一株马里亚纳海沟来源的糖多孢菌(Saccharopolyspora sp.) BM8-3的全基因组测序与分析

Whole-genome sequencing and analysis of Saccharopolyspora sp. BM8-3 from the Mariana Trench

摘要:

背景 糖多孢菌属(Saccharopolyspora)是一类重要的稀有放线菌资源，菌株BM8-3分离自马里亚纳海沟沉积物，具有较强的耐盐特性和病原菌拮抗活性。目前尚无对深海来源糖多孢菌的功能基因、基因组学分析以及代谢产物合成的相关研究。目的 分析Saccharopolyspora sp. BM8-3的基因组序列和代谢功能基因，评估次级代谢合成潜力，为深入揭示其深海极端环境适应机制和挖掘新颖次级代谢产物基因资源奠定基础。方法 利用PacBio平台对菌株BM8-3进行全基因组测序，使用SMRT Link 5.0.1对测序数据进行基因组组装，并通过蛋白质直系同源簇(cluster of orthologous groups of proteins, COG)、京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)等数据库进行基因预测及功能注释。结果 菌株BM8-3基因组全长6 344 421 bp，G+C含量为72.5%，共注释到5 620个基因、51个tRNA基因和12个rRNA基因。分别有4 137、2 677个基因在COG、KEGG数据库中提取到注释信息。基因组分析表明，该菌基因组中富含与渗透压、高静水压适应相关的基因，包括海藻糖(otsAB)、甘氨酸甜菜碱(betAB)、四氢嘧啶(ectABCD)、二甲基甘氨酸和肌氨酸(gsmt-sdmt)等相容溶质合成和转运基因，以及与钠钾离子运输系统(如钠离子/质子逆向转运蛋白Mrp)和有机溶质运输通道(如MscL)相关的基因；同时基因组中还注释到了与冷适应相关的基因包括冷休克蛋白编码基因cspA、GroEL-GroES分子伴侣蛋白的编码基因和多种参与不饱和脂肪酸代谢的编码基因(如desC、fabF)；此外，KEGG注释结果显示菌株BM8-3具有完整的牛磺酸转运和代谢的TauABCD途径以及硫胺素回收途径(thiamine salvage pathway)；基因组中还预测到24个次级代谢产物合成基因簇，50%以上与已知化合物合成基因簇相似度低于60%，说明该菌株可能具备合成多种新颖次级代谢产物的能力。结论 本研究分析了菌株BM8-3的全基因组信息，揭示了菌株的代谢多样性及其在极端环境中的适应能力，为深海放线菌的环境适应策略及其在硫循环中的生态功能提供了重要参考。

Abstract:

Background Saccharopolyspora is an important genus of rare actinomycetes. Strain BM8-3, isolated from sediments of the Mariana Trench, exhibits strong salt tolerance and antagonistic activity against pathogens. Currently, studies are limited regarding the functional genes, genomics, and metabolite biosynthesis of Saccharopolyspora from deep sea environments.Objective To analyze the genome sequence and functional genes and evaluate the secondary metabolite synthesis of Saccharopolyspora sp. BM8-3, thus laying a foundation for exploring the strategies of this strain for adapting to extreme environments and mining the gene resources involved in the synthesis of novel secondary metabolites.Methods The whole genome of strain BM8-3 was sequenced on the PacBio platform. Genome assembly was performed by SMRT Link 5.0.1, and gene prediction and functional annotation were conducted with cluster of orthologous groups of proteins (COG) and Kyoto encyclopedia of genes and genomes (KEGG).Results The genome of strain BM8-3 had a total length of 6 344 421 bp, with the G+C content of 72.5%. A total of 5 620 genes, 51 tRNA genes, and 12 rRNA genes were annotated. The annotation against COG and KEGG predicted 4 137 and 2 677 genes, respectively. The genome of strain BM8-3 contained rich genes related to osmotic pressure and high hydrostatic pressure adaptation, including genes involved in the synthesis and transport of compatible solutes such as trehalose (otsAB), glycine betaine (betAB), ectoine (ectABCD), and dimethylglycine/sarcosine (gsmt-sdmt). Additionally, the genome contained genes associated with sodium and potassium ion transport systems (e.g., multiple resistance and pH-related antiporter) and organic solute transport channels (e.g., MscL). Furthermore, the genes associated with cold adaptation were annotated, including cspA encoding cold shock protein, genes encoding the GroEL-GroES chaperonin system, and multiple genes involved in the metabolism of unsaturated fatty acids (e.g., desC and fabF). KEGG annotation revealed that strain BM8-3 possessed a complete taurine transport and metabolism pathway (TauABCD) as well as a thiamine salvage pathway. Additionally, 24 biosynthetic gene clusters (BGCs) for secondary metabolites were predicted in the genome, with more than 50% showing less than 60% similarity to known BGCs. This finding suggested the potential of strain BM8-3 to produce novel secondary metabolites.Conclusion We analyzed the whole-genome sequence of Saccharopolyspora sp. BM8-3, revealing its metabolic diversity and adaptation mechanisms in extreme environments. This study provides critical insights into the environmental adaptation strategies of deep-sea actinomycetes and their roles in sulfur cycling.