Cell Factory Engineering

Cell Systems

Volumn 4, Issue 3, 2017, Pages 262-275

  Davy, Anne Mathilde ^a   Kildegaard, Helene Faustrup ^b   Andersen, Mikael Rørdam ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b Chalmers University of Technology   (Denmark)

Author keywords

Aspergillus; Bacillus subtilis; cell factory; cell factory engineering; CHO cells; Escherichia coli; metabolic engineering; Pichia; protein secretion; Saccharomyces cerevisiae

Indexed keywords

ALGORITHM; BIOCOMPATIBILITY; BIOSYNTHESIS; CELL ENGINEERING; CELLS BY BODY ANATOMY; HETEROLOGOUS EXPRESSION; METABOLITE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; REVIEW; ANIMAL; GENETIC ENGINEERING; GENETICS; HUMAN; METABOLIC ENGINEERING; PHYSIOLOGY; PROCEDURES; PROTEIN ENGINEERING;

ANIMALS; BIOSYNTHETIC PATHWAYS; CELL ENGINEERING; GENETIC ENGINEERING; HUMANS; METABOLIC ENGINEERING; PROTEIN ENGINEERING;

EID: 85016050928     PISSN: 24054712     EISSN: 24054720     Source Type: Journal    
DOI: 10.1016/j.cels.2017.02.010     Document Type: Review

References (137)

1. Ailor, E., Betenbaugh, M.J., Overexpression of a cytosolic chaperone to improve solubility and secretion of a recombinant IgG protein in insect cells. Biotechnol. Bioeng. 58 (1998), 196–203.
2. Ailor, E., Pathmanathan, J., Jongbloed, J.D., Betenbaugh, M.J., A bacterial signal peptidase enhances processing of a recombinant single chain antibody fragment in insect cells. Biochem. Biophys. Res. Commun. 255 (1999), 444–450.
3. Andersen, M.R., Nam, J.H., Sharfstein, S.T., Protein glycosylation: analysis, characterization, and engineering. Flickinger, M.C., (eds.) Encyclopedia of Industrial Biotechnology, Bioprocess, Bioseparation, and Cell Technology, 2011, John Wiley, 1–50.
4. Anyaogu, D.C., Mortensen, U.H., Heterologous production of fungal secondary metabolites in Aspergilli. Front. Microbiol., 6, 2015, 77.
5. Asadollahi, M.A., Maury, J., Patil, K.R., Schalk, M., Clark, A., Nielsen, J., Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab. Eng. 11 (2009), 328–334.
6. Association of Manufacturers and Formulators of Enzyme Products, 2009. List of commercial enzymes. http://www.amfep.org/content/list-enzymes.
7. Bai, Y., Yin, H., Bi, H., Zhuang, Y., Liu, T., Ma, Y., De novo biosynthesis of gastrodin in Escherichia coli. Metab. Eng. 35 (2016), 138–147.
8. Bailey, J.E., Toward a science of metabolic engineering. Science 252 (1991), 1668–1675.
9. Bailey, J.E., Sburlati, A., Hatzimanikatis, V., Lee, K., Renner, W.A., Tsai, P.S., Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol. Bioeng. 79 (2002), 568–579.
10. Baltz, R.H., Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes. J. Ind. Microbiol. Biotechnol. 43 (2016), 343–370.
11. Barnstable, C.J., Bodmer, W.F., Brown, G., Galfre, G., Milstein, C., Williams, A.F., Ziegler, A., Production of monoclonal antibodies to group A erythrocytes, HLA and other human cell surface antigen-new tools for genetic analysis. Cell 14 (1978), 9–18.
12. Bashor, C.J., Horwitz, A.A., Peisajovich, S.G., Lim, W.A., et al. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annu. Rev. Biophys. 39 (2010), 515–537.
13. Becker, J., Schäfer, R., Kohlstedt, M., Harder, B.J., Borchert, N.S., Stöveken, N., Bremer, E., Wittmann, C., Systems metabolic engineering of Corynebacterium glutamicum for production of the chemical chaperone ectoine. Microb. Cell Fact., 12, 2013, 110.
