1887

Abstract

Synthetic Biology is the ‘Engineering of Biology’ – it aims to use a forward-engineering design cycle based on specifications, modelling, analysis, experimental implementation, testing and validation to modify natural or design new, synthetic biology systems so that they behave in a predictable fashion. Motivated by the need for truly plug-and-play synthetic biological components, we present a comprehensive review of ways in which the various parts of a biological system can be modified systematically. In particular, we review the list of ‘dials’ that are available to the designer and discuss how they can be modelled, tuned and implemented. The dials are categorized according to whether they operate at the global, transcriptional, translational or post-translational level and the resolution that they operate at. We end this review with a discussion on the relative advantages and disadvantages of some dials over others.

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2013-07-01
2024-12-07
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References

  1. Alberts B., Johnson A., Lewis J., Raff M.,, Roberts K. &, Walter P. ( 2002). Molecular Biology of the Cell, 4th edn. New York: Garland Science;
    [Google Scholar]
  2. Alon U. ( 2007). An Introduction to Systems Biology Boca Raton, FL: Chapman & Hall/CRC Press;
    [Google Scholar]
  3. Alper H., Fischer C., Nevoigt E., Stephanopoulos G. ( 2005). Tuning genetic control through promoter engineering. Proc Natl Acad Sci U S A 102:12678–12683 [View Article][PubMed]
    [Google Scholar]
  4. Andersen J. B., Sternberg C., Poulsen L. K., Bjorn S. P., Givskov M., Molin S. ( 1998). New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ Microbiol 64:2240–2246[PubMed]
    [Google Scholar]
  5. Anderson J., Strelkowa N., Stan G.-B., Douglas T., Savulescu J., Barahona M., Papachristodoulou A. ( 2012). Engineering and ethical perspectives in synthetic biology. Rigorous, robust and predictable designs, public engagement and a modern ethical framework are vital to the continued success of synthetic biology. EMBO Rep 13:584–590 [View Article][PubMed]
    [Google Scholar]
  6. Andrianantoandro E., Basu S., Karig D. K., Weiss R. ( 2006). Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2:0028 [View Article][PubMed]
    [Google Scholar]
  7. Angov E. ( 2011). Codon usage: nature’s roadmap to expression and folding of proteins. Biotechnol J 6:650–659 [View Article][PubMed]
    [Google Scholar]
  8. Arnold T. E. T., Yu J. J., Belasco J. G. J. ( 1998). mRNA stabilization by the ompA 5′ untranslated region: two protective elements hinder distinct pathways for mRNA degradation. RNA 4:319–330[PubMed]
    [Google Scholar]
  9. Atkinson M. R. M., Savageau M. A. M., Myers J. T. J., Ninfa A. J. A. ( 2003). Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. . Cell 113:597–607 [View Article][PubMed]
    [Google Scholar]
  10. Balbás M. D., Evans M. J., Hosfield D. J., Wongvipat J., Arora V. K., Watson P. A., Chen Y., Greene G. L., Shen Y., Sawyers C. L. ( 2013). Overcoming mutation-based resistance to antiandrogens with rational drug design. Elife 2:e00499 [View Article][PubMed]
    [Google Scholar]
  11. Becker G., Hengge-Aronis R. ( 2001). What makes an Escherichia coli promoter σS dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of σS.. Mol Microbiol 39:1153–1165 [View Article][PubMed]
    [Google Scholar]
  12. Beguerisse-Díaz M., Wang B., Desikan R., Barahona M. ( 2012). Squeeze-and-breathe evolutionary Monte Carlo optimization with local search acceleration and its application to parameter fitting. J R Soc Interface 9:1925–1933 [View Article][PubMed]
    [Google Scholar]
  13. Beisel C. L., Smolke C. D. ( 2009). Design principles for riboswitch function. PLOS Comput Biol 5:e1000363 [View Article][PubMed]
    [Google Scholar]
  14. Bernardo L. M., Johansson L. U., Skärfstad E., Shingler V. ( 2009). σ54-promoter discrimination and regulation by ppGpp and DksA. J Biol Chem 284:828–838 [View Article][PubMed]
    [Google Scholar]
