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Genomic analysis suggests Salinispora is a rich source of novel lanthipeptides

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Abstract

Lanthipeptides are a subgroup of ribosomally encoded and post-translationally modified peptides (RiPPs) which frequently possess potent biological activity. Here we provide the first comprehensive bioinformatic analysis of the lanthipeptide-producing capability of the Salinispora genus, a marine actinomycete. One hundred twenty-two Salinispora arenicola, tropica, and pacifica genomic sequences were analyzed for lanthipeptide gene clusters, and the resulting 182 clusters were divided into seven groups based on sequence similarities. Group boundaries were defined based on LanB and LanM sequences with greater than 80% similarity within groups. Of the seven groups, six are predicted to encode class I lanthipeptides while only one group is predicted to encode class II lanthipeptides. Leader and core peptides were predicted for each cluster along with the number of possible lanthionine bridges. Notably, all of the predicted products of these clusters would represent novel lanthipeptide scaffolds. Of the 122 Salinispora genomes analyzed in this study, 92% contained at least one lanthipeptide gene cluster suggesting that Salinispora is a rich, yet untapped, source of lanthipeptides.

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Availability of data and material

Data generated and analysed during this study are included in the supplementary information file associated with this publication. Any additional datasets (such as antiSMASH results or MultiGeneBlast results) are available from the corresponding author on reasonable request.

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Acknowledgements

We thank Kevin Bucholtz, Garland Crawford, David Goode, and Jeff Hugdahl for helpful conversations and valuable feedback.

Funding

This study was funded by Mercer University’s Provost Office, Research that Reaches Out office, and the Department of Chemistry.

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Authors and Affiliations

  1. Department of Chemistry, Mercer University, Macon, GA, USA

    Caroline G. Kittrell, Shailey C. Shah, Matthew E. Halbert, Dylan H. Scott & Emilianne M. Limbrick

Authors
  1. Caroline G. Kittrell
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  2. Shailey C. Shah
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  3. Matthew E. Halbert
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  4. Dylan H. Scott
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  5. Emilianne M. Limbrick
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Contributions

All authors contributed to the study design and analysis of data. Data collection and analysis were performed by CGK, MEH, DHS, SCS, and EML. The first draft of the manuscript was written by EML and CGK, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Emilianne M. Limbrick.

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Conflict of interest

Caroline G. Kittrell declares that she has no conflict of interest. Shailey C. Shah declares that she has no conflict of interest. Matthew E. Halbert declares that he has no conflict of interest. Dylan H. Scott declares that he has no conflict of interest. Emilianne M. Limbrick declares that she has no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Communicated by Stefan Hohmann.

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Kittrell, C.G., Shah, S.C., Halbert, M.E. et al. Genomic analysis suggests Salinispora is a rich source of novel lanthipeptides. Mol Genet Genomics 295, 1529–1535 (2020). https://doi.org/10.1007/s00438-020-01718-1

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  • DOI: https://doi.org/10.1007/s00438-020-01718-1

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