14. Behnsen, J., Deriu, E., Sassone-Corsi, M., Raffatellu, M., Probiotics: properties, examples, and specific applications. Cold Spring Harb. Perspect. Med., 3, 2013, a010074.
15. Bekiesch, P., Basitta, P., Apel, A.K., Challenges in the heterologous production of antibiotics in Streptomyces. Arch. Pharm. (Weinheim) 349 (2016), 594–601.
16. Berkmen, M., Production of disulfide-bonded proteins in Escherichia coli. Protein Expr. Purif. 82 (2012), 240–251.
17. Borkovich, K.A., Alex, L.A., Yarden, O., Freitag, M., Turner, G.E., Read, N.D., Seiler, S., Bell-Pedersen, D., Paietta, J., Plesofsky, N., et al. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol. Mol. Biol. Rev. 68 (2004), 1–108.
18. Borodina, I., Siebring, J., Zhang, J., Smith, C.P., van Keulen, G., Dijkhuizen, L., Nielsen, J., Antibiotic overproduction in Streptomyces coelicolor A3(2) mediated by phosphofructokinase deletion. J. Biol. Chem. 283 (2008), 25186–25199.
19. Borth, N., Mattanovich, D., Kunert, R., Katinger, H., Effect of increased expression of protein disulfide isomerase and heavy chain binding protein on antibody secretion in a recombinant CHO cell line. Biotechnol. Prog. 21 (2005), 106–111.
20. Burgard, A.P., Pharkya, P., Maranas, C.D., Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84 (2003), 647–657.
21. Calfon, M., Zeng, H., Urano, F., Till, J.H., Hubbard, S.R., Harding, H.P., Clark, S.G., Ron, D., IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA. Nature 415 (2002), 92–96.
22. Cambray, G., Guimaraes, J.C., Mutalik, V.K., Lam, C., Mai, Q.A., Thimmaiah, T., Carothers, J.M., Arkin, A.P., Endy, D., Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res. 41 (2013), 5139–5148.
23. Carvalho, N.D., Jørgensen, T.R., Arentshorst, M., Nitsche, B.M., van den Hondel, C.A., Archer, D.B., Ram, A.F., Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress. BMC Genomics, 13, 2012, 350.
24. Cavallaro, G., Decaria, L., Rosato, A., Genome-based analysis of heme biosynthesis and uptake in prokaryotic systems. J. Proteome Res. 7 (2008), 4946–4954.
25. Celik, E., Calık, P., Production of recombinant proteins by yeast cells. Biotechnol. Adv. 30 (2011), 1108–1118.
26. Chemier, J.A., Fowler, Z.L., Koffas, M.A., Leonard, E., Trends in microbial synthesis of natural products and biofuels. Adv. Enzymol. Relat. Areas Mol. Biol. 76 (2009), 151–217.
27. Chen, X., Dong, X., Wang, Y., Zhao, Z., Liu, L., Mitochondrial engineering of the TCA cycle for fumarate production. Metab. Eng., 31, 2015, 62.
28. Choi, B.-K., Bobrowicz, P., Davidson, R.C., Hamilton, S.R., Kung, D.H., Li, H., Miele, R.G., Nett, J.H., Wildt, S., Gerngross, T.U., Use of combinatorial genetic libraries to humanize N-linked glycosylation in the yeast Pichia pastoris. Proc. Natl. Acad. Sci. USA 100 (2003), 5022–5027.
29. Cui, Y.-Y., Ling, C., Zhang, Y.Y., Huang, J., Liu, J.Z., Production of shikimic acid from Escherichia coli through chemically inducible chromosomal evolution and cofactor metabolic engineering. Microb. Cell Fact., 13, 2014, 21.
30. Curran, K.A., Karim, A.S., Gupta, A., Alper, H.S., Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications. Metab. Eng. 19 (2013), 88–97.
31. Damasceno, L.M., Huang, C.-J.J., Batt, C.A., Protein secretion in Pichia pastoris and advances in protein production. Appl. Microbiol. Biotechnol. 93 (2012), 31–39.
