Biotechnology Bulletin ›› 2017, Vol. 33 ›› Issue (1): 58-64.doi: 10.13560/j.cnki.biotech.bull.1985.2017.01.006
• Orignal Article • Previous Articles Next Articles
PANG Qing-xiao, LIANG Quan-feng, QI Qing-sheng
Received:
2016-10-18
Online:
2017-01-25
Published:
2017-01-19
PANG Qing-xiao, LIANG Quan-feng, QI Qing-sheng. Application of Switch for Synthetic Biology in Metabolic Engineering[J]. Biotechnology Bulletin, 2017, 33(1): 58-64.
[1] Denard CA, Ren H, Zhao H. Improving and repurposing biocatalysts via directed evolution[J]. Curr Opin Chem Biol, 2015, 25:55-64. [2] Way JC, Collins JJ, Keasling JD, et al. Integrating biological redesign:where synthetic biology came from and where it needs to go[J]. Cell, 2014, 157:151-161. [3] Cobb RE, Sun N, Zhao H. Directed evolution as a powerful synthetic biology tool[J]. Methods, 2013, 60:81-90. [4] Dragosits M, Mattanovich D. Adaptive laboratory evolution principles and applications for biotechnology[J]. Microb Cell Fact, 2013, 12:64. [5] Tenaillon O, Rodriguez-Verdugo A, Gaut RL, et al. The molecular diversity of adaptive convergence[J]. Science, 2012, 335:457-461. [6] Hu H, Wood TK. An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol[J]. Biochem Biophys Res Commun, 2010, 391:1033-1038. [7] Bassalo MC, Liu RM, Gill RT. Directed evolution and synthetic biology applications to microbial systems[J]. Curr Opin Biotechnol, 2016, 39:126-133. [8] Wang Y, Manow R, Finan C, et al. Adaptive evolution of nontransgenic Escherichia coli KC01 for improved ethanol tolerance and homoethanol fermentation from xylose[J]. J Ind Microbiol Biotechnol, 2011, 38:1371-1377. [9] Khalil AS, Collins JJ. Synthetic biology:applications come of age[J]. Nat Rev Genet, 2010, 11:367-379. [10] Cadwell RC, Joyce GF. Randomization of genes by PCR mutagenesis[J]. PCR Methods Appl, 1992, 2:28-33. [11] van Summeren-Wesenhagen PV, Marienhagen J. Metabolic engineering of Escherichia coli for the synthesis of the plant polyphenol pinosylvin[J]. Appl Environ Microbiol, 2015, 81:840-849. [12] Wang W, Malcolm BA. Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using QuikChange site-directed mutagenesis[J]. Biotechniques, 1999, 26:680-682. [13] Bastian S, Liu X, Meyerowitz JT, et al. Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli[J]. Metab Eng, 2011, 13:345-352. [14] Firnberg E, Ostermeier M. PFunkel:efficient, expansive, user-defined mutagenesis[J]. PLoS One, 2012, 7:e52031. [15] Wang HH, Isaacs FJ, Carr PA, et al. Programming cells by multiplex genome engineering and accelerated evolution[J]. Nature, 2009, 460:894-898. [16] Ng CY, Farasat I, Maranas CD, et al. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration[J]. Metab Eng, 2015, 29:86-96. [17] Raman S, Rogers JK, Taylor ND, et al. Evolution-guided optimization of biosynthetic pathways[J]. Proc Natl Acad Sci USA, 2014, 111:17803-17808. [18] Isaacs FJ, Carr PA, Wang HH, et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement[J]. Science, 2011, 333:348-353. [19] Rovner AJ, Haimovich AD, Katz SR, et al. Recoded organisms engineered to depend on synthetic amino acids[J]. Nature, 2015, 518:89-93. [20] DiCarlo JE, Conley AJ, Penttila M, et al. Yeast oligo-mediated genome engineering(YOGE)[J]. ACS Synth Biol, 2013, 2:741-749. [21] Zhang