Considerations for the design and construction of a synthetic platform cell for biotechnological applications

Biotechnology and Bioengineering

Volumn 105, Issue 1, 2010, Pages 26-36

  Foley, P L ^a   Shuler, M L ^a  

^a School of Chemical and Molecular Engineering   (United States)

Author keywords

Metabolic engineering; Minimal cell; Synthetic biology; Synthetic platform cell

Indexed keywords

BACTERIAL CELLS; BIOTECHNOLOGICAL APPLICATIONS; BIOTECHNOLOGICAL PROCESS; CELL ENVELOPES; CELL REPRODUCTION; DESIGN AND CONSTRUCTION; EXPERIMENTAL APPROACHES; GENETIC DRIFTS; METABOLIC ENGINEERING; METABOLIC INTERACTIONS; MINIMAL CELL; MODEL ORGANISMS; REGULATORY STRUCTURE; STATE OF RESEARCH; SYNTHETIC BIOLOGY; TRANSLATION CONTROL; WASTE STREAM;

BIODEGRADATION; CYTOLOGY; ESCHERICHIA COLI; GENES; GENETIC ENGINEERING; METABOLISM;

CELLS;

BACTERIAL CELL; BACTERIAL GENETICS; BACTERIAL GENOME; BIOLOGICAL MODEL; BIOTECHNOLOGICAL PRODUCTION; CELL DIVISION; CELL GROWTH; CELL MEMBRANE; ESCHERICHIA COLI; GENETIC DRIFT; GENETIC REGULATION; MATHEMATICAL MODEL; METABOLIC REGULATION; MINIMAL CELL; NONHUMAN; PLATFORM CELL; REVIEW;

BIOREACTORS; BIOTECHNOLOGY; ESCHERICHIA COLI; MODELS, THEORETICAL; PROTEIN ENGINEERING;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 73949123429     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.22575     Document Type: Review

References (117)

