合成生物学 ›› 2020, Vol. 1 ›› Issue (4): 454-469.DOI: 10.12211/2096-8280.2020-026
田荣臻1,2, 刘延峰1,2, 李江华2, 刘龙1,2, 堵国成1,2
收稿日期:
2020-03-15
修回日期:
2020-06-21
出版日期:
2020-08-31
发布日期:
2020-10-09
通讯作者:
堵国成
作者简介:
田荣臻(1995—),男,博士研究生,研究方向为发酵工程。E-mail:基金资助:
Rongzhen TIAN1,2, Yanfeng LIU1,2, Jianghua LI2, Long LIU1,2, Guocheng DU1,2
Received:
2020-03-15
Revised:
2020-06-21
Online:
2020-08-31
Published:
2020-10-09
Contact:
Guocheng DU
摘要:
以大肠杆菌、枯草芽孢杆菌和酿酒酵母等为代表的典型模式微生物是合成生物学研究中的重要底盘细胞。典型模型微生物的新型基因表达调控工具开发与应用实现了细胞代谢途径的精确工程设计和新型遗传回路的设计,极大促进了合成生物学和代谢工程的发展。本文针对典型模式微生物基因表达精细调控工具,特别是人工基因表达调控元件和精确调控的工具进行了系统总结和讨论。首先总结了经典的基因表达调控元件,然后介绍和讨论了基于中心法则创建的新型基因表达调控元件、基于全局调控蛋白的基因表达全局调控工具,以及响应特定信号的基因表达调控工具三个方面的最新研究进展,最后展望了如何通过新型天然基因表达调控元件的发现和响应代谢压力等细胞生理特性的基因表达调控系统的开发,进一步提升基因表达精细调控的范围和精度。通过将系统生物学数据与生物信息学相结合,能够进一步促进基因表达调控元件的标准化和多元化,提升基因表达精细调控的效率。
中图分类号:
田荣臻, 刘延峰, 李江华, 刘龙, 堵国成. 典型模式微生物基因表达精细调控工具的研究进展[J]. 合成生物学, 2020, 1(4): 454-469.
Rongzhen TIAN, Yanfeng LIU, Jianghua LI, Long LIU, Guocheng DU. Progress in the regulatory tools of gene expression for model microorganisms[J]. Synthetic Biology Journal, 2020, 1(4): 454-469.
1 |
KENT R, DIXON N. Contemporary tools for regulating gene expression in bacteria [J]. Trends in Biotechnology, 2020, 38(3): 316-333. DOI: 10.1016/j.tibtech.2019.09.007.
DOI |
2 |
TYO K E, ALPER H S, STEPHANOPOULOS G N. Expanding the metabolic engineering toolbox: more options to engineer cells [J]. Trends in Biotechnology, 2007, 25(3): 132-137. DOI: 10.1016/j.tibtech.2007.01.003.
DOI |
3 |
YANG Sen, DU Guocheng, CHEN Jian, et al. Characterization and application of endogenous phase-dependent promoters in Bacillus subtilis [J]. Applied Microbiology and Biotechnology, 2017, 101(10): 4151-4161. DOI: 10.1007/s00253-017-8142-7.
DOI |
4 |
ALPER H, FISCHER C, NEVOIGT E, et al. Tuning genetic control through promoter engineering [J]. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(36): 12678. DOI: 10.1073/pnas.0504604102.
DOI |
5 |
REZNIKOFF W S. The lactose operon-controlling elements: a complex paradigm [J]. Molecular Microbiology, 1992, 6(17): 2419-2422. DOI: 10.1111/j.1365-2958.1992.tb01416.x.
DOI |
6 |
GUIZIOU S, SAUVEPLANE V, CHANG Hung-Ju, et al. A part toolbox to tune genetic expression in Bacillus subtilis [J]. Nucleic Acids Research, 2016, 44(15): 7495-7508. DOI: 10.1093/nar/gkw624.
