Advertisement

Gene Expression Engineering

  • Nicholas J. Morse
  • Hal S. Alper
Chapter

Abstract

Cellular systems can become platforms for chemical production. Over the last four years, over 50 biopharmaceuticals have been approved for production, ranging in scope from hormones, enzymes, fusion proteins, antibodies, and vaccines. However, each of these applications—whether chemicals or pharmaceuticals, requires both a host organism and tools to engineer pathways in this chosen organism. The cellular hosts for these processes range in scope and complexity to include bacterial systems like Escherichia coli, yeast systems like Saccharomyces cerevisiae, and a variety of mammalian cell systems. To accomplish these production goals, it is necessary to control gene expression (especially of heterologous genes and pathways). This chapter will evaluate methods for controlling gene expression in the context of heterologous genes, endogenous genes, pathway expression and provide insight into new paradigms for flux control through gene expression circuits. A focus of this chapter will be on the various synthetic tools available for gene expression control. Although these basic principles are broadly applicable to multiple organisms, the predominant focus of this chapter will be on microbial systems, particularly E. coli and S. cerevisiae.

Keywords

Itaconic Acid Constitutive Promoter Inducible Promoter Control Gene Expression Plasmid Copy Number 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Abe H, Aiba H (1996) Differential contributions of two elements of rho-independent terminator to transcription termination and mRNA stabilization. Biochimie 78(11–12):1035–1042PubMedCrossRefGoogle Scholar
  2. Adams BG (1972) Induction of galactokinase in Saccharomyces cerevisiae: kinetics of induction and glucose effects. J Bacteriol 111(2):308–315PubMedPubMedCentralGoogle Scholar
  3. Agnew DE, Pfleger BF (2011) Optimization of synthetic operons using libraries of post-transcriptional regulatory elements. Methods Mol Biol 765:99–111PubMedCrossRefGoogle Scholar
  4. Ajikumar PK et al (2010) Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 330(6000):70–74PubMedPubMedCentralCrossRefGoogle Scholar
  5. Alper H et al (2005) Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA 102(36):12678–12683PubMedPubMedCentralCrossRefGoogle Scholar
  6. Amit R (2012) Towards synthetic gene circuits with enhancers: biology’s multi-input integrators. Subcell Biochem 64:3–20PubMedCrossRefGoogle Scholar
  7. Anthony JR et al (2009) Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene. Metab Eng 11(1):13–19PubMedCrossRefGoogle Scholar
  8. Atkinson MR et al (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113(5):597–607PubMedCrossRefGoogle Scholar
  9. Baneyx F (1999) Recombinant protein expression in Escherichia coli. Curr Opin Biotechnol 10(5):411–421PubMedCrossRefGoogle Scholar
  10. Bassel J, Mortimer R (1971) Genetic order of the galactose structural genes in Saccharomyces cerevisiae. J Bacteriol 108(1):179–183PubMedPubMedCentralGoogle Scholar
  11. Batard Y et al (2000) Increasing expression of P450 and P450-reductase proteins from monocots in heterologous systems. Arch Biochem Biophys 379(1):161–169PubMedCrossRefGoogle Scholar
  12. Berlec A, Strukelj B (2013) Current state and recent advances in biopharmaceutical production in Escherichia coli, yeasts and mammalian cells. J Ind Microbiol Biotechnol 40(3–4):257–274PubMedCrossRefGoogle Scholar
  13. Blazeck J, Alper HS (2013) Promoter engineering: recent advances in controlling transcription at the most fundamental level. Biotechnol J 8(1):46–58PubMedCrossRefGoogle Scholar
  14. Blazeck J et al (2011) Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl Environ Microbiol 77(22):7905–7914PubMedPubMedCentralCrossRefGoogle Scholar
