技术情报 |
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合成生物学领域技术发展态势与研究进展* |
江洪1,2,3,**( ),李晓南1,2,3,高倩1,3 |
1 中国科学院武汉文献情报中心 武汉 430071 2 中国科学院大学经济与管理学院信息资源管理系 北京 101408 3 科技大数据湖北省重点实验室 武汉 430071 |
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Technology Development Trend and Research Progress of Synthetic Biology |
JIANG Hong1,2,3,**( ),LI Xiaonan1,2,3,GAO Qian1,3 |
1 Wuhan Library,Chinese Academy of Sciences,Wuhan 430071, China 2 Department of Information Resources Management, School of Economics and Management, University of Chinese Academy of Sciences, Beijing 100190, China 3 Hubei Key Laboratory of Big Data in Science and Technology, Wuhan 430071, China |
[1] |
赵国屏. 合成生物学: 开启生命科学“会聚” 研究新时代. 中国科学院院刊, 2018, 33(11): 1135-1149.
|
|
Zhao G P. Synthetic biology: unsealing the convergence era of life science research. Bulletin of Chinese Academy of Sciences, 2018, 33(11): 1135-1149.
|
[2] |
Rawis R L. ‘synthetic biology’ makes its debut. Chemical & Engineering News Archive, 2000, 78(17): 49-53.
|
[3] |
辛竹琳, 何微, 王晓梅, 等.全球合成生物学专利发展格局及对中国的启示. 农业展望, 2023, 19(7): 105-113.
|
|
Xin Z L, He W, Wang X M, et al. Landscape of synthetic biology based on global patents and its enlightenment to China. Agricultural Outlook, 2023, 19(7): 105-113.
|
[4] |
严伟, 信丰学, 董维亮, 等. 合成生物学及其研究进展. 生物学杂志, 2020, 37(5): 1-9.
|
|
Yan W, Xin F X, Dong W L, et al. Synthetic biology and research progress. Journal of Biology, 2020, 37(5): 1-9.
|
[5] |
Wu X X, Li F Z, Yang R F, et al. Identification of a bidirectional promoter from Trichoderma reesei and its application in dual gene expression. Journal of Fungi, 2022, 8(10): 1059.
|
[6] |
Liu T S, Wu K F, Jiang H W, et al. Identification of a far-red light-inducible promoter that exhibits light intensity dependency and reversibility in a Cyanobacterium. ACS Synthetic Biology, 2023, 12(4): 1320-1330.
|
[7] |
Forestier E C F, Cording A C, Loake G J, et al. An engineered heat-inducible expression system for the production of casbene in Nicotiana benthamiana. International Journal of Molecular Sciences, 2023, 24(14): 11425.
|
[8] |
于慧敏, 郑煜堃, 杜岩, 等. 合成生物学研究中的微生物启动子工程策略. 合成生物学, 2021, 2(4): 598-611.
doi: 10.12211/2096-8280.2020-092
|
|
Yu H M, Zheng Y K, Du Y, et al. Microbial promoter engineering strategies in synthetic biology. Synthetic Biology Journal, 2021, 2(4): 598-611.
doi: 10.12211/2096-8280.2020-092
|
[9] |
Vidal L, Lebrun E, Park Y K, et al. Bidirectional hybrid erythritol-inducible promoter for synthetic biology in Yarrowia lipolytica. Microbial Cell Factories, 2023, 22(1): 7.
doi: 10.1186/s12934-023-02020-6
pmid: 36635727
|
[10] |
Guo X, Bai Z Z, Zhang Y, et al. Mining and application of constitutive promoters from Rhodosporidium toruloides. AMB Express, 2023, 13(1): 17.
|
[11] |
Milito A, Aschern M, McQuillan J L, et al. Challenges and advances towards the rational design of microalgal synthetic promoters in Chlamydomonas reinhardtii. Journal of Experimental Botany, 2023, 74(13): 3833-3850.
|
[12] |
Chen C, Chen J, Wu G X, et al. A blue light-responsive strong synthetic promoter based on rational design in Chlamydomonas reinhardtii. International Journal of Molecular Sciences, 2023, 24(19): 14596.