DOI |
7 |
SALIS H M, MIRSKY E A, VOIGT C A. Automated design of synthetic ribosome binding sites to control protein expression [J]. Nature Biotechnology, 2009, 27(10): 946-950. DOI: 10.1038/nbt.1568.
DOI |
8 |
SINUMVAYO J P, 杨森, 陈坚, 等. 枯草芽孢杆菌168新型转录终止子的构建与表征[J]. 生物工程学报, 2017, 33(7): 1091-1100. DOI: 10.13345/j.cjb.160484.
DOI |
SINUMVAYO J P, YANG S, CHEN J, et al. Engineering and characterization of new intrinsic transcriptional terminators in Bacillus subtilis 168 [J]. Chinese Journal of Biotechnology, 2017, 33(7): 1091-1100. DOI: 10.13345/j.cjb.160484.
DOI |
|
9 |
POPE S D, MEDZHITOV R. Emerging principles of gene expression programs and their regulation [J]. Molecular Cell, 2018, 71(3): 389-397. DOI: 10.1016/j.molcel.2018.07.017.
DOI |
10 |
LU Zhenghui, YANG Shihui, YUAN Xin, et al. CRISPR-assisted multi-dimensional regulation for fine-tuning gene expression in Bacillus subtilis [J]. Nucleic acids research, 2019, 47(7): e40. DOI: 10.1093/nar/gkz072.
DOI |
11 |
YANG Sen, LIU Qingtao, ZHANG Yunfeng, et al. Construction and characterization of broad-spectrum promoters for synthetic biology [J]. ACS Synthetic Biology, 2018, 7(1): 287-291. DOI: 10.1021/acssynbio.7b00258.
DOI |
12 |
PAPENFORT K, VANDERPOOL C K. Target activation by regulatory RNAs in bacteria [J]. FEMS Microbiology Reviews, 2015, 39(3): 362-378. DOI: 10.1093/femsre/fuv016.
DOI |
13 |
BREAKER R R. Riboswitches and translation control [J]. Cold Spring Harbor Perspectives in Biology, 2018, 10(11). DOI: 10.1101/cshperspect.a032797.
DOI |
14 |
MANDAL M, BREAKER R R. Gene regulation by riboswitches [J]. Nature Reviews Molecular Cell Biology, 2004, 5(6): 451-463. DOI: 10.1038/nrm1403.
DOI |
15 |
CARON M P, BASTET L, LUSSIER A, et al. Dual-acting riboswitch control of translation initiation and mRNA decay [J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(50): E3444-E3453. DOI: 10.1073/pnas.1214024109.
DOI |
16 |
JANG Sungho, JUNG Gyoo Yeol. Systematic optimization of L-tryptophan riboswitches for efficient monitoring of the metabolite in Escherichia coli [J]. Biotechnology and Bioengineering, 2018, 115(1): 266-271. DOI: 10.1002/bit.26448.
DOI |
17 |
JANG Sungho, JANG Sungyeon, XIU Yu, et al. Development of artificial riboswitches for monitoring of naringenin in vivo [J]. ACS Synthetic Biology, 2017, 6(11): 2077-2085. DOI: 10.1021/acssynbio.7b00128.
DOI |
18 |
XIU Yu, JANG Sungho, JONES J A, et al. Naringenin-responsive riboswitch-based fluorescent biosensor module for Escherichia coli co-cultures [J]. Biotechnology and Bioengineering, 2017, 114(10): 2235-2244. DOI: 10.1002/bit.26340.
DOI |
19 |
CAI Yao, HU Huasi, PAN Ziheng, et al. Metaheuristic optimization in shielding design for neutrons and gamma rays reducing dose equivalent as much as possible [J]. Annals of Nuclear Energy, 2018, 120: 27-34. DOI: 10.1016/j.anucene.2018.05.038.