1. Agapakis CM, Silver PA. 2009. Synthetic biology: Exploring and exploiting genetic modularity through the design of novel biological networks. Mol Biosyst 5(7):704-713.
2. Ara K, Ozaki K, Nakamura K, Yamane K, Sekiguchi J, Ogasawara N. 2007. Bacillus minimum genome factory: Effective utilization of microbial genome information. Biotechnol Appl Biochem 46:169-178.
3. Atlas JC, Nikolaev EV, Browning ST, Shuler ML. 2008. Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli: Application to DNA replication. IET Syst Biol 2(5):369-382.
4. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko K, Tomita M, Wanner B, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Syst Biol 2:8.
5. Bashor CJ, Helman NC, Yan SD, Lim WA. 2008. Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319(5869):1539-1543.
6. Bernhardt TG, de Boer PAJ. 2005. SimA, a nucleoid-associated, FtsZ binding protein required for blocking septal ring assembly over chromosomes in E coli. Mol Cell 18(5):555-564.
7. Browning ST, Shuler ML. 2001. Towards the development of a minimal cell model by generalization of a model of Escherichia coli: Use of dimensionless rate parameters. Biotechnol Bioeng 76(3):187-192.
8. Browning ST, Castellanos M, Shuler ML. 2004. Robust control of initiation of prokaryotic chromosome replication: Essential considerations for a minimal cell. Biotechnol Bioeng 88(5):575-584.
9. Burgess-BrownNA, SharmaS, Sobott F, Loenarz C,Oppermann U,GileadiO. 2008. Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study. Protein Expr Purif 59(1):94-102.
10. Camara JE, Breier AM, Brendler T, Austin S, Cozzarelli NR, Crooke E. 2005. Hda inactivation of DnaA is the predominant mechanism preventing hyperinitiation of Escherichia coli DNA replication. EMBO Rep 6(8):736-741.
11. Capaldo-Kimball F, Barbour SD. 1971. Involvement of recombination genes in growth and viability of Escherichia coli K-12. J Bacteriol 106:204-212.
12. Castellanos M, Wilson DB, Shuler ML. 2004. A modular minimal cell model: Purine and pyrimidine transport and metabolism. Proc Natl Acad Sci USA 101(17):6681-6686.
13. Castellanos M, Kushiro K, Lai SK, Shuler ML. 2007. A genomically/ chemically complete module for synthesis of lipid membrane in a minimal cell. Biotechnol Bioeng 97(2):397-409.
14. Chalmers JJ, Kim E, Telford JN, Wong EY, Tacon WC, Shuler ML, Wilson DB. 1990. Effects of temperature on Escherichia coli overproducing beta-lactamase or human epidermal growth-factor. Appl Environ Microbiol 56(1):104-111.
15. Cortazzo P, Cervenansky C, Marin M, Reiss C, Ehrlich R, Deana A. 2002. Silent mutations affect in vivo protein folding in Escherichia coli. Biochem Biophys Res Commun 293(1):537-541.
16. de Bont JAM. 1998. Solvent-tolerant bacteria in biocatalysis. Trends Biotechnol 16(12):493-499.
17. Drubin DA, Way JC, Silver PA. 2007. Designing biological systems. Genes Dev 21(3):242-254.
18. Ellis T, Wang X, Collins JJ. 2009. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol 27(5):465-471.
19. Elowitz MB, Leibler S. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335-338.
20. Feher T, Papp B, Pal C, Posfai G. 2007. Systematic genome reductions: Theoretical and experimental approaches. Chem Rev 107(8):3498-3513.
21. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. 2007. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121.
22. Fischer CR, Klein-Marcuschamer D, Stephanopoulos G. 2008. Selection and optimization of microbial hosts for biofuels production. Metabol Eng 10(6):295-304.
23. Forster AC, Church GM. 2006. Towards synthesis of a minimal cell. Mol Syst Biol Article 2:45.
24. Forster AC, Church GM. 2007. Synthetic biology projects in vitro. Genome Res 17(1):1-6.
25. Forsyth RA, Haselbeck RJ, Ohlsen KL, Yamamoto RT, Xu H, Trawick JD, Wall D, Wang LS, Brown-Driver V, Froelich JM, Kedar GC, King P, McCarthy M, Malone C, Misiner B, Robbins D, Tan ZH, Zhu ZY, Carr G, Mosca DA, Zamudio C, Foulkes JG, Zyskind JW. 2002. A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol 43(6):1387-1400.
26. Foster PL. 2007. Stress-induced mutagenesis in bacteria. Crit Rev Biochem Mol Biol 42(5):373-397.
27. French CE. 2009. Synthetic biology and biomass conversion: A match made in heaven? J Roy Soc Interface 6:S547-S558.
28. French CT, Lao P, Loraine AE, Matthews BT, Yu HL, Dybvig K. 2008. Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol 69(1):67-76.
29. Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. 2009. Synthetic gene networks that count. Science 324(5931):1199-1202.