  15. Bouvet P. P., Belasco J. G. J. ( 1992). Control of RNase E-mediated RNA degradation by 5′-terminal base pairing in E. coli. Nature 360:488–491 [View Article][PubMed]
    [Google Scholar]
  16. Boyd S., Vandenberghe L. ( 2004). Convex Optimisation Cambridge, UK: Cambridge University Press; [CrossRef]
    [Google Scholar]
  17. Brannigan J. A., Wilkinson A. J. ( 2002). Protein engineering 20 years on. Nat Rev Mol Cell Biol 3:964–970 [View Article][PubMed]
    [Google Scholar]
  18. Brewster R. C., Jones D. L., Phillips R. ( 2012). Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. PLOS Comput Biol 8:e1002811 [View Article][PubMed]
    [Google Scholar]
  19. Buck M., Gallegos M. T., Studholme D. J., Guo Y., Gralla J. D. ( 2000). The bacterial enhancer-dependent σ54N) transcription factor. J Bacteriol 182:4129–4136 [View Article][PubMed]
    [Google Scholar]
  20. Callura J. M., Cantor C. R., Collins J. J. ( 2012). Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci U S A 109:5850–5855 [View Article][PubMed]
    [Google Scholar]
  21. Canton B., Labno A., Endy D. ( 2008). Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 26:787–793 [View Article][PubMed]
    [Google Scholar]
  22. Carrier T. A., Keasling J. D. ( 1997a). Controlling messenger RNA stability in bacteria: strategies for engineering gene expression. Biotechnol Prog 13:699–708 [View Article][PubMed]
    [Google Scholar]
  23. Carrier T. A., Keasling J. D. ( 1997b). Controlling messenger RNA stability in bacteria: strategies for engineering gene expression. Biotechnol Prog 13:699–708 [View Article][PubMed]
    [Google Scholar]
  24. Chang A. C., Cohen S. N. ( 1978). Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol 134:1141–1156[PubMed]
    [Google Scholar]
  25. Chau A. H., Walter J. M., Gerardin J., Tang C., Lim W. A. ( 2012). Designing synthetic regulatory networks capable of self-organizing cell polarization. Cell 151:320–332 [View Article][PubMed]
    [Google Scholar]
  26. Chen H. H., Bjerknes M. M., Kumar R. R., Jay E. E. ( 1994). Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res 22:4953–4957 [View Article][PubMed]
    [Google Scholar]
  27. Chen S., Zhang H., Shi H., Ji W., Feng J., Gong Y., Yang Z., Ouyang Q. ( 2012). Automated design of genetic toggle switches with predetermined bistability. ACS Synth Biol 1:284–290 [View Article][PubMed]
    [Google Scholar]
  28. Choi Y. J., Bourque D., Morel L., Groleau D., Míguez C. B. ( 2006). Multicopy integration and expression of heterologous genes in Methylobacterium extorquens ATCC 55366. Appl Environ Microbiol 72:753–759 [View Article][PubMed]
    [Google Scholar]
  29. Cookson N. A., Mather W. H., Danino T., Mondragón-Palomino O., Williams R. J., Tsimring L. S., Hasty J. ( 2011). Queueing up for enzymatic processing: correlated signaling through coupled degradation. Mol Syst Biol [View Article]
    [Google Scholar]
  30. Cornish-Bowden A. ( 2004). Fundamentals of Enzyme Kinetics, 3rd edn. London: Portland Press;
    [Google Scholar]
  31. Cosentino C., Bates D. G. ( 2012). Feedback Control in Systems Biology Boca Raton, FL: Taylor & Francis/CRC Press.;
    [Google Scholar]
  32. Cox R. S., Surette M. G., Elowitz M. B. ( 2007). Programming gene expression with combinatorial promoters. Mol Syst Biol3
    [Google Scholar]
  33. Davis J. H., Rubin A. J., Sauer R. T. ( 2011). Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res 39:1131–1141 [View Article][PubMed]
    [Google Scholar]
  34. Del Vecchio D., Ninfa A. J., Sontag E. D. ( 2008). Modular cell biology: retroactivity and insulation. Mol Syst Biol
    [Google Scholar]
  35. Deuschle U., Kammerer W., Gentz R., Bujard H. ( 1986). Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. EMBO J 5:2987–2994[PubMed]
    [Google Scholar]
  36. Dixon N., Duncan J. N., Geerlings T., Dunstan M. S., McCarthy J. E. G., Leys D., Micklefield J. ( 2010). Reengineering orthogonally selective riboswitches. Proc Natl Acad Sci U S A 107:2830–2835 [View Article][PubMed]
    [Google Scholar]