DOI |
20 |
BURKE-AGUERO D H. Methods in enzymology : riboswitches as targets and tools [J]. Methods in Enzymology, 2015. DOI: 10.1016/S0076-6879(15)00012-9.
DOI |
21 | SEDLYAROVA N, SHAMOVSKY I, BHARATI B K, et al. sRNA-mediated control of transcription termination in E. coli [J]. Cell, 2016, 167(1): 111-121. e13. DOI: 10.1016/j.cell.2016.09.004. |
22 |
Young Je LEE, HOYNES-O'CONNOR A, LEONG M C, et al. Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system [J]. Nucleic Acids Research, 2016, 44(5): 2462-2473. DOI: 10.1093/nar/gkw056.
DOI |
23 |
YANG Yaping, LIN Yuheng, LI Lingyun, et al. Regulating malonyl-CoA metabolism via synthetic antisense RNAs for enhanced biosynthesis of natural products [J]. Metabolic Engineering, 2015, 29: 217-226. DOI: 10.1016/j.ymben.2015.03.018.
DOI |
24 |
NAKASHIMA N, TAMURA T, GOOD L. Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli [J]. Nucleic Acids Research, 2006, 34(20): e138-e138. DOI: 10.1093/nar/gkl697.
DOI |
25 |
SHERWOOD A V, HENKIN T M. Riboswitch-mediated gene regulation: novel RNA architectures dictate gene expression responses [J]. Annual Review of Microbiology, 2016, 70(1): 361-374. DOI: 10.1146/annurev-micro-091014-104306.
DOI |
26 |
RÖTHLISBERGER P, HOLLENSTEIN M. Aptamer chemistry [J]. Advanced Drug Delivery Reviews, 2018, 134: 3-21. DOI: 10.1016/j.addr.2018.04.007.
DOI |
27 |
ABOUL-ELA F, HUANG Wei, ELRAHMAN M A, et al. Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design [J]. Wiley Interdisciplinary Reviews. RNA, 2015, 6(6): 631-650. DOI: 10.1002/wrna.1300.
DOI |
28 |
WANG j, YANG Le, CUI Xun, et al. A DNA bubble-mediated gene regulation system based on thrombin-bound DNA aptamers [J]. ACS Synthetic Biology, 2017, 6(5): 758-765. DOI: 10.1021/acssynbio.6b00391.
DOI |
29 |
DENG Jieying, CHEN Chunmei, GU Yang, et al. Creating an in vivo bifunctional gene expression circuit through an aptamer-based regulatory mechanism for dynamic metabolic engineering in Bacillus subtilis [J]. Metabolic Engineering, 2019, 55: 179-190. DOI: 10.1016/j.ymben.2019.07.008.
DOI |
30 |
GOODMAN D B, CHURCH G M, KOSURI S. Causes and effects of N-terminal codon bias in bacterial genes [J]. Science, 2013, 342(6157): 475. DOI: 10.1126/science.1241934.
DOI |
31 |
KUDLA G, MURRAY A W, TOLLERVEY D, et al. Coding-sequence determinants of gene expression in Escherichia coli [J]. Science, 2009, 324(5924): 255. DOI: 10.1126/science.1170160.
DOI |
32 |
SAUER C, THEMAAT E V L VAN, BOENDER L G M, et al. Exploring the nonconserved sequence space of synthetic expression modules in Bacillus subtilis [J]. ACS Synthetic Biology, 2018, 7(7): 1773-1784. DOI: 10.1021/acssynbio.8b00110.
DOI |
33 |
ESPAH BORUJENI A, SALIS H M. Translation initiation is controlled by RNA folding kinetics via a ribosome drafting mechanism [J]. Journal of the American Chemical Society, 2016, 138(22): 7016-7023. DOI: 10.1021/jacs.6b01453.
DOI |
34 |
BORUJENI A E, CETNAR D, FARASAT I, et al. Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences [J]. Nucleic Acids Research, 2017, 45(9): 5437-5448. DOI: 10.1093/nar/gkx061.
