紫黑链霉菌进化枝菌株Streptomyces solisilvae HNM0141^(T)的全基因组分析

Analysis of Complete Genome Sequence of Streptomyces solisilvae HNM0141^(T) of the Streptomyces violaceusniger Clade

链霉菌属放线菌是最重要的抗生素产生菌,也是包含放线菌种类最多的放线菌属。链霉菌属的有效发表种的模式菌株在16S rRNA基因序列系统发育树上分散归簇于不同的进化分枝。紫黑链霉菌16S rRNA基因进化枝(Streptomyces violaceusniger 16S rRNA gene clade)是其中的一个分枝。该分枝菌株在燕麦培养基上基内菌丝淡黄色,气生菌丝发育成灰色,表面皱纹的螺旋状孢子丝,培养后期呈黑色。该分枝中的菌株普遍具有丰富的生物活性,能产生抗菌、抗寄生虫、抗肿瘤、免疫抑制等多种活性物质,是新型抗生素开发与利用的重要菌源。Streptomyces solisilvae HNM0141^(T)是紫黑链霉菌16S rRNA基因进化枝放线菌的模式菌株。采用第三代全基因组测序技术,首次获得了菌株S.solisilvae HNM0141^(T)的基因组完成图,其线状基因组长度11639536 bp,GC含量为71.03%,包含9363个蛋白编码基因(CDS),18个rRNA基因和67个tRNA基因。其中有6376、5886、3246个CDS分别在COG、GO和KEGG数据库中得到功能注释。除了一般功能预测之外,有大部分基因参与转录、氨基酸转运和代谢、碳水化合物转运和代谢以及次级代谢生物合成和代谢,基因数占比分别为12.91%、10.25%、8.89%、7.59%。利用antiSMASH软件,预测到48个次级代谢产物合成基因簇,其类型包括8个聚酮(PKS)型、7个非核糖体肽(NRPS)型、14个杂合型、6个terpene、3个siderophore、2个butyrolactone,其余NAPAA、ectoine、lanthipeptide-class-i、ladderane、indole、RiPP-like、hserlactone、redox-cofactor各1个。其中聚酮类(PKS)和非核糖体肽(NRPS)类(包括杂合类型)的基因簇含量丰富,占总基因簇的50%以上。7个基因簇与已知代谢物(pristinol、ectoine、geosmin、desferrioxamin B、echoside A/B/C/D/E、nigericin、coelichelin)基因簇的相似性为100%,34个基因簇的相似性在2%~96%之间,剩余的7个基因簇无法匹配到已知基因簇。全基因组分析表明菌株S.solisilvae HNM0141T具有强大次级代谢产物合成的能力,预示该菌株在新颖抗生素的挖掘上具有良好的研究潜力。

Actinomycetes belonging to Streptomyces are the most important antibiotic producing bacteria and also the actinomycete genus with the largest number of species.Many streptomycete type strains can be assigned to distinct evolutionary clades on the 16S rRNA gene phylogenetic tree,and the S.violaceusniger 16S rRNA gene clade is one of them.Members of the clade form a greyish yellow substrate mycelium and a grayish aerial hyphae on oatmeal agar that develop into spiral chains of rugose ornamented spores that become black on prolonged incubation.Members of the S.violaceusniger 16S rRNA gene clade have abundant biological activities and produce antibacterial metabolites,anti-parasitic metabolites,antitumour compounds and immunosuppressants as important sources for the development and utilization of new antibiotics.S.solisilvae HNM0141^(T) is a type strain assigned to the S.violaceusniger 16S rRNA gene clade.Here,we present the complete genome sequence of it,which is generated using the third sequencing technology and consists of a linear chromosome of 11639536 bp with a GC content of 71.3%,9363 protein coding genes(CDS),18 rRNA genes,and 67 tRNA genes.The identified CDS were classified into 6376,5886,and 3246 categories based on clusters of orthologous genes of proteins(COG),gene ontology(GO),and Kyoto Encyclopedia of Genes and Genomes(KEGG)designation,respectively.In addition to the general function prediction only,most of the genes involved in transcription,amino acid transport and metabolism,carbohydrate transport and metabolism and secondary metabolic biosynthesis and metabolism were accounted for 12.91%,10.25%,8.89%and 7.59%respectively.Forty-eight putative secondary metabolite biosynthetic gene clusters were found in the genome using the online antiSMASH software,in-cluding eight PKS,seven NRPS,fourteen hybrid gene clusters,six terpenes,three siderophores,two butyrolactones,one NAPAA,one ectoine,one lanthipeptide-class-i,one ladderane,one indole,one RiPP-like,one hserlactone and one re-dox-cofactor.Polyketone(PKS)and non-ribosomal peptide(NRPS)gene clusters(including heterozygous types)were abundant and accounted for more than 50%of the total gene clusters.Seven putative gene clusters showed 100%simi-larities to known gene clusters:pristinol,ectoine,geosmin,desferrioxamin B,echoside A/B/C/D/E,nigericin,and coelichelin gene clusters.Thirty-four putative gene clusters showed 2%–96%similarities to known gene clusters.The remaining seven gene clusters could not be matched to known gene clusters.Genome-wide analysis showed that S.solisilvae HNM0141^(T) had strong ability of the biosynthesis of secondary metabolites,indicated that it should be good research potential for mining of the novel antibiotics.