动态调控策略在代谢工程中的应用研究进展
Application of dynamic regulation strategies in metabolic engineering
- 合成生物学 2020年1卷第4期 页码：440-453
- 作者机构：
北京化工大学化工资源有效利用国家重点实验室，北京 100029
- 作者简介：
[ "于政（1998—），男，硕士研究生。研究方向为代谢工程及合成生物学。E-mail：2016018277@mail.buct.edu.cn" ]
[ "王佳（1989—），女，博士，副教授。研究方向为代谢工程及合成生物学。E-mail：wangjia@mail.buct.edu.cn" ]
[ "袁其朋（1969—），男，博士生导师，教授。研究方向为生物化工。E-mail：yuanqp@mail.buct.edu.cn" ]
- 基金信息：国家自然科学基金(21908003);国家重点研发计划(2018YFA0903000)
DOI：10.12211/2096-8280.2020-029
中图分类号： Q812收稿：2020-03-19，
修回：2020-04-29，
纸质出版：2020-08-31
- 稿件说明：
移动端阅览
于政, 申晓林, 孙新晓, 王佳, 袁其朋. 动态调控策略在代谢工程中的应用研究进展[J]. 合成生物学, 2020, 1(4): 440-453
Yu Zheng, SHEN Xiaolin, Sun Xinxiao, Wang Jia, Yuan Qipeng. Application of dynamic regulation strategies in metabolic engineering[J]. Synthetic Biology Journal, 2020, 1(4): 440-453
于政, 申晓林, 孙新晓, 王佳, 袁其朋. 动态调控策略在代谢工程中的应用研究进展[J]. 合成生物学, 2020, 1(4): 440-453 DOI： 10.12211/2096-8280.2020-029.
Yu Zheng, SHEN Xiaolin, Sun Xinxiao, Wang Jia, Yuan Qipeng. Application of dynamic regulation strategies in metabolic engineering[J]. Synthetic Biology Journal, 2020, 1(4): 440-453 DOI： 10.12211/2096-8280.2020-029.
摘要
微生物细胞工厂作为一种可持续的生化反应器，被广泛应用于天然产物、药品、营养保健品等高附加值产物的生产中。为了使细胞工厂在生产过程中以最大的产量、产率和生产能力生产目标化合物，往往需要利用代谢工程方法对细胞工厂进行合理的改造和调控。以基因敲除和过表达为主要策略的静态调控不可避免地带来了细胞代谢流与能量流失衡、生长阻滞和毒性中间体积累等问题，限制了细胞工厂的生产能力、碳收率和产物产量。为了解决这一问题，构建调控元件并设计基因线路以精确调节物质流及能量流的动态调控策略被普遍应用于代谢工程领域，成为调控微生物细胞工厂的常用方法之一。本文依据不同动态调控策略的特点，将动态调控策略分为代谢物响应、群体感应响应、环境响应和蛋白质水平调控四种类型，重点介绍了各种调控元件的构建方法及其在代谢工程中的应用，分析了不同调控策略在工业化应用中面临的挑战。同时，指出了高通量筛选和蛋白质工程方法、计算机模拟和数学模型分析、耦合基因控制元件等方面的策略在解决动态调控工具响应阈值窄、调控范围有限等问题中的应用潜力。
Abstract
As a sustainable biochemical reactor
microbial cell factories are widely used in the production of value-added compounds such as natural products
pharmaceuticals and nutraceuticals. In order to make microbial cell factories produce target compounds with high titer
productivity and yield
metabolic engineering strategies are employed to rationally modify and regulate their metabolism. However
knockout and overexpression of genes inevitably bring stresses such as redox imbalance and toxic intermediate accumulation. While dynamic control strategy has been proven as a promising tool to address these challenges by balancing carbon flux and energy generation and dissipation for cell growth and generation of target compounds. As a result
many dynamic regulation elements and gene circuits have been developed and widely used in metabolic engineering so far. In this review
we summarize four types of attractive dynamic regulation systems based on metabolite-response
quorum sensing-response
environmental parameter-response and protein level regulation
with a focus on the construction method of various regulatory elements and their applications in metabolic engineering. In addition
challenges faced by different dynamic control strategies in industrial applications are analyzed. At the same time
we prospect the application potentials of some strategies such as high-throughput screening
protein engineering
computer simulation and mathematical model analysis coupled with gene control elements in solving the problems of narrow response threshold and limited control range of dynamic regulation tools. With the further development of synthetic biology and metabolic engineering
we believe that dynamic control strategy will be widely used for the construction of microbial cell factories in the near future.