DOI |
35 |
DOUGAN D A, TRUSCOTT K N, ZETH K. The bacterial N-end rule pathway: expect the unexpected [J]. Molecular Microbiology, 2010, 76(3): 545-558. DOI: 10.1111/j.1365-2958.2010.07120.x.
DOI |
36 |
LU Jianli, DEUTSCH C. Electrostatics in the ribosomal tunnel modulate chain elongation rates [J]. Journal of Molecular Biology, 2008, 384(1): 73-86. DOI: 10.1016/j.jmb.2008.08.089.
DOI |
37 |
SHARMA A K, BUKAU B, O'BRIEN E P. Physical origins of codon positions that strongly influence cotranslational folding: a framework for controlling nascent-protein folding [J]. Journal of the American Chemical Society, 2016, 138(4): 1180-1195. DOI: 10.1021/jacs.5b08145.
DOI |
38 | TOBIAS J W, SHRADER T E, ROCAP G, et al. The N-end rule in bacteria [J]. Science, 1991, 254(5036): 1374-1377. |
39 |
ZADEH J N, STEENBERG C D, BOIS J S, et al. NUPACK: analysis and design of nucleic acid systems [J]. Journal of Computational Chemistry, 2011, 32(1): 170-173. DOI: 10.1002/jcc.21596.
DOI |
40 |
CAMBRAY G, GUIMARAES J C, ARKIN A P. Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli [J]. Nature Biotechnology, 2018, 36(10): 1005-1015. DOI: 10.1038/nbt.4238.
DOI |
41 |
TIAN Rongzhen, LIU Yanfeng, CHEN Junrong, et al. Synthetic N-terminal coding sequences for fine-tuning gene expression and metabolic engineering in Bacillus subtilis [J]. Metabolic Engineering, 2019, 55: 131-141. DOI: 10.1016/j.ymben.2019.07.001.
DOI |
42 |
XU Peng. Production of chemicals using dynamic control of metabolic fluxes [J]. Current Opinion in Biotechnology, 2018, 53: 12-19. DOI: 10.1016/j.copbio.2017.10.009.
DOI |
43 |
HOLTZ W J, KEASLING J D. Engineering static and dynamic control of synthetic pathways [J]. Cell, 2010, 140(1): 19-23. DOI: 10.1016/j.cell.2009.12.029.
DOI |
44 |
ALPER H, STEPHANOPOULOS G. Global transcription machinery engineering: a new approach for improving cellular phenotype [J]. Metabolic Engineering, 2007, 9(3): 258-267. DOI: 10.1016/j.ymben.2006.12.002.
DOI |
45 |
MY L, ACHKAR N G, VIALA J P, et al. Reassessment of the genetic regulation of fatty acid synthesis in Escherichia coli: global positive control by the dual functional regulator FadR [J]. Journal of Bacteriology, 2015, 197(11): 1862-1872. DOI: 10.1128/JB.00064-15.
DOI |
46 |
KURODA K, UEDA M. Engineering of global regulators and cell surface properties toward enhancing stress tolerance in Saccharomyces cerevisiae [J]. Journal of Bioscience and Bioengineering, 2017, 124(6): 599-605. DOI: 10.1016/j.jbiosc.2017.06.010.
DOI |
47 |
NGUYEN-VO T P, LIANG Yunxiao, SANKARANARAYANAN M, et al. Development of 3-hydroxypropionic-acid-tolerant strain of Escherichia coli W and role of minor global regulator yieP [J]. Metabolic Engineering, 2019, 53: 48-58. DOI: 10.1016/j.ymben.2019.02.001.
DOI |
48 |
BRINSMADE S R, ALEXANDER E L, LIVNY J, et al. Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY [J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(22): 8227. DOI: 10.1073/pnas.1321308111.
