Exploring the Diversity and Specificity of Secondary Biosynthetic Potential in <i>Rhodococcus</i>
Gang-Ao Hu,
Yue Song,
Shi-Yi Liu,
Wen-Chao Yu,
Yan-Lei Yu,
Jian-Wei Chen,
Hong Wang,
Bin Wei
Affiliations
Gang-Ao Hu
College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang Key Laboratory of Green, Low-Carbon, and Efficient Development of Marine Fishery Resources, Zhejiang University of Technology (ZJUT), Hangzhou 310014, China
Yue Song
College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang Key Laboratory of Green, Low-Carbon, and Efficient Development of Marine Fishery Resources, Zhejiang University of Technology (ZJUT), Hangzhou 310014, China
Shi-Yi Liu
College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang Key Laboratory of Green, Low-Carbon, and Efficient Development of Marine Fishery Resources, Zhejiang University of Technology (ZJUT), Hangzhou 310014, China
Wen-Chao Yu
College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang Key Laboratory of Green, Low-Carbon, and Efficient Development of Marine Fishery Resources, Zhejiang University of Technology (ZJUT), Hangzhou 310014, China
Yan-Lei Yu
College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang Key Laboratory of Green, Low-Carbon, and Efficient Development of Marine Fishery Resources, Zhejiang University of Technology (ZJUT), Hangzhou 310014, China
Jian-Wei Chen
College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang Key Laboratory of Green, Low-Carbon, and Efficient Development of Marine Fishery Resources, Zhejiang University of Technology (ZJUT), Hangzhou 310014, China
Hong Wang
College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang Key Laboratory of Green, Low-Carbon, and Efficient Development of Marine Fishery Resources, Zhejiang University of Technology (ZJUT), Hangzhou 310014, China
Bin Wei
College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang Key Laboratory of Green, Low-Carbon, and Efficient Development of Marine Fishery Resources, Zhejiang University of Technology (ZJUT), Hangzhou 310014, China
The actinomycete genus Rhodococcus is known for its diverse biosynthetic enzymes, with potential in pollutant degradation, chemical biocatalysis, and natural product exploration. Comparative genomics have analyzed the distribution patterns of non-ribosomal peptide synthetases (NRPSs) in Rhodococcus. The diversity and specificity of its secondary metabolism offer valuable insights for exploring natural products, yet remain understudied. In the present study, we analyzed the distribution patterns of biosynthetic gene clusters (BGCs) in the most comprehensive Rhodococcus genome data to date. The results show that 86.5% of the gene cluster families (GCFs) are only distributed in a specific phylogenomic-clade of Rhodococcus, with the most predominant types of gene clusters being NRPS and ribosomally synthesized and post-translationally modified peptides (RiPPs). In-depth mining of RiPP gene clusters revealed that Rhodococcus encodes many clade-specific novel RiPPs, with thirteen core peptides showing antibacterial potential. High-throughput elicitor screening (HiTES) and non-targeted metabolomics revealed that a marine-derived Rhodococcus strain produces a large number of new aurachin-like compounds when exposed to specific elicitors. The present study highlights the diversity and specificity of secondary biosynthetic potential in Rhodococcus, and provides valuable information for the targeted exploration of novel natural products from Rhodococcus, especially for phylogenomic-clade-specific metabolites.