2
关键词
Keywords
references
SUN X , SHEN X , JAIN R , et al . Synthesis of chemicals by metabolic engineering of microbes [J ] . Chemical Society Reviews , 2015 , 44 ( 11 ): 3760 - 3785 .
SHEN X , WANG J , WANG J , et al . High-level de novo biosynthesis of arbutin in engineered Escherichia coli [J ] . Metabolic Engineering , 2017 , 42 : 52 - 58 .
WANG J , SHEN X , YUAN Q , et al . Microbial synthesis of pyrogallol using genetically engineered Escherichia coli [J ] . Metabolic Engineering , 2018 , 45 : 134 - 141 .
ATSUMI S , HANAI T , LIAO J C . Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels [J ] . Nature , 2008 , 451 ( 7174 ): 86 - 89 .
CHEN X , GAO C , GUO L , et al . DCEO biotechnology: tools to design, construct, evaluate, and optimize the metabolic pathway for biosynthesis of chemicals [J ] . Chemical Reviews , 2018 , 118 ( 1 ): 4 - 72 .
SHEN X , WANG J , LI C , et al . Dynamic gene expression engineering as a tool in pathway engineering [J ] . Current Opinion in Biotechnology , 2019 , 59 : 122 - 129 .
TAN S Z , PRATHER K L . Dynamic pathway regulation: recent advances and methods of construction [J ] . Current Opinion in Chemical Biology , 2017 , 41 : 28 - 35 .
XU P , GU Q , WANG W , et al . Modular optimization of multi-gene pathways for fatty acids production in E. coli [J ] . Nature Communications , 2013 , 4 : 1409 .
FARMER W R , LIAO J C . Improving lycopene production in Escherichia coli by engineering metabolic control [J ] . Nature Biotechnology , 2000 , 18 ( 5 ): 533 - 537 .
DOONG S J , GUPTA A , PRATHER K L J . Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2018 , 115 ( 12 ): 2964 - 2969 .
WU J , LIU Y , ZHAO S , et al . Application of dynamic regulation to increase L-phenylalanine production in Escherichia coli [J ] . Journal of Microbiology and Biotechnology , 2019 , 29 ( 6 ): 923 - 932 .
SPITZ F , FURLONG E E . Transcription factors: from enhancer binding to developmental control [J ] . Nature Reviews Genetics , 2012 , 13 ( 9 ): 613 - 626 .
ZHANG F , KEASLING J . Biosensors and their applications in microbial metabolic engineering [J ] . Trends in Microbiology , 2011 , 19 ( 7 ): 323 - 329 .
XU P . Production of chemicals using dynamic control of metabolic fluxes [J ] . Current Opinion in Biotechnology , 2018 , 53 : 12 - 19 .
WU J , YU O , DU G , et al . Fine-tuning of the fatty acid pathway by synthetic antisense RNA for enhanced (2 S )-naringenin production from L-tyrosine in Escherichia coli [J ] . Applied and Environmental Microbiology , 2014 , 80 ( 23 ): 7283 - 7292 .
CHEN Z , HUANG J , WU Y , et al . Metabolic engineering of Corynebacterium glutamicum for the production of 3-hydroxypropionic acid from glucose and xylose [J ] . Metabolic Engineering , 2017 , 39 : 151 - 158 .
SHEN X , MAHAJANI M , WANG J , et al . Elevating 4-hydroxycoumarin production through alleviating thioesterase-mediated salicoyl-CoA degradation [J ] . Metabolic Engineering , 2017 , 42 : 59 - 65 .
XU P , LI L , ZHANG F , et al . Improving fatty acids production by engineering dynamic pathway regulation and metabolic control [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2014 , 111 ( 31 ): 11299 - 11304 .
LIU D , XIAO Y , EVANS B S , et al . Negative feedback regulation of fatty acid production based on a malonyl-CoA sensor-actuator [J ] . ACS Synthetic Biology , 2015 , 4 ( 2 ): 132 - 140 .
HANKO E K R , MINTON N P , MALYS N . A transcription factor-based biosensor for detection of itaconic acid [J ] . ACS Synthetic Biology , 2018 , 7 ( 5 ): 1436 - 1446 .
KOCH M , PANDI A , BORKOWSKI O , et al . Custom-made transcriptional biosensors for metabolic engineering [J ] . Current Opinion in Biotechnology , 2019 , 59 : 78 - 84 .