DOI |
49 |
CAO Haojie, KUIPERS O P. Influence of global gene regulatory networks on single cell heterogeneity of green fluorescent protein production in Bacillus subtilis [J]. Microbial Cell Factories, 2018, 17(1): 134. DOI: 10.1186/s12934-018-0985-9.
DOI |
50 |
ZHU Liying, GAO Shan, ZHANG Hongman, et al. Improvement of lead tolerance of Saccharomyces cerevisiae by random mutagenesis of transcription regulator SPT3 [J]. Applied Biochemistry and Biotechnology, 2018, 184(1): 155-167. DOI: 10.1007/s12010-017-2531-3.
DOI |
51 |
PARK Kyung-Soon, Dong-ki LEE, Horim LEE, et al. Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors [J]. Nature Biotechnology, 2003, 21(10): 1208-1214. DOI: 10.1038/nbt868.
DOI |
52 |
ALPER H, MOXLEY J, NEVOIGT E, et al. Engineering yeast transcription machinery for improved ethanol tolerance and production [J]. Science, 2006, 314(5805): 1565. DOI: 10.1126/science.1131969.
DOI |
53 |
BURGESS R R, ANTHONY L. How sigma docks to RNA polymerase and what sigma does [J]. Current Opinion in Microbiology, 2001, 4(2): 126-131. DOI: 10.1016/S1369-5274(00)00177-6.
DOI |
54 |
GAO Xi, JIANG Ling, ZHU Liying, et al. Tailoring of global transcription sigma D factor by random mutagenesis to improve Escherichia coli tolerance towards low-pHs [J]. Journal of Biotechnology, 2016, 224: 55-63. DOI: 10.1016/j.jbiotec.2016.03.012.
DOI |
55 |
ADHIKARI S, CURTIS P D. DNA methyltransferases and epigenetic regulation in bacteria [J]. FEMS Microbiology Reviews, 2016, 40(5): 575-591. DOI: 10.1093/femsre/fuw023.
DOI |
56 |
KANG Jeong Gu, PARK Jin Suk, Jeong-Heosn KO, et al. Regulation of gene expression by altered promoter methylation using a CRISPR/Cas9-mediated epigenetic editing system [J]. Scientific Reports, 2019, 9(1): 11960. DOI: 10.1038/s41598-019-48130-3.
DOI |
57 |
GRUNSTEIN M, GASSER S M. Epigenetics in Saccharomyces cerevisiae [J]. Cold Spring Harbor Perspectives in Biology, 2013, 5(7): a017491. DOI: 10.1101/cshperspect.a017491.
DOI |
58 |
CHEN Chao, WANG Lianrong, CHEN Si, et al. Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes [J]. Proceedings of the National Academy of Sciences of the United States of America, 2017, 114(17): 4501-4506. DOI: 10.1073/pnas.1702450114.
DOI |
59 |
LAL A, KRISHNA S, SESHASAYEE A S N. Regulation of global transcription in Escherichia coli by Rsd and 6S RNA [J]. G3: Genes, Genomes, Genetics, 2018, 8(6): 2079-2089. DOI: 10.1534/g3.118.200265.
DOI |
60 |
WASSARMAN K M, STORZ G. 6S RNA Regulates E. coli RNA polymerase activity [J]. Cell, 2000, 101(6): 613-623. DOI: 10.1016/S0092-8674(00)80873-9.
DOI |
61 |
WASSARMAN K M. 6S RNA, a global regulator of transcription [J]. Microbiology Spectrum, 2018, 6(3): 10.1128/microbiolspec. RWR-0019-2018. DOI: 10.1128/microbiolspec.RWR-0019-2018.
DOI |
62 |
CAVANAGH A T, WASSARMAN K M. 6S RNA, a global regulator of transcription in Escherichia coli, Bacillus subtilis, and beyond [J]. Annual Review of Microbiology, 2014, 68(1): 45-60. DOI: 10.1146/annurev-micro-092611-150135.
