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Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting

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Abstract

Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.

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Acknowledgements

The authors thank the authorities of Sathyabama Institute of Science and Technology, Tamil Nadu, India, for the research facilities provided.

Funding

This study receives financial support from the Ministry of Earth Science – National Centre for Polar and Ocean Research, Goa, India, in terms of the extramural research project (Ref. NCPOR/2019/PACER-POP/BS-08) to work on Southern Ocean bacterial diversity.

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  1. Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India

    Manigundan Kaari, Radhakrishnan Manikkam & Abirami Baskaran

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  1. Manigundan Kaari
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  2. Radhakrishnan Manikkam
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Correspondence to Radhakrishnan Manikkam.

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Glossary

Biosynthetic gene cluster

Physical grouping of two or more genes responsible for the production of secondary metabolites.

Natural product

A chemical compound or substance produced by a living organism found in nature.

Secondary metabolites

Small organic molecules produced by an organism that are not essential for their growth, development, and reproduction.

Metagenomics

The study of genetic material recovered directly from environmental samples.

Genome shuffling

A method to increase the production of metabolites by microbial strain.

antiSMASH

antiSMASH is a bioinformatics software to identify, annotate, and compare gene clusters that encode the biosynthesis of secondary metabolites in microbial genomes.

EvoMining

To study the expansion-and-recruitment events in enzyme families in archaea and bacteria lineages, with the goal of providing both evolutionary insights and a genome mining approach for the discovery of novel natural product biosynthetic gene clusters.

Genome mining

The identification of previously uncharacterized natural product biosynthetic gene clusters within the genomes of sequenced organisms, sequence analysis of the enzymes encoded by these gene clusters, and the experimental identification of the products of the gene clusters.

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Kaari, M., Manikkam, R. & Baskaran, A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. Mar Biotechnol 24, 448–467 (2022). https://doi.org/10.1007/s10126-022-10118-y

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