  15. Blazeck J et al (2012) Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters. Biotechnol Bioeng 109(11):2884–2895PubMedCrossRefGoogle Scholar
  16. Blazeck J et al (2014a) Metabolic engineering of Saccharomyces cerevisiae for itaconic acid production. Appl Microbiol Biotechnol 98(19):8155–8164PubMedCrossRefGoogle Scholar
  17. Blazeck J et al (2014b) Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nat Commun 5:3131PubMedCrossRefGoogle Scholar
  18. Bolivar F et al (1976) Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene 2(2):95–113Google Scholar
  19. Brophy JA, Voigt CA (2014) Principles of genetic circuit design. Nat Methods 11(5):508–520PubMedPubMedCentralCrossRefGoogle Scholar
  20. Cambray G et al (2013) Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res 41(9):5139–5148PubMedPubMedCentralCrossRefGoogle Scholar
  21. Camps M (2009) Modulation of ColE1-like plasmid replication for recombinant gene expression. Recent Pat DNA Gene Sequences 4(1):58–73CrossRefGoogle Scholar
  22. Celik E, Calik P (2012) Production of recombinant proteins by yeast cells. Biotechnol Adv 30(5):1108–1118PubMedCrossRefGoogle Scholar
  23. Chang AC, Cohen SN (1978) Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol 134(3):1141–1156PubMedPubMedCentralGoogle Scholar
  24. Chao YP, Wen CS, Wang JY (2004) A facile and efficient method to achieve LacZ overproduction by the expression vector carrying the thermoregulated promoter and plasmid copy number. Biotechnol Prog 20(2):420–425PubMedCrossRefGoogle Scholar
  25. Chen R (2012) Bacterial expression systems for recombinant protein production: E. coli and beyond. Biotechnol Adv 30(5):1102–1107PubMedCrossRefGoogle Scholar
  26. Chen D, Arkin AP (2012) Sequestration-based bistability enables tuning of the switching boundaries and design of a latch. Mol Syst Biol 8:620PubMedPubMedCentralCrossRefGoogle Scholar
  27. Chen X et al (2013) Metabolic engineering of Escherichia coli: a sustainable industrial platform for bio-based chemical production. Biotechnol Adv 31(8):1200–1223PubMedCrossRefGoogle Scholar
  28. Cherest H, Kerjan P, Surdin-Kerjan Y (1987) The Saccharomyces cerevisiae MET3 gene: nucleotide sequence and relationship of the 5’ non-coding region to that of MET25. Molecular & general genetics: MGG 210(2):307–313CrossRefGoogle Scholar
  29. Chou CP (2007) Engineering cell physiology to enhance recombinant protein production in Escherichia coli. Appl Microbiol Biotechnol 76(3):521–532PubMedCrossRefGoogle Scholar
  30. Cigan AM, Pabich EK, Donahue TF (1988) Mutational analysis of the HIS4 translational initiator region in Saccharomyces cerevisiae. Mol Cell Biol 8(7):2964–2975PubMedPubMedCentralCrossRefGoogle Scholar
  31. Clarke L, Carbon J (1980) Isolation of a yeast centromere and construction of functional small circular chromosomes. Nature 287(5782):504–509PubMedCrossRefGoogle Scholar
  32. Crook NC, Schmitz AC, Alper HS (2014) Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering. ACS Synth Biol 3(5):307–313PubMedCrossRefGoogle Scholar
  33. Curran KA et al (2013a) Metabolic engineering of muconic acid production in Saccharomyces cerevisiae. Metab Eng 15:55–66PubMedCrossRefGoogle Scholar
  34. Curran KA et al (2013b) Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications. Metab Eng 19:88–97PubMedPubMedCentralCrossRefGoogle Scholar
  35. Curran KA et al (2014) Design of synthetic yeast promoters via tuning of nucleosome architecture. Nat Commun 5:4002PubMedPubMedCentralCrossRefGoogle Scholar
  36. Curry KA, Tomich CS (1988) Effect of ribosome binding site on gene expression in Escherichia coli. DNA 7(3):173–179PubMedCrossRefGoogle Scholar