  37. Dolan, J., Anderson, J. & Papachristodoulou, A. (2012).Proceedings of the IEEE Conference on Decision and Control
  38. Dougan D. A. D., Reid B. G. B., Horwich A. L. A., Bukau B. B. ( 2002). ClpS, a substrate modulator of the ClpAP machine. Mol Cell 9:673–683 [View Article][PubMed]
    [Google Scholar]
  39. Driessen A. J. M., Nouwen N. ( 2008). Protein translocation across the bacterial cytoplasmic membrane. Annu Rev Biochem 77:643–667 [View Article][PubMed]
    [Google Scholar]
  40. Ebersbach G., Gerdes K. ( 2005). Plasmid segregation mechanisms. Annu Rev Genet 39:453–479 [View Article][PubMed]
    [Google Scholar]
  41. Egbert R. G. R., Klavins E. E. ( 2012). Fine-tuning gene networks using simple sequence repeats. Proc Natl Acad Sci U S A 109:16817–16822 [View Article][PubMed]
    [Google Scholar]
  42. Elleuche S., Pöggeler S. ( 2010). Inteins, valuable genetic elements in molecular biology and biotechnology. Appl Microbiol Biotechnol 87:479–489 [View Article][PubMed]
    [Google Scholar]
  43. Ellis T., Wang X., Collins J. J. ( 2009). Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol 27:465–471 [View Article][PubMed]
    [Google Scholar]
  44. Erbse A., Schmidt R., Bornemann T., Schneider-Mergener J., Mogk A., Zahn R., Dougan D. A., Bukau B. ( 2006). ClpS is an essential component of the N-end rule pathway in Escherichia coli. . Nature 439:753–756 [View Article][PubMed]
    [Google Scholar]
  45. Figurski D. H., Meyer R. J., Helinski D. R. ( 1979). Suppression of Co1E1 replication properties by the Inc P-1 plasmid RK2 in hybrid plasmids constructed in vitro. J Mol Biol 133:295–318 [View Article][PubMed]
    [Google Scholar]
  46. Flynn J. M. J., Levchenko I. I., Seidel M. M., Wickner S. H. S., Sauer R. T. R., Baker T. A. T. ( 2001). Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc Natl Acad Sci U S A 98:10584–10589 [View Article][PubMed]
    [Google Scholar]
  47. Gardner T. S., Cantor C. R., Collins J. J. ( 2000). Construction of a genetic toggle switch in Escherichia coli. . Nature 403:339–342 [View Article][PubMed]
    [Google Scholar]
  48. Gillespie D. T. ( 1992). A rigorous derivation of the chemical master equation. Physica A: Statist. Mechanics Applic 188:404–425 [View Article]
    [Google Scholar]
  49. Gogarten J. P., Senejani A. G., Zhaxybayeva O., Olendzenski L., Hilario E. ( 2002). Inteins: structure, function, and evolution. Annu Rev Microbiol 56:263–287 [View Article][PubMed]
    [Google Scholar]
  50. Gotta S. L., Miller O. L. Jr, French S. L. ( 1991). rRNA transcription rate in Escherichia coli. . J Bacteriol 173:6647–6649[PubMed]
    [Google Scholar]
  51. Grossman A. D., Straus D. B., Walter W. A., Gross C. A. ( 1987). Sigma 32 synthesis can regulate the synthesis of heat shock proteins in Escherichia coli. . Genes Dev 1:179–184 [View Article][PubMed]
    [Google Scholar]
  52. Gruber T. M., Gross C. A. ( 2003). Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol 57:441–466 [View Article][PubMed]
    [Google Scholar]
  53. Grünwald D., Singer R. H. ( 2010). In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport. Nature 467:604–607 [View Article][PubMed]
    [Google Scholar]
  54. Gur E., Sauer R. T. ( 2008). Recognition of misfolded proteins by Lon, a AAA(+) protease. Genes Dev 22:2267–2277 [View Article][PubMed]
    [Google Scholar]
  55. Hakkaart M. J. J., van Gemen B., Veltkamp E., Nijkamp H. J. J. ( 1985). Maintenance of multicopy plasmid Clo DF13 III. Role of plasmid size and copy number in partitioning. Mol Gen Genet 198:364–366 [View Article][PubMed]
    [Google Scholar]
  56. Hansen M. J., Chen L. H., Fejzo M. L., Belasco J. G. ( 1994). The ompA 5′ untranslated region impedes a major pathway for mRNA degradation in Escherichia coli. . Mol Microbiol 12:707–716 [View Article][PubMed]
    [Google Scholar]
  57. Hasunuma K. K., Sekiguchi M. M. ( 1979). Effect of dna mutations on the replication of plasmid pSC101 in Escherichia coli K-12. J Bacteriol 137:1095–1099[PubMed]
    [Google Scholar]
  58. Herman C. C., Thévenet D. D., Bouloc P. P., Walker G. C. G., D’Ari R. R. ( 1998). Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH). Genes Dev 12:1348–1355 [View Article][PubMed]
