Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

Abstract

BackgroundBacteria of the genus Rhodococcus are well known for their ability to degrade a large range of organic compounds. Some rhodococci are free-living, saprophytic bacteria; others are animal and plant pathogens. Recently, several studies have shown that their genomes encode putative pathways for the synthesis of a large number of specialized metabolites that are likely to be involved in microbe-microbe and host-microbe interactions. To systematically explore the specialized metabolic potential of this genus, we here performed a comprehensive analysis of the biosynthetic coding capacity across publicly available rhododoccal genomes, and compared these with those of several Mycobacterium strains as well as that of their mutual close relative Amycolicicoccus subflavus.ResultsComparative genomic analysis shows that most predicted biosynthetic gene cluster families in these strains are clade-specific and lack any homology with gene clusters encoding the production of known natural products. Interestingly, many of these clusters appear to encode the biosynthesis of lipopeptides, which may play key roles in the diverse environments were rhodococci thrive, by acting as biosurfactants, pathogenicity factors or antimicrobials. We also identified several gene cluster families that are universally shared among all three genera, which therefore may have a more ‘primary’ role in their physiology. Inactivation of these clusters by mutagenesis might help to generate weaker strains that can be used as live vaccines.ConclusionsThe genus Rhodococcus thus provides an interesting target for natural product discovery, in view of its large and mostly uncharacterized biosynthetic repertoire, its relatively fast growth and the availability of effective genetic tools for its genomic modification.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3966-1) contains supplementary material, which is available to authorized users.

Production of Lipopeptide Biosurfactant by a Hydrocarbon-Degrading Antarctic Rhodococcus

“…Secondary metabolites prediction using both the anti-SMASH and the anti-SMASH-incorporated NaPDoS pipelines revealed the presence of several major BGCs such as PKS, terpene, saccharides, siderophores, ribosomally synthesised and post-translationally modified peptides (RiPPs) and a noticeably high number of NRPS ( Table 2 ). The data obtained are in agreement with the observation of both Ceniceros et al [ 53 ] and Doroghazi and Metcalf [ 54 ], where high numbers were predicted for NRPS clusters compared to the PKS clusters in Rhodococci genomic sequences. Nonetheless, because the analysis was performed on drafted genome sequences, the ratio of core BGCs like NRPS to PKS might be overestimated (contigs splitting).…”

“…According to Peng et al [ 15 ], the absence of glycolipids in the sample was not related to the extraction method, but rather to the lack of corresponding synthetic pathways in the bacterium itself. A genome-based study by Ceniceros et al [ 53 ] on the metabolic capacities of the genus Rhodococcus revealed a great number of putative BGCs in their genome which includes a considerable number of BGCs that putatively encode the lipopeptide synthesis. This genomic exploration of the Rhodococci genome provides the base for further research focusing on the assessment of biosurfactant production, particularly the less-studied Rhodococci lipopeptides.…”

Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

“…This population level approach shows that the P. fluorescens population in a single field is highly complex, heterogeneous and dynamic (Figures 2, 3 and 8). The genetic and metabolic diversity of various genera or species groups have previously been investigated in detail for several bacteria, including Salinospora (86), Rhodococcus (87) and Pseudoalteromonas (88), Burkholderia (89) as well as prior studies on P. fluorescens (7, 14, 15) and wider analyses of prokaryote secondary metabolism (41) and its biogeographic distribution (90). However, these studies typically focus on the biosynthetic capacity and associated phylogenetic relationships of globally distributed strains rather than addressing the distribution and dynamics of natural product production for bacteria within a defined geographic region.…”

Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites

“…The distribution of all identified BGCs of the AntiSMASH analysis was visualized in a circular chord diagram using Circos table viewer, whereby the putative BGCs were not considered 32 . A similarity network of the BGCs among different genomes was obtained using a modified Pfam domain similarity metric implemented in BigScape 33 , 34 . A cut-off of 0.75 was used for the analysis 34 .…”