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Whole-Genome Sequence Analysis of Paenibacillus alvei JR949 Revealed Biosynthetic Gene Clusters Coding for Novel Antimicrobials

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Abstract

The increased prevalence of multidrug-resistant pathogens poses a significant clinical threat, and hence, the discovery of novel antibiotics is the need of the hour. Several attempts are being made worldwide to screen and identify newer antibiotics from various microbial sources. The genus Paenibacillus is known for its biosynthetic potential and metabolic versatility in producing several secondary metabolites. In this study, we isolated Paenibacillus alvei strain JR949 from the soil, which exhibited antimicrobial activity against Enteropathogenic Escherichia coli (EPEC), Pseudomonas aeruginosa (PAO1), and methicillin-resistant Staphylococcus aureus (MRSA). The whole genome of this strain was sequenced using the Illumina platform. The genome mining of the draft genome sequence revealed a total of 31 biological gene clusters (BGCs) responsible for the synthesis of secondary metabolites. The construction of the similarity network of the BGCs and the comparative analysis with the genetically related strains aided the identification of metabolites produced by this strain. We identified BGCs coding for paenibactin, paenibacterin, anabaenopeptin NZ857, icosalide A/B, polymyxin, and bicornutinA1/A2 with 100% similarity. The BGCs with lower sequence similarity to paenibacterin, polymyxin B, colistin A/B, pellasoren, tridecaptin, pelgipeptin, and marthiapeptide were also identified. Furthermore, 13 putative NRPS BGCs, 3 NRPS-T1PKS hybrid clusters, a T1PKS, and a bacteriocin BGC were identified with very low similarity (≤ 25%) or no similarity with known antibiotics. Further experimental investigations may result in the discovery of novel antimicrobial drugs.

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source genomes and the node shapes indicate the biosynthetic classes

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Acknowledgements

The authors acknowledge the UGC-NRCBS, DBT-IPLS, DST-PURSE, and DST-FIIST Programs of the School of Biological Sciences, Madurai Kamaraj University.

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Madurai Kamaraj University.

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Authors and Affiliations

  1. Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India

    Parameswaran Sree Pranav, Balasubramanian Mahalakshmi, Ramamoorthy Sivakumar, Raman Karthikeyan & Jeyaprakash Rajendhran

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  1. Parameswaran Sree Pranav
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  2. Balasubramanian Mahalakshmi
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  3. Ramamoorthy Sivakumar
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Contributions

JR, RS, and RK: designed the experiments. PSP, BM, RS: performed experiments. PSP and JR: wrote the experiment. All authors read and approved the final manuscript.

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Correspondence to Jeyaprakash Rajendhran.

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Pranav, P.S., Mahalakshmi, B., Sivakumar, R. et al. Whole-Genome Sequence Analysis of Paenibacillus alvei JR949 Revealed Biosynthetic Gene Clusters Coding for Novel Antimicrobials. Curr Microbiol 78, 1168–1176 (2021). https://doi.org/10.1007/s00284-021-02393-0

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