    [Google Scholar]
  59. Hirschberg K., Lippincott-Schwartz J. ( 1999). Secretory pathway kinetics and in vivo analysis of protein traffic from the Golgi complex to the cell surface. FASEB J 13:Suppl 2S251–S256[PubMed]
    [Google Scholar]
  60. Hoskins J. R., Singh S. K., Maurizi M. R., Wickner S. ( 2000). Protein binding and unfolding by the chaperone ClpA and degradation by the protease ClpAP. Proc Natl Acad Sci U S A 97:8892–8897 [View Article][PubMed]
    [Google Scholar]
  61. Isaacs F. J., Dwyer D. J., Ding C., Pervouchine D. D., Cantor C. R., Collins J. J. ( 2004). Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 22:841–847 [View Article][PubMed]
    [Google Scholar]
  62. Jensen P. R., Hammer K. ( 1998). The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters. Appl Environ Microbiol 64:82–87[PubMed]
    [Google Scholar]
  63. Kelly J. R., Rubin A. J., Davis J. H., Ajo-Franklin C. M., Cumbers J., Czar M. J., de Mora K., Glieberman A. L., Monie D. D., Endy D. ( 2009). Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng 3:4 [View Article][PubMed]
    [Google Scholar]
  64. Kirstein J., Molière N., Dougan D. A., Turgay K. ( 2009). Adapting the machine: adaptor proteins for Hsp100/Clp and AAA+ proteases 1–11. . Nat Rev Microbiol. 7:589–599 [View Article]
    [Google Scholar]
  65. Kittleson J. T., Cheung S., Anderson J. C. ( 2011). Rapid optimization of gene dosage in E. coli using DIAL strains. J Biol Eng 5:10 [View Article][PubMed]
    [Google Scholar]
  66. Klumpp S. ( 2011). Growth-rate dependence reveals design principles of plasmid copy number control. PLoS ONE 6:e20403 [View Article][PubMed]
    [Google Scholar]
  67. Klumpp S., Zhang Z., Hwa T. ( 2009). Growth rate-dependent global effects on gene expression in bacteria. Cell 139:1366–1375 [View Article][PubMed]
    [Google Scholar]
  68. Koch B., Liljefors T., Persson T., Nielsen J., Kjelleberg S., Givskov M. ( 2005). The LuxR receptor: the sites of interaction with quorum-sensing signals and inhibitors. Microbiology 151:3589–3602 [View Article][PubMed]
    [Google Scholar]
  69. Köhler J., Baumbach J., Taubert J., Specht M., Skusa A., Rüegg A., Rawlings C., Verrier P., Philippi S. ( 2006). Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics 22:1383–1390 [View Article][PubMed]
    [Google Scholar]
  70. Komarova A. V., Tchufistova L. S., Dreyfus M., Boni I. V. ( 2005). AU-rich sequences within 5′ untranslated leaders enhance translation and stabilize mRNA in Escherichia coli. . J Bacteriol 187:1344–1349 [View Article][PubMed]
    [Google Scholar]
  71. Kool A. J. A., Nijkamp H. J. H. ( 1974). Isolation and characterization of a copy mutant of the bacteriocinogenic plasmid Clo DF13. J Bacteriol 120:569–578[PubMed]
    [Google Scholar]
  72. Kudla G., Murray A. W., Tollervey D., Plotkin J. B. ( 2009). Coding-sequence determinants of gene expression in Escherichia coli. . Science 324:255–258 [View Article][PubMed]
    [Google Scholar]
  73. Kües U., Stahl U. ( 1989). Replication of plasmids in gram-negative bacteria. Microbiol Rev 53:491–516[PubMed]
    [Google Scholar]
  74. Lanzer M., Bujard H. ( 1988). Promoters largely determine the efficiency of repressor action. Proc Natl Acad Sci U S A 85:8973–8977 [View Article][PubMed]
    [Google Scholar]
  75. Lederer T., Kintrup M., Takahashi M., Sum P.-E., Ellestad G. A., Hillen W. ( 1996). Tetracycline analogs affecting binding to Tn10-Encoded Tet repressor trigger the same mechanism of induction. Biochemistry 35:7439–7446 [View Article][PubMed]
    [Google Scholar]
  76. Lehmann M., Wyss M. ( 2001). Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. Curr Opin Biotechnol 12:371–375 [View Article][PubMed]
    [Google Scholar]
  77. Lestas I., Vinnicombe G., Paulsson J. ( 2010). Fundamental limits on the suppression of molecular fluctuations. Nature 467:174–178 [View Article][PubMed]
    [Google Scholar]