  37. Da Silva NA, Srikrishnan S (2012) Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae. FEMS Yeast Res 12(2):197–214PubMedCrossRefGoogle Scholar
  38. Dalton AC, Barton WA (2014) Over-expression of secreted proteins from mammalian cell lines. Protein Sci 23(5):517–525PubMedPubMedCentralCrossRefGoogle Scholar
  39. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97(12):6640–6645PubMedPubMedCentralCrossRefGoogle Scholar
  40. Dehli T, Solem C, Jensen PR (2012) Tunable promoters in synthetic and systems biology. Subcell Biochem 64:181–201PubMedCrossRefGoogle Scholar
  41. del Solar G, Espinosa M (2000) Plasmid copy number control: an ever-growing story. Mol Microbiol 37(3):492–500PubMedCrossRefGoogle Scholar
  42. del Solar G et al (1998) Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62(2):434–464PubMedPubMedCentralGoogle Scholar
  43. DiCarlo JE et al (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41(7):4336–4343PubMedPubMedCentralCrossRefGoogle Scholar
  44. Dunlop MJ, Keasling JD, Mukhopadhyay A (2010) A model for improving microbial biofuel production using a synthetic feedback loop. Syst Synth Biol 4(2):95–104PubMedPubMedCentralCrossRefGoogle Scholar
  45. Ellefson JW et al (2014) Directed evolution of genetic parts and circuits by compartmentalized partnered replication. Nat Biotechnol 32(1):97–101PubMedCrossRefGoogle Scholar
  46. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335–338PubMedCrossRefGoogle Scholar
  47. Feklistov A (2013) RNA polymerase: in search of promoters. Ann N Y Acad Sci 1293:25–32PubMedCrossRefGoogle Scholar
  48. Fung E et al (2005) A synthetic gene-metabolic oscillator. Nature 435(7038):118–122PubMedCrossRefGoogle Scholar
  49. Futcher B, Carbon J (1986) Toxic effects of excess cloned centromeres. Mol Cell Biol 6(6):2213–2222PubMedPubMedCentralCrossRefGoogle Scholar
  50. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767):339–342PubMedCrossRefGoogle Scholar
  51. Genbauffe FS, Chisholm GE, Cooper TG (1984) Tau, sigma, and delta. A family of repeated elements in yeast. J Biol Chem 259(16):10518–10525PubMedGoogle Scholar
  52. Giaever G, Nislow C (2014) The yeast deletion collection: a decade of functional genomics. Genetics 197(2):451–465PubMedPubMedCentralCrossRefGoogle Scholar
  53. Giaever G et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387–391PubMedCrossRefGoogle Scholar
  54. Goh S, Good L (2008) Plasmid selection in Escherichia coli using an endogenous essential gene marker. BMC Biotechnol 8:61PubMedPubMedCentralCrossRefGoogle Scholar
  55. Gorgoni B et al (2014) Controlling translation elongation efficiency: tRNA regulation of ribosome flux on the mRNA. Biochem Soc Trans 42(1):160–165PubMedCrossRefGoogle Scholar
  56. Graumann K, Premstaller A (2006) Manufacturing of recombinant therapeutic proteins in microbial systems. Biotechnol J 1(2):164–186PubMedCrossRefGoogle Scholar
  57. Gustafsson C, Govindarajan S, Minshull J (2004) Codon bias and heterologous protein expression. Trends Biotechnol 22(7):346–353PubMedCrossRefGoogle Scholar
  58. Guzman LM et al (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 177(14):4121–4130PubMedPubMedCentralGoogle Scholar
  59. Hägg P et al (2004) A host/plasmid system that is not dependent on antibiotics and antibiotic resistance genes for stable plasmid maintenance in Escherichia coli. J Biotechnol 111(1):17–30PubMedCrossRefGoogle Scholar
  60. Hamilton R, Watanabe CK, de Boer HA (1987) Compilation and comparison of the sequence context around the AUG startcodons in Saccharomyces cerevisiae mRNAs. Nucleic Acids Res 15(8):3581–3593PubMedPubMedCentralCrossRefGoogle Scholar
  61. Harrison ME, Dunlop MJ (2012) Synthetic feedback loop model for increasing microbial biofuel production using a biosensor. Front Microbiol 3:360PubMedPubMedCentralCrossRefGoogle Scholar