LIANG C , ZHANG X , WU J , et al . Dynamic control of toxic natural product biosynthesis by an artificial regulatory circuit [J ] . Metabolic Engineering , 2020 , 57 : 239 - 246 .
DABIRIAN Y , LI X , CHEN Y , et al . Expanding the dynamic range of a transcription factor-based biosensor in Saccharomyces cerevisiae [J ] . ACS Synthetic Biology , 2019 , 8 ( 9 ): 1968 - 1975 .
CHEN Y , HO J M L , SHIS D L , et al . Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors [J ] . Nature Communications , 2018 , 9 ( 1 ): 64 .
MANNAN A A , LIU D , ZHANG F , et al . Fundamental design principles for transcription-factor-based metabolite biosensors [J ] . ACS Synthetic Biology , 2017 , 6 ( 10 ): 1851 - 1859 .
TIAN J , YANG G , GU Y , et al . Developing an endogenous quorum-sensing based CRISPRi circuit for autonomous and tunable dynamic regulation of multiple targets in industrial Streptomyces [J ] . Nucleic Acids Research , 2020 . DOI: 10.1093/nar/gkaa602 http://dx.doi.org/10.1093/nar/gkaa602 .
CHO S , SHIN J , CHO B K . Applications of CRISPR/Cas system to bacterial metabolic engineering [J ] . International Journal of Molecular Sciences , 2018 , 19 ( 4 ): 1089 .
WU Y , CHEN T , LIU Y , et al . Design of a programmable biosensor-CRISPRi genetic circuits for dynamic and autonomous dual-control of metabolic flux in Bacillus subtilis [J ] . Nucleic Acids Research , 2020 , 48 ( 2 ): 996 - 1009 .
YANG Y , LIN Y , WANG J , et al . Sensor-regulator and RNAi based bifunctional dynamic control network for engineered microbial synthesis [J ] . Nature Communications , 2018 , 9 ( 1 ): 3043 .
GALIZI R , JARAMILLO A . Engineering CRISPR guide RNA riboswitches for in vivo applications [J ] . Current Opinion in Biotechnology , 2019 , 55 : 103 - 113 .
LIU D , EVANS T , ZHANG F . Applications and advances of metabolite biosensors for metabolic engineering [J ] . Metabolic Engineering , 2015 , 31 : 35 - 43 .
JANG S , JANG S , XIU Y , et al . Development of artificial riboswitches for monitoring of naringenin in vivo [J ] . ACS Synthetic Biology , 2017 , 6 ( 11 ): 2077 - 2085 .
BREAKER R R . Riboswitches and translation control [J ] . Cold Spring Harbor Perspectives in Biology , 2018 , 10 ( 11 ): a032797 .
LOTZ T S , SUESS B . Small-molecule-binding riboswitches [J ] . Microbiology Spectrum , 2018 , 6 ( 4 ): 75 - 88 .
WACHSMUTH M , FINDEISS S , WEISSHEIMER N , et al . De novo design of a synthetic riboswitch that regulates transcription termination [J ] . Nucleic Acids Research , 2013 , 41 ( 4 ): 2541 - 2551 .
MASUDA S , LZAWA S . Applied RNA bioscience [M ] . Singapore : Springer , 2018 : 33 - 46 .
ZHOU L B , ZENG A P . Exploring lysine riboswitch for metabolic flux control and improvement of L-lysine synthesis in Corynebacterium glutamicum [J ] . ACS Synthetic Biology , 2015 , 4 ( 6 ): 729 - 734 .
ZHOU L , REN J , LI Z , et al . Characterization and engineering of a Clostridium glycine riboswitch and its use to control a novel metabolic pathway for 5-aminolevulinic acid production in Escherichia coli [J ] . ACS Synthetic Biology , 2019 , 8 ( 10 ): 2327 - 2335 .
PANG Q , HAN H , LIU X , et al . In vivo evolutionary engineering of riboswitch with high-threshold for N -acetylneuraminic acid production [J ] . Metabolic Engineering , 2020 , 59 : 36 - 43 .
HAN L , HAN D , LI L , et al . Discovery and identification of medium‐chain fatty acid responsive promoters in Saccharomyces cerevisiae [J ] . Engineering in Life Sciences , 2020 , 5 : 186 - 196 .
MAURY J , KANNAN S , JENSEN N B , et al . Glucose-dependent promoters for dynamic regulation of metabolic pathways [J ] . Frontiers in Bioengineering and Biotechnology , 2018 , 6 : 63 .