|
[13] |
Feng X J, Jia L, Cai Y T, et al. ABA-inducible DEEPER ROOTING 1 improves adaptation of maize to water deficiency. Plant Biotechnology Journal, 2022, 20(11): 2077-2088.
doi: 10.1111/pbi.13889
pmid: 35796628
|
[14] |
Kar S, Bordiya Y, Rodriguez N, et al. Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors. Plant Methods, 2022, 18(1): 42.
doi: 10.1186/s13007-022-00867-1
pmid: 35351174
|
[15] |
Moreno-Giménez E, Selma S, Calvache C, et al. GB_SynP: a modular dCas9-regulated synthetic promoter collection for fine-tuned recombinant gene expression in plants. ACS Synthetic Biology, 2022, 11(9): 3037-3048.
doi: 10.1021/acssynbio.2c00238
pmid: 36044643
|
[16] |
Danila F, Schreiber T, Ermakova M, et al. A single promoter-TALE system for tissue-specific and tuneable expression of multiple genes in rice. Plant Biotechnology Journal, 2022, 20(9): 1786-1806.
|
[17] |
Jameel A, Ketehouli T, Wang Y F, et al. Detection and validation of cis-regulatory motifs in osmotic stress-inducible synthetic gene switches via computational and experimental approaches. Functional Plant Biology, 2022, 49(12): 1043-1054.
doi: 10.1071/FP21314
pmid: 35940614
|
[18] |
Song H Y, Yang Y F, Li H, et al. Determination of nucleotide sequences within promoter regions affecting promoter compatibility between zymomonas mobilis and Escherichia coli. ACS Synthetic Biology, 2022, 11(8): 2811-2819.
|
[19] |
Liu J, Liu M S, Shi T, et al. CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an l-proline exporter for l-proline hyperproduction. Nature Communications, 2022, 13: 891.
doi: 10.1038/s41467-022-28501-7
pmid: 35173152
|
[20] |
Ni X X, Liu Z Y, Guo J T, et al. Development of Terminator-promoter bifunctional elements for application in Saccharomyces cerevisiae pathway engineering. International Journal of Molecular Sciences, 2023, 24(12): 9870.
|
[21] |
LaFleur T L, Hossain A, Salis H M. Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria. Nature Communications, 2022, 13: 5159.
doi: 10.1038/s41467-022-32829-5
pmid: 36056029
|
[22] |
Zhang P C, Wang H C, Xu H W, et al. Deep flanking sequence engineering for efficient promoter design using DeepSEED. Nature Communications, 2023, 14: 6309.
doi: 10.1038/s41467-023-41899-y
pmid: 37813854
|
[23] |
Vaishnav E D, de Boer C G, Molinet J, et al. The evolution, evolvability and engineering of gene regulatory DNA. Nature, 2022, 603: 455-463.
|
[24] |
Zrimec J, Fu X Z, Muhammad A S, et al. Controlling gene expression with deep generative design of regulatory DNA. Nature Communications, 2022, 13: 5099.
doi: 10.1038/s41467-022-32818-8
pmid: 36042233
|
[25] |
Zhao S Q, Hong C K Y, Myers C A, et al. A single-cell massively parallel reporter assay detects cell-type-specific gene regulation. Nature Genetics, 2023, 55: 346-354.
doi: 10.1038/s41588-022-01278-7
pmid: 36635387
|
[26] |
Gallego Romero I, Lea A J. Leveraging massively parallel reporter assays for evolutionary questions. Genome Biology, 2023, 24(1): 26.
doi: 10.1186/s13059-023-02856-6
pmid: 36788564
|
[27] |
Xiao F X, Zhang Y P, Zhang L, et al. Construction of the genetic switches in response to mannitol based on artificial MtlR box. Bioresources and Bioprocessing, 2023, 10(1): 9.
|
[28] |
Li H, Yan Y, Chen J, et al. Artificial receptor-mediated phototransduction toward protocellular subcompartmentalization and signaling-encoded logic gates. Science Advances, 2023, 9(9): eade5853.