  62. Holladay JE et al (2007) Top value-added chemicals from biomass: results of screening for potential candidates from biorefinery lignin. Pacific Northwest National LaboratoryGoogle Scholar
  63. Holtz WJ, Keasling JD (2010) Engineering static and dynamic control of synthetic pathways. Cell 140(1):19–23PubMedCrossRefGoogle Scholar
  64. Ito Y et al (2013) Characterization of five terminator regions that increase the protein yield of a transgene in Saccharomyces cerevisiae. J Biotechnol 168(4):486–492PubMedCrossRefGoogle Scholar
  65. Jackson RJ, Hellen CU, Pestova TV (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11(2):113–127PubMedPubMedCentralCrossRefGoogle Scholar
  66. Jiang W et al (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31(3):233–239PubMedPubMedCentralCrossRefGoogle Scholar
  67. Johnston M (1987) A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cerevisiae. Microbiol Rev 51(4):458–476PubMedPubMedCentralGoogle Scholar
  68. Jones KL, Kim SW, Keasling JD (2000) Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metab Eng 2(4):328–338PubMedCrossRefGoogle Scholar
  69. Kane JF (1995) Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr Opin Biotechnol 6(5):494–500PubMedCrossRefGoogle Scholar
  70. Karim AS, Curran KA, Alper HS (2013) Characterization of plasmid burden and copy number in Saccharomyces cerevisiae for optimization of metabolic engineering applications. FEMS Yeast Res 13(1):107–116PubMedCrossRefGoogle Scholar
  71. Kobori S et al (2013) A controllable gene expression system in liposomes that includes a positive feedback loop. Mol BioSyst 9(6):1282–1285PubMedCrossRefGoogle Scholar
  72. Kozak M (2002) Pushing the limits of the scanning mechanism for initiation of translation. Gene 299(1–2):1–34PubMedCrossRefGoogle Scholar
  73. Kroll J et al (2009) Establishment of a novel anabolism-based addiction system with an artificially introduced mevalonate pathway: Complete stabilization of plasmids as universal application in white biotechnology. Metab Eng 11(3):168–177PubMedCrossRefGoogle Scholar
  74. Kroll J et al (2010) Plasmid addiction systems: perspectives and applications in biotechnology. Microb Biotechnol 3(6):634–657PubMedPubMedCentralCrossRefGoogle Scholar
  75. Kroll J, Klinter S, Steinbuchel A (2011) A novel plasmid addiction system for large-scale production of cyanophycin in Escherichia coli using mineral salts medium. Appl Microbiol Biotechnol 89(3):593–604PubMedCrossRefGoogle Scholar
  76. Labbe S, Thiele DJ (1999) Copper ion inducible and repressible promoter systems in yeast. Methods Enzymol 306:145–153PubMedCrossRefGoogle Scholar
  77. Lee C et al (2006) Absolute and relative QPCR quantification of plasmid copy number in Escherichia coli. J Biotechnol 123(3):273–280PubMedCrossRefGoogle Scholar
  78. Levin-Karp A et al (2013) Quantifying translational coupling in E. coli synthetic operons using RBS modulation and fluorescent reporters. ACS Synth. Biol 2(6):327–336Google Scholar
  79. Lewis M (2005) The lac repressor. C R Biol 328(6):521–548PubMedCrossRefGoogle Scholar
  80. Lewis M (2011) A tale of two repressors. J Mol Biol 409(1):14–27PubMedPubMedCentralCrossRefGoogle Scholar
  81. Li Z et al (2013) Direct and efficient xylitol production from xylan by Saccharomyces cerevisiae through transcriptional level and fermentation processing optimizations. Bioresour Technol 149:413–419PubMedCrossRefGoogle Scholar
  82. Liang S et al (1999) Activities of constitutive promoters in Escherichia coli. J Mol Biol 292(1):19–37PubMedCrossRefGoogle Scholar
  83. Lim HN, Lee Y, Hussein R (2011) Fundamental relationship between operon organization and gene expression. Proc Natl Acad Sci USA 108(26):10626–10631PubMedPubMedCentralCrossRefGoogle Scholar