ABISADO R G , BENOMAR S , KLAUS J R , et al . Bacterial quorum sensing and microbial community interactions [J ] . mBio , 2018 , 9 ( 3 ): e02331-17 .
DANG H T , KOMATSU S , MASUDA H , et al . Characterization of LuxI and LuxR protein homologs of N -Acylhomoserine lactone-dependent quorum sensing system in Pseudoalteromonas sp. 520P1 [J ] . Marine Biotechnology , 2017 , 19 ( 1 ): 1 - 10 .
WHITELEY M , DIGGLE S P , GREENBERG E P . Progress in and promise of bacterial quorum sensing research [J ] . Nature , 2017 , 551 ( 7680 ): 313 - 320 .
KIM E M , WOO H M , TIAN T , et al . Autonomous control of metabolic state by a quorum sensing (QS)-mediated regulator for bisabolene production in engineered E. coli [J ] . Metabolic Engineering , 2017 , 44 : 325 - 336 .
BAO S H , LI W Y , LIU C J , et al . Quorum-sensing based small RNA regulation for dynamic and tuneable gene expression [J ] . Biotechnology Letters , 2019 , 41 ( 10 ): 1147 - 1154 .
KIMATU J N . Advances in plant pathology [M ] . London : IntechOpen , 2018 : 68 - 89 .
PAPENFORT K , BASSLER B L . Quorum sensing signal-response systems in Gram-negative bacteria [J ] . Nature Reviews Microbiology , 2016 , 14 ( 9 ): 576 - 588 .
SHEN Y P , FONG L S , YAN Z B , et al . Combining directed evolution of pathway enzymes and dynamic pathway regulation using a quorum-sensing circuit to improve the production of 4-hydroxyphenylacetic acid in Escherichia coli [J ] . Biotechnology for Biofuels , 2019 , 12 : 94 .
GU F , JIANG W , MU Y , et al . Quorum sensing-based dual-function switch and its application in solving two key metabolic engineering problems [J ] . ACS Synthetic Biology , 2020 , 9 ( 2 ): 209 - 217 .
GUPTA A , REIZMAN I M , REISCH C R , et al . Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit [J ] . Nature Biotechnology , 2017 , 35 ( 3 ): 273 - 279 .
DOONG S J , GUPTA A , PRATHER K L J . Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2018 , 115 ( 12 ): 2964 - 2969 .
DINH C V , PRATHER K L J . Development of an autonomous and bifunctional quorum-sensing circuit for metabolic flux control in engineered Escherichia coli [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2019 , 116 ( 51 ): 25562 - 25568 .
ZENG W , DU P , LOU Q , et al . Rational design of an ultrasensitive quorum-sensing switch [J ] . ACS Synthetic Biology , 2017 , 6 ( 8 ): 1445 - 1452 .
DAER R , BARRETT C M , MELENDEZ E L , et al . Characterization of diverse homoserine lactone synthases in Escherichia coli [J ] . Plos One , 2018 , 13 ( 8 ): e0202294 .
TEKEL S J , SMITH C L , LOPEZ B , et al . Engineered orthogonal quorum sensing systems for synthetic gene regulation in Escherichia coli [J ] . Frontiers in Bioengineering and Biotechnology , 2019 , 7 : 80 .
SCOTT S R , HASTY J . Quorum sensing communication modules for microbial consortia [J ] . ACS Synthetic Biology , 2016 , 5 ( 9 ): 969 - 977 .
HARDER B J , BETTENBROCK K , KLAMT S . Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli [J ] . Biotechnology and Bioengineering , 2018 , 115 ( 1 ): 156 - 164 .
ZHOU P , XIE W , YAO Z , et al . Development of a temperature-responsive yeast cell factory using engineered Gal4 as a protein switch [J ] . Biotechnology and Bioengineering , 2018 , 115 ( 5 ): 1321 - 1330 .
HWANG H J , KIM J W , JU S Y , et al . Application of an oxygen-inducible nar promoter system in metabolic engineering for production of biochemicals in Escherichia coli [J ] . Biotechnology and Bioengineering , 2017 , 114 ( 2 ): 468 - 473 .
YIN X , SHIN H D , LI J , et al . Pgas, a low-pH-induced promoter, as a tool for dynamic control of gene expression for metabolic engineering of Aspergillus niger [J ] . Applied and Environmental Microbiology , 2017 , 83 ( 6 ): e03222-16 .
