Genomic analysis suggests Salinispora is a rich source of novel lanthipeptides
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ORIGINAL ARTICLE
Genomic analysis suggests Salinispora is a rich source of novel lanthipeptides Caroline G. Kittrell1 · Shailey C. Shah1 · Matthew E. Halbert1 · Dylan H. Scott1 · Emilianne M. Limbrick1 Received: 4 February 2020 / Accepted: 17 August 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
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. Keywords Lanthipeptide · Salinispora · Genomic analysis · Biosynthesis · Actinomycete
Introduction With the increasing prevalence of antibacterial resistance in the clinical setting, new antibiotics are desperately needed. Microbial secondary metabolites have long been a source of pharmaceutically important compounds with a wide range of biological activities. Lanthipeptides are cyclic peptides, characterized by lanthionine and methyl lanthionine residues, belonging to the large class of ribosomally encoded and post-translationally modified peptides (RiPPs). These compounds display diverse biological activities with the largest subgroup of known lanthipeptides possessing antimicrobial activity (Piper et al. 2009; Knerr and van der Donk 2012; Arnison et al. 2012; Dischinger et al. 2014; Zhang Communicated by Stefan Hohmann. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00438-020-01718-1) contains supplementary material, which is available to authorized users. * Emilianne M. Limbrick [email protected] 1
Department of Chemistry, Mercer University, Macon, GA, USA
et al. 2015). Nisin is the most well-studied lanthipeptide and has been used by the food industry as a preservative for more than 40 years. Intriguingly, no substantial resistance to nisin has been reported (Piper et al. 2009; Arnison et al. 2012). Other lanthipeptides have been shown to possess potent activity against medically important bacteria such as Staphylococcus, Streptococcus, Enterococcus, Clost
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