Engineering Cellular Metabolism

Cell

Volumn 164, Issue 6, 2016, Pages 1185-1197

  Nielsen, Jens ^a,b,c   Keasling, Jay D ^b,d,e,f,g  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^d JOINT BIOENERGY INSTITUTE   (United States)

^e University of California at Berkeley   (United States)

^f LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

cell factories; industrial biotechnology; metabolic engineering; metabolism; regulation; synthetic biology

Indexed keywords

ASPERGILLUS NIGER; BACILLUS SUBTILIS; BIOINFORMATICS; BIOPROCESS; BIOSYNTHESIS; CELL METABOLISM; CHEMICAL INDUSTRY; CHO CELL LINE; CORYNEBACTERIUM GLUTAMICUM; DNA SEQUENCE; ESCHERICHIA COLI; GENE EXPRESSION; HIGH THROUGHPUT SCREENING; METABOLIC ENGINEERING; METABOLITE; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; RNA SEQUENCE; SACCHAROMYCES CEREVISIAE; ANIMAL; BACTERIUM; CLASSIFICATION; CRICETULUS; DRUG DEVELOPMENT; FUNGUS; METABOLISM; MICROBIOLOGY; PROCEDURES;

BIOLOGICAL PRODUCT;

ANIMALS; BACTERIA; BIOLOGICAL PRODUCTS; BIOSYNTHETIC PATHWAYS; CHO CELLS; CRICETULUS; DRUG DISCOVERY; ESCHERICHIA COLI; FUNGI; INDUSTRIAL MICROBIOLOGY; METABOLIC ENGINEERING; SACCHAROMYCES CEREVISIAE;

EID: 84960460639     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2016.02.004     Document Type: Review

References (112)

