Biotechnology Bulletin ›› 2017, Vol. 33 ›› Issue (1): 83-92.doi: 10.13560/j.cnki.biotech.bull.1985.2017.01.009
• Orignal Article • Previous Articles Next Articles
MA Fu-qiang1, YANG Guang-yu1, 2
Received:
2016-10-14
Online:
2017-01-25
Published:
2017-01-19
MA Fu-qiang, YANG Guang-yu. Ultra-high-throughput Screening System Based on Droplet Microfluidics and Its Applications in Synthetic Biology[J]. Biotechnology Bulletin, 2017, 33(1): 83-92.
[1] Lartigue C, Glass JI, Alperovich N, et al. Genome transplantation in bacteria:Changing one species to another[J]. Science, 2007, 317(5838):632-638. [2] Annaluru N, Muller H, Mitchell LA, et al. Total synthesis of a functional designer eukaryotic chromosome[J]. Science, 2014, 344(6179):55-58. [3] Ro DK, Paradise EM, Ouellet M, et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast[J]. Nature, 2006, 440(7086):940-943. [4] 陈大明, 刘晓, 毛开云, 等. 合成生物学应用产品开发现状与趋势[J]. 中国生物工程杂志, 2016, 7:117-126. [5] Manyika J, Chui M, Bughin J, et al. Disruptive technologies:Advances that will transform life, business, and the global economy[M]. McKinsey Global Institute San Francisco, CA, 2013. [6] Denard CA, Ren H, Zhao H. Improving and repurposing biocatalysts via directed evolution[J]. Current Opinion in Chemical Biology, 2015, 25:55-64. [7] Currin A, Swainston N, Day PJ, et al. Synthetic biology for the directed evolution of protein biocatalysts:Navigating sequence space intelligently[J]. Chemical Society Reviews, 2014, 44(5):1172-239. [8] Tizei PAG, Csibra E, Torres L, et al. Selection platforms for directed evolution in synthetic biology[J]. Biochemical Society Transactions, 2016, 44(4):1165-1175. [9] Williams TC, Pretorius IS, Paulsen IT. Synthetic evolution of metabolic productivity using biosensors[J]. Trends in biotechnology, 2016, 34(5):371-381. [10] 林炳承, 秦建华. 图解微流控芯片实验室[M]. 北京:科学出版社, 2008. [11] Kintses B, Vliet LDV, Devenish SR, et al. Microfluidic droplets:New integrated workflows for biological experiments[J]. Current Opinion in Chemical Biology, 2010, 14(5):548-555. [12] Wen N, Zhao Z, Fan B, et al. Development of droplet microfluidics enabling high-throughput single-cell analysis[J]. Molecules, 2016, 21(7):E881. [13] Kaminski TS, Scheler O, Garstecki P. Droplet microfluidics for microbiology:Techniques, applications and challenges[J]. Lab on A Chip, 2016, 16(12):2168-2187. [14] Chou WL, Lee PY, Yang CL, et al. Recent advances in applications of droplet microfluidics[J]. Micromachines, 2015, 6(9):1249-1271. [15] Mastrobattista E, Taly V, Chanudet E, et al. High-throughput screening of enzyme libraries:In vitro evolution of a β-galactosidase by fluorescence-activated sorting of double emulsions[J]. Chemistry & Biology, 2005, 12(12):1291-1300. [16] Hardiman E, Gibbs M, Reeves R, et al. Directed evolution of a thermophilic β-glucosidase for cellulosic bioethanol production[J]. Applied Biochemistry and Biotechnology, 2010, 161(1-8):301-312. [17] Ma F, Xie Y, Huang C, et al. An improved single cell ultrahigh throughput screening method based on in vitro compartmentalization[J]. PLoS One, 2014, 9(2):e89785. [18] Tu R, Martinez R, Prodanovic R, et al. A flow cytometry-based screening system for directed evolution of proteases[J]. Journal of Biomolecular Screening, 2011, 16(3):285-294. [19] Agresti JJ, Antipov E, Abate AR, et al. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution[J]. Proceedings of the National Academy of Sciences, 2010, 107(9):4004-4009. [20] Aharoni A, Amitai G, Bernath K, et al. High-throughput screening of enzyme libraries:Thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments[J]. Chemistry & Biology, 2005, 12(12):1281-1289. [21] Varadarajan N, Gam J, Olsen MJ, et al. Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity[J]. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(19):6855-6860. [22] Varadarajan N, Rodriguez S, Hwang BY, et al. Highly active and selective endopeptidases with programmed substrate specificities[J]. Nature Chemical Biology, 2008, 4(5):290-294. [23] Varadarajan N, Georgiou G, Iverson BL, et al. An engineered protease that cleaves specifically after sulfated tyrosine[J]. Angewandte Chemie, 2007, 47(41):7861-7863. [24] Yang Y, Babiak P, Reymond JL. Low background fret-substrates for lipases and esterases suitable for high-throughput screening under basic(pH 11)conditions[J]. Organic & Biomolecular Chemistry, 2006, 4(9):1746-1754. [25] Mizukami S, Watanabe S, Hori Y, et al. Covalent protein labeling based on noncatalytic β-lactamase and a designed fret substrate[J]. Journal of the American Chemical Society, 2009, 131(14):5016-5017. [26] Yang GY, Li C, Fischer M, et al. A fret probe for cell-based imaging of ganglioside-processing enzyme activity and high-throughput screening[J]. Angewandte Chemie International Edition in English, 2015, 54(18):5389-5893. [27] Bjerregaard S, Pedersen H, Vedstesen H, et al. Parenteral water/oil emulsions containing hydrophilic compounds with enhanced in vivo retention:Formulation, rheological characterisation and study of in vivo fate using whole body gamma-scintigraphy[J]. International Journal of Pharmaceutics, 2001, 215(1):13-27. [28] Pays K, Giermanska-Kahn J, Pouligny B, et al. Double emulsions:How does release occur?[J]. Journal of Controlled Release, 2002, 79(1):193-205. [29] Cheng J, Chen JF, Zhao M, et al. Transport of ions through the oil phase of w 1/o/w 2 double emulsions[J]. Journal of Colloid and Interface Science, 2007, 305(1):175-182. [30] Wen L, Papadopoulos KD. Visualization of water transport in w 1/o/w 2 emulsions[J]. Colloids and surfaces A:Physicochemical and Engineering Aspects, 2000, 174(1):159-167. [31] Prodanovic R, Ostafe R, Blanusa M, et al. Vanadium bromoperoxi-dase-coupled fluorescent assay for flow cytometry sorting of glucose oxidase gene libraries in double emulsions[J]. Analytical and Bioanalytical Chemistry, 2012, 404(5):1439-1447. [32] Woronoff G, El Harrak A, Mayot E, et al. New generation of amino coumarin methyl sulfonate-based fluorogenic substrates for amidase assays in droplet-based microfluidic applications[J]. Analytical Chemistry, 2011, 83(8):2852-2857. [33] Najah M, Mayot E, Mahendra-Wijaya IP, et al. New glycosidase substrates for droplet-based microfluidic screening[J]. Analytical Chemistry, 2013, 85(20):9807-9814. [34] Ma F, Fischer M, Han Y, et al. Substrate engineering enabling fluorescence droplet entrapment for ivc-facs based ultrahigh-throughput screening[J]. Analytical Chemistry, 2016, 88(17):8587-8595. [35] Hammar P, Angermayr SA, Sjostrom SL, et al. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria[J]. Biotechnology for Biofuels, 2015, 8(1):193-201. [36] Wang BL, Ghaderi A, Zhou H, et al. Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption[J]. Nature Biotechnology, 2014, 32(5):473-478. [37] Abalde-Cela S, Gould A, Liu X, et al. High-throughput detection of ethanol-producing cyanobacteria in a microdroplet platform[J]. Journal of The Royal Society Interface, 2015, 12(106):20150216. [38] Ostafe R, Prodanovic R, Nazor J, et al. Ultra-high-throughput screening method for the directed evolution of glucose oxidase[J]. Chemistry & Biology, 2014, 21(3):414-421. [39] Ostafe R, Prodanovic R, Ung WL, et al. A high-throughput cellulase screening system based on droplet microfluidics[J]. Biomicrofluidics, 2014, 8(4):041102. [40] The lac operon:A short history of a genetic paradigm[M]. Walter de Gruyter, 1996. [41] Gallegos MT, Schleif R, Bairoch A, et al. Arac/xyls family of transcriptional regulators[J]. Microbiology & Molecular Biology Reviews Mmbr, 1997, 61(4):393-410. [42] Ramos JL, Martínezbueno M, Molinahenares AJ, et al. The tetr family of transcriptional repressors[J]. Microbiology & Molecular Biology Reviews, 2005, 69(2):326-356. [43] Tropel D, Jr VDM. Bacterial transcriptional regulators for degradation pathways of aromatic compounds[J]. Microbiology & Molecular Biology Reviews, 2004, 68(3):474-500. [44] Link KH, Breaker RR. Engineering ligand-responsive gene-control elements:Lessons learned from natural riboswitches[J]. Gene Therapy, 2009, 16(10):1189-1201. [45] Sudarsan N, Wickiser JK, Nakamura S, et al. An mrna structure in bacteria that controls gene expression by binding lysine[J]. Genes & Development, 2003, 17(21):2688-2697. [46] Cheng F, Kardashliev T, Pitzler C, et al. A competitive flow cytometry screening system for directed evolution of therapeutic enzyme[J]. Acs SyntheticBiology, 2015, 4(7):768-775. [47] Siedler S, Schendzielorz G, Binder S, et al. Soxr as a single-cell biosensor for nadph-consuming enzymes in Escherichia coli[J]. Acs Synthetic Biology, 