DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Sci Rep. 2022 Nov 7;12(1):18909. doi: 10.1038/s41598-022-21731-1.
Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.
链霉菌是具有高度代谢能力的细菌，能够产生具有深远经济和社会重要性的生物制品。这些生物制品是通过代谢途径产生的，包括次生代谢物生物合成途径和植物生物质成分的分解代谢途径。基因组测序技术的进步揭示了来自链霉菌基因组的大量未开发的代谢潜力。在这里，我们报告了使用 205 个完整基因组生成的最大的链霉菌泛基因组。分析了泛基因组和单个基因组的代谢潜力，揭示了单个代谢途径的保守程度和潜在适合代谢工程的菌株。其中，链霉菌 bingchenggensis 被鉴定为一种有效的植物生物质降解菌。聚酮、非核糖体肽和γ-丁内酯生物合成酶主要是菌株特异性的，而章鱼胺和一些萜烯生物合成途径则高度保守。与次生代谢物相关的大量转录因子是菌株特异性的，而那些控制基本生物过程的转录因子则高度保守。尽管参与形态发育的大多数基因高度保守，但也存在菌株特异性的变体，这可能有助于精细调节细胞分化的时间。总的来说，这些结果为链霉菌的代谢潜力、调控和生理学提供了深入的了解，这将有助于进一步开发这些重要的细菌。
