Metagenomic approaches for the discovery of pollutant-remediating enzymes: Recent trends and challenges

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Date
2022-09-27
Authors
Mukherjee, Arghya
Cotter, Paul D.
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Springer Nature Ltd.
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Abstract
Metagenomic studies in diverse environments have generated petabytes of sequencing data, allowing biologists to peer into the uncultivated microbial majority with unprecedented clarity. Such advances have heralded a new era of enzyme discovery where proteins of interest can be directly extracted from metagenomic sequencing data, although this remains a challenging task. Traditionally, metagenomic enzyme discovery, including that involved in xenobiotic degradation, has largely relied on functional insights derived from activity-guided or PCR-based metagenomics. Due to its untargeted and holistic nature, metagenomics allows us to probe the unknown and underexplored microbial diversity, which represents a key resource for novel biocatalyst discovery. Metagenomic shotgun sequencing-based enzyme discovery, additionally, avoids common biases introduced through PCR-based or activity-guided functional genomic methods. In this chapter, we have provided an overview of metagenomics in novel enzyme discovery with discussions on both the experimental and computational aspects of the same. We discuss in detail computational strategies for identifying possible enzyme candidates from shotgun sequencing data and experimental strategies for characterizing candidate enzymes once they have been identified. Finally, we review emerging methods of metagenomic enzyme discovery as well as future goals and challenges with an emphasis on metagenomic-based approaches.
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Metagenomics , Xenobiotics , Pollution , Enzyme discovery , Shotgun sequencing , Protein function
Citation
Mukherjee, A. and Cotter, P. D. (2022) 'Metagenomic approaches for the discovery of pollutant-remediating enzymes: Recent trends and challenges', in Kumar, V. and Thakur, I. S. (eds) Omics Insights in Environmental Bioremediation. Springer, Singapore, pp. 571-604. doi: 10.1007/978-981-19-4320-1_24
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© 2022, Springer Nature Singapore Pte Ltd. This is a post-peer-review, pre-copyedit version of a chapter published in Kumar, V. and Thakur, I. S. (eds) Omics Insights in Environmental Bioremediation. Springer, Singapore, pp. 571-604, doi: 10.1007/978-981-19-4320-1_24. The final authenticated version is available online at: https://doi.org/10.1007/978-981-19-4320-1_24