  78. Lewis M., Chang G., Horton N. C., Kercher M. A., Pace H. C., Schumacher M. A., Brennan R. G., Lu P. ( 1996). Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271:1247–1254 [View Article][PubMed]
    [Google Scholar]
  79. Lim H. N., Lee Y., Hussein R. ( 2011). Fundamental relationship between operon organization and gene expression. Proc Natl Acad Sci U S A 108:10626–10631 [View Article][PubMed]
    [Google Scholar]
  80. Lim W. A., Alvania R., Marshall W. F. ( 2012). Cell biology 2.0. Trends Cell Biol 22:611–612 [View Article][PubMed]
    [Google Scholar]
  81. Lin-Chao S., Chen W. T., Wong T. T. ( 1992). High copy number of the pUC plasmid results from a Rom/Rop-suppressible point mutation in RNA II. Mol Microbiol 6:3385–3393 [View Article][PubMed]
    [Google Scholar]
  82. Litcofsky K. D., Afeyan R. B., Krom R. J., Khalil A. S., Collins J. J. ( 2012). Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nat Methods 9:1077–1080 [View Article][PubMed]
    [Google Scholar]
  83. Lloyd G., Landini P., Busby S. ( 2001). Activation and repression of transcription initiation in bacteria. Essays Biochem 37:17–31[PubMed]
    [Google Scholar]
  84. Lockless S. W., Muir T. W. ( 2009). Traceless protein splicing utilizing evolved split inteins. Proc Natl Acad Sci U S A 106:10999–11004 [View Article][PubMed]
    [Google Scholar]
  85. Lutz R., Bujard H. ( 1997). Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res 25:1203–1210 [View Article][PubMed]
    [Google Scholar]
  86. Lutz S., Patrick W. M. ( 2004). Novel methods for directed evolution of enzymes: quality, not quantity. Curr Opin Biotechnol 15:291–297 [View Article][PubMed]
    [Google Scholar]
  87. Lynch S. A., Desai S. K., Sajja H. K., Gallivan J. P. ( 2007). A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem Biol 14:173–184 [View Article][PubMed]
    [Google Scholar]
  88. Ma W., Trusina A., El-Samad H., Lim W. A., Tang C. ( 2009). Defining network topologies that can achieve biochemical adaptation. Cell 138:760–773 [View Article][PubMed]
    [Google Scholar]
  89. MacDonald J. T., Barnes C., Kitney R. I., Freemont P. S., Stan G.-B. V. ( 2011). Computational design approaches and tools for synthetic biology. Integr Biol (Camb) 3:97–108 [View Article][PubMed]
    [Google Scholar]
  90. Mackie G. A. ( 2013). RNase E: at the interface of bacterial RNA processing and decay. Nat Rev Microbiol 11:45–57 [View Article][PubMed]
    [Google Scholar]
  91. Martoglio B., Dobberstein B. ( 1998). Signal sequences: more than just greasy peptides. Trends Cell Biol 8:410–415 [View Article][PubMed]
    [Google Scholar]
  92. Mather W., Bennett M. R., Hasty J., Tsimring L. S. ( 2009). Delay-induced degrade-and-fire oscillations in small genetic circuits. Phys Rev Lett 102:068105 [View Article][PubMed]
    [Google Scholar]
  93. McGinness K. E., Baker T. A., Sauer R. T. ( 2006). Engineering controllable protein degradation. Mol Cell 22:701–707 [View Article][PubMed]
    [Google Scholar]
  94. Menart V., Jevševar S., Vilar M., Trobiš A., Pavko A. ( 2003). Constitutive versus thermoinducible expression of heterologous proteins in Escherichia coli based on strong PR,PL promoters from phage lambda. Biotechnol Bioeng 83:181–190 [View Article][PubMed]
    [Google Scholar]
  95. Mileyko Y. Y., Joh R. I. R., Weitz J. S. J. ( 2008). Small-scale copy number variation and large-scale changes in gene expression. Proc Natl Acad Sci U S A 105:16659–16664 [View Article][PubMed]
    [Google Scholar]
  96. Mirasoli M., Feliciano J., Michelini E., Daunert S., Roda A. ( 2002). Internal response correction for fluorescent whole-cell biosensors. Anal Chem 74:5948–5953 [View Article][PubMed]
    [Google Scholar]
  97. Moon T. S., Lou C., Tamsir A., Stanton B. C., Voigt C. A. ( 2012). Genetic programs constructed from layered logic gates in single cells. Nature 491:249–253 [View Article][PubMed]
    [Google Scholar]
  98. Mootz H. D., Muir T. W. ( 2002). Protein splicing triggered by a small molecule. J Am Chem Soc 124:9044–9045 [View Article][PubMed]
    [Google Scholar]