YX, Perry K, Vinci VA, et al. Genome shuffling leads to rapid phenotypic improvement in bacteria[J]. Nature, 2002, 415:644-646. [22] Biot-Pelletier D, Martin VJJ. Evolutionary engineering by genome shuffling[J]. Appl Microbiol Biotechnol, 2014, 98:3877-3887. [23] Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013, 339:819-823. [24] Mali P, Yang L, Esvelt KM, et al. RNA-guided human genome engineering via Cas9[J]. Science, 2013, 339:823-826. [25] Shalem O, Sanjana NE, Hartenian E, et al. Genome-scale CRISPR-Cas9 knockout screening in humancells[J]. Science, 2014, 343:84-87. [26] Konermann S, Brigham MD, Trevino AE, et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex[J]. Nature, 2015, 517:583-588. [27] Jiang W, Bikard D, Cox D, et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems[J]. Nat Biotechnol, 2013, 31:233-239. [28] Findlay GM, Boyle EA, Hause RJ, et al. Saturation editing of genomic regions by multiplex homology-directed repair[J]. Nature, 2014, 513:120-123. [29] Pines G, Pines A, Garst AD, et al. Codon compression algorithms for saturation mutagenesis[J]. ACS Synth Biol, 2015, 4:604-614. [30] Horwitz AA, Walter JM, Schubert MG, et al. Efficient multiplexed integration ofsynergistic alleles and metabolic pathways in yeasts via CRISPR-Cas[J]. Cell Syst, 2015, 1:88-96. [31] Des Soye BJ, Patel JR, Isaacs FJ, et al. Repurposing the translation apparatus for synthetic biology[J]. Curr Opin Chem Biol, 2015, 28:83-90. [32] Orelle C, Carlson ED, Szal T, et al. Protein synthesis by ribosomes with tethered subunits[J]. Nature, 2015, 524:119-124. [33] Santos CNS, Regitsky DD, Yoshikuni Y. Implementation of stable and complex biological systems through recombinase-assisted genome engineering[J]. Nat Commun, 2013, 4:2503. [34] Gaida SM, Sandoval NR, Nicolaou SA, et al. Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries[J]. Nat Commun, 2015, 6:7045. [35] Zingaro KA, Nicolaou SA, Yuan Y, et al. Exploring the heterologous genomic space for building, stepwise, complex, multicomponent tolerance to toxic chemicals[J]. ACS Synth Biol, 2014, 3:476-486. [36] Xiao H, Bao Z, Zhao H. High throughput screening and selection methods for directed enzyme evolution[J]. Ind Eng Chem Res, 2015, 54:4011-4020. [37] Liu Y, Li Q, Zheng P, et al. Developing a high-throughputscreening method for threonine overproduction based on an artificial promoter[J]. Microb Cell Fact, 2015, 14:121. [38] Yang J, Seo SW, Jang S, et al. Synthetic RNA devices to expedite the evolution of metabolite-producing microbes[J]. Nat Commun, 2013, 4:1413. [39] Carothers JM, Goler JA, Juminaga D, et al. Model-driven engineering of RNA devices to quantitatively program gene expression[J]. Science, 2011, 334:1716-1719. [40] Tinberg CE, Khare SD, Dou J, et al. Computational design of ligand-binding proteins with high affinity and selectivity[J]. Nature, 2013, 501:212-216. [41] Brophy JAN, Voigt CA. Principles of genetic circuit design[J]. Nat Methods, 2014, 11:508-520. [42] Soma Y, Hanai T. Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production[J]. Metab Eng, 2015, 30:7-15. [43] Hoynes-O'Connor A, Hinman K, Kirchner L, et al. De novo design of heat-repressible RNA thermosensors in E. coli[J]. Nucleic Acids Res, 2015, 43:6166-6179. [44] Esvelt KM, Carlson JC, Liu DR. A system for the continuous directed evolution of biomolecules[J]. Nature, 2011, 472:499-503. [45] Carlson JC, Badran AH, Guggiana-Nilo DA, et al. Negative selection and stringency modulation in phage-assisted continuous evolution[J]. Nat Chem Biol, 2014, 10:216-222. [46] Xiao H, Nasertorabi F, Choi SH, et al. Exploring the potential impact of an expanded genetic code on protein function[J]. Proc Natl Acad Sci USA, 2015, 112:6961-6966. [47] Xu P, Vansiri A, Bhan N, et al. ePathBrick:a synthetic biology platform for engineering metabolic pathways in E. coli[J]. ACS Synth Biol, 2012, 1:256-266. [48] Jakociunas T, Rajkumar AS, Zhang J, et al. CasEMBLR:Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae[J]. ACS Synth Biol, 2015, 4(11):1226-1234. [49] Ajikumar PK, Xiao WH, Tyo KEJ, et al. Isoprenoid pathway optimization for taxol precursor verproduction in Escherichia coli[J]. Science, 2010, 330:70-74. [50] Dueber JE, Wu GC, Malmirchegini GR, et al. Synthetic protein scaffolds provide modular control over metabolic flux[J]. Nat Biotechnol, 2009, 27:753-759. [51] Martin VJJ, Pitera DJ, Withers ST, et al. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids[J]. Nat Biotechnol, 2003, 21:796-802. [52] Xu P, Gu Q, Wang W, et al. Modular optimization of multi-gene pathways for fatty acids production in E. coli[J]. Nat Commun, 2013, 4:1409. [53] Temme K, Zhao D, Voigt CA. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca[J]. Proc Natl Acad Sci USA, 2012, 109:7085-7090. [54] Gimpel JA, Nour-Eldin HH, Scranton MA, et al. Refactoring the six-gene photosystem II core in the chloroplast of the green algae Chlamydomonas reinhardtii[J]. ACS Synth Biol, 2015, 5(7):589-596. [55] Zhang H, Wang Y, Wu J, et al. Complete biosynthesis of erythromycin A and designed analogs using E. coli as a heterologous host[J]. Chem Biol, 2010, 17:1232-1240. [56] Ma NJ, Moonan DW, Isaacs FJ. Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering[J]. Nat Protoc, 2014, 9(10):2285-300. [57] Mandell DJ, Lajoie MJ, Mee MT, et al. Biocontainment of genetically modified organisms by synthetic protein design[J]. Nature, 2015, 518:55-60. [58] Gibson DG, Glass JI, Lartigue C, et al. Creation of a bacterial cell controlled by a chemicallysynthesized genome[J]. Science, 2010, 329:52-56. [59] Annaluru N, Muller H, Mitchell LA, et al. Total synthesis of a functional designer eukaryotic chromosome[J]. Science, 2014, 344:55-58. [60] Christen M, Deutsch S, Christen B. Genome calligrapher:a web tool for refactoring bacterial genome sequences for de novo DNA synthesis[J]. ACS Synth Biol, 2015, 4:927-934. [61] Mee MT, Collins JJ, Church GM, et al. Syntrophic exchange in synthetic microbial communities[J]. Proc Natl Acad Sci USA, 2014, 111:E2149-E2156. [62] Youk H, Lim WA. Secreting and sensing the same molecule allows cells to achieve versatile social behaviors[J]. Science, 2014, 343:1242782. [63] Minty JJ, Singer ME, Scholz SA, et al. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass[J]. Proc Natl Acad Sci USA, 2013, 110:14592-14597. [64] Zhang H, Pereira B, Li Z, et al. Engineering Escherichia coli coculture systems for the production of biochemical products[J]. Proc Natl Acad Sci USA, 2015, 112:8266-8271. |