1. P.K. Ajikumar, W.-H. Xiao, K.E. Tyo, Y. Wang, F. Simeon, E. Leonard, O. Mucha, T.H. Phon, B. Pfeifer, and G. Stephanopoulos Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli Science 330 2010 70 74
2. J. Alonso-Gutierrez, E.-M. Kim, T.S. Batth, N. Cho, Q. Hu, L.J.G. Chan, C.J. Petzold, N.J. Hillson, P.D. Adams, J.D. Keasling, and et al. Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering Metab. Eng. 28 2015 123 133
3. H. Alper, and G. Stephanopoulos Global transcription machinery engineering: a new approach for improving cellular phenotype Metab. Eng. 9 2007 258 267
4. J.L. Avalos, G.R. Fink, and G. Stephanopoulos Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols Nat. Biotechnol. 31 2013 335 341
5. J.E. Bailey Toward a science of metabolic engineering Science 252 1991 1668 1675
6. I. Bakke, L. Berg, T.E. Aune, T. Brautaset, H. Sletta, A. Tondervik, and S. Valla Random mutagenesis of the PM promoter as a powerful strategy for improvement of recombinant-gene expression Appl. Environ. Microbiol. 75 2009 2002 2011
7. V.M. Boer, C.A. Crutchfield, P.H. Bradley, D. Botstein, and J.D. Rabinowitz Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations Mol. Biol. Cell 21 2010 198 211
8. M.P. Brynildsen, J.A. Winkler, C.S. Spina, I.C. MacDonald, and J.J. Collins Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production Nat. Biotechnol. 31 2013 160 165
9. L. Caspeta, and J. Nielsen Economic and environmental impacts of microbial biodiesel Nat. Biotechnol. 31 2013 789 793
10. L. Caspeta, Y. Chen, P. Ghiaci, A. Feizi, S. Buskov, B.M. Hallström, D. Petranovic, and J. Nielsen Biofuels. Altered sterol composition renders yeast thermotolerant Science 346 2014 75 78
11. Y. Chen, V. Siewers, and J. Nielsen Profiling of cytosolic and peroxisomal acetyl-CoA metabolism in Saccharomyces cerevisiae PLoS ONE 7 2012 e42475
12. J. Chen, D. Densmore, T.S. Ham, J.D. Keasling, and N.J. Hillson DeviceEditor visual biological CAD canvas J. Biol. Eng. 6 2012 1
13. X. Chen, L. Zhou, K. Tian, A. Kumar, S. Singh, B.A. Prior, and Z. Wang Metabolic engineering of Escherichia coli: a sustainable industrial platform for bio-based chemical production Biotechnol. Adv. 31 2013 1200 1223
14. Y. Chen, L. Daviet, M. Schalk, V. Siewers, and J. Nielsen Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism Metab. Eng. 15 2013 48 54
15. Y.J. Choi, and S.Y. Lee Microbial production of short-chain alkanes Nature 502 2013 571 574
16. H.H. Chou, and J.D. Keasling Programming adaptive control to evolve increased metabolite production Nat. Commun. 4 2013 2595
17. L. Crawford, A.M. Stepan, P.C. McAda, J.A. Rambosek, M.J. Conder, V.A. Vinci, and C.D. Reeves Production of cephalosporin intermediates by feeding adipic acid to recombinant Penicillium chrysogenum strains expressing ring expansion activity Biotechnology (N. Y.) 13 1995 58 62
18. R.H. Dahl, F. Zhang, J. Alonso-Gutierrez, E. Baidoo, T.S. Batth, A.M. Redding-Johanson, C.J. Petzold, A. Mukhopadhyay, T.S. Lee, P.D. Adams, and J.D. Keasling Engineering dynamic pathway regulation using stress-response promoters Nat. Biotechnol. 31 2013 1039 1046
19. F. David, and V. Siewers Advances in yeast genome engineering FEMS Yeast Res. 15 2014 1 14
20. W.A. de Jongh, C. Bro, S. Ostergaard, B. Regenberg, L. Olsson, and J. Nielsen The roles of galactitol, galactose-1-phosphate, and phosphoglucomutase in galactose-induced toxicity in Saccharomyces cerevisiae Biotechnol. Bioeng. 101 2008 317 326
21. J.A. Dietrich, D.L. Shis, A. Alikhani, and J.D. Keasling Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis ACS Synth. Biol. 2 2013 47 58
22. K.A. Donald, R.Y. Hampton, and I.B. Fritz Effects of overproduction of the catalytic domain of 3-hydroxy-3-methylglutaryl coenzyme A reductase on squalene synthesis in Saccharomyces cerevisiae Appl. Environ. Microbiol. 63 1997 3341 3344