  99. Morcos P. A. ( 2007). Achieving targeted and quantifiable alteration of mRNA splicing with Morpholino oligos. Biochem Biophys Res Commun 358:521–527 [View Article][PubMed]
    [Google Scholar]
  100. Murphy K. F., Balázsi G., Collins J. J. ( 2007). Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A 104:12726–12731 [View Article][PubMed]
    [Google Scholar]
  101. Murray J. D. ( 2002). Mathematical Biology Berlin, Heidelberg: Springer Verlag;
    [Google Scholar]
  102. Na D., Lee S., Lee D. ( 2010). Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. BMC Syst Biol 4:71 [View Article][PubMed]
    [Google Scholar]
  103. Newbury S. F. S., Smith N. H. N., Higgins C. F. C. ( 1987). Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell 51:1131–1143 [View Article][PubMed]
    [Google Scholar]
  104. Neylon C. ( 2004). Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. Nucleic Acids Res 32:1448–1459 [View Article][PubMed]
    [Google Scholar]
  105. Nichols J. C., Matthews K. S. ( 1997). Combinatorial mutations of lac repressor. Stability of monomer-monomer interface is increased by apolar substitution at position 84. J Biol Chem 272:18550–18557 [View Article][PubMed]
    [Google Scholar]
  106. Nordström K. K., Uhlin B. E. B. ( 1992). Runaway-replication plasmids as tools to produce large quantities of proteins from cloned genes in bacteria. Biotechnology (N Y) 10:661–666 [View Article][PubMed]
    [Google Scholar]
  107. Oeffinger M., Zenklusen D. ( 2012). To the pore and through the pore: a story of mRNA export kinetics. Biochim Biophys Acta 1819:494–506 [View Article][PubMed]
    [Google Scholar]
  108. Orth P., Schnappinger D., Hillen W., Saenger W., Hinrichs W. ( 2000). Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat Struct Biol 7:215–219 [View Article][PubMed]
    [Google Scholar]
  109. Osterman I. A., Evfratov S. A., Sergiev P. V., Dontsova O. A. ( 2013). Comparison of mRNA features affecting translation initiation and reinitiation. Nucleic Acids Res 41:474–486 [View Article][PubMed]
    [Google Scholar]
  110. Panayotatos N. ( 1984). DNA replication regulated by the priming promoter. Nucleic Acids Res 12:2641–2648 [View Article][PubMed]
    [Google Scholar]
  111. Papanikou E., Karamanou S., Economou A. ( 2007). Bacterial protein secretion through the translocase nanomachine. Nat Rev Microbiol 5:839–851 [View Article][PubMed]
    [Google Scholar]
  112. Parsell D. A., Silber K. R., Sauer R. T. ( 1990). Carboxy-terminal determinants of intracellular protein degradation. Genes Dev 4:277–286 [View Article][PubMed]
    [Google Scholar]
  113. Penumetcha P., Lau K., Zhu X., Davis K., Eckdahl T. T., Campbell A. M. ( 2010). Improving the Lac system for synthetic biology. BIOS 81:7–15 [View Article]
    [Google Scholar]
  114. Perler F. B. ( 2002). InBase: the intein database. Nucleic Acids Res 30:383–384 [View Article][PubMed]
    [Google Scholar]
  115. Perry R. H., Green D. W. ( 1999). Perry’s Chemical Engineers’ Handbook, 7th edn. New York: McGraw-Hill;
    [Google Scholar]
  116. Peterson J., Phillips G. J. ( 2008). New pSC101-derivative cloning vectors with elevated copy numbers. Plasmid 59:193–201 [View Article][PubMed]
    [Google Scholar]
  117. Pfeuty B., Kaneko K. ( 2009). The combination of positive and negative feedback loops confers exquisite flexibility to biochemical switches. Phys Biol 6:046013 [View Article][PubMed]
    [Google Scholar]
  118. Prindle A., Selimkhanov J., Danino T., Samayoa P., Goldberg A., Bhatia S. N., Hasty J. ( 2012). Genetic circuits in Salmonella typhimurium . ACS Synth Biol 1:458–464 [View Article][PubMed]
    [Google Scholar]
  119. Purcell O., Savery N. J., Grierson C. S., di Bernardo M. ( 2010). A comparative analysis of synthetic genetic oscillators. J R Soc Interface 7:1503–1524 [View Article][PubMed]
    [Google Scholar]
  120. Purcell O., Grierson C. S., Bernardo M., Savery N. J. ( 2012). . J Biol Eng6 [View Article]
    [Google Scholar]
  121. Purnick P. E. M., Weiss R. ( 2009). The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10:410–422 [View Article][PubMed]
    [Google Scholar]