30. Fukuoka T, Moriya S, Yoshikawa H, Ogasawara N. 1990. Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis. J Biochem 107(5):732-739.
31. Gabaldon T, Pereto J, Montero F, Gil R, Latorre A, Moya A. 2007. Structural analyses of a hypothetical minimal metabolism. Phil T Roy Soc B 362(1486):1751-1762.
32. Galhardo RS, Hastings PJ, Rosenberg SM. 2007. Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol 42(5):399-435.
33. Georgiou G, Segatori L. 2005. Preparative expression of secreted proteins in bacteria: Status report and future prospects. Curr Opin Biotechnol 16(5):538-545.
34. Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL. 2003. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185(19):5673-5684.
35. Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA. 2008a. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci USA 105(51):20404-20409.
36. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA, Smith HO. 2008b. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319(5867):1215-1220.
37. Giga-Hama Y, Tohda H, Takegawa K, Kumagai H. 2007. Schizosoccharomyces pombe minimum genome factory. Biotechnol Appl Biochem 46:147-155.
38. Gil R, Silva FJ, Pereto J, Moya A. 2004. Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68(3):518-537.
39. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Ca H III, Smith HO, Venter JC. 2006. Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 103(2):425-430.
40. Gustafsson C, Govindarajan S, Minshull J. 2004. Codon bias and heterologous protein expression. Trends Biotechnol 22(7):346-353.
41. Hanczyc MM, Szostak JW. 2004. Replicating vesicles as models of primitive cell growth and division. Curr Opin Chem Biol 8(6):660-664.
42. Harry E, Monahan L, Thompson L. 2006. Bacterial cell division: The mechanism and its precison. Int Rev Cytol 253:27-94.
43. Hashimoto M, Ichimura T, Mizoguchi H, Tanaka K, Fujimitsu K, Keyamura K, Ote T, Yamakawa T, Yamazaki Y, Mori H, Katayama T, Kato J. 2005. Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 55(1):137-149.
44. Ishii N, Robert M, Nakayama Y, Kanai A, Tomita M. 2004. Toward large-scale modeling of the microbial cell for computer simulation. J Biotechnol 113(1-3):281-294.
45. Itaya M, Fujita K, Kuroki A, Tsuge K. 2008. Bottom-up genome assembly using the Bacillus subtilis genome vector. Nat Methods 5(1):41-43.
46. Kaguni JM. 2006. DnaA: Controlling the initiation of bacterial DNA replication and more. Annu Rev Microbiol 60:351-371.
47. Kahali B, Basak S, Ghosh TC. 2008. Delving deeper into the unexpected correlation between gene expressivity and codon usage bias of the Escherichia coli genome. J Biomol Struct Dyn 25(6):655-661.
48. Kato J. 2005. Regulatory network of the initiation of chromosomal replication in Escherichia coli. Crit Rev Biochem Mol Biol 40(6):331-342.
49. Kato JI, Hashimoto M. 2007. Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol 3:132.
50. Keasling JD. 2008. Synthetic biology for synthetic chemistry. ACS Chem Biol 3(1):64-76.
51. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Debarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauel C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers J, Sekiguchi J, Sekowska A, Seror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, YamamotoH, YamamotoM, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N. 2003. Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100(8):4678-4683.
52. Koob MD, Shaw AJ, Cameron DC. 1994. Minimizing the genome of Escherichia coli - Motivation and Strategy. Biochem Eng Viii:1-3.
53. Koonin EV. 2003. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1(2):127-136.
54. Ladjimi MM, Ghellis C, Feller A, Cunin R, Glansdorff N, Pierard A, Herve G. 1985. Structure-function relationship in allosteric aspartate carbamoyltransferase from Escherichia coli .2. Involvement of the C-terminal region of the regulatory chain in homotropic and heterotropic interactions. J Mol Biol 186(4):715-724.
55. Lange H, Taillandier P, Riba JP. 2001. Effect of high sheer stress on microbial viability. J Chem Technol Biotechnol 76(5):501-505.
56. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA, Smith HO, Venter JC. 2007. Genome transplantation in bacteria: Changing one species to another. Science 317(5838):632-638.
57. Lee SJ, Kim DM, Bae KH, Byun SM, Chung JH. 2000. Enhancement of secretion and extracellular stability of staphylokinase in Bacillus subtilis by wprA gene disruption. Appl Environ Microbiol 66(2):476-480.