32. Davis, R., Schooley, K., Rasmussen, B., Thomas, J., Reddy, P., Effect of PDI overexpression on recombinant protein secretion in CHO cells. Biotechnol. Prog. 16 (2000), 736–743.
33. de Marco, A., Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli. Microb. Cell Fact., 8, 2009, 26.
34. Dehli, T., Solem, C., Jensen, P.R., Tunable promoters in synthetic and systems biology. Subcell Biochem. 64 (2012), 181–201.
35. Dueber, J.E., Wu, G.C., Malmirchegini, G.R., Moon, T.S., Petzold, C.J., Ullal, A.V., Prather, K.L., Keasling, J.D., Synthetic protein scaffolds provide modular control over metabolic flux. Nat. Biotechnol. 27 (2009), 753–759.
36. Dunlop, M.J., Dossani, Z.Y., Szmidt, H.L., Chu, H.C., Lee, T.S., Keasling, J.D., Hadi, M.Z., Mukhopadhyay, A., Engineering microbial biofuel tolerance and export using efflux pumps. Mol. Syst. Biol., 7, 2011, 487.
37. Edwards, A.M., Arrowsmith, C.H., Christendat, D., Dharamsi, A., Friesen, J.D., Greenblatt, J.F., Vedadi, M., Protein production: feeding the crystallographers and NMR spectroscopists. Nat. Struct. Biol. 7 (2000), 970–972.
38. Fisher, A.K., Freedman, B.G., Bevan, D.R., Senger, R.S., A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories. Comput. Struct. Biotechnol. J. 11 (2014), 91–99.
39. Fleissner, A., Dersch, P., Expression and export: recombinant protein production systems for Aspergillus. Appl. Microbiol. Biotechnol. 87 (2010), 1255–1270.
40. Franken, A.C.W., Lokman, B.C., Ram, A.F., Punt, P.J., van den Hondel, C.A., de Weert, S., Heme biosynthesis and its regulation: towards understanding and improvement of heme biosynthesis in filamentous fungi. Appl. Microbiol. Biotechnol. 91 (2011), 447–460.
41. Galanie, S., Thodey, K., Trenchard, I.J., Filsinger Interrante, M., Smolke, C.D., Complete biosynthesis of opioids in yeast. Science 349 (2015), 1095–1100.
42. Gasser, B., Saloheimo, M., Rinas, U., Dragosits, M., Rodríguez-Carmona, E., Baumann, K., Giuliani, M., Parrilli, E., Branduardi, P., Lang, C., et al. Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview. Microb. Cell Fact., 7, 2008, 11.
43. Ghosh, A., Zhao, H., Price, N.D., Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. PLoS One, 6, 2011, e27316.
44. Hamann, T., Lange, L., Discovery, cloning and heterologous expression of secreted potato proteins reveal erroneous pre-mRNA splicing in Aspergillus oryzae. J. Biotechnol. 126 (2006), 265–276.
45. Hamilton, S.R., Davidson, R.C., Sethuraman, N., Nett, J.H., Jiang, Y., Rios, S., Bobrowicz, P., Stadheim, T.A., Li, H., Choi, B.K., et al. Humanization of yeast to produce complex terminally sialylated glycoproteins. Science 313 (2006), 1441–1443.
46. Hienonen, E., Romantschuk, M., Fenel, F., Taira, S., Transcript stabilization by mRNA sequences from hrpA of Pseudomonas syringae. J. Biotechnol. 128 (2007), 258–267.
47. Hossler, P., Protein glycosylation control in mammalian cell culture: past precedents and contemporary prospects. Adv. Biochem. Eng. Biotechnol. 127 (2012), 187–219.
48. Hossler, P., Khattak, S.F., Li, Z.J., Optimal and consistent protein glycosylation in mammalian cell culture. Glycobiology 19 (2009), 936–949.
49. Hou, J., Tyo, K., Liu, Z., Petranovic, D., Nielsen, J., Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae. Metab. Eng. 14 (2012), 120–127.