DOI |
63 |
QI Lei S, LARSON M H, GILBERT L A, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression [J]. Cell, 2013, 152(5): 1173-1183. DOI: 10.1016/j.cell.2013.02.022.
DOI |
64 |
RAN F A, HSU P D, WRIGHT J, et al. Genome engineering using the CRISPR-Cas9 system [J]. Nature Protocols, 2013, 8(11): 2281-2308. DOI: 10.1038/nprot.2013.143.
DOI |
65 |
HSU P D, LANDER E S, ZHANG Feng. Development and applications of CRISPR-Cas9 for genome engineering [J]. Cell, 2014, 157(6): 1262-1278. DOI: 10.1016/j.cell.2014.05.010.
DOI |
66 |
LIU Yang, WAN Xinyi, WANG Baojun. Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria [J]. Nature Communications, 2019, 10(1): 3693. DOI: 10.1038/s41467-019-11479-0.
DOI |
67 |
LIAN Jiazhang, HAMEDIRAD M, HU Sumeng, et al. Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system [J]. Nature Communications, 2017, 8(1): 1688. DOI: 10.1038/s41467-017-01695-x.
DOI |
68 |
WU Yaokang, CHEN Taichi, LIU Yanfeng, 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, 2019, 48(2): 996-1009. DOI: 10.1093/nar/gkz1123.
DOI |
69 |
FENNO L, YIZHAR O, DEISSEROTH K. The development and application of optogenetics [J]. Annual Review of Neuroscience, 2011, 34: 389-412. DOI: 10.1146/annurev-neuro-061010-113817.
DOI |
70 |
BACCHUS W, FUSSENEGGER M. The use of light for engineered control and reprogramming of cellular functions [J]. Current Opinion in Biotechnology, 2012, 23(5): 695-702. DOI: 10.1016/j.copbio.2011.12.004.
DOI |
71 |
OLSON E J, TABOR J J. Optogenetic characterization methods overcome key challenges in synthetic and systems biology [J]. Nature Chemical Biology, 2014, 10(7): 502-511. DOI: 10.1038/nchembio.1559.
DOI |
72 |
PATHAK G P, VRANA J D, TUCKER C L. Optogenetic control of cell function using engineered photoreceptors [J]. Biology of the Cell, 2013, 105(2): 59-72. DOI: 10.1111/boc.201200056.
DOI |
73 |
ZHAO E M, ZHANG Yanfei, MEHL J, et al. Optogenetic regulation of engineered cellular metabolism for microbial chemical production [J]. Nature, 2018, 555(7698): 683-687. DOI: 10.1038/nature26141.
DOI |
74 |
SHIMIZU-SATO S, HUQ E, TEPPERMAN J M, et al. A light-switchable gene promoter system [J]. Nature Biotechnology, 2002, 20(10): 1041-1044. DOI: 10.1038/nbt734.
DOI |
75 |
MOTTA-MENA L B, READE A, MALLORY M J, et al. An optogenetic gene expression system with rapid activation and deactivation kinetics [J]. Nature Chemical Biology, 2014, 10(3): 196-202. DOI: 10.1038/nchembio.1430.
DOI |
76 |
SHIN Yongdae, BERRY J, PANNUCCI N, et al. Spatiotemporal control of intracellular phase transitions using light-activated optoDroplets [J]. Cell, 2017, 168(1/2): 159-171.e14. DOI: 10.1016/j.cell.2016.11.054.
DOI |
77 |
TABOR J J, LEVSKAYA A, VOIGT C A. Multichromatic control of gene expression in Escherichia coli [J]. Journal of Molecular Biology, 2011, 405(2): 315-324. DOI: 10.1016/j.jmb.2010.10.038.
DOI |
78 |
MILIAS-ARGEITIS A, RULLAN M, AOKI S K, et al. Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth [J]. Nature Communications, 2016, 7: 12546. DOI: 10.1038/ncomms12546.