  84. Liu L et al (2013a) How to achieve high-level expression of microbial enzymes: strategies and perspectives. Bioengineered 4(4):212–223PubMedPubMedCentralCrossRefGoogle Scholar
  85. Liu L, Redden H, Alper HS (2013b) Frontiers of yeast metabolic engineering: diversifying beyond ethanol and Saccharomyces. Curr Opin Biotechnol 24(6):1023–1030PubMedCrossRefGoogle Scholar
  86. Lu WC, Ellington AD (2014) Design and selection of a synthetic operon. ACS Synth Biol 3(6):410–415PubMedCrossRefGoogle Scholar
  87. Madyagol M et al (2011) Gene replacement techniques for Escherichia coli genome modification. Folia Microbiol (Praha) 56(3):253–263CrossRefGoogle Scholar
  88. Makoff AJ, Oxer MD (1991) High level heterologous expression in E. coli using mutant forms of the lac promoter. Nucleic Acids Res 19(9):2417–2421PubMedPubMedCentralCrossRefGoogle Scholar
  89. Makrides SC (1996) Strategies for achieving high-level expression of genes in Escherichia coli. Microbiol Rev 60(3):512–538PubMedPubMedCentralGoogle Scholar
  90. Malys N (2012) Shine-Dalgarno sequence of bacteriophage T4: GAGG prevails in early genes. Mol Biol Rep 39(1):33–39PubMedCrossRefGoogle Scholar
  91. Martinez JL et al (2012) Pharmaceutical protein production by yeast: towards production of human blood proteins by microbial fermentation. Curr Opin Biotechnol 23(6):965–971PubMedCrossRefGoogle Scholar
  92. Matsumoto Y et al (2011) Bacterial cells carrying synthetic dual-function operon survived starvation. J Biomed Biotechnol 2011:489265PubMedPubMedCentralCrossRefGoogle Scholar
  93. Mead DJ, Gardner DC, Oliver SG (1986) The yeast 2 micron plasmid: strategies for the survival of a selfish DNA. Mol Gen Genet 205(3):417–421PubMedCrossRefGoogle Scholar
  94. Mieschendahl M, Petri T, Hanggi U (1986) A Novel prophage independent Trp regulated lambda-Pl expression system. Bio-Technology 4(9):802–809CrossRefGoogle Scholar
  95. Minton NP (1984) Improved plasmid vectors for the isolation of translational lac gene fusions. Gene 31(1–3):269–273PubMedCrossRefGoogle Scholar
  96. Morris MK et al (2010) Logic-based models for the analysis of cell signaling networks. Biochemistry 49(15):3216–3224PubMedPubMedCentralCrossRefGoogle Scholar
  97. Muller PP, Trachsel H (1990) Translation and regulation of translation in the yeast Saccharomyces cerevisiae. Eur J Biochem 191(2):257–261PubMedCrossRefGoogle Scholar
  98. Mumberg D, Muller R, Funk M (1995) Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 156(1):119–122PubMedCrossRefGoogle Scholar
  99. Nevoigt E et al (2006) Engineering of promoter replacement cassettes for fine-tuning of gene expression in Saccharomyces cerevisiae. Appl Environ Microbiol 72(8):5266–5273PubMedPubMedCentralCrossRefGoogle Scholar
  100. Nevoigt E et al (2007) Engineering promoter regulation. Biotechnol Bioeng 96(3):550–558PubMedCrossRefGoogle Scholar
  101. Nielsen J (2013) Production of biopharmaceutical proteins by yeast: advances through metabolic engineering. Bioengineered 4(4):207–211PubMedCrossRefGoogle Scholar
  102. Nielsen AA et al (2016) Genetic circuit design automation. Science 352(6281):aac7341Google Scholar
  103. Nordstrom K (2006) Plasmid R1–replication and its control. Plasmid 55(1):1–26PubMedCrossRefGoogle Scholar
  104. Okuda S et al (2007) Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genom 8:48CrossRefGoogle Scholar
  105. Partow S et al (2010) Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast 27(11):955–964PubMedCrossRefGoogle Scholar
  106. Peubez I et al (2010) Antibiotic-free selection in E. coli: new considerations for optimal design and improved production. Microb Cell Fact 9:65PubMedPubMedCentralCrossRefGoogle Scholar