50. Hsu, P.D., Lander, E.S., Zhang, F., Development and applications of CRISPR-Cas9 for genome engineering. Cell 157 (2014), 1262–1278.
51. Hwang, K.-S., Kim, H.U., Charusanti, P., Palsson, B.Ø., Lee, S.Y., Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites. Biotechnol. Adv. 32 (2014), 255–268.
52. Idiris, A., Tohda, H., Sasaki, M., Okada, K., Kumagai, H., Giga-Hama, Y., Takegawa, K., Enhanced protein secretion from multiprotease-deficient fission yeast by modification of its vacuolar protein sorting pathway. Appl. Microbiol. Biotechnol. 85 (2010), 667–677.
53. Innis, M.A., Holland, M.J., McCabe, P.C., Cole, G.E., Wittman, V.P., Tal, R., Watt, K.W., Gelfand, D.H., Holland, J.P., Meade, J.H., Expression, glycosylation, and secretion of an Aspergillus glucoamylase by Saccharomyces cerevisiae. Science 228 (1985), 21–26.
54. Jakočiūnas, T., Jensen, M.K., Keasling, J.D., CRISPR/Cas9 advances engineering of microbial cell factories. Metab. Eng. 34 (2016), 44–59.
55. Jin, F.J., Watanabe, T., Juvvadi, P.R., Maruyama, J., Arioka, M., Kitamoto, K., Double disruption of the proteinase genes, tppA and pepE, increases the production level of human lysozyme by Aspergillus oryzae. Appl. Microbiol. Biotechnol. 76 (2007), 1059–1068.
56. de Jongh, W.A., Nielsen, J., Enhanced citrate production through gene insertion in Aspergillus niger. Metab. Eng. 10 (2008), 87–96.
57. Jossé, L., Smales, C.M., Tuite, M.F., Engineering the chaperone network of CHO cells for optimal recombinant protein production and authenticity. Methods Mol. Biol. 824 (2012), 595–608.
58. Keasling, J.D., Synthetic biology for synthetic chemistry. ACS Chem. Biol. 3 (2008), 64–76.
59. Keasling, J.D., Synthetic biology and the development of tools for metabolic engineering. Metab. Eng. 14 (2012), 189–195.
60. Kiel, C., Yus, E., Serrano, L., Engineering signal transduction pathways. Cell 140 (2010), 33–47.
61. Kim, S.H., Lee, G.M., Down-regulation of lactate dehydrogenase-A by siRNAs for reduced lactic acid formation of Chinese hamster ovary cells producing thrombopoietin. Appl. Microbiol. Biotechnol. 74 (2007), 152–159.
62. Kind, S., Jeong, W.K., Schröder, H., Wittmann, C., Systems-wide metabolic pathway engineering in Corynebacterium glutamicum for bio-based production of diaminopentane. Metab. Eng. 12 (2010), 341–351.
63. Kind, S., Neubauer, S., Becker, J., Yamamoto, M., Völkert, M., Abendroth, Gv, Zelder, O., Wittmann, C., From zero to hero – production of bio-based nylon from renewable resources using engineered Corynebacterium glutamicum. Metab. Eng. 25 (2014), 113–123.
64. Ku, S.C.Y., Ng, D.T., Yap, M.G., Chao, S.H., Effects of overexpression of X-box binding protein 1 on recombinant protein production in Chinese hamster ovary and NS0 myeloma cells. Biotechnol. Bioeng. 99 (2008), 155–164.
65. Lee, S.Y., Kim, H.U., Systems strategies for developing industrial microbial strains. Nat. Biotechnol. 33 (2015), 1061–1072.
66. Lee, J.H., Lee, D.E., Lee, B.U., Kim, H.S., Global analyses of transcriptomes and proteomes of a parent strain and an L-threonine-overproducing mutant strain. J. Bacteriol. 185 (2003), 5442–5451.
67. Lee, K.H., Park, J.H., Kim, T.Y., Kim, H.U., Lee, S.Y., Systems metabolic engineering of Escherichia coli for L-threonine production. Mol. Syst. Biol., 3, 2007, 149.