23. M. Dragosits, and D. Mattanovich Adaptive laboratory evolution - principles and applications for biotechnology Microb. Cell Fact. 12 2013 64
24. J.E. Dueber, G.C. Wu, G.R. Malmirchegini, T.S. Moon, C.J. Petzold, A.V. Ullal, K.L. Prather, and J.D. Keasling Synthetic protein scaffolds provide modular control over metabolic flux Nat. Biotechnol. 27 2009 753 759
25. M. Farhi, E. Marhevka, T. Masci, E. Marcos, Y. Eyal, M. Ovadis, H. Abeliovich, and A. Vainstein Harnessing yeast subcellular compartments for the production of plant terpenoids Metab. Eng. 13 2011 474 481
26. W.R. Farmer, and J.C. Liao Improving lycopene production in Escherichia coli by engineering metabolic control Nat. Biotechnol. 18 2000 533 537
27. S. Galanie, K. Thodey, I.J. Trenchard, M. Filsinger Interrante, and C.D. Smolke Complete biosynthesis of opioids in yeast Science 349 2015 1095 1100
28. M.A. Garcia-Albornoz, and J. Nielsen Application of genome-scale metabolic models in metabolic engineering J. Ind. Microbiol. Biotechnol. 9 2013 203 214
29. L.A. Gilbert, M.H. Larson, L. Morsut, Z. Liu, G.A. Brar, S.E. Torres, N. Stern-Ginossar, O. Brandman, E.H. Whitehead, J.A. Doudna, and et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes Cell 154 2013 442 451
30. R.T. Gill, J.J. Valdes, and W.E. Bentley A comparative study of global stress gene regulation in response to overexpression of recombinant proteins in Escherichia coli Metab. Eng. 2 2000 178 189
31. N. Hadadi, and V. Hatzimanikatis Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways Curr. Opin. Chem. Biol. 28 2015 99 104
32. K.-K. Hong, W. Vongsangnak, G.N. Vemuri, and J. Nielsen Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis Proc. Natl. Acad. Sci. USA 108 2011 12179 12184
33. M. Huang, Y. Bai, S.L. Sjostrom, B.M. Hallström, Z. Liu, D. Petranovic, M. Uhlén, H.N. Joensson, H. Andersson-Svahn, and J. Nielsen Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast Proc. Natl. Acad. Sci. USA 112 2015 E4689 E4696
34. R.U. Ibarra, J.S. Edwards, and B.O. Palsson Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth Nature 420 2002 186 189
35. T. Jakočiunas, I. Bonde, M. Herrgård, S.J. Harrison, M. Kristensen, L.E. Pedersen, M.K. Jensen, and J.D. Keasling Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae Metab. Eng. 28 2015 213 222
36. P.R. Jensen, and K. Hammer The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters Appl. Environ. Microbiol. 64 1998 82 87
37. M.K. Jensen, and J.D. Keasling Recent applications of synthetic biology tools for yeast metabolic engineering FEMS Yeast Res. 15 2014 1 10
38. M. Jinek, K. Chylinski, I. Fonfara, M. Hauer, J.A. Doudna, and E. Charpentier A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity Science 337 2012 816 821
39. J.D. Keasling Manufacturing molecules through metabolic engineering Science 330 2010 1355 1358
40. A. Khlebnikov, K.A. Datsenko, T. Skaug, B.L. Wanner, and J.D. Keasling Homogeneous expression of the P(BAD) promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter Microbiology 147 2001 3241 3247
41. T.Y. Kim, S.B. Sohn, Y.B. Kim, W.J. Kim, and S.Y. Lee Recent advances in reconstruction and applications of genome-scale metabolic models Curr. Opin. Biotechnol. 23 2012 617 623
42. L. Kizer, D.J. Pitera, B.F. Pfleger, and J.D. Keasling Application of functional genomics to pathway optimization for increased isoprenoid production Appl. Environ. Microbiol. 74 2008 3229 3241
43. A.A. Komar, and M. Hatzoglou Internal ribosome entry sites in cellular mRNAs: mystery of their existence J. Biol. Chem. 280 2005 23425 23428
44. F. Koopman, J. Beekwilder, B. Crimi, A. van Houwelingen, R.D. Hall, D. Bosch, A.J.A. van Maris, J.T. Pronk, and J.-M. Daran De novo production of the flavonoid naringenin in engineered Saccharomyces cerevisiae Microb. Cell Fact. 11 2012 155
