卡奇霉素产生菌棘孢小单胞菌ATCC 15837的全基因组测序及序列分析
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摘要
棘孢小单胞菌(Micromonospora echinospora) ATCC 15837是一种高GC含量的革兰氏阳性稀有放线菌,能够合成烯二炔类抗肿瘤抗生素卡奇霉素(calicheamicin, CLM)。目前,还没有相关研究报道棘孢小单胞菌ATCC 15837的全基因组序列,这限制了其代谢产物合成途径和比较基因组学等研究。本研究首次通过高通量测序技术对棘孢小单胞菌ATCC 15837进行全基因组测序,使用相关生物信息学软件对数据进行组装和注释等分析。使用Velvet软件进行组装拼接得到77个Contigs,GC含量为72.36%,基因组大小约为7.69 Mb。序列已提交至美国国立生物技术信息中心(NCBI)的GenBank数据库(登录号为NGNT00000000)。本研究首次报道了一株烯二炔类抗肿瘤抗生素卡奇霉素产生菌棘孢小单胞菌ATCC 15837的全基因组序列,分析了基因组基本特征,预测了该菌株的次级代谢产物生物合成基因簇,为后续的进一步代谢调控与合成生物学提供了理论基础。
Micromonospora echinospora ATCC 15837 is a high GC content rare Gram-positive actinomycetes,which can synthesize calicheamicin(CLM), an anti-tumor antibiotic of enediyne. Currently, there are no studies reporting the complete genome sequence of Micromonospora echinospora ATCC 15837, which limits the studies on metabolite biosynthesis and comparative genomics. For the first, this research used high-throughput sequencing technology to uncover the genome sequences of Micromonospora echinospora ATCC 15837, and used bioinformatics software to analyze and annotate the data. We used velvet software for assembly and splicing to get 77 contigs with a GC content of 72.36% and a genome size of approximately 7.69 Mb. The sequence had been submitted to the NCBI GenBank database(NGNT00000000). This study first reported the whole-genome sequence of a enediyne anti-tumor antibiotic calicheamicin-producing strain ATCC 15837. The basic characteristics of the genome were analyzed, and the secondary metabolite biosynthesis gene cluster of the strain was predicted. This study could provide a theoretical basis for subsequent further metabolic regulation and synthetic biology.
Micromonospora echinospora ATCC 15837 is a high GC content rare Gram-positive actinomycetes,which can synthesize calicheamicin(CLM), an anti-tumor antibiotic of enediyne. Currently, there are no studies reporting the complete genome sequence of Micromonospora echinospora ATCC 15837, which limits the studies on metabolite biosynthesis and comparative genomics. For the first, this research used high-throughput sequencing technology to uncover the genome sequences of Micromonospora echinospora ATCC 15837, and used bioinformatics software to analyze and annotate the data. We used velvet software for assembly and splicing to get 77 contigs with a GC content of 72.36% and a genome size of approximately 7.69 Mb. The sequence had been submitted to the NCBI GenBank database(NGNT00000000). This study first reported the whole-genome sequence of a enediyne anti-tumor antibiotic calicheamicin-producing strain ATCC 15837. The basic characteristics of the genome were analyzed, and the secondary metabolite biosynthesis gene cluster of the strain was predicted. This study could provide a theoretical basis for subsequent further metabolic regulation and synthetic biology.