DOI |
79 |
CASTILLO-HAIR S M, BAERMAN E A, FUJITA M, et al. Optogenetic control of Bacillus subtilis gene expression [J]. Nature Communications, 2019, 10(1): 3099. DOI: 10.1038/s41467-019-10906-6.
DOI |
80 |
GAO Cong, HOU Jianshen, XU Peng, et al. Programmable biomolecular switches for rewiring flux in Escherichia coli [J]. Nature Communications, 2019, 10(1): 3751. DOI: 10.1038/s41467-019-11793-7.
DOI |
81 |
CAMERON D E, COLLINS J J. Tunable protein degradation in bacteria [J]. Nature Biotechnology, 2014, 32(12): 1276-1281. DOI: 10.1038/nbt.3053.
DOI |
82 |
CHUNG Hokyung K, JACOBS C L, HUO Yunwen, et al. Tunable and reversible drug control of protein production via a self-excising degron [J]. Nature Chemical Biology, 2015, 11(9): 713-720. DOI: 10.1038/nchembio.1869.
DOI |
83 |
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. DOI: 10.1073/pnas.1716920115.
DOI |
84 |
MARTÍNEZ V, LAURITSEN I, HOBEL T, et al. CRISPR/Cas9-based genome editing for simultaneous interference with gene expression and protein stability [J]. Nucleic Acids Research, 2017, 45(20): e171-e171. DOI: 10.1093/nar/gkx797.
DOI |
85 |
FERNANDEZ-RODRIGUEZ J, VOIGT C A. Post-translational control of genetic circuits using Potyvirus proteases [J]. Nucleic Acids Research, 2016, 44(13): 6493-6502. DOI: 10.1093/nar/gkw537.
DOI |
86 |
TAN S Z, PRATHER K L J. Dynamic pathway regulation:recent advances and methods of construction [J]. Current Opinion in Chemical Biology, 2017, 41: 28-35. DOI: 10.1016/j.cbpa.2017.10.004.
DOI |
87 |
WHITELEY M, DIGGLE S P, GREENBERG E P. Progress in and promise of bacterial quorum sensing research [J]. Nature, 2017, 551(7680): 313-320. DOI: 10.1038/nature24624.
DOI |
88 |
SOMA Y, HANAI T. Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production [J]. Metabolic Engineering, 2015, 30: 7-15. DOI: 10.1016/j.ymben.2015.04.005.
DOI |
89 |
GUPTA A, REIZMAN I M B, 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. DOI: 10.1038/nbt.3796.
DOI |
90 |
CUI Shixiu, Xueqin LÜ, WU Yaokang, et al. Engineering a bifunctional Phr60-Rap60-Spo0A quorum-sensing molecular switch for dynamic fine-tuning of menaquinone-7 synthesis in Bacillus subtilis [J]. ACS Synthetic Biology, 2019, 8(8): 1826-1837. DOI: 10.1021/acssynbio.9b00140.
DOI |
91 |
WILLIAMS T C, AVERESCH N, WINTER G, et al. Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae [J]. Metabolic Engineering, 2015, 29: 124-134. DOI: 10.1016/j.ymben.2015.03.008.
DOI |
92 |
XU Peng, LI Lingyun, ZHANG Fuming, 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. DOI: 10.1073/pnas.1406401111.
DOI |
93 |
RUGBJERG P, SARUP-LYTZEN K, NAGY M, et al. Synthetic addiction extends the productive life time of engineered Escherichia coli populations [J]. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(10): 2347. DOI: 10.1073/pnas.1718622115.
DOI |
94 |
SANDBERG T E, SALAZAR M J, WENG L L, et al. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology [J]. Metabolic Engineering, 2019, 56: 1-16. DOI: 10.1016/j.ymben.2019.08.004.
DOI |
95 |
BUERGER J, GRONENBERG L S, GENEE H J, et al. Wiring cell growth to product formation [J]. Current Opinion in Biotechnology, 2019, 59: 85-92. DOI: 10.1016/j.copbio.2019.02.014.