45. S. Kosuri, and G.M. Church Large-scale de novo DNA synthesis: technologies and applications Nat. Methods 11 2014 499 507
46. B.U. Kozak, H.M. van Rossum, K.R. Benjamin, L. Wu, J.M. Daran, J.T. Pronk, and A.J. van Maris Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis Metab. Eng. 21 2014 46 59
47. B.U. Kozak, H.M. van Rossum, M.A.H. Luttik, M. Akeroyd, K.R. Benjamin, L. Wu, S. de Vries, J.-M. Daran, J.T. Pronk, and A.J.A. van Maris Engineering acetyl coenzyme A supply: functional expression of a bacterial pyruvate dehydrogenase complex in the cytosol of Saccharomyces cerevisiae MBio 5 2014 e01696-e14
48. A. Krivoruchko, Y. Zhang, V. Siewers, Y. Chen, and J. Nielsen Microbial acetyl-CoA metabolism and metabolic engineering Metab. Eng. 28 2015 28 42
49. M. Kuyper, M.J. Toirkens, J.A. Diderich, A.A. Winkler, J.P. van Dijken, and J.T. Pronk Evolutionary engineering of mixed-sugar utilization by a xylose-fermenting Saccharomyces cerevisiae strain FEMS Yeast Res. 5 2005 925 934
50. E.S. Langer Biomanufacturing outsourcing outlook Biopharm International 25 2012 http://www.biopharminternational.com/biomanufacturing-outsourcing-outlook
51. S.K. Lee, and J.D. Keasling A propionate-inducible expression system for enteric bacteria Appl. Environ. Microbiol. 71 2005 6856 6862
52. S.Y. Lee, and H.U. Kim Systems strategies for developing industrial microbial strains Nat. Biotechnol. 33 2015 1061 1072
53. T.S. Lee, R.A. Krupa, F. Zhang, M. Hajimorad, W.J. Holtz, N. Prasad, S.K. Lee, and J.D. Keasling BglBrick vectors and datasheets: A synthetic biology platform for gene expression J. Biol. Eng. 5 2011 12
54. M.E. Lee, W.C. DeLoache, B. Cervantes, and J.E. Dueber A highly characterized yeast toolkit for modular, multipart assembly ACS Synth. Biol. 4 2015 975 986
55. M. Li, K.R. Kildegaard, Y. Chen, A. Rodriguez, I. Borodina, and J. Nielsen De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae Metab. Eng. 32 2015 1 11
56. V.J.J. Martin, D.J. Pitera, S.T. Withers, J.D. Newman, and J.D. Keasling Engineering a mevalonate pathway in Escherichia coli for production of terpenoids Nat. Biotechnol. 21 2003 796 802
57. D. Murdock, B.D. Ensley, C. Serdar, and M. Thalen Construction of metabolic operons catalyzing the de novo biosynthesis of indigo in Escherichia coli Biotechnology (N. Y.) 11 1993 381 386
58. D. Na, S.M. Yoo, H. Chung, H. Park, J.H. Park, and S.Y. Lee Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Nat. Biotechnol. 31 2013 170 174
59. C.E. Nakamura, and G.M. Whited Metabolic engineering for the microbial production of 1,3-propanediol Curr. Opin. Biotechnol. 14 2003 454 459
60. F.C. Neidhardt, J.L. Ingraham, and M. Schaechter Physiology of the Bacterial Cell 1990 Sinauer Associates Sunderland, MA
61. J. Nielsen Metabolic engineering Appl. Microbiol. Biotechnol. 55 2001 263 283
62. J. Nielsen It is all about metabolic fluxes J. Bacteriol. 185 2003 7031 7035
63. J. Nielsen Systems biology of lipid metabolism: from yeast to human FEBS Lett. 583 2009 3905 3913
64. J. Nielsen Synthetic biology for engineering acetyl coenzyme A metabolism in yeast MBio 5 2014 e02153
65. J. Nielsen BIOENGINEERING. Yeast cell factories on the horizon Science 349 2015 1050 1051
66. T.L. Nissen, M.C. Kielland-Brandt, J. Nielsen, and J. Villadsen Optimization of ethanol production in Saccharomyces cerevisiae by metabolic engineering of the ammonium assimilation Metab. Eng. 2 2000 69 77
67. E.J. O'Brien, and B.O. Palsson Computing the functional proteome: recent progress and future prospects for genome-scale models Curr. Opin. Biotechnol. 34 2015 125 134
68. E.J. O'Brien, J.M. Monk, and B.O. Palsson Using genome-scale models to predict biological capabilities Cell 161 2015 971 987