引文
A hler t J.,Shepard E.,Lomovskaya N.,Zazopoulos E.,Staffa A.,Bachmann B.O.,Huang K.,Fonstein L.,Czisny A.,and Whitwam R.E.,2002,The calicheamicin gene cluster and its iterative typeⅠenediyne PKS,Science,297(5584):1173-1176
Annm H.,and Maria V.,2010,Micromonospora:an important microbe for biomedicine and potentially for biocontrol and biofuels,Soil Biology Biochemistry,42(4):536-542
Berdy J.,2005,Bioactive microbial metabolites:a personal view,The Journal of Antibiotics,58(1):1-26
Bredholt H.,Fjaervik E.,Johnsen G.,and Zotchev S.B.,2008,Actinomycetes from sediments in the Trondheim fjord,norway:diversity and biological activity,Marine Drugs,6(1):12
Cheng Y.R.,and Zheng W.,2006,Micromonospora spp.and their secondary bioactive metabolites,Zhongguo Kangshengsu Zazhi(Chinese Journal of Antibiotics),31(6):321-327(程元荣,郑卫,2006,小单孢菌及其产生的次级生物活性代谢产物,中国抗生素杂志,31(6):321-327)
Freel K.C.,Nam S.J.,Fenical W.,and Jensen P.R.,2011,Evolution of secondary metabolite genes in three closely related marine actinomycete species,Applied and Environmental Microbiology,77(20):7261-7270
He X.F.,Yang H.L.,Zhang Z.B.,Wang Y.,Yan R.M.,and Zhu D.,2016,Whole-genome sequencing and analysis of Micromonospora rosaria DSM 803,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(8):2055-2063(何小峰,杨慧琳,张志斌,汪涯,颜日明,朱笃,2016,小单孢菌(Micromonospora rosaria)DSM 803全基因组测序及分析,基因组学与应用生物学,35(8):2055-2063)
Jones P.,Binns D.,Chang H.Y.,Fraser M.,Li W.,Mcanulla C.,Mcwilliam H.,Maslen J.,Mitchell A.,and Nuka G.,2014,InterProScan 5:genome-scale protein function classification,Bioinformatics,30(9):1236-1240
Li Y.,Yang H.L.,Zhang Z.B.,Yan R.M.,Wang Y.,and Zhu D.,2016,Whole-genome sequencing and sequence analysis of Micromonospora rifamycinica AM105,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(4):858-866(李怡,杨慧林,张志斌,颜日明,汪涯,朱笃,2016,小单孢菌(Micromonospora rifamycinica)AM105全基因组测序及分析,基因组学与应用生物学,35(4):858-866)
Medema M.H.,Kai B.,Cimermancic P.,Jager V.D.,Zakrzewski P.,Fischbach M.A.,Weber T.,Takano E.,and Breitling R.,2011,AntiSMASH:rapid identification,annotation and analysis of sec ondary metabolite biosynthesis gene clusters in bacterial and fun gal genome sequences,Nucleic Acids Research,39:339-346
Schuster S.C.,2008,Next-generation sequencing transforms today's biology,Nature Methods,5(1):16-18
Wang X.C.,Yang Z.R.,Wang M.,Li W.,and Li S.C.,2012,High throughput sequencing technology and its application,Zhongguo Shengwu Gongcheng Zazhi(Journal of Chinese Biotechnology),32(1):109-114(王兴春,杨致荣,王敏,李玮,李生才,2012,高通量测序技术及其应用,中国生物工程杂志,32(1):109-114)
Yang H.L.,Zhang Z.B.,Yan R.M.,Wang Y.,and Zhu D.,2015,Whole-genome sequencing and analysis of an endophytic actinomycete Streptomyces sp.PRh5 from Dongxiang wild rice,Weishengwuxue Tongbao(Microbiology China),42(4):801-809(杨慧林,张志斌,颜日明,汪涯,朱笃,2015,东乡野生稻内生放线菌Streptomyces sp.PRh5的全基因组测序及序列分析,微生物学通报,42(4):801-809)
Ye J.,Fang L.,Zheng H.,Zhang Y.,Chen J.,Zhang Z.,Wang J.,Li S.,Li R.,and Bolund L.,2006,WEGO:a web tool for plotting GO annotations,Nucleic Acids Research,34(S2):293-297
Zerbino D.R.,and Birney E.,2008,Velvet:algorithms for de novo short read assembly using de Bruijn graphs,Genome Research,18(5):821-829
Zhou D.G.,Zhao Q.Y.,Fu C.Y.,Li H.,Cai X.F.,Luo D.,and Zhou X.C.,2008,The next generation sequencing and its effect on the rice molecular design breeding,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),6(4):619-630(周德贵,赵琼一,付崇允,李宏,蔡学飞,罗达,周小川,2008,新一代测序技术及其对水稻分子设计育种的影响,分子植物育种,6(4):619-630)