58. Lee SY, Lee DY, Kim TY. 2005. Systems biotechnology for strain improvement. Trends Biotechnol 23(7):349-358.
59. Lee J, Yun H, Feist AM, Palsson BO, Lee SY. 2008a. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol 80(5):849-862.
60. Lee SK, Chou H, Ham TS, Lee TS, Keasling JD. 2008b. Metabolic engineering of microorganisms for biofuels production: From bugs to synthetic biology to fuels. Curr Opin Biotechnol 19(6):556-563.
61. Lee JH, Sung BH, Kim MS, Blattner FR, Yoon BH, Kim JH, Kim SC. 2009. Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production. Microb Cell Fact 8:2.
62. Leonard E, Nielsen D, Solomon K, Prather KJ. 2008. Engineering microbes with synthetic biology frameworks. Trends Biotechnol 26(12):674-681.
63. Loakes D, Holliger P. 2009. Darwinian chemistry: Towards the synthesis of a simple cell. Mol Biosyst 5(7):686-694.
64. Loeb J. 1906. The dynamics of living matter. New York, NY: Macmillan, 221-223 p.
65. Luisi PL, Ferri F, Stano P. 2006. Approaches to semi-synthetic minimal cells: A review. Naturwissenschaften 93(1):1-13.
66. Lutkenhaus J. 2007. Assembly dynamics of the bacterial MinCDE system and spatial regulation of the Z ring. Annu Rev Biochem 76:539-562.
67. Ma NN, Koelling KW, Chalmers JJ. 2002. Fabrication and use of a transient contractional flow device to quantify the sensitivity of mammalian and insect cells to hydrodynamic forces. Biotechnol Bioeng 80(4):428-437.
68. Margolin W. 2005. FtsZ and the division of prokaryotic cells and organelles. Nat Rev Mol Cell Biol 6(11):862-871.
69. Miller EN, Jarboe LR, Turner PC, Pharkya P, Yomano LP, York SW, Nunn D, Shanmugam KT, Ingram LO. 2009. Furfural inhibits growth by limiting sulfur assimilation in ethanolgenic Escherichia coli strain LY180. Appl Environ Microbiol 75(19):6132-6141.
70. Mizoguchi H, Mori H, Fujio T. 2007. Escherichia coli minimum genome factory. Biotechnol Appl Biochem 46:157-167.
71. Morimoto T, Kadoya R, Endo K, Tohata M, Sawada K, Liu S, Ozawa T, Kodama T, Kakeshita H, Kageyama Y, Manabe K, Kanaya S, Ara K, Ozaki K, Ogasawara N. 2008. Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res 15(2):73-81.
72. Morris DM, Jensen GJ. 2008. Toward a biomechanical understanding of whole bacterial cells. Annu Rev Biochem 77:583-613.
73. Moya A, Gil R, Latorre A, Pereto J, Garcillan-Barcia MP, de la Cruz F. 2009. Toward minimal bacterial cells: Evolution vs. design. FEMS Microbiol Rev 33(1):225-235.
74. Mushegian AR, Koonin EV. 1996. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 93(19):10268-10273.
75. Nikolaev E, Altas JC, Shuler ML. 2006. Computer models of bacterial cells: From generalized coarse-grained to genome-specific modular models. J Phys Conf Ser 4b:322-326.
76. Noireaux V, Libchaber A. 2004. A vesicle bioreactor as a step toward an artificial cell assembly. Proc Natl Acad Sci USA 101(51):17669-17674.
77. Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R. 2007. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 282(39):28791-28799.
78. Park JH, Lee SY, Kim TY, Kim HU. 2008. Application of systems biology for bioprocess development. Trends Biotechnol 26(8):404-412.
79. Pohorille A, Deamer D. 2002. Artificial cells: Prospects for biotechnology. Trends Biotechnol 20(3):123-128.
80. Pósfai G, Plunkett G, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR. 2006. Emergent properties of reduced-genome Escherichia coli. Science 312(5776):1044-1046.
81. Prather KLJ, Martin CH. 2008. De novo biosynthetic pathways: Rational design of microbial chemical factories. Curr Opin Biotechnol 19:468-474.
82. Puchalka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D, Timmis KN, Papin JA, dos Santos V. 2008. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 4:10.
83. Purnick PEM, Weiss R. 2009. The second wave of synthetic biology: From modules to systems. Nat Rev Mol Cell Biol 10(6):410-422.
84. Ramos JL, Duque E, Gallegos MT, Godoy P, Ramos-Gonzalez MI, Rojas A, Teran W, Segura A. 2002. Mechanisms of solvent tolerance in gramnegative bacteria. Annu Rev Microbiol 56:743-768.
85. Rasmussen S, Chen LH, Deamer D, Krakauer DC, Packard NH, Stadler PF, Bedau MA. 2004. Transitions from nonliving to living matter. Science 303(5660):963-965.
86. Rusk N. 2009. Synthetic life. Nat Methods 6:33.
87. Salama NR, Shepherd B, Falkow S. 2004. Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. J Bacteriol 186(23): 7926-7935.
88. Sardessai Y, Bhosle S. 2002. Tolerance of bacteria to organic solvents. Res Microbiol 153(5):263-268.
