Isolation of multi-metal tolerant ubiquitin fusion protein from metal polluted soil by metatranscriptomic approach

Thakur, Bharti; Yadav, Ravi; Fraissinet‐Tachet, Laurence; Marmeisse, Roland; Reddy, M. Sudhakara

doi:10.1016/j.mimet.2018.08.001

Cited by 16 publications

(12 citation statements)

References 62 publications

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“…Further, functional metatranscriptomics approach allows identification of genes from microbial communities responsible for adapting to extreme environmental conditions. A protocol for functional metatranscriptomics study would involve isolation of total RNA from an environmental sample, construction of cDNA library, screening for HM tolerance transcripts through bacterial or yeast complementation system, and finally sequencing for identification of transcripts of interest (Thakur et al, 2018;Mukherjee and Reddy, 2020). Thakur et al (2018) used this approach to screen cDNA library prepared from Cd contaminated site.…”

Section: Metatranscriptomicsmentioning

confidence: 99%

“…A protocol for functional metatranscriptomics study would involve isolation of total RNA from an environmental sample, construction of cDNA library, screening for HM tolerance transcripts through bacterial or yeast complementation system, and finally sequencing for identification of transcripts of interest (Thakur et al, 2018;Mukherjee and Reddy, 2020). Thakur et al (2018) used this approach to screen cDNA library prepared from Cd contaminated site. The study revealed a yeast transformant that exhibited significant tolerance against multiple stresses (2-4 mM Co, 150-300 µM Cu, and 10-12 mM Zn; Thakur et al, 2018).…”

Section: Metatranscriptomicsmentioning

confidence: 99%

“…Thakur et al (2018) used this approach to screen cDNA library prepared from Cd contaminated site. The study revealed a yeast transformant that exhibited significant tolerance against multiple stresses (2-4 mM Co, 150-300 µM Cu, and 10-12 mM Zn; Thakur et al, 2018). Lehembre et al (2013) used the functional metatranscriptomics approach to decipher the functional contribution of microbiota toward HM resistance.…”

Section: Metatranscriptomicsmentioning

confidence: 99%

See 2 more Smart Citations

Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome

Phurailatpam

Dalal

Singh

et al. 2022

Front. Sustain. Food Syst.

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Heavy metal (HM) contamination of soil and water resources is a global concern, which not only limits crop yield and quality, but also has serious environmental effects. Due to the non-biodegradable nature and toxicity, high concentration of HMs in food and environment is a serious threat to the entire ecosystem. Moreover, the target of supplying safe and quality food to the rising human population (expected to reach ~9–10 bn by the year 2050), necessitates effective treatment of the HM-contaminated soil. Various microbe-mediated bioremediation strategies such as biosorption, bioprecipiation, biostimulation, etc., have been found to be effective in uptake and conversion of HMs to less toxic forms. Further, in the past few years, the use of soil and plant-associated microbiome for HM stress alleviation is gaining attention among the scientific community. In general, microbes are spectacular in being dynamic and more responsive to environmental conditions in comparison to their host plants. Moreover, with the advancements in high throughput sequencing technologies, the focus is eventually shifting from just structural characterization to functional insights into the microbiome. The microbes inhabiting the HM-contaminated environments or associated with HM-tolerant plants are a source for exploring HM-tolerant microbial communities, which could be used for enhancing bioremediation efficiency and conferring HM tolerance in plants. This review discusses the application of omics techniques including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, for rapid and robust identification of HM-tolerant microbial communities, mining novel HM resistance genes, and fabricating the HM resistome.

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Section: Metatranscriptomicsmentioning

confidence: 99%

Section: Metatranscriptomicsmentioning

confidence: 99%

Section: Metatranscriptomicsmentioning

confidence: 99%

See 1 more Smart Citation

Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome

Phurailatpam

Dalal

Singh

et al. 2022

Front. Sustain. Food Syst.

View full text Add to dashboard Cite

show abstract

“…On the other hand, metatranscriptomics provides data related to the real physiological activity of organisms in the environmental samples by RNA extraction from a microbial community, whose mRNA or cDNA, after sequencing, indicates the protein encoded by a gene, which can express a real or future quantitative or qualitative activity. This tool allows determining potential genes in microorganisms to apply in the bioremediation of environmentally hazardous compounds (Thakur et al 2018).…”

Section: Application Of Omics Tools In Environmental Biotechnologymentioning

confidence: 99%

Environmental Biotechnology

et al. 2020

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The various industrial sectors, as well as livestock and agricultural activities, are increasing the production of inputs to meet the demand of the worldwide demographic explosion, making a challenge the clean maintenance of water, soil, and air. Therefore, the search for solutions for a pollutant-free environment without compromising economic development has become extremely important. Thereby, biotechnological studies in order to solve environmental issues have been gaining extensive attention through the coupling of technology procedures to biological systems as sustainable solutions to remediate contaminated areas. In this sense, this review covers topics such as the role of Omics era in microbial environmental biotechnology for pollution control as well as the microbial fuel cell use in energy production. Moreover, phytoremediation and the perspective of applying chemical methods are approached as environmentally friendly tools for the pollutant control to improve remediation processes.

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“…Function-based approach of metagenomics involves conversion of mRNAs into complementary DNA libraries followed by transcription and expression in suitable hosts (Bailly et al 2007;Grant et al 2006). It has been reported that function-based metagenomic approach may explore the functional diversity by directly using mRNAs, thus providing actively expressed gene repertoire in environmental samples (Bailly et al 2007;Thakur et al 2018). 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).…”

Section: Introductionmentioning

confidence: 99%

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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Isolation of multi-metal tolerant ubiquitin fusion protein from metal polluted soil by metatranscriptomic approach

Cited by 16 publications

References 62 publications

Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome

Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome

Environmental Biotechnology

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

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