69. S. Ostergaard, L. Olsson, M. Johnston, and J. Nielsen Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network Nat. Biotechnol. 18 2000 1283 1286
70. T. Österlund, S. Bordel, and J. Nielsen Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors Integr Biol (Camb) 7 2015 560 568
71. J.M. Otero, D. Cimini, K.R. Patil, S.G. Poulsen, L. Olsson, and J. Nielsen Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory PLoS ONE 8 2013 e54144
72. C.J. Paddon, P.J. Westfall, D.J. Pitera, K. Benjamin, K. Fisher, D. McPhee, M.D. Leavell, A. Tai, A. Main, D. Eng, and et al. High-level semi-synthetic production of the potent antimalarial artemisinin Nature 496 2013 528 532
73. J.H. Park, K.H. Lee, T.Y. Kim, and S.Y. Lee Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation Proc. Natl. Acad. Sci. USA 104 2007 7797 7802
74. S.H. Park, H.U. Kim, T.Y. Kim, J.S. Park, S.-S. Kim, and S.Y. Lee Metabolic engineering of Corynebacterium glutamicum for L-arginine production Nat. Commun. 5 2014 4618
75. K.R. Patil, and J. Nielsen Uncovering transcriptional regulation of metabolism by using metabolic network topology Proc. Natl. Acad. Sci. USA 102 2005 2685 2689
76. R. Patnaik, and J.C. Liao Engineering of Escherichia coli central metabolism for aromatic metabolite production with near theoretical yield Appl. Environ. Microbiol. 60 1994 3903 3908
77. R. Patnaik, R.G. Spitzer, and J.C. Liao Pathway engineering for production of aromatics in Escherichia coli: Confirmation of stoichiometric analysis by independent modulation of AroG, TktA, and Pps activities Biotechnol. Bioeng. 46 1995 361 370
78. B.F. Pfleger, D.J. Pitera, C.D. Smolke, and J.D. Keasling Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes Nat. Biotechnol. 24 2006 1027 1032
79. J. Qin, Y.J. Zhou, A. Krivoruchko, M. Huang, L. Liu, S. Khoomrung, V. Siewers, B. Jiang, and J. Nielsen Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine Nat. Commun. 6 2015 8224
80. H. Redden, and H.S. Alper The development and characterization of synthetic minimal yeast promoters Nat. Commun. 6 2015 7810
81. H. Redden, N. Morse, and H.S. Alper The synthetic biology toolbox for tuning gene expression in yeast FEMS Yeast Res. 15 2014 1 10
82. A.M. Redding-Johanson, T.S. Batth, R. Chan, R. Krupa, H.L. Szmidt, P.D. Adams, J.D. Keasling, T.S. Lee, A. Mukhopadhyay, and C.J. Petzold Targeted proteomics for metabolic pathway optimization: application to terpene production Metab. Eng. 13 2011 194 203
83. B. Regenberg, T. Grotkjaer, O. Winther, A. Fausbøll, M. Åkesson, C. Bro, L.K. Hansen, S. Brunak, and J. Nielsen Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae Genome Biol. 7 2006 R107
84. H. Renata, Z.J. Wang, and F.H. Arnold Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution Angew. Chem. Int. Ed. Engl. 54 2015 3351 3367
85. D.-K. Ro, E.M. Paradise, M. Ouellet, K.J. Fisher, K.L. Newman, J.M. Ndungu, K.A. Ho, R.A. Eachus, T.S. Ham, J. Kirby, and et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast Nature 440 2006 940 943
86. A. Rodriguez, K.R. Kildegaard, M. Li, I. Borodina, and J. Nielsen Establishment of a yeast platform strain for production of p-coumaric acid through metabolic engineering of aromatic amino acid biosynthesis Metab. Eng. 31 2015 181 188
87. P. Saling Eco-Efficiency Analysis of biotechnological processes Appl. Microbiol. Biotechnol. 68 2005 1 8
88. H.M. Salis The ribosome binding site calculator Methods Enzymol. 498 2011 19 42
89. H.M. Salis, E.A. Mirsky, and C.A. Voigt Automated design of synthetic ribosome binding sites to control protein expression Nat. Biotechnol. 27 2009 946 950
90. G. Scalcinati, C. Knuf, S. Partow, Y. Chen, J. Maury, M. Schalk, L. Daviet, J. Nielsen, and V. Siewers Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode Metab. Eng. 14 2012 91 103