Annm H.,and Maria V.,2010,Micromonospora:an important microbe for biomedicine and potentially for biocontrol and biofuels,Soil Biology Biochemistry,42(4):536-542
Berdy J.,2005,Bioactive microbial metabolites:a personal view,The Journal of Antibiotics,58(1):1-26
Bredholt H.,Fjaervik E.,Johnsen G.,and Zotchev S.B.,2008,Actinomycetes from sediments in the Trondheim fjord,norway:diversity and biological activity,Marine Drugs,6(1):12
Cheng Y.R.,and Zheng W.,2006,Micromonospora spp.and their secondary bioactive metabolites,Zhongguo Kangshengsu Zazhi(Chinese Journal of Antibiotics),31(6):321-327(程元荣,郑卫,2006,小单孢菌及其产生的次级生物活性代谢产物,中国抗生素杂志,31(6):321-327)
Freel K.C.,Nam S.J.,Fenical W.,and Jensen P.R.,2011,Evolution of secondary metabolite genes in three closely related marine actinomycete species,Applied and Environmental Microbiology,77(20):7261-7270
He X.F.,Yang H.L.,Zhang Z.B.,Wang Y.,Yan R.M.,and Zhu D.,2016,Whole-genome sequencing and analysis of Micromonospora rosaria DSM 803,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(8):2055-2063(何小峰,杨慧琳,张志斌,汪涯,颜日明,朱笃,2016,小单孢菌(Micromonospora rosaria)DSM 803全基因组测序及分析,基因组学与应用生物学,35(8):2055-2063)
Jones P.,Binns D.,Chang H.Y.,Fraser M.,Li W.,Mcanulla C.,Mcwilliam H.,Maslen J.,Mitchell A.,and Nuka G.,2014,InterProScan 5:genome-scale protein function classification,Bioinformatics,30(9):1236-1240
Li Y.,Yang H.L.,Zhang Z.B.,Yan R.M.,Wang Y.,and Zhu D.,2016,Whole-genome sequencing and sequence analysis of Micromonospora rifamycinica AM105,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(4):858-866(李怡,杨慧林,张志斌,颜日明,汪涯,朱笃,2016,小单孢菌(Micromonospora rifamycinica)AM105全基因组测序及分析,基因组学与应用生物学,35(4):858-866)
Medema M.H.,Kai B.,Cimermancic P.,Jager V.D.,Zakrzewski P.,Fischbach M.A.,Weber T.,Takano E.,and Breitling R.,2011,AntiSMASH:rapid identification,annotation and analysis of sec ondary metabolite biosynthesis gene clusters in bacterial and fun gal genome sequences,Nucleic Acids Research,39:339-346
Schuster S.C.,2008,Next-generation sequencing transforms today's biology,Nature Methods,5(1):16-18
Wang X.C.,Yang Z.R.,Wang M.,Li W.,and Li S.C.,2012,High throughput sequencing technology and its application,Zhongguo Shengwu Gongcheng Zazhi(Journal of Chinese Biotechnology),32(1):109-114(王兴春,杨致荣,王敏,李玮,李生才,2012,高通量测序技术及其应用,中国生物工程杂志,32(1):109-114)
Yang H.L.,Zhang Z.B.,Yan R.M.,Wang Y.,and Zhu D.,2015,Whole-genome sequencing and analysis of an endophytic actinomycete Streptomyces sp.PRh5 from Dongxiang wild rice,Weishengwuxue Tongbao(Microbiology China),42(4):801-809(杨慧林,张志斌,颜日明,汪涯,朱笃,2015,东乡野生稻内生放线菌Streptomyces sp.PRh5的全基因组测序及序列分析,微生物学通报,42(4):801-809)
Ye J.,Fang L.,Zheng H.,Zhang Y.,Chen J.,Zhang Z.,Wang J.,Li S.,Li R.,and Bolund L.,2006,WEGO:a web tool for plotting GO annotations,Nucleic Acids Research,34(S2):293-297
Zerbino D.R.,and Birney E.,2008,Velvet:algorithms for de novo short read assembly using de Bruijn graphs,Genome Research,18(5):821-829
Zhou D.G.,Zhao Q.Y.,Fu C.Y.,Li H.,Cai X.F.,Luo D.,and Zhou X.C.,2008,The next generation sequencing and its effect on the rice molecular design breeding,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),6(4):619-630(周德贵,赵琼一,付崇允,李宏,蔡学飞,罗达,周小川,2008,新一代测序技术及其对水稻分子设计育种的影响,分子植物育种,6(4):619-630)
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