68. Lee, J.W., Na, D., Park, J.M., Lee, J., Choi, S., Lee, S.Y., Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat. Chem. Biol. 8 (2012), 536–546.
69. Li, H., Sethuraman, N., Stadheim, T.A., Zha, D., Prinz, B., Ballew, N., Bobrowicz, P., Choi, B.K., Cook, W.J., Cukan, M., et al. Optimization of humanized IgGs in glycoengineered Pichia pastoris. Nat. Biotechnol. 24 (2006), 210–215.
70. Li, A., Pfelzer, N., Zuijderwijk, R., Brickwedde, A., van Zeijl, C., Punt, P., Reduced by-product formation and modified oxygen availability improve itaconic acid production in Aspergillus niger. Appl. Microbiol. Biotechnol. 97 (2013), 3901–3911.
71. Liu, L., Yang, H., Shin, H.D., Li, J., Du, G., Chen, J., Recent advances in recombinant protein expression by Corynebacterium, Brevibacterium, and Streptomyces: from transcription and translation regulation to secretion pathway selection. Appl. Microbiol. Biotechnol. 97 (2013), 9597–9608.
72. Lubertozzi, D., Keasling, J.D., Developing Aspergillus as a host for heterologous expression. Biotechnol. Adv. 27 (2009), 53–75.
73. Martin, V.J.J., Pitera, D.J., Withers, S.T., Newman, J.D., Keasling, J.D., Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21 (2003), 796–802.
74. Martínez, I., Mohamed Mel, S., Rozas, D., García, J.L., Díaz, E., Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds. Metab. Eng. 35 (2016), 46–54.
75. Mattanovich, D., Branduardi, P., Dato, L., Gasser, B., Sauer, M., Porro, D., Recombinant protein production in yeasts. Methods Mol. Biol. 824 (2012), 329–358.
76. McKeague, M., Wang, Y.H., Cravens, A., Win, M.N., Smolke, C.D., Engineering a microbial platform for de novo biosynthesis of diverse methylxanthines. Metab. Eng. 38 (2016), 191–203.
77. Meerman, H.J., Georgiou, G., Construction and characterization of a set of E. coli strains deficient in all known loci affecting the proteolytic stability of secreted recombinant proteins. Biotechnology (N Y) 12 (1994), 1107–1110.
78. Meta, A., Nakatake, H., Imamura, T., Nozaki, C., Sugimura, K., High-yield production and characterization of biologically active recombinant aprotinin expressed in Saccharomyces cerevisiae. Protein Expr. Purif. 66 (2009), 22–27.
79. Mohan, C., Park, S.H., Chung, J.Y., Lee, G.M., Effect of doxycycline-regulated protein disulfide isomerase expression on the specific productivity of recombinant CHO cells: thrombopoietin and antibody. Biotechnol. Bioeng. 98 (2007), 611–615.
80. Molnár, I., Jungmann, V., Stege, J., Trefzer, A., Pachlatko, J.P., Biocatalytic conversion of avermectin into 4″-oxo-avermectin: discovery, characterization, heterologous expression and specificity improvement of the cytochrome P450 enzyme. Biochem. Soc. Trans. 34 (2006), 1236–1240.
81. Müller, J.E.N., Meyer, F., Litsanov, B., Kiefer, P., Potthoff, E., Heux, S., Quax, W.J., Wendisch, V.F., Brautaset, T., Portais, J.C., et al. Engineering Escherichia coli for methanol conversion. Metab. Eng. 28 (2015), 190–201.
82. Nerem, R.M., Cellular engineering. Ann. Biomed. Eng. 19 (1991), 529–545.
83. Nielsen, J., Metabolic engineering: techniques for analysis of targets for genetic manipulations. Biotechnol. Bioeng. 58 (1998), 125–132.
84. Nielsen, J., Synthetic biology for engineering acetyl coenzyme a metabolism in yeast. mBio, 5, 2014, e02153.
85. Nielsen, M.T., Nielsen, J.B., Anyaogu, D.C., Holm, D.K., Nielsen, K.F., Larsen, T.O., Mortensen, U.H., Heterologous reconstitution of the intact geodin gene cluster in Aspergillus nidulans through a simple and versatile PCR based approach. PLoS One, 8, 2013, e72871.