  107. Price VL et al (1990) Expression of heterologous proteins in Saccharomyces cerevisiae using the ADH2 promoter. Methods Enzymol 185:308–318PubMedCrossRefGoogle Scholar
  108. Rajkumar AS, Maerkl SJ (2012) Rapid synthesis of defined eukaryotic promoter libraries. ACS Synth Biol 1(10):483–490PubMedCrossRefGoogle Scholar
  109. Ramalingam KI et al (2009) Forward engineering of synthetic bio-logical AND gates. Biochem Eng J 47(1–3):38–47CrossRefGoogle Scholar
  110. Redden H, Alper HS (2015) The development and characterization of synthetic minimal yeast promoters. Nat Commun 6:7810PubMedPubMedCentralCrossRefGoogle Scholar
  111. Redden H, Morse N, Alper HS (2014) The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast ResGoogle Scholar
  112. Ro DK et al (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440(7086):7940–7943CrossRefGoogle Scholar
  113. Rosano GL, Ceccarelli EA (2014) Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol 5:172PubMedPubMedCentralGoogle Scholar
  114. Salis HM (2011) The ribosome binding site calculator. Methods Enzymol 498:19–42PubMedCrossRefGoogle Scholar
  115. Sanchez S, Demain A (2012) Special issue on the production of recombinant proteins. Biotechnol Adv 30(5):1100–1101PubMedCrossRefGoogle Scholar
  116. Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32(4):347–355PubMedPubMedCentralCrossRefGoogle Scholar
  117. Sangsoda S, Cherest H, Surdin-Kerjan Y (1984) The expression of the MET25 gene of Saccharomyces cerevisiae is regulated transcriptionally. Molecular & general genetics: MGG 200(3):407–414CrossRefGoogle Scholar
  118. Sauer B (1987) Functional expression of the cre-lox site-specific recombination system in the yeast Saccharomyces cerevisiae. Mol Cell Biol 7(6):2087–2096PubMedPubMedCentralCrossRefGoogle Scholar
  119. Shah P et al (2013) Rate-limiting steps in yeast protein translation. Cell 153(7):1589–1601PubMedPubMedCentralCrossRefGoogle Scholar
  120. Shine J, Dalgarno L (1975) Determinant of cistron specificity in bacterial ribosomes. Nature 254(5495):34–38PubMedCrossRefGoogle Scholar
  121. Silva-Rocha R, de Lorenzo V (2014) Chromosomal integration of transcriptional fusions. Methods Mol Biol 1149:479–489PubMedCrossRefGoogle Scholar
  122. Silverstone AE, Arditti RR, Magasanik B (1970) Catabolite-insensitive revertants of lac promoter mutants. Proc Natl Acad Sci U S A 66(3):773–779PubMedPubMedCentralCrossRefGoogle Scholar
  123. Singh V (2014) Recent advancements in synthetic biology: current status and challenges. Gene 535(1):1–11PubMedCrossRefGoogle Scholar
  124. Sorensen HP, Mortensen KK (2005) Advanced genetic strategies for recombinant protein expression in Escherichia coli. J Biotechnol 115(2):113–128PubMedCrossRefGoogle Scholar
  125. Stoker NG, Fairweather NF, Spratt BG (1982) Versatile low-copy-number plasmid vectors for cloning in Escherichia coli. Gene 18(3):335–341PubMedCrossRefGoogle Scholar
  126. Stricker J et al (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456(7221):516–519PubMedCrossRefGoogle Scholar
  127. Suess B et al (2012) Aptamer-regulated expression of essential genes in yeast. Methods Mol Biol 824:381–391PubMedCrossRefGoogle Scholar
  128. Sun J et al (2012) Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae. Biotechnol Bioeng 109(8):2082–2092PubMedCrossRefGoogle Scholar
  129. Taxis C, Knop M (2006) System of centromeric, episomal, and integrative vectors based on drug resistance markers for Saccharomyces cerevisiae. Biotechniques 40(1):73–78PubMedCrossRefGoogle Scholar
  130. Temme K, Zhao D, Voigt CA (2012) Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci U S A 109(18):7085–7090PubMedPubMedCentralCrossRefGoogle Scholar
  131. Terpe K (2006) Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 72(2):211–222PubMedCrossRefGoogle Scholar