BANARES A B , VALDEHUESA K N G , RAMOS K R M , et al . A pH-responsive genetic sensor for the dynamic regulation of D-xylonic acid accumulation in Escherichia coli [J ] . Applied Microbiology and Biotechnology , 2020 , 104 ( 5 ): 2097 - 2108 .
LIU Z , ZHANG J , JIN J , et al . Programming bacteria with light-sensors and applications in synthetic biology [J ] . Frontiers in Microbiology , 2018 , 9 : 2692 .
TANDAR S T , SENOO S , TOYA Y , et al . Optogenetic switch for controlling the central metabolic flux of Escherichia coli [J ] . Metabolic Engineering , 2019 , 55 : 68 - 75 .
RAMAKRISHNAN P , TABOR J J . Repurposing Synechocystis PCC6803 UirS-UirR as a UV-violet/Green p hotoreversible transcriptional regulatory tool in E. coli [J ] . ACS Synthetic Biology , 2016 , 5 ( 7 ): 733 - 740 .
BAUMSCHLAGER A , AOKI S K , KHAMMASH M . Dynamic blue light-inducible T7 RNA polymerases (Opto-T7RNAPs) for precise spatiotemporal gene expression control [J ] . ACS Synthetic Biology , 2017 , 6 ( 11 ): 2157 - 2167 .
ZHAO E M , ZHANG Y , MEHL J , et al . Optogenetic regulation of engineered cellular metabolism for microbial chemical production [J ] . Nature , 2018 , 555 ( 7698 ): 683 - 687 .
SHEETS M B , WONG W W , DUNLOP M J . Light-inducible recombinases for bacterial optogenetics [J ] . ACS Synthetic Biology , 2020 , 9 ( 2 ): 227 - 235 .
BOTHFELD W , KAPOV G , TYO K E J . A glucose-sensing toggle switch for autonomous, high productivity genetic control [J ] . ACS Synthetic Biology , 2017 , 6 ( 7 ): 1296 - 1304 .
DAVID F , NIELSEN J , SIEWERS V . Flux control at the malonyl-CoA node through hierarchical dynamic pathway regulation in Saccharomyces cerevisiae [J ] . ACS Synthetic Biology , 2016 , 5 ( 3 ): 224 - 233 .
MOTLAGH H N , WRABL J O , LI J , et al . The ensemble nature of allostery [J ] . Nature , 2014 , 508 ( 7496 ): 331 - 339 .
DOKHOLYAN N V . Controlling allosteric networks in proteins [J ] . Chemical Reviews , 2016 , 116 ( 11 ): 6463 - 6487 .
CHEN Z , RAPPERT S , ZENG A P . Rational design of allosteric regulation of homoserine dehydrogenase by a nonnatural inhibitor L-lysine [J ] . ACS Synthetic Biology , 2015 , 4 ( 2 ): 126 - 131 .
GAO C , HOU J , XU P , et al . Programmable biomolecular switches for rewiring flux in Escherichia coli [J ] . Nature Communications , 2019 , 10 ( 1 ): 3751 .
BROCKMAN I M , PRATHER K L J . Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites [J ] . Metabolic Engineering , 2015 , 28 : 104 - 113 .
HE F , STUMPF M P H . Quantifying dynamic regulation in metabolic pathways with nonparametric flux inference [J ] . Biophysical Journal , 2019 , 116 ( 10 ): 2035 - 2046 .
JABARIVELISDEH B , WALDHERR S . Optimization of bioprocess productivity based on metabolic-genetic network models with bilevel dynamic programming [J ] . Biotechnology and Bioengineering , 2018 , 115 ( 7 ): 1829 - 1841 .
0
浏览量
1
下载量
0
CSCD
- 网络PDF下载
- WORD下载
- Meta-XML下载
- BibTeX下载
- Endnote下载
- RefMan 下载
- NoteExpress下载
- NoteFirst下载
关联资源
相关文章
相关作者
相关机构
- 地址：北京市东城区青年湖南街13号 邮编：100000
- 联系电话：010-64519339
- 技术支持由北京北大方正电子有限公司提供 京ICP备09064830号-19
京公网安备11010802024621 - 本系统建议在Chrome、 IE9+ 以上版本浏览器阅读本站内容，360浏览器请切换至极速模式
- Cookies帮助我们提供服务并提供个性化体验。使用本网站，即表示您同意我们使用Cookies