86. Nieuwenhuizen, P.J., Lyon, D., Anticipating opportunities in industrial biotechnology: sizing the market and growth scenarios. J. Commer. Biotechnol. 17 (2011), 159–164.
87. Nocon, J., Steiger, M.G., Pfeffer, M., Sohn, S.B., Kim, T.Y., Maurer, M., Rußmayer, H., Pflügl, S., Ask, M., Haberhauer-Troyer, C., et al. Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production. Metab. Eng. 24 (2014), 129–138.
88. Ohya, T., Hayashi, T., Kiyama, E., Nishii, H., Miki, H., Kobayashi, K., Honda, K., Omasa, T., Ohtake, H., Improved production of recombinant human antithrombin III in Chinese hamster ovary cells by {ATF}4 overexpression. Biotechnol. Bioeng. 100 (2008), 317–324.
89. Ostergaard, S., Olsson, L., Johnston, M., Nielsen, J., Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network. Nat. Biotechnol. 18 (2000), 1283–1286.
90. Park, J.H., Oh, J.E., Lee, K.H., Kim, J.Y., Lee, S.Y., Rational design of Escherichia coli for L-isoleucine production. ACS Synth. Biol. 1 (2012), 532–540.
91. Pfeifer, B.A., Khosla, C., Biosynthesis of polyketides in heterologous hosts. Microbiol. Mol. Biol. Rev. 65 (2001), 106–118.
92. Pfleger, B.F., Pitera, D.J., Smolke, C.D., Keasling, J.D., Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 24 (2006), 1027–1032.
93. Pfleger, B.F., Gossing, M., Nielsen, J., Metabolic engineering strategies for microbial synthesis of oleochemicals. Metab. Eng. 29 (2015), 1–11.
94. Pharkya, P., Maranas, C.D., An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab. Eng. 8 (2006), 1–13.
95. Pickens, L.B., Tang, Y., Chooi, Y.H., Metabolic engineering for the production of natural products. Annu. Rev. Chem. Biomol. Eng. 2 (2011), 211–236.
96. Punt, P.J., Schuren, F.H., Lehmbeck, J., Christensen, T., Hjort, C., van den Hondel, C.A., Characterization of the Aspergillus niger prtT, a unique regulator of extracellular protease encoding genes. Fungal Genet. Biol. 45 (2008), 1591–1599.
97. Pybus, L.P., Dean, G., West, N.R., Smith, A., Daramola, O., Field, R., Wilkinson, S.J., James, D.C., Model-directed engineering of “difficult-to-express” monoclonal antibody production by Chinese hamster ovary cells. Biotechnol. Bioeng. 111 (2013), 372–385.
98. Qi, K., Zhong, J.J., Xia, X.X., Triggering respirofermentative metabolism in the crabtree-negative yeast Pichia guilliermondii by disrupting the CAT8 gene. Appl. Environ. Microbiol. 80 (2014), 3879–3887.
99. Qian, Z.G., Xia, X.X., Lee, S.Y., Metabolic engineering of Escherichia coli for the production of cadaverine: a five carbon diamine. Biotechnol. Bioeng. 108 (2011), 93–103.
100. Ranganathan, S., Suthers, P.F., Maranas, C.D., OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput. Biol., 6, 2010, e1000744.
101. Ratner, M., Genentech's glyco-engineered antibody to succeed Rituxan. Nat. Biotechnol. 32 (2014), 6–7.
102. Ribela, M.T., Bianco, A.C., Bartolini, P., The use of recombinant human thyrotropin produced by Chinese hamster ovary cells for the preparation of immunoassay reagents. J. Clin. Endocrinol. Metab. 81 (1996), 249–256.
103. Rodrigues, A.L., Trachtmann, N., Becker, J., Lohanatha, A.F., Blotenberg, J., Bolten, C.J., Korneli, C., de Souza Lima, A.O., Porto, L.M., Sprenger, G.A., et al. Systems metabolic engineering of Escherichia coli for production of the antitumor drugs violacein and deoxyviolacein. Metab. Eng. 20 (2013), 29–41.
