function-driven approach and recognized as an authoritative tool in unearthing various functional genes playing fundamental role in numerous phenomena including biological response mechanisms to environmental conditions (Damon et al 2011;de Menezes et al 2012;Zielinski et al 2016). Function-based metagenomics has identified numerous ecologically significant genes as those encoding for oligopeptide transporters (Damon et al 2011), cysteine-rich metallothioneins (Ziller et al 2017) and candidate proteins involved in metal tolerance (Thakur et al 2019). This approach provided an unprecedented overview of gene expression profiling in microbial communities, thus providing huge information on functional microbial diversity.…”

Section: Introductionmentioning

confidence: 99%

“…These proteins accumulate in a wide range of plant and animal species in response to environmental stressors to maintain cellular homeostasis (Gillis et al 2013;Gupta et al 2010). Screening of yeast cDNA library constructed from RNA isolated from a metal-contaminated site allowed us to identify several genes involved in Cd tolerance when expressed in yeast (Thakur et al 2018(Thakur et al , 2019Mukherjee et al 2019). In the present study, one of the cDNAs, PLCc43, whose deduced protein sequence showed partial sequence similarity to eukaryotic type I Hsp40 proteins, was characterized and its role in providing tolerance to potentially toxic metals in metal-sensitive yeast mutants was assessed.…”

Section: Introductionmentioning

confidence: 99%

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Protection from metal toxicity by Hsp40-like protein isolated from contaminated soil using functional metagenomic approach

Thakur

Yadav

Mukherjee

et al. 2021

Environ Sci Pollut Res

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Pollution in the environment due to accumulation of potentially toxic metals results in deterioration of soil and water quality, thus impacting health of all living organisms including microbes. In the present investigation, a functional metagenomics approach was adopted to mine functional genes involved in metal tolerance from potentially toxic metal contaminated site. Eukaryotic cDNA library (1.0-4.0 kb) was screened for the genes providing tolerance to cadmium (Cd) toxicity through a functional complementation assay using Cd-sensitive Saccharomyces cerevisiae mutant ycf1 Δ . Out of the 98 clones able to recover growth on Cd-supplemented selective medium, one clone designated as PLCc43 showed more tolerance to Cd along with some other clones. Sequence analysis revealed that cDNA PLCc43 encodes a 284 amino acid protein harbouring four characteristic zinc finger motif repeats (CXXCXGXG) and showing partial homology with heat shock protein (Hsp40) of Acanthamoeba castellanii. qPCR analysis revealed the induction of PLCc43 in the presence of Cd, which was further supported by accumulation of Cd in ycf1 Δ /PLCc43 mutant. Cu-sensitive (cup1 Δ ), Zn-sensitive (zrc1 Δ ) and Co-sensitive (cot1 Δ ) yeast mutant strains were rescued from sensitivity when transformed with cDNA PLCc43 indicating its ability to confer tolerance to various potentially toxic metals. Oxidative stress tolerance potential of PLCc43 was also confirmed in the presence of H2O2. Present study results suggest that PLCc43 originating from a functional eukaryotic gene of soil community play an important role in detoxification of potentially toxic metals and may be used as biomarker in various contaminated sites.

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Meta‐omics assisted microbial gene and strain resources mining in contaminant environment

Huang,

Hu,

Zhang

et al. 2023

Engineering in Life Sciences

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Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta‐omics provided culture‐independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta‐omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.

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Multi-metal tolerance of von Willebrand factor type D domain isolated from metal contaminated site by metatranscriptomics approach

Cited by 9 publications

References 60 publications

Metagenomic analysis of heavy metal-contaminated soils reveals distinct clades with adaptive features

Metagenomic analysis of heavy metal-contaminated soils reveals distinct clades with adaptive features

Protection from metal toxicity by Hsp40-like protein isolated from contaminated soil using functional metagenomic approach

Meta‐omics assisted microbial gene and strain resources mining in contaminant environment

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