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Genome mining to identify valuable secondary metabolites and their regulation in Actinobacteria from different niches

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Abstract

Actinobacteria are the largest bacteria group with 18 significant lineages, which are ubiquitously distributed in all the possible terrains. They are known to produce more than 10,000 medically relevant compounds. Despite their ability to make critical secondary metabolites and genome sequences' availability, these two have not been linked with certainty. With this intent, our study aims at understanding the biosynthetic capacity in terms of secondary metabolite production in 528 Actinobacteria species from five different habitats, viz., soil, water, plants, animals, and humans. In our analysis of 9,646 clusters of 59 different classes, we have documented 64,000 SMs, of which more than 74% were of unique type, while 19% were partially conserved and 7% were conserved compounds. In the case of conserved compounds, we found the highest distribution in soil, 79.12%. We found alternate sources of antibiotics, such as viomycin, vancomycin, teicoplanin, fosfomycin, ficellomycin and patulin, and antitumour compounds, such as doxorubicin and tacrolimus in the soil. Also our study reported alternate sources for the toxin cyanobactin in water and plant isolates. We further analysed the clusters to determine their regulatory pathways and reported the prominent presence of the two component system of TetR/AcrR family, as well as other partial domains like CitB superfamily and HTH superfamily, and discussed their role in secondary metabolite production. This information will be helpful in exploring Actinobacteria from other environments and in discovering new chemical moieties of clinical significance.

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Acknowledgements

We thank the Director, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, India, for his consistent encouragement and support.

Funding

A.B. and M.V.D. were supported by CSIR-NET Fellowship, while S.S. and T.S. were supported by DST-INSPIRE fellowships (IF-170007 and IF-160438). DST-SERB supports B.D. This work was funded by the Council of Scientific and Industrial Research (CSIR), New Delhi (OLP-2035), and the Department of Science and Technology-SERB (GPP-0329) to A.K.S.

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  1. Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India

    Abhilash Bhattacharjee, Sangita Sarma, Tejosmita Sen, Moirangthem Veigyabati Devi, Banani Deka & Anil Kumar Singh

  2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India

    Abhilash Bhattacharjee, Sangita Sarma, Tejosmita Sen, Moirangthem Veigyabati Devi, Banani Deka & Anil Kumar Singh

  3. Department of Botany, Dibrugarh Hanumanbax Surajmall Kanoi College, Dibrugarh, 786001, Assam, India

    Abhilash Bhattacharjee

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Contributions

AB and AKS planned and prepared the design of the experiment. AB, SS, TS, MVD, and BD screened relevant literature and collected relevant data, while AB and SS performed bioinformatics analysis. AB performed the statistical analysis, while AB, SS, and AKS designed and prepared the figures. AB and AKS wrote the main manuscript. AKS supervised the work.

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Correspondence to Anil Kumar Singh.

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Bhattacharjee, A., Sarma, S., Sen, T. et al. Genome mining to identify valuable secondary metabolites and their regulation in Actinobacteria from different niches. Arch Microbiol 205, 127 (2023). https://doi.org/10.1007/s00203-023-03482-3

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