DOI |
96 |
CHOU H H, KEASLING J D. Programming adaptive control to evolve increased metabolite production [J]. Nature Communications, 2013, 4(1): 2595. DOI: 10.1038/ncomms3595.
DOI |
97 |
LEAVITT J M, WAGNER J M, TU C C, et al. Biosensor-enabled directed evolution to improve muconic acid production in Saccharomyces cerevisiae [J]. Biotechnology Journal, 2017, 12(10): 1600687. DOI: 10.1002/biot.201600687.
DOI |
[1] | 刁志钿, 王喜先, 孙晴, 徐健, 马波. 单细胞拉曼光谱测试分选装备研制及应用进展[J]. 合成生物学, 2023, 4(5): 1020-1035. |
[2] | 卢挥, 张芳丽, 黄磊. 合成生物学自动化装置iBioFoundry的构建与应用[J]. 合成生物学, 2023, 4(5): 877-891. |
[3] | 白仲虎, 任和, 聂简琪, 孙杨. 高通量平行发酵技术的发展与应用[J]. 合成生物学, 2023, 4(5): 904-915. |
[4] | 吴玉洁, 刘欣欣, 刘健慧, 杨开广, 随志刚, 张丽华, 张玉奎. 基于高通量液相色谱质谱技术的菌株筛选与关键分子定量分析研究进展[J]. 合成生物学, 2023, 4(5): 1000-1019. |
[5] | 胡哲辉, 徐娟, 卞光凯. 自动化高通量技术在天然产物生物合成中的应用[J]. 合成生物学, 2023, 4(5): 932-946. |
[6] | 刘欢, 崔球. 原位电离质谱技术在微生物菌株筛选中的应用进展[J]. 合成生物学, 2023, 4(5): 980-999. |
[7] | 王雁南, 孙宇辉. 碱基编辑技术及其在微生物合成生物学中的应用[J]. 合成生物学, 2023, 4(4): 720-737. |
[8] | 刘晚秋, 季向阳, 许慧玲, 卢屹聪, 李健. 限制性内切酶的无细胞快速制备研究[J]. 合成生物学, 2023, 4(4): 840-851. |
[9] | 孙美莉, 王凯峰, 陆然, 纪晓俊. 解脂耶氏酵母底盘细胞的工程改造及应用[J]. 合成生物学, 2023, 4(4): 779-807. |
[10] | 程真真, 张健, 高聪, 刘立明, 陈修来. 代谢工程改造微生物利用甲酸研究进展[J]. 合成生物学, 2023, 4(4): 756-778. |
[11] | 孙智, 杨宁, 娄春波, 汤超, 杨晓静. 功能拓扑的理性设计及其在合成生物学中的应用[J]. 合成生物学, 2023, 4(3): 444-463. |
[12] | 赖奇龙, 姚帅, 查毓国, 白虹, 宁康. 微生物组生物合成基因簇发掘方法及应用前景[J]. 合成生物学, 2023, 4(3): 611-627. |
[13] | 孟巧珍, 郭菲. “可折叠性”在酶智能设计改造中的应用研究——以AlphaFold2为例[J]. 合成生物学, 2023, 4(3): 571-589. |
[14] | 王晟, 王泽琛, 陈威华, 陈珂, 彭向达, 欧发芬, 郑良振, 孙瑨原, 沈涛, 赵国屏. 基于人工智能和计算生物学的合成生物学元件设计[J]. 合成生物学, 2023, 4(3): 422-443. |
[15] | 吕海龙, 王建, 吕浩, 王金, 徐勇, 顾大勇. 合成生物学在下一代基因诊断技术中的应用进展[J]. 合成生物学, 2023, 4(2): 318-332. |
阅读次数 | ||||||
全文 |
|
|||||
摘要 |
|
|||||