|
[29] |
Ghataora J S, Gebhard S, Reeksting B J. Chimeric MerR-family regulators and logic elements for the design of metal sensitive genetic circuits in Bacillus subtilis. ACS Synthetic Biology, 2023, 12(3): 735-749.
doi: 10.1021/acssynbio.2c00545
pmid: 36629785
|
[30] |
Kameda S, Ohno H, Saito H. Synthetic circular RNA switches and circuits that control protein expression in mammalian cells. Nucleic Acids Research, 2023, 51(4): e24.
|
[31] |
Zhou Z, Liu Y T, Feng Y S, et al. Engineering longevity-design of a synthetic gene oscillator to slow cellular aging. Science, 2023, 380(6643): 376-381.
doi: 10.1126/science.add7631
pmid: 37104589
|
[32] |
Kawasaki S, Ono H, Hirosawa M, et al. Programmable mammalian translational modulators by CRISPR-associated proteins. Nature Communications, 2023, 14: 2243.
doi: 10.1038/s41467-023-37540-7
pmid: 37076490
|
[33] |
Zhu R H, Del Rio-Salgado J M, Garcia-Ojalvo J, et al. Synthetic multistability in mammalian cells. Science, 2022, 375(6578): eabg9765.
|
[34] |
Ning H, Liu G, Li L, et al. Rational design of microRNA-responsive switch for programmable translational control in mammalian cells. Nature Communications, 2023, 14: 7193.
doi: 10.1038/s41467-023-43065-w
pmid: 37938567
|
[35] |
Kamel N, Kharma N, Perreault J. Evolutionary design and analysis of ribozyme-based logic gates. Genetic Programming and Evolvable Machines, 2023, 24(2): 11.
|
[36] |
Zhu J W, Chu P, Fu X F. Unbalanced response to growth variations reshapes the cell fate decision landscape. Nature Chemical Biology, 2023, 19: 1097-1104.
doi: 10.1038/s41589-023-01302-9
pmid: 36959461
|
[37] |
Sun Z, Wei W J, Zhang M Y, et al. Synthetic robust perfect adaptation achieved by negative feedback coupling with linear weak positive feedback. Nucleic Acids Research, 2022, 50(4): 2377-2386.
doi: 10.1093/nar/gkac066
pmid: 35166832
|
[38] |
Qin C R, Xiang Y H, Liu J, et al. Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system. Nature Communications, 2023, 14: 1500.
doi: 10.1038/s41467-023-37244-y
pmid: 36932109
|
[39] |
Sequeiros C, Vázquez C, Banga J R, et al. Automated design of synthetic gene circuits in the presence of molecular noise. ACS Synthetic Biology, 2023, 12(10): 2865-2876.
doi: 10.1021/acssynbio.3c00033
pmid: 37812682
|
[40] |
Chen Z B, Kibler R D, Hunt A, et al. De novo design of protein logic gates. Science, 2020, 368(6486): 78-84.
doi: 10.1126/science.aay2790
pmid: 32241946
|
[41] |
Watson J L, Juergens D, Bennett N R, et al. De novo design of protein structure and function with RFdiffusion. Nature, 2023, 620: 1089-1100.
|
[42] |
Lee J S, Kim J, Kim P M. Score-based generative modeling for de novo protein design. Nature Computational Science, 2023, 3: 382-392.
|
[43] |
Praetorius F, Leung P J Y, Tessmer M H, et al. Design of stimulus-responsive two-state hinge proteins. Science, 2023, 381(6659): 754-760.
doi: 10.1126/science.adg7731
pmid: 37590357
|
[44] |
Guo Z, Smutok O, Ayva C E, et al. Development of epistatic YES and AND protein logic gates and their assembly into signalling cascades. Nature Nanotechnology, 2023, 18: 1327-1334.
|
[45] |
Tan K X, Hu Y X, Liang Z H, et al. Dual input-controlled synthetic mRNA circuit for bidirectional protein expression regulation. ACS Synthetic Biology, 2023, 12(9): 2516-2523.