104. Rodrigues, A.L., Becker, J., de Souza Lima, A.O., Porto, L.M., Wittmann, C., Systems metabolic engineering of Escherichia coli for gram scale production of the antitumor drug deoxyviolacein from glycerol. Biotechnol. Bioeng. 111 (2014), 2280–2289.
105. Rosano, G.L., Ceccarelli, E.A., Recombinant protein expression in Escherichia coli: advances and challenges. Front. Microbiol., 5, 2014, 172.
106. Ruohonen, L., Toikkanen, J., Tieaho, V., Outola, M., Soderlund, H., Keranen, S., Enhancement of protein secretion in Saccharomyces cerevisiae by overproduction of Sso protein, a late-acting component of the secretory machinery. Yeast 13 (1997), 337–351.
107. Sathyamurthy, M., Lee, J.S., Park, J.H., Kim, Y.J., Jeong, J.Y., Jang, J.W., Lee, G.M., Overexpression of PACEsol improves BMP-7 processing in recombinant CHO cells. J. Biotechnol. 164 (2012), 336–339.
108. Schröder, M., Engineering eukaryotic protein factories. Biotechnol. Lett. 30 (2008), 187–196.
109. Siddiqui, M.S., Thodey, K., Trenchard, I., Smolke, C.D., Advancing secondary metabolite biosynthesis in yeast with synthetic biology tools. FEMS Yeast Res. 12 (2012), 144–170.
110. Stephanopoulos, G., Vallino, J.J., Network rigidity and metabolic engineering in metabolite overproduction. Science 252 (1991), 1675–1681.
111. Thodey, K., Galanie, S., Smolke, C.D., A microbial biomanufacturing platform for natural and semisynthetic opioids. Nat. Chem. Biol. 10 (2014), 1–10.
112. Tigges, M., Fussenegger, M., Xbp1-based engineering of secretory capacity enhances the productivity of Chinese hamster ovary cells. Metab. Eng. 8 (2006), 264–272.
113. Trosset, J.Y., Carbonell, P., Synthetic biology for pharmaceutical drug discovery. Drug Des. Dev. Ther. 9 (2015), 6285–6302.
114. Tyo, K.E., Liu, Z., Magnusson, Y., Petranovic, D., Nielsen, J., Impact of protein uptake and degradation on recombinant protein secretion in yeast. Appl. Microbiol. Biotechnol. 98 (2014), 7149–7159.
115. Valkonen, M., Ward, M., Wang, H., Penttilä, M., Saloheimo, M., Improvement of foreign-protein production in Aspergillus niger var. awamori by constitutive induction of the unfolded-protein response. Appl. Environ. Microbiol. 69 (2003), 6979–6986.
116. Valkonen, M., Penttilä, M., Saloheimo, M., Effects of inactivation and constitutive expression of the unfolded- protein response pathway on protein production in the yeast Saccharomyces cerevisiae. Appl. Environ. Microbiol. 69 (2003), 2065–2072.
117. van Dijl, J.M., de Jong, A., Smith, H., Bron, S., Venema, G., Signal peptidase I overproduction results in increased efficiencies of export and maturation of hybrid secretory proteins in Escherichia coli. Mol. Gen. Genet. 227 (1991), 40–48.
118. van Rossum, H.M., Kozak, B.U., Pronk, J.T., van Maris, A.J., Engineering cytosolic acetyl-coenzyme A supply in Saccharomyces cerevisiae: pathway stoichiometry, free-energy conservation and redox-cofactor balancing. Metab. Eng. 36 (2016), 99–115.
119. Vogl, T., Hartner, F.S., Glieder, A., New opportunities by synthetic biology for biopharmaceutical production in Pichia pastoris. Curr. Opin. Biotechnol. 24 (2013), 1094–1101.
120. Waegeman, H., Soetaert, W., Increasing recombinant protein production in Escherichia coli through metabolic and genetic engineering. J. Ind. Microbiol. Biotechnol. 38 (2011), 1891–1910.
