微生物,高智商,大产业——合成生物学助力阿维菌素的高效智能制造
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摘要
合成生物学研究具有两种属性,即生命本质的认识提升属性与生物制造属性。以阿维菌素产生的生命过程复杂性为例,几乎可用"高智商"来形容。通过系统认知微生物的"智商",从"格物致知"到"建物致用",实现师法自然,让微生物更高效地为人类服务。在人工工业大规模制造时,上述生命本质的认识无疑是有帮助的,但在微生物与生物反应器组成的复杂系统中,如何从基因到代谢的细胞生理状态到胞外的环境影响中,由"格物致知"的因果关系找到可人工操作的生物智能制造(智造),这又是极其困难的科学问题,这就是合成生物学的生物制造属性。因此,必须开展生物过程大数据分析,克服基因、代谢、过程到生产组织中产生的大量互不联系的数据孤岛。近年来,合成生物学的蓬勃发展掀起的技术革命已经彻底颠覆了人们过去对于生物和生物技术的认识。该文以阿维菌素的研究为例,讨论在合成生物学时代如何利用微生物的"智商"来加速实现微生物药物高效智能制造的研发过程,并为其他微生物天然产物药物的智能化生产提供可借鉴的思路和方法。
There are two important properties in synthetic biology, which are understanding the nature of life and the corresponding biological manufacturing. Here we choose the bio-production of avermectin as a case because its production involves the complexity of life process with the "high intelligence quotient(IQ)" of microorganisms. By understanding this IQ, we could evolve the "building to understand" to "building to apply" and finally better serve human beings. Although understanding the nature of life is helpful to the large-scale manufacturing industry, the complex system is involved in the microorganisms and bioreactor such as the relationship, the interaction between intracellular environment(gene regulation, metabolic regulation and physiological state of the cell, etc.) and extracellular environment. It is very complicate. So far, these data were not linked to each other. How to reveal such kind of black-boxes to realize the intelligent bio-manufacture process for manual manipulation is an extremely difficult scientific problem. Therefore, it is necessary for us to investigate the complete bioprocess steps by the big data analysis which integrates all kinds of massive data produced by cells(such as gene transcription, metabolic profiling, etc.), fermentation process(parameters such as OUR, CER, RQ etc.), and even comprehensive system management. In recent years, the technological advancement initiated by synthetic biology has completely revolutionized our understanding of biotechnology. Therefore, this article will take the latest research progress of avermectin as an example, focusing on how to use the "high intelligence quotient" of microorganisms to speed up the development of microbial drug efficient manufacturing process in the age of synthetic biology.
There are two important properties in synthetic biology, which are understanding the nature of life and the corresponding biological manufacturing. Here we choose the bio-production of avermectin as a case because its production involves the complexity of life process with the "high intelligence quotient(IQ)" of microorganisms. By understanding this IQ, we could evolve the "building to understand" to "building to apply" and finally better serve human beings. Although understanding the nature of life is helpful to the large-scale manufacturing industry, the complex system is involved in the microorganisms and bioreactor such as the relationship, the interaction between intracellular environment(gene regulation, metabolic regulation and physiological state of the cell, etc.) and extracellular environment. It is very complicate. So far, these data were not linked to each other. How to reveal such kind of black-boxes to realize the intelligent bio-manufacture process for manual manipulation is an extremely difficult scientific problem. Therefore, it is necessary for us to investigate the complete bioprocess steps by the big data analysis which integrates all kinds of massive data produced by cells(such as gene transcription, metabolic profiling, etc.), fermentation process(parameters such as OUR, CER, RQ etc.), and even comprehensive system management. In recent years, the technological advancement initiated by synthetic biology has completely revolutionized our understanding of biotechnology. Therefore, this article will take the latest research progress of avermectin as an example, focusing on how to use the "high intelligence quotient" of microorganisms to speed up the development of microbial drug efficient manufacturing process in the age of synthetic biology.