|
[46] |
Hu S L, Fei M Y, Fu B B, et al. Development of probiotic E. coli Nissle 1917 for β-alanine production by using protein and metabolic engineering. Applied Microbiology and Biotechnology, 2023, 107(7): 2277-2288.
|
[47] |
Zhou C, Chen T J, Gu A D, et al. Combining protein and metabolic engineering to achieve green biosynthesis of 12β-O-Glc-PPD in Saccharomyces cerevisiae. Green Chemistry, 2023, 25(4): 1356-1367.
|
[48] |
An T, Lin G Y, Liu Y, et al. De novo biosynthesis of anticarcinogenic icariin in engineered yeast. Metabolic Engineering, 2023, 80: 207-215.
doi: 10.1016/j.ymben.2023.10.003
pmid: 37852432
|
[49] |
Chen Y M, Han A, Wang M, et al. Metabolic engineering of Trichoderma reesei for l-malic acid production. Journal of Agricultural and Food Chemistry, 2023, 71(9): 4043-4050.
|
[50] |
Garg A, Jers C, Hwang H J, et al. Engineering Bacillus subtilis for production of 3-hydroxypropanoic acid. Frontiers in Bioengineering and Biotechnology, 2023, 11: 1101232.
|
[51] |
Wu Y K, Li Y, Jin K, et al. CRISPR-dCas12a-mediated genetic circuit cascades for multiplexed pathway optimization. Nature Chemical Biology, 2023, 19: 367-377.
doi: 10.1038/s41589-022-01230-0
pmid: 36646959
|
[52] |
Zhang J, Hansen L G, Gudich O, et al. A microbial supply chain for production of the anti-cancer drug vinblastine. Nature, 2022, 609: 341-347.
|
[53] |
Du H M, Qiao J F, Qi Y T, et al. Reprogramming the sulfur recycling network to improve l-cysteine production in Corynebacterium glutamicum. Green Chemistry, 2023, 25(8): 3152-3165.
|
[54] |
Wang Y P, Ferrinho S, Connaris H, et al. The impact of viral infection on the chemistries of the earth’s most abundant photosynthesizes: metabolically talented aquatic cyanobacteria. Biomolecules, 2023, 13(8): 1218.
|
[55] |
Liang H Y, Chen H J, Liu X Y, et al. Heterologous production in the Synechocystis chassis suggests the biosynthetic pathway of astaxanthin in cyanobacteria. Antioxidants, 2023, 12(10): 1826.
|
[56] |
Russo M T, Rogato A, Jaubert M, et al. Phaeodactylum tricornutum: an established model species for diatom molecular research and an emerging chassis for algal synthetic biology. Journal of Phycology, 2023, 59(6): 1114-1122.
doi: 10.1111/jpy.13400
pmid: 37975560
|
[57] |
Kallam K, Moreno-Giménez E, Mateos-Fernández R, et al. Tunable control of insect pheromone biosynthesis in Nicotiana benthamiana. Plant Biotechnology Journal, 2023, 21(7): 1440-1453.
|
[58] |
Chen Q, Liu D Q, Qu Y, et al. Construction of plant cell factory for biosynthesis of ginsenoside Rh 2 in tobacco. Industrial Crops and Products, 2023, 192: 116057.
|
[59] |
Ma Y S, Liu N, Greisen P, et al. Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica. Nature Communications, 2022, 13: 572.
|
[60] |
Kang Q, Fang H, Xiang M J, et al. A synthetic cell-free 36-enzyme reaction system for vitamin B12 production. Nature Communications, 2023, 14: 5177.
|
[61] |
Tian X T, Liu W Q, Xu H L, et al. Cell-free expression of NO synthase and P 450 enzyme for the biosynthesis of an unnatural amino acid L-4-nitrotryptophan. Synthetic and Systems Biotechnology, 2022, 7(2): 775-783.
|
[62] |
Yeh A H W, Norn C, Kipnis Y, et al. De novo design of luciferases using deep learning. Nature, 2023, 614: 774-780.