  122. Qi L. S., Larson M. H., Gilbert L. A., Doudna J. A., Weissman J. S., Arkin A. P., Lim W. A. ( 2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–1183 [View Article][PubMed]
    [Google Scholar]
  123. RAEng ( 2009). Synthetic Biology: Scope, Applications and Implications . . London: Royal Academy of Engineering;
    [Google Scholar]
  124. Raghavan R., Minnick M. F. ( 2009). Group I introns and inteins: disparate origins but convergent parasitic strategies. J Bacteriol 191:6193–6202 [View Article][PubMed]
    [Google Scholar]
  125. Raj A., van Oudenaarden A. ( 2008). Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135:216–226 [View Article][PubMed]
    [Google Scholar]
  126. Salis H. M., Mirsky E. A., Voigt C. A. ( 2009). Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27:946–950 [View Article][PubMed]
    [Google Scholar]
  127. Satya Lakshmi O., Rao N. M. ( 2009). Evolving Lac repressor for enhanced inducibility. Protein Eng Des Sel 22:53–58 [View Article][PubMed]
    [Google Scholar]
  128. Schleif R. ( 2000). Regulation of the L-arabinose operon of Escherichia coli. . Trends Genet 16:559–565 [View Article][PubMed]
    [Google Scholar]
  129. Schmidt L., Inselburg J. ( 1982). ColE1 copy number mutants. J Bacteriol 151:845–854[PubMed]
    [Google Scholar]
  130. Scott M., Gunderson C. W., Mateescu E. M., Zhang Z., Hwa T. ( 2010). Interdependence of cell growth and gene expression: origins and consequences. Science 330:1099–1102 [View Article][PubMed]
    [Google Scholar]
  131. ).Decision and Control (CDC), 2012 IEEE 51st Annual Conference http://www.cds.caltech.edu/~murray/papers/sm12-cdc.html
  132. Seo S. W., Yang J.-S., Kim I., Yang J., Min B. E., Kim S., Jung G. Y. ( 2013). Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. Metab Eng 15:67–74 [View Article][PubMed]
    [Google Scholar]
  133. Shi J., Muir T. W. ( 2005). Development of a tandem protein trans-splicing system based on native and engineered split inteins. J Am Chem Soc 127:6198–6206 [View Article][PubMed]
    [Google Scholar]
  134. Shizuya H., Birren B., Kim U. J., Mancino V., Slepak T., Tachiiri Y., Simon M. ( 1992). Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci U S A 89:8794–8797 [View Article][PubMed]
    [Google Scholar]
  135. Shong J., Jimenez Diaz M. R., Collins C. H. ( 2012). Towards synthetic microbial consortia for bioprocessing. Curr Opin Biotechnol 23:798–802 [View Article][PubMed]
    [Google Scholar]
  136. Silber K. R. K., Keiler K. C. K., Sauer R. T. R. ( 1992). Tsp: a tail-specific protease that selectively degrades proteins with nonpolar C termini. Proc Natl Acad Sci U S A 89:295–299 [View Article][PubMed]
    [Google Scholar]
  137. Silva-Rocha R., Martínez-García E., Calles B., Chavarría M., Arce-Rodríguez A., de Las Heras A., Páez-Espino A. D., Durante-Rodríguez G., Kim J. et al. ( 2013). The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res 41:Database issueD666–D675 [View Article][PubMed]
    [Google Scholar]
  138. Skretas G., Wood D. W. ( 2005). Regulation of protein activity with small-molecule-controlled inteins. Protein Sci 14:523–532 [View Article][PubMed]
    [Google Scholar]
  139. Slusarczyk A. L., Lin A., Weiss R. ( 2012). Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet 13:406–420 [View Article][PubMed]
    [Google Scholar]
  140. Smith R. N., Aleksic J., Butano D., Carr A., Contrino S., Hu F., Lyne M., Lyne R., Kalderimis A. et al. ( 2012). InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics 28:3163–3165 [View Article][PubMed]
    [Google Scholar]
  141. Sternberg N. ( 1990). Bacteriophage P1 cloning system for the isolation, amplification, and recovery of DNA fragments as large as 100 kilobase pairs. Proc Natl Acad Sci U S A 87:103–107 [View Article][PubMed]
    [Google Scholar]
  142. Strelkowa N., Barahona M. ( 2010). Switchable genetic oscillator operating in quasi-stable mode. J R Soc Interface 7:1071–1082 [View Article][PubMed]
    [Google Scholar]
  143. Stricker J., Cookson S., Bennett M. R., Mather W. H., Tsimring L. S., Hasty J. ( 2008). A fast, robust and tunable synthetic gene oscillator. Nature 456:516–519 [View Article][PubMed]