89. Schumann W. 2007. Production of recombinant proteins in Bacillus subtilis. Adv Appl Microbiol 62:137-189.
90. Schwille P, Diez S. 2009. Synthetic biology of minimal systems. Crit Rev Biochem Mol Biol 44(4):223-242.
91. Segré D, Ben-Eli D, Deamer DW, Lancet D. 2001. The lipid world. Orig Life Evol Biosph 31(1-2):119-145.
92. Seto S, Miyata M. 1998. Cell reproduction and morphological changes in Mycoplasma capricolum. J Bacteriol 180(2):256-264.
93. Sharma SS, Blattner FR, Harcum SW. 2007. Recombinant protein production in an Escherichia coli reduced genome strain. Metab Eng 9(2):133-141.
94. Shuler ML, Marvin J. 1986. Johnson award lecture. Anaheim, CA: American Chemical Society.
95. Sikkema J, de Bont JAM, Poolman B. 1995. Mechanisms of membrane toxicity of hydrocarbons. Microbiol Rev 59(2):201-222.
96. Smith HO, Hutchison CA, Pfannkoch C, Venter JC. 2003. Generating a synthetic genome by whole genome assembly: phi X174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci USA 100(26):15440-15445.
97. Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J. 2008. A fast, robust and tunable synthetic gene oscillator. Nature 456(7221):516-520.
98. Sundin GW, Weigand MR. 2007. The microbiology of mutability. FEMS Microbiol Lett 277(1):11-20.
99. Suthers PF, Dasika MS, Kumar VS, Denisov G, Glass JI, Maranas CD. 2009. A Genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput Biol 5(2).
100. Tian JD, Gong H, Sheng NJ, Zhou XC, Gulari E, Gao XL, Church G. 2004. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432(7020):1050-1054.
101. Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA. 1999. E-CELL: Software environment for whole-cell simulation. Bioinformatics 15(1):72-84.
102. Trinh CT, Unrean P, Srienc F. 2008. Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses. Appl Environ Microbiol 74(12):3634-3643.
103. Ullner E, Koseska A, Kurths J, Volkov E, Kantz H, Garcia-Ojalvo J. 2008. Multistability of synthetic genetic networks with repressive cell-to-cell communication. Phys Rev E 78(3):031904.
104. van Dalen A, de Kruijff B. 2004. The role of lipids in membrane insertion and translocation of bacterial proteins. Biochim Biophys Acta 1694(1-3):97-109.
105. Vicente M, Rico AI, Martinez-Arteaga R, Mingorance J. 2006. Septum enlightenment: Assembly of bacterial division proteins. J Bacteriol 188(1):19-27.
106. Wang WD, Chen ZT, Kang BG, Li R. 2008. Construction of an artificial intercellular communication network using the nitric oxide signaling elements in mammalian cells. Exp Cell Res 314(4):699-706.
107. Westers H, Dorenbos R, van Dijl JM, Kabel J, Flanagan T, Devine KM, Jude F, Seror SJ, Beekman AC, Darmon E, et al. 2003. Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol 20(12):2076-2090.
108. Westers L, Westers H, Quax WJ. 2004. Bacillus subtilis as cell factory for pharmaceutical proteins: A biotechnological approach to optimize the host organism. Biochim Biophys Acta 1694(1-3):299-310.
109. Wu S-C, Yeung JC, Duan Y, Ye R, Szarka SJ, Habibi HR, Wong S-L. 2002. Functional production and characterization of a fibrin-specific single-chain antibody fragment from Bacillus subtilis: Effects of molecular chaperones and a wall-bound protease on antibody fragment production. Appl Environ Microbiol 68(7):3261-3269.
110. Ye HY, Huang MC, Li MH, Ying JY. 2009. Experimental analysis of gene assembly with TopDown one-step real-time gene synthesis. Nucleic Acids Res 37:7.
111. Yomano LP, York SW, Ingram LO. 1998. Isolation and characterization of ethanol-tolerant mutants of Escherichia coli KO11 for fuel ethanol production. J Ind Microbiol Biotechnol 20(2):132-138.
112. Yu BJ, Sung BH, Koob MD, Lee CH, Lee JH, Lee WS, Kim MS, Kim SC. 2002. Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system. Nat Biotechnol 20(10):1018-1023.
113. Zakrzewska-Czerwinska J, Jakimowicz D, Zawilak-Pawlik A, Messer W. 2007. Regulation of the initiation of chromosomal replication in bacteria. FEMS Microbiol Rev 31(4):378-387.
114. Zalucki YM, Jennings MP. 2007. Experimental confirmation of a key role for non-optimal codons in protein export. Biochem Biophys Res Commun 355(1):143-148.
115. Zalucki YM, Gittins KL, Jennings MP. 2008. Secretory signal sequence nonoptimal codons are required for expression and export of beta-lactamase. Biochem Biophys Res Commun 366(1):135-141.
116. Zimmer C. 2003. Genomics - Tinker, tailor: Can Venter stitch together a genome from scratch? Science 299(5609):1006-1007.
117. Zweers JC, Barak I, Becher D, Driessen AJM, Hecker M, Kontinen VP, Saller MJ, Vavrova L, van Dijl