  132. Voss I, Steinbuchel A (2006) Application of a KDPG-aldolase gene-dependent addiction system for enhanced production of cyanophycin in Ralstonia eutropha strain H16. Metab Eng 8(1):66–78PubMedCrossRefGoogle Scholar
  133. Walsh G (2010) Biopharmaceutical benchmarks 2010. Nat Biotechnol 28(9):917–924PubMedCrossRefGoogle Scholar
  134. Walsh G (2014) Biopharmaceutical benchmarks 2014. Nat Biotechnol 32(10):992–1000PubMedCrossRefGoogle Scholar
  135. Wang B, Buck M (2012) Customizing cell signaling using engineered genetic logic circuits. Trends Microbiol 20(8):376–384PubMedCrossRefGoogle Scholar
  136. Wang RF, Kushner SR (1991) Construction of versatile low-copy-number vectors for cloning, sequencing and gene expression in Escherichia coli. Gene 100:195–199PubMedCrossRefGoogle Scholar
  137. Wang SH, Shih YH, Lin LY (1998) Yeast consensus initiator sequence markedly enhances the synthesis of metallothionein III in Saccharomyces cerevisiae. Biotechnol Lett 20(1):9–13CrossRefGoogle Scholar
  138. Wang Z et al (2012) Expression and production of recombinant cis-epoxysuccinate hydrolase in Escherichia coli under the control of temperature-dependent promoter. J Biotechnol 162(2–3):232–236PubMedCrossRefGoogle Scholar
  139. Welch M et al (2009) You’re one in a googol: optimizing genes for protein expression. J R Soc Interface 6(Suppl 4):S467–S476PubMedPubMedCentralCrossRefGoogle Scholar
  140. Werpy T et al (2004) Top value added chemicals from biomass: results of screening for potential candidates from sugars and synthesis gas. [U.S. Department of Energy [Office of] Energy Efficiency and Renewable EnergyGoogle Scholar
  141. Westfall PJ et al (2012) Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl Acad Sci U S A 109(3):E111–E118PubMedPubMedCentralCrossRefGoogle Scholar
  142. Winzeler EA et al (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285(5429):5901–5906CrossRefGoogle Scholar
  143. Wu X et al (2014) Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32(7):670–676PubMedPubMedCentralCrossRefGoogle Scholar
  144. Yamanishi M, Katahira S, Matsuyama T (2011) TPS1 terminator increases mRNA and protein yield in a Saccharomyces cerevisiae expression system. Biosci Biotechnol Biochem 75(11):2234–2236PubMedCrossRefGoogle Scholar
  145. Yamanishi M et al (2013) A genome-wide activity assessment of terminator regions in Saccharomyces cerevisiae provides a “terminatome” toolbox. ACS Synth Biol 2(6):337–347PubMedCrossRefGoogle Scholar
  146. Yao YF et al (2013) Metabolic engineering of Escherichia coli for production of salvianic acid A via an artificial biosynthetic pathway. Metab Eng 19:79–87PubMedCrossRefGoogle Scholar
  147. Yokobayashi Y, Weiss R, Arnold FH (2002) Directed evolution of a genetic circuit. Proc Natl Acad Sci USA 99(26):16587–16591PubMedPubMedCentralCrossRefGoogle Scholar
  148. Yoon H, Donahue TF (1992) Control of translation initiation in Saccharomyces cerevisiae. Mol Microbiol 6(11):1413–1419PubMedCrossRefGoogle Scholar
  149. Zhang F, Carothers JM, Keasling JD (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30(4):354–359PubMedCrossRefGoogle Scholar
  150. Zhu J (2012) Mammalian cell protein expression for biopharmaceutical production. Biotechnol Adv 30(5):1158–1170PubMedCrossRefGoogle Scholar
  151. Zielenkiewicz U, Cegłowski P (2001) Mechanisms of plasmid stable maintenance with special focus on plasmid addiction systems. Acta Biochim Pol 48(4):1003–1023PubMedGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Department of Chemical EngineeringThe University of Texas at AustinAustinUSA
  2. 2.Institute for Cellular and Molecular BiologyThe University of Texas at AustinAustinUSA

Personalised recommendations