91. S.W. Seo, D. Kim, H. Latif, E.J. O'Brien, R. Szubin, and B.O. Palsson Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli Nat. Commun. 5 2014 4910
92. S.W. Seo, D. Kim, R. Szubin, and B.O. Palsson Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655 Cell Rep. 12 2015 1289 1299
93. S. Shi, Y. Chen, V. Siewers, and J. Nielsen Improving production of malonyl coenzyme A-derived metabolites by abolishing Snf1-dependent regulation of Acc1 MBio 5 2014 e01130-e14
94. Y. Shiba, E.M. Paradise, J. Kirby, D.K. Ro, and J.D. Keasling Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids Metab. Eng. 9 2007 160 168
95. S.C. Shih, G. Goyal, P.W. Kim, N. Koutsoubelis, J.D. Keasling, P.D. Adams, N.J. Hillson, and A.K. Singh A versatile microfluidic device for automating synthetic biology ACS Synth. Biol. 4 2015 1151 1164
96. J.B. Siegel, A. Zanghellini, H.M. Lovick, G. Kiss, A.R. Lambert, J.L. St Clair, J.L. Gallaher, D. Hilvert, M.H. Gelb, B.L. Stoddard, and et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction Science 329 2010 309 313
97. M.L. Simpson, G.S. Sayler, B.M. Applegate, S. Ripp, D.E. Nivens, M.J. Paulus, and G.E. Jellison Bioluminescent-bioreporter integrated circuits from novel whole-cell biosensors Trends Biotechnol. 16 1998 332 338
98. C.D. Smolke, T.A. Carrier, and J.D. Keasling Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures Appl. Environ. Microbiol. 66 2000 5399 5405
99. G. Stephanopoulos, and J.J. Vallino Network rigidity and metabolic engineering in metabolite overproduction Science 252 1991 1675 1681
100. A.L. Tarca, V.J. Carey, X.W. Chen, R. Romero, and S. Drəghici Machine learning and its applications to biology PLoS Comput. Biol. 3 2007 e116 10.1371/journal.pcbi.0030116
101. J. Thykaer, and J. Nielsen Metabolic engineering of β-lactam production Metab. Eng. 5 2003 56 69
102. C.Y. Tsao, S. Hooshangi, H.C. Wu, J.J. Valdes, and W.E. Bentley Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli Metab. Eng. 12 2010 291 297
103. K.E. Tyo, P.K. Ajikumar, and G. Stephanopoulos Stabilized gene duplication enables long-term selection-free heterologous pathway expression Nat. Biotechnol. 27 2009 760 765
104. R. Usaite, M.C. Jewett, A.P. Oliveira, J.R. Yates 3rd, L. Olsson, and J. Nielsen Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator Mol. Syst. Biol. 5 2009 319
105. Z. Waks, and P.A. Silver Engineering a synthetic dual-organism system for hydrogen production Appl. Environ. Microbiol. 75 2009 1867 1875
106. T. Wang, X. Ma, G. Du, and J. Chen Overview of regulatory strategies and molecular elements in metabolic engineering of bacteria Mol. Biotechnol. 52 2012 300 308
107. B.L. Wang, A. Ghaderi, H. Zhou, J. Agresti, D.A. Weitz, G.R. Fink, and G. Stephanopoulos Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption Nat. Biotechnol. 32 2014 473 478
108. P.J. Westfall, D.J. Pitera, J.R. Lenihan, D. Eng, F.X. Woolard, R. Regentin, T. Horning, H. Tsuruta, D.J. Melis, A. Owens, and et al. Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin Proc. Natl. Acad. Sci. USA 109 2012 E111 E118
109. H. Yim, R. Haselbeck, W. Niu, C. Pujol-Baxley, A. Burgard, J. Boldt, J. Khandurina, J.D. Trawick, R.E. Osterhout, R. Stephen, and et al. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol Nat. Chem. Biol. 7 2011 445 452
110. H. Yu, and M. Gerstein Genomic analysis of the hierarchical structure of regulatory networks Proc. Natl. Acad. Sci. USA 103 2006 14724 14731
111. F. Zhang, J.M. Carothers, and J.D. Keasling Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids Nat. Biotechnol. 30 2012 354 359
112. Y. Zhang, Z. Dai, A. Krivoruchko, Y. Chen, V. Siewers, and J. Nielsen Functional pyruvate formate lyase pathway expressed with two different electron donors in Saccharomyces cerevisiae at aerobic growth FEMS Yeast Res. 15 2015 fov024