2014, 3(1):41-47. [48] Schallmey M, Frunzke J, Eggeling L, et al. Looking for the pick of the bunch:High-throughput screening of producing microorganisms with biosensors[J]. Current Opinion in Biotechnology, 2014, 26C(26C):148-154. [49] Binder S, Schendzielorz G, Stäbler N, et al. A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level[J]. Genome Biology, 2012, 13(5):405-413. [50] Fang M, Wang T, Chong Z, et al. Intermediate-sensor assisted push-pull strategy and its application in heterologous deoxyviolacein production in Escherichia coli[J]. Metabolic Engineering, 2015, 33:41-51. [51] Pitzler C, Wirtz G, Vojcic L, et al. A fluorescent hydrogel-based flow cytometry high-throughput screening platform for hydrolytic enzymes[J]. Chemistry & Biology, 2014, 21(12):1733-1742. [52] Larsen AC, Dunn MR, Hatch A, et al. A general strategy for expanding polymerase function by droplet microfluidics[J]. Nature Communications, 2016, 7:11235. [53] Fischlechner M, Schaerli Y, Mohamed MF, et al. Evolution of enzyme catalysts caged in biomimetic gel-shell beads[J]. Nature Chemistry, 2014, 6(9):791-796. [54] Woronoff G, Ryckelynck M, Wessel J, et al. Activity-fed translation(aft)assay:A new high-throughput screening strategy for enzymes in droplets[J]. Chembiochem, 2015, 16(9):1343-1349. [55] 韩云宾, 黄琛, 冯雁. 催化元件和途径的人工设计与组装[J]. 生命科学, 2011, 23(9):869-874. [56] Kintses B, Hein C, Mohamed MF, et al. Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution[J]. Chemistry & Biology, 2012, 19(8):1001-1009. [57] Hosokawa M, Hoshino Y, Nishikawa Y, et al. Droplet-based microfluidics for high-throughput screening of a metagenomic library for isolation of microbial enzymes[J]. Biosensors and Bioelectronics, 2015, 67:379-385. [58] Colin PY, Kintses B, Gielen F, et al. Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics[J]. Nature Communications, 2015, 6:10008. [59] Stapleton JA, Swartz JR. Development of an in vitro compartmentalization screen for high-throughput directed evolution of[FeFe]hydrogenases[J]. PLoS One, 2010, 5(12):e15275. [60] Ryckelynck M, Baudrey S, Rick C, et al. Using droplet-based microfluidics to improve the catalytic properties of rna under multiple-turnover conditions[J]. RNA, 2015, 21(3):458-469. [61] Obexer R, Pott M, Zeymer C, et al. Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated droplet sorting[J]. Protein Engineering Design and Selection, 2016, 29(9):355-366. [62] Sjostrom SL, Bai Y, Huang M, et al. High-throughput screening for industrial enzyme production hosts by droplet microfluidics[J]. Lab on a Chip, 2014, 14(4):806-813. [63] Huang M, Bai Y, Sjostrom SL, et al. Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast[J]. Proceedings of the National Academy of Sciences, 2015, 112(34):E4689-E4696. [64] Jang S, Lee B, Jeong HH, et al. On-chip analysis, indexing and screening for chemical producing bacteria in microfluidic static droplet array[J]. Lab on a Chip, 2016, 16(10):1909-1916. [65] Smith CA, Li X, Mize TH, et al. Sensitive, high throughput detection of proteins in individual, surfactant-stabilized picoliter droplets using nanoelectrospray ionization mass spectrometry[J]. Analytical Chemistry, 2013, 85(8):3812-3816. [66] Sun S, Kennedy RT. Droplet electrospray ionization mass spectrometry for high throughput screening for enzyme inhibitors[J]. Analytical Chemistry, 2014, 86(18):9309-9314. [67] Meier TA, Beulig R, Klinge E, et al. On-chip monitoring of chemical syntheses in microdroplets via surface-enhanced raman spectroscopy[J]. Chemical Communications, 2015, 51(41):8588-8591. [68] Stehle R, Goerigk G, Wallacher D, et al. Small-angle x-ray scattering in droplet-based microfluidics[J]. Lab on a Chip, 2013, 13(8):1529-1537. [69] Cheow LF, Viswanathan R, Chin CS, et al. Multiplexed analysis of protein-ligand interactions by fluorescence anisotropy in a microfluidic platform[J]. Analytical Chemistry, 2014, 86(19):9901-9908. [70] Choi JW, Min KM, Hengoju S, et al. A droplet-based microfluidic immunosensor for high efficiency melamine analysis[J]. Biosensors & Bioelectronics, 2015, 80:182-186. [71] Niu X, Pereira F, Edel JB, et al. Droplet-interfaced microchip and capillary electrophoretic separations[J]. Analytical Chemistry, 2013, 85(18):8654-8660. |
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