引文
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[29]Zhang S,Chu J,Zhuang Y.A multi-scale study of industrial fermentation processes and their optimization.Adv Biochem Eng Biotechnol,2004,87:97-150
[30]Lara AR,Galindo E,Ramirez OT,et al.Living with heterogeneities in bioreactors.Mol Biotechnol,2006,34:355-81
[31]Xia JY,Wang YH,Zhang SL,et al.Fluid dynamics investigation of variant impeller combinations by simulation and fermentation experiment.Biochem Eng J,2008,43:252-60
[32]Yugi K,Kubota H,Hatano A,et al.Trans-Omics:how to reconstruct biochemical networks across multiple'Omic layers.Trends Biotechnol,2016,34:276-90
[33]文莹,张立新.阿维菌素的中国“智”造.遗传学报,2018,40:888-9
[34]Zhuo Y,Zhang W,Chen D,et al.Reverse biological engineering of hrd B to enhance the production of avermectins in an industrial strain of Streptomyces avermitilis.Proc Natl Acad Sci USA,2010,107:11250-4
[35]Zhuo Y,Zhang T,Wang Q,et al.Synthetic biology of avermectin for production improvement and structure diversification.Biotechnol J,2014,9:316-25
[36]Wang F,Wang Y,Ji J,et al.Structural and functional analysis of the loading acyltransferase from avermectin modular polyketide synthase.ACS Chem Biol,2015,10:1017-25
[37]Naimi AI,Westreich DJ.Big Data:a revolution that will transform how we live,work,and think.Am J Epidemiol,2014,179:1143-4
[38]Dong XL,Gabrilovich E,Heitz G,et al.From data fusion to knowledge fusion.Proceedings VLDB Endowment,2014,7:881-92
[39]Shimizu K,Ye K.Development of intelligent control systems for bioreactors.IFAC Proceedings Volumes,1995,28:89-94
[40]Liu M,Huang P,Wang Q,et al.Synergistic antifungal indolecarbazoles from Streptomyces sp.CNS-42 associated with traditional Chinese medicine Alisma orientale.JAntibiot,2017,70:715-7
[41]Chen J,Liu M,Liu X,et al.Interrogation of Streptomyces avermitilis for efficient production of avermectins.Synth Syst Biotechnol,2016,1:7-16
[42]Qiu J,Zhuo Y,Zhu D,et al.Overexpression of the ABCtransporter AvtAB increases avermectin production in Streptomyces avermitilis.Appl Microbiol Biotechnol,2011,92:337-45
[43]Gao Q,Tan GY,Xia X,et al.Learn from microbial intelligence for avermectins overproduction.Curr Opin Biotechnol,2017,48:251-7
[44]沈寅初.阿维菌素的发展史——在“2009阿维菌素类360°产业论坛”上的讲话.世界农药,2009,31:1
[45]陈芝,宋渊,文莹,等.阿维菌素的生物合成研究进展与展望.自然科学进展,2007,17:290-6
[46]Guo H,Ren B,Dai H,et al.Reversal of meticillin resistance in Staphylococcus aureus by the anthelmintic avermectin.Int J Antimicrob Agents,2014,44:274-6
[47]Chen J,Miao J,Liu M,et al.Different fates of avermectin and artemisinin in China.Sci China Life Sci,2016,59:634-6
[48]陈金松,刘梅,张立新.从阿维菌素获得诺贝尔奖到中国创造.微生物学报,2016,56:543-58
[49]胡栋,柯灵超,张敬宇,等.响应面法设计优化阿维菌素化学合成发酵培养基.中国抗生素杂志,2018,43:1055-61
[50]陈金松,苗靳,刘梅,等.2015年诺贝尔奖分子阿维菌素与青蒿素不同在哪里?中国科学:生命科学,2016,46:346-8
[2]Shen Y,Wang Y,Chen T,et al.Deep functional analysis of synII,a 770-kilobase synthetic yeast chromosome.Science,2017,355:eaaf4791
[3]李诗渊,赵国屏,王金.合成生物学技术的研究进展——DNA合成、组装与基因组编辑.生物工程学报,2017,33:343-60
[4]Cello J,Paul AV,Wimmer E.Chemical synthesis of poliovirus cDNA:generation of infectious virus in the absence of natural template.Science,2002,297:1016-8