121. Walsh, G., Biopharmaceutical benchmarks 2010. Nat. Biotechnol. 28 (2010), 917–924.
122. Walsh, G., Biopharmaceutical benchmarks 2014. Nat. Biotechnol. 32 (2014), 992–1000.
123. Wang, Y., Yu, O., Synthetic scaffolds increased resveratrol biosynthesis in engineered yeast cells. J. Biotechnol. 157 (2012), 258–260.
124. Wang, J., Liu, W., Ding, W., Zhang, G., Liu, J., Increasing ethanol titer and yield in a gpd1Δ gpd2Δ strain by simultaneous overexpression of GLT1 and STL1 in Saccharomyces cerevisiae. Biotechnol. Lett. 35 (2013), 1859–1864.
125. Ward, O.P., Production of recombinant proteins by filamentous fungi. Biotechnol. Adv. 30 (2011), 1119–1139.
126. Ward, M., Wilson, L.J., Kodama, K.H., Rey, M.W., Berka, R.M., Improved production of chymosin in Aspergillus by expression as a glucoamylase-chymosin fusion. Biotechnology (N Y) 8 (1990), 435–440.
127. Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H.U., Bruccoleri, R., Lee, S.Y., Fischbach, M.A., Müller, R., Wohlleben, W., et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43 (2015), W237–W243.
128. Westwood, A.D., Rowe, D.A., Clarke, H.R.G., Improved recombinant protein yield using a codon deoptimized DHFR selectable marker in a CHEF1 expression plasmid. Biotechnol. Prog. 26 (2010), 1558–1566.
129. Wu, J., Du, G., Zhou, J., Chen, J., Systems metabolic engineering of microorganisms to achieve large-scale production of flavonoid scaffolds. J. Biotechnol. 188 (2014), 72–80.
130. Wurm, F.M., Production of recombinant protein therapeutics in cultivated mammalian cells. Nat. Biotechnol. 22 (2004), 1393–1398.
131. Xiao, H., Zhong, J.J., Production of useful terpenoids by higher-fungus cell factory and synthetic biology approaches. Trends Biotechnol. 34 (2016), 242–255.
132. Xu, J.W., Xu, Y.N., Zhong, J.J., Enhancement of ganoderic acid accumulation by overexpression of an n-terminally truncated 3-hydroxy-3-methylglutaryl coenzyme a reductase gene in the basidiomycete Ganoderma lucidum. Appl. Environ. Microbiol. 78 (2012), 7968–7976.
133. Yamauchi, Y., Hirasawa, T., Nishii, M., Furusawa, C., Shimizu, H., Enhanced acetic acid and succinic acid production under microaerobic conditions by Corynebacterium glutamicum harboring Escherichia coli transhydrogenase gene pntAB. J. Gen. Appl. Microbiol. 60 (2014), 112–118.
134. Yang, Z., Wang, S., Halim, A., Schulz, M.A., Frodin, M., Rahman, S.H., Vester-Christensen, M.B., Behrens, C., Kristensen, C., Vakhrushev, S.Y., et al. Engineered CHO cells for production of diverse, homogeneous glycoproteins. Nat. Biotechnol. 33 (2015), 842–844.
135. Yoon, J., Aishan, T., Maruyama, J., Kitamoto, K., Enhanced production and secretion of heterologous proteins by the filamentous fungus Aspergillus oryzae via disruption of vacuolar protein sorting receptor gene Aovps10. Appl. Environ. Microbiol. 76 (2010), 5718–5727.
136. Yu, J.L., Xia, X.X., Zhong, J.J., Qian, Z.G., Direct biosynthesis of adipic acid from a synthetic pathway in recombinant Escherichia coli. Biotechnol. Bioeng. 111 (2014), 2580–2586.
137. Zabala, D., Braña, A.F., Flórez, A.B., Salas, J.A., Méndez, C., Engineering precursor metabolite pools for increasing production of antitumor mithramycins in Streptomyces argillaceus. Metab. Eng. 20 (2013), 187–197.