|
[63] |
Cao F F, Jin L L, Gao Y, et al. Artificial-enzymes-armed Bifidobacterium longum probiotics for alleviating intestinal inflammation and microbiota dysbiosis. Nature Nanotechnology, 2023, 18: 617-627.
|
[64] |
Zhao P X, Kong F H, Jiang Y P, et al. Enabling peroxygenase activity in cytochrome P 450 monooxygenases by engineering hydrogen peroxide tunnels. Journal of the American Chemical Society, 2023, 145(9): 5506-5511.
|
[65] |
Hassani D, Taheri A, Fu X Q, et al. Elevation of artemisinin content by co-transformation of artemisinin biosynthetic pathway genes and trichome-specific transcription factors in Artemisia annua. Frontiers in Plant Science, 2023, 14: 1118082.
|
[66] |
Wu Y T, Liu J Q, Han X, et al. Eliminating host-guest incompatibility via enzyme mining enables the high-temperature production of N-acetylglucosamine. iScience, 2023, 26(1): 105774.
|
[67] |
Yu H, Deng H X, He J H, et al. UniKP: a unified framework for the prediction of enzyme kinetic parameters. Nature Communications, 2023, 14: 8211.
doi: 10.1038/s41467-023-44113-1
pmid: 38081905
|
[68] |
Mao Z T, Yuan Q Q, Li H R, et al. CAVE: a cloud-based platform for analysis and visualization of metabolic pathways. Nucleic Acids Research, 2023, 51(W1): W70-W77.
doi: 10.1093/nar/gkad360
pmid: 37158271
|
[69] |
Shen Y, Gao F, Wang Y, et al. Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast. Cell Genomics, 2023, 3(11): 100364.
|
[70] |
Williams T C, Kroukamp H, Xu X, et al. Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects. Cell Genomics, 2023, 3(11): 100379.
|
[71] |
McCulloch L H, Sambasivam V, Hughes A L, et al. Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains. Cell Genomics, 2023, 3(11): 100419.
|
[72] |
Blount B A, Lu X Y, Driessen M R M, et al. Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics. Cell Genomics, 2023, 3(11): 100418.
|
[73] |
Nurk S, Koren S, Rhie A, et al. The complete sequence of a human genome. Science, 2022, 376(6588): 44-53.
doi: 10.1126/science.abj6987
pmid: 35357919
|
[74] |
Rautiainen M, Nurk S, Walenz B P, et al. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nature Biotechnology, 2023, 41: 1474-1482.
doi: 10.1038/s41587-023-01662-6
pmid: 36797493
|
[75] |
Yang C T, Zhou Y, Song Y N, et al. The complete and fully-phased diploid genome of a male Han Chinese. Cell Research, 2023, 33: 745-761.
doi: 10.1038/s41422-023-00849-5
pmid: 37452091
|
[76] |
Gao Y, Yang X F, Chen H, et al. A pangenome reference of 36 Chinese populations. Nature, 2023, 619: 112-121.
|
[77] |
Chen J, Wang Z J, Tan K W, et al. A complete telomere-to-telomere assembly of the maize genome. Nature Genetics, 2023, 55: 1221-1231.
doi: 10.1038/s41588-023-01419-6
pmid: 37322109
|
[78] |
Huang Z, Xu Z X, Bai H, et al. Evolutionary analysis of a complete chicken genome. Proceedings of the National Academy of Sciences of the United States of America, 2023, 120(8): e2216641120.
|
[79] |
Coradini A L V, Ville C N, Krieger Z A, et al. Building synthetic chromosomes from natural DNA. Nature Communications, 2023, 14: 8337.
doi: 10.1038/s41467-023-44112-2
pmid: 38123566
|
[80] |
Sun C, Lei Y, Li B S, et al. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors. Nature Biotechnology, 2024, 42: 316-327.
|
[81] |
Zürcher J F, Kleefeldt A A, Funke L F H, et al. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature, 2023, 619: 555-562.