[5]Gibson DG,Glass JI,Lartigue C,et al.Creation of a bacterial cell controlled by a chemically synthesized genome.Science,2010,329:52-6
[6]Gibson DG,Benders GA,Andrews-Pfannkoch C,et al.Complete chemical synthesis,assembly,and cloning of a Mycoplasma genitalium genome.Science,2008,319:1215-20
[7]Gibson DG,Smith HO,Hutchison CA 3rd,et al.Chemical synthesis of the mouse mitochondrial genome.Nat Methods,2010,7:901-3
[8]Martin VJJ,Pitera DJ,Withers ST,et al.Engineering a mevalonate pathway in Escherichia coli for production of terpenoids.Nat Biotechnol,2003,21:796-802
[9]Ro DK,Paradise EM,Ouellet M,et al.Production of the antimalarial drug precursor artemisinic acid in engineered yeast.Nature,2006,440:940-3
[10]Wu Y,Li BZ,Zhao M,et al.Bug mapping and fitness testing of chemically synthesized chromosome X.Science,2017,355:eaaf4706
[11]Xie ZX,Li BZ,Mitchell LA,et al.“Perfect”designer chromosome V and behavior of a ring derivative.Science,2017,355:eaaf4704
[12]Zhang W,Zhao G,Luo Z,et al.Engineering the ribosomal DNA in a megabase synthetic chromosome.Science,2017,355:eaaf3981
[13]Khalil AS,Collins JJ.Synthetic biology:applications come of age.Nat Rev Genet,2010,11:367-79
[14]章竞思,李梦霞.当代智力测验研究的现状与发展趋势.科技情报开发与经济,2002,12:93-4
[15]Wang W,Li S,Li Z,et al.Harnessing cellular triacylglycerol pool for titer improvement of polyketides in Streptomyces.(待发表)
[16]Tan GY,Bai LQ,Zhong JJ.Exogenous 1,4-butyrolactone stimulates a-factor-like cascade and validamycin biosynthesis in Streptomyces hygroscopicus 5008.Biotechnol Bioeng,2013,110:2984-93
[17]Siegl T,Tokovenko B,Myronovskyi M,et al.Design,construction and characterisation of a synthetic promoter library for fine-tuned gene expression in actinomycetes.Metab Eng,2013,19:98-106
[18]Wang W,Li X,Wang J,et al.An engineered strong promoter for Streptomycetes.Appl Environ Microbiol,2013,79:4484-92
[19]Bai C,Zhang Y,Zhao X,et al.Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in Streptomyces.Proc Natl Acad Sci USA,2015,112:12181-6
[20]Li S,Zhou L,Yao Y,et al.A platform for the development of novel biosensors by configuring allosteric transcription factor recognition with amplified luminescent proximity homogeneous assays.Chem Commun,2017,53:99-102
[21]Cao J,Yao Y,Fan K,et al.Harnessing bacterial allosteric transcription factors for biosensing diverse small molecules via mature DNA detection methods.Science Adv,2018,4:eaau4602
[22]Zhao Y,Wang A,Zou Y,et al.In vivo monitoring of cellular energy metabolism using SoNar,a highly responsive sensor for NAD+/NADH redox state.Nat Protoc,2016,11:1345-59
[23]Tao RK,Zhao YZ,Chu HY,et al.Genetically encoded fluorescent sensors reveal dynamic regulation of NADPHmetabolism.Nat Methods,2017,14:720-8
[24]Zhao Y,Hu Q,Cheng F,et al.SoNar,a highly responsive NAD+/NADH sensor,allows high-throughput metabolic screening of anti-tumor agents.Cell Metab,2015,21:777-89
[25]Gao H,Liu M,Liu J,et al.Medium optimization for the production of avermectin B1a by Streptomyces avermitilis14-12A using response surface methodology.Bioresour Technol,2009,100:4012-6