    [Google Scholar]
  144. Swinburne I. A., Miguez D. G., Landgraf D., Silver P. A. ( 2008). Intron length increases oscillatory periods of gene expression in animal cells. Genes Dev 22:2342–2346 [View Article][PubMed]
    [Google Scholar]
  145. Tan C., Marguet P., You L. ( 2009). Emergent bistability by a growth-modulating positive feedback circuit. Nat Chem Biol 5:842–848 [View Article][PubMed]
    [Google Scholar]
  146. Tian T., Burrage K. ( 2006). Stochastic models for regulatory networks of the genetic toggle switch. Proc Natl Acad Sci U S A 103:8372–8377 [View Article][PubMed]
    [Google Scholar]
  147. Tolia N. H., Joshua-Tor L. ( 2006). Strategies for protein coexpression in Escherichia coli. . Nat Methods 3:55–64 [View Article][PubMed]
    [Google Scholar]
  148. Topp S., Reynoso C. M. K., Seeliger J. C., Goldlust I. S., Desai S. K., Murat D., Shen A., Puri A. W., Komeili A. et al. ( 2010). Synthetic riboswitches that induce gene expression in diverse bacterial species. Appl Environ Microbiol 76:7881–7884 [View Article][PubMed]
    [Google Scholar]
  149. Tyson J. J., Chen K. C., Novak B. ( 2003). Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15:221–231 [View Article][PubMed]
    [Google Scholar]
  150. Urbanowski M. L., Lostroh C. P., Greenberg E. P. ( 2004). Reversible acyl-homoserine lactone binding to purified Vibrio fischeri LuxR protein. J Bacteriol 186:631–637 [View Article][PubMed]
    [Google Scholar]
  151. Villaverde A. A., Benito A. A., Viaplana E. E., Cubarsi R. R. ( 1993). Fine regulation of cI857-controlled gene expression in continuous culture of recombinant Escherichia coli by temperature. Appl Environ Microbiol 59:3485–3487[PubMed]
    [Google Scholar]
  152. Vitreschak A. G., Rodionov D. A., Mironov A. A., Gelfand M. S. ( 2004). Riboswitches: the oldest mechanism for the regulation of gene expression?. Trends Genet 20:44–50 [View Article][PubMed]
    [Google Scholar]
  153. Vogel U., Jensen K. F. ( 1994). The RNA chain elongation rate in Escherichia coli depends on the growth rate. J Bacteriol 176:2807–2813[PubMed]
    [Google Scholar]
  154. Wachsmuth M., Findeiß S., Weissheimer N., Stadler P. F., Mörl M. ( 2013). De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res 41:2541–2551 [View Article][PubMed]
    [Google Scholar]
  155. Wang Y., deHaseth P. L. ( 2003). Sigma 32-dependent promoter activity in vivo: sequence determinants of the groE promoter. J Bacteriol 185:5800–5806 [View Article][PubMed]
    [Google Scholar]
  156. Wang K. H., Sauer R. T., Baker T. A. ( 2007). ClpS modulates but is not essential for bacterial N-end rule degradation. Genes Dev 21:403–408 [View Article][PubMed]
    [Google Scholar]
  157. Wang B., Barahona M., Buck M. ( 2013). A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals. Biosens Bioelectron 40:368–376 [View Article][PubMed]
    [Google Scholar]
  158. Welch M., Govindarajan S., Ness J. E., Villalobos A., Gurney A., Minshull J., Gustafsson C. ( 2009). Design parameters to control synthetic gene expression in Escherichia coli. PLoS ONE 4:e7002 [View Article][PubMed]
    [Google Scholar]
  159. Wilkinson D. J. ( 2011). Stochastic Modelling for Systems Biology, , 2nd edn. Boca Raton, FL: Chapman & Hall/CRC Press.;
    [Google Scholar]
  160. Wilson C., Agard D. A. ( 1991). Engineering substrate specificity. Curr Opin Struct Biol 1:617–623 [View Article]
    [Google Scholar]
  161. Yabuta M., Onai-Miura S., Ohsuye K. ( 1995). Thermo-inducible expression of a recombinant fusion protein by Escherichia coli lac repressor mutants. J Biotechnol 39:67–73 [View Article][PubMed]
    [Google Scholar]
  162. Zhong C., Peng D., Ye W., Chai L., Qi J., Yu Z., Ruan L., Sun M. ( 2011). Determination of plasmid copy number reveals the total plasmid DNA amount is greater than the chromosomal DNA amount in Bacillus thuringiensis YBT-1520. PLoS ONE 6:e16052 [View Article]
    [Google Scholar]
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