Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite

Abstract

Natural products (NPs) are synthesized by biosynthetic gene clusters (BGCs), whose genes are involved in producing one or a family of chemically related metabolites. Advances in comparative genomics have been favourable for exploiting huge amounts of data and discovering previously unknown BGCs. Nonetheless, studying distribution patterns of novel BGCs and elucidating the biosynthesis of orphan metabolites remains a challenge. To fill this knowledge gap, our study developed a pipeline for high-quality comparative genomics for the actinomycete genus Rhodococcus , which is metabolically versatile, yet understudied in terms of NPs, leading to a total of 110 genomes, 1891 BGCs and 717 non-ribosomal peptide synthetases (NRPSs). Phylogenomic inferences showed four major clades retrieved from strains of several ecological habitats. BiG-SCAPE sequence similarity BGC networking revealed 44 unidentified gene cluster families (GCFs) for NRPS, which presented a phylogenomic-dependent evolution pattern, supporting the hypothesis of vertical gene transfer. As a proof of concept, we analysed in-depth one of our marine strains, Rhodococcus sp. H-CA8f, which revealed a unique BGC distribution within its phylogenomic clade, involved in producing a chloramphenicol-related compound. While this BGC is part of the most abundant and widely distributed NRPS GCF, corason analysis unveiled major differences regarding its genetic context, co-occurrence patterns and modularity. This BGC is composed of three sections, two well-conserved right/left arms flanking a very variable middle section, composed of nrps genes. The presence of two non-canonical domains in H-CA8f’s BGC may contribute to adding chemical diversity to this family of NPs. Liquid chromatography-high resolution MS and dereplication efforts retrieved a set of related orphan metabolites, the corynecins, which to our knowledge are reported here for the first time in Rhodococcus . Overall, our data provide insights to connect BGC uniqueness with orphan metabolites, by revealing key comparative genomic features supported by models of BGC distribution along phylogeny.

iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments

“…Chloramphenicol is a dichloro-substituted acetamide with broad-spectrum antibacterial activity [ 64 ]. Corynecin I is a chloramphenicol-like acyl-nitrophenylpropylamine that also has broad-spectrum antibacterial activity [ 65 , 66 ].…”

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

“…High-quality comparative genome mining allowed the identification of a number of biosynthetic gene clusters in Rhodococcus sp. H-CA8f involved in producing corynecins (N-acyl derivatives of D-threop-nitrophenylserinol compounds structurally similar to the antibiotic chloramphenicol), which exhibit antimicrobial properties (Undabarrena et al, 2021). Currently, bacteria from rare or challenging (i.e., nutritional imbalance, waterlogging, hypoxia and anoxia, pollution, salinity, heat, and cold) conditions attract particular interest in searching for biosynthetic genes and novel natural products, which avoids the replication of already known molecules.…”

“…The main function of pigments is to protect cells from reactive oxygen species produced by UV radiation and toxic substances (Cappelletti et al, 2020). The pigments extracted Antimicrobials synthetized by rhodococci (Iwatsuki et al, 2006;Kurosawa et al, 2008;Nachtigall et al, 2010;Chu et al, 2016;Shim, 2016;Undabarrena et al, 2021;Harunari et al, 2022). Ivshina et al 10.3389/fmicb.2022.967127 Frontiers in Microbiology 14 frontiersin.org from a soil bacterium, Rhodococcus sp.…”

“… Antimicrobials synthetized by rhodococci ( Iwatsuki et al, 2006 ; Kurosawa et al, 2008 ; Nachtigall et al, 2010 ; Chu et al, 2016 ; Shim, 2016 ; Undabarrena et al, 2021 ; Harunari et al, 2022 ). …”

Role is in the eye of the beholder—the multiple functions of the antibacterial compound tropodithietic acid produced by marine Rhodobacteraceae

“… 2021 ; Undabarrena et al . 2021 ). Genetic diversification of the salinosporamides A biosynthetic gene cluster, found in the marine Salinispora genus, had direct consequences on the secondary metabolite production (Chase et al .…”