[26]Liu M,Gao H,Shang P,et al.Magnetic field is the dominant factor to induce the response of Streptomyces avermitilis in altered gravity simulated by diamagnetic levitation.PLoS One,2011,6:e24697
[27]张嗣良.工业生物过程优化与放大研究中的科学问题——生物过程环境组学与多尺度方法原理研究.中国基础科学,2009,11:27-31
[28]张嗣良.大数据时代的生物过程研究.生物产业技术,2016,03:34-9
[29]Zhang S,Chu J,Zhuang Y.A multi-scale study of industrial fermentation processes and their optimization.Adv Biochem Eng Biotechnol,2004,87:97-150
[30]Lara AR,Galindo E,Ramirez OT,et al.Living with heterogeneities in bioreactors.Mol Biotechnol,2006,34:355-81
[31]Xia JY,Wang YH,Zhang SL,et al.Fluid dynamics investigation of variant impeller combinations by simulation and fermentation experiment.Biochem Eng J,2008,43:252-60
[32]Yugi K,Kubota H,Hatano A,et al.Trans-Omics:how to reconstruct biochemical networks across multiple'Omic layers.Trends Biotechnol,2016,34:276-90
[33]文莹,张立新.阿维菌素的中国“智”造.遗传学报,2018,40:888-9
[34]Zhuo Y,Zhang W,Chen D,et al.Reverse biological engineering of hrd B to enhance the production of avermectins in an industrial strain of Streptomyces avermitilis.Proc Natl Acad Sci USA,2010,107:11250-4
[35]Zhuo Y,Zhang T,Wang Q,et al.Synthetic biology of avermectin for production improvement and structure diversification.Biotechnol J,2014,9:316-25
[36]Wang F,Wang Y,Ji J,et al.Structural and functional analysis of the loading acyltransferase from avermectin modular polyketide synthase.ACS Chem Biol,2015,10:1017-25
[37]Naimi AI,Westreich DJ.Big Data:a revolution that will transform how we live,work,and think.Am J Epidemiol,2014,179:1143-4
[38]Dong XL,Gabrilovich E,Heitz G,et al.From data fusion to knowledge fusion.Proceedings VLDB Endowment,2014,7:881-92
[39]Shimizu K,Ye K.Development of intelligent control systems for bioreactors.IFAC Proceedings Volumes,1995,28:89-94
[40]Liu M,Huang P,Wang Q,et al.Synergistic antifungal indolecarbazoles from Streptomyces sp.CNS-42 associated with traditional Chinese medicine Alisma orientale.JAntibiot,2017,70:715-7
[41]Chen J,Liu M,Liu X,et al.Interrogation of Streptomyces avermitilis for efficient production of avermectins.Synth Syst Biotechnol,2016,1:7-16
[42]Qiu J,Zhuo Y,Zhu D,et al.Overexpression of the ABCtransporter AvtAB increases avermectin production in Streptomyces avermitilis.Appl Microbiol Biotechnol,2011,92:337-45
[43]Gao Q,Tan GY,Xia X,et al.Learn from microbial intelligence for avermectins overproduction.Curr Opin Biotechnol,2017,48:251-7
[44]沈寅初.阿维菌素的发展史——在“2009阿维菌素类360°产业论坛”上的讲话.世界农药,2009,31:1
[45]陈芝,宋渊,文莹,等.阿维菌素的生物合成研究进展与展望.自然科学进展,2007,17:290-6
[46]Guo H,Ren B,Dai H,et al.Reversal of meticillin resistance in Staphylococcus aureus by the anthelmintic avermectin.Int J Antimicrob Agents,2014,44:274-6
[47]Chen J,Miao J,Liu M,et al.Different fates of avermectin and artemisinin in China.Sci China Life Sci,2016,59:634-6
[48]陈金松,刘梅,张立新.从阿维菌素获得诺贝尔奖到中国创造.微生物学报,2016,56:543-58
[49]胡栋,柯灵超,张敬宇,等.响应面法设计优化阿维菌素化学合成发酵培养基.中国抗生素杂志,2018,43:1055-61
[50]陈金松,苗靳,刘梅,等.2015年诺贝尔奖分子阿维菌素与青蒿素不同在哪里?中国科学:生命科学,2016,46:346-8