[1] | XUE Ning, WANG Jin, LI Shi-xin, LIU Ye, CHENG Hai-jiao, ZHANG Yue, MAO Yu-feng, WANG Meng. Construction of L-phenylalanine High-producing Corynebacterium glutamicum Engineered Strains via Multi-gene Simultaneous Regulation Combined with High-throughput Screening [J]. Biotechnology Bulletin, 2023, 39(9): 268-280. |
[2] | CHENG Ya-nan, ZHANG Wen-cong, ZHOU Yuan, SUN Xue, LI Yu, LI Qing-gang. Synthetic Pathway Construction of Producing 2'-fucosyllactose by Lactococcus lactis and Optimization of Fermentation Medium [J]. Biotechnology Bulletin, 2023, 39(9): 84-96. |
[3] | ZHAO Si-jia, WANG Xiao-lu, SUN Ji-lu, TIAN Jian, ZHANG Jie. Modification of Pichia pastoris for Erythritol Production by Metabolic Engineering [J]. Biotechnology Bulletin, 2023, 39(8): 137-147. |
[4] | LI Yu-zhen, MEI Tian-xiu, LI Zhi-wen, WANG Qi, LI Jun, ZOU Yue, ZHAO Xin-qing. Advances in Genomic Studies and Metabolic Engineering of Red Yeasts [J]. Biotechnology Bulletin, 2023, 39(7): 67-79. |
[5] | CHENG Ting, YUAN Shuai, ZHANG Xiao-yuan, LIN Liang-cai, LI Xin, ZHANG Cui-ying. Research Progress in the Regulation of Isobutanol Synthesis Pathway in Saccharomyces cerevisiae [J]. Biotechnology Bulletin, 2023, 39(7): 80-90. |
[6] | YU Hui-li, LI Ai-tao. Application of Cytochrome P450 in the Biosynthesis of Flavors and Fragrances [J]. Biotechnology Bulletin, 2023, 39(4): 24-37. |
[7] | WANG Xiao-mei, YANG Xiao-wei, LI Hui-shang, HE Wei, XIN Zhu-lin. Development Status of Synthetic Biology in Globe and Its Enlightenment [J]. Biotechnology Bulletin, 2023, 39(2): 292-302. |
[8] | CHEN Xiao-lin, LIU Yang-er, XU Wen-tao, GUO Ming-zhang, LIU Hui-lin. Application of Synthetic Biology Based Whole-cell Biosensor Technology in the Rapid Detection of Food Safety [J]. Biotechnology Bulletin, 2023, 39(1): 137-149. |
[9] | ZHOU Lin, LIANG Xuan-ming, ZHAO Lei. Biosynthesis of Natural Carotenoids:Progress and Perspective [J]. Biotechnology Bulletin, 2022, 38(7): 119-127. |
[10] | QIU Yi-bin, MA Yan-qin, SHA Yuan-yuan, ZHU Yi-fan, SU Er-zheng, LEI Peng, LI Sha, XU Hong. Research Progress in Molecular Genetic Manipulation Technology of Bacillus amyloliquefaciens and Its Application [J]. Biotechnology Bulletin, 2022, 38(2): 205-217. |
[11] | MA Yan-qin, QIU Yi-bin, LI Sha, XU Hong. Research Progress in the Biosynthesis and Metabolic Engineering of Hyaluronic Acid [J]. Biotechnology Bulletin, 2022, 38(2): 252-262. |
[12] | GUO Xiao-zhen, ZHANG Xue-fu. Analysis of the Development Trend in the Field of Plant Synthetic Biology [J]. Biotechnology Bulletin, 2022, 38(2): 289-296. |
[13] | ZHAO Yu-xue, WANG Yun, YU Lu-yao, LIU Jing-jing, SI Jin-ping, ZHANG Xin-feng, ZHANG Lei. Structure and Application of C-glycosyltransferases in Plants [J]. Biotechnology Bulletin, 2022, 38(10): 18-28. |
[14] | YE Min, GAO Jiao-qi, ZHOU Yong-jin. Engineering Non-conventional Yeast Cell Factory for the Biosynthesis of Natural Products [J]. Biotechnology Bulletin, 2021, 37(8): 12-24. |
[15] | ZHANG Chan, YAO Guang-long, ZHANG Jun-feng, YU Jing, YANG Dong-mei, CHEN Ping, WU You-gen. Research Progress on Patchoulol Molecular Regulation and Synthetic Biology in Pogostemon cablin [J]. Biotechnology Bulletin, 2021, 37(8): 55-64. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||