|
[82] |
Zhao Y C, Han J L, Tan J T, et al. Efficient assembly of long DNA fragments and multiple genes with improved nickase-based cloning and Cre/loxP recombination. Plant Biotechnology Journal, 2022, 20(10): 1983-1995.
doi: 10.1111/pbi.13882
pmid: 35767383
|
[83] |
Zhang W M, Golynker I, Brosh R, et al. Mouse genome rewriting and tailoring of three important disease loci. Nature, 2023, 623: 423-431.
|
[84] |
Kretzmann J A, Liedl A, Monferrer A, et al. Gene-encoding DNA origami for mammalian cell expression. Nature Communications, 2023, 14: 1017.
doi: 10.1038/s41467-023-36601-1
pmid: 36823187
|
[85] |
Moger-Reischer R Z, Glass J I, Wise K S, et al. Evolution of a minimal cell. Nature, 2023, 620: 122-127.
|
[86] |
Belluati A, Jimaja S, Chadwick R J, et al. Artificial cell synthesis using biocatalytic polymerization-induced self-assembly. Nature Chemistry, 2024, 16: 564-574.
|
[87] |
Ji Y, Lin Y Y, Qiao Y. Plant cell-inspired membranization of coacervate protocells with a structured polysaccharide layer. Journal of the American Chemical Society, 2023, 145(23): 12576-12585.
doi: 10.1021/jacs.3c01326
pmid: 37267599
|
[88] |
包心茹, 陈卯森, 钟洁, 等. CRISPR/Cas12a基因组编辑技术及应用. 中国生物工程杂志, 2023, 43(10): 32-42.
|
|
Bao X R, Chen M S, Zhong J, et al. Characteristics and application of CRISPR/Cas12a genome editing technology. China Biotechnology, 2023, 43(10): 32-42.
|
[89] |
Banskota S, Raguram A, Suh S, et al. Engineered virus-like particles for efficient in vivo delivery of therapeutic proteins. Cell, 2022, 185(2): 250-265.e16.
doi: 10.1016/j.cell.2021.12.021
pmid: 35021064
|
[90] |
Kreitz J, Friedrich M J, Guru A, et al. Programmable protein delivery with a bacterial contractile injection system. Nature, 2023, 616: 357-364.
|
[91] |
Tang J C, Li W C, Chiu T Y, et al. Synthesis of portimines reveals the basis of their anti-cancer activity. Nature, 2023, 622: 507-513.
|
[92] |
Sha G, Sun P, Kong X J, et al. Genome editing of a rice CDP-DAG synthase confers multipathogen resistance. Nature, 2023, 618: 1017-1023.
|
[93] |
2022年中国合成生物学绿色应用与产业感知调研组. 合成生物企业与产品分析. 中国生物工程杂志, 2023, 43(4): 141-147.
|
|
2022 China Synthetic Biology Green Application and Industry Perception Research Group. Synthetic biological enterprises and product analysis. China Biotechnology, 2023, 43(4): 141-147.
|
[94] |
Nguyen P Q, Soenksen L R, Donghia N M, et al. Wearable materials with embedded synthetic biology sensors for biomolecule detection. Nature Biotechnology, 2021, 39: 1366-1374.
doi: 10.1038/s41587-021-00950-3
pmid: 34183860
|
[95] |
“中国学科及前沿领域发展战略研究(2021-2035)”项目组. 中国合成生物学2035发展战略. 北京: 科学出版社, 2023:493-500.
|
|
“Research on the Development Strategy of China’s Disciplines and Frontier Fields (2021-2035)” Project Team. China synthetic biology 2035 development strategy. Beijing: Science Press, 2023:493-500.
|
[96] |
赵国屏. 从定量合成生物学“出圈儿”谈起:我国迎来定量合成生物学发展重要契机.[2023-12-24]. https://www.cas.cn/zjs/202112/t20211206_4817121.shtml.
|
|
Zhao G P. Starting from the “out of the circle” of quantitative synthetic biology: China has ushered in an important opportunity for the development of quantitative synthetic biology.[2023-12-24]. https://www.cas.cn/zjs/202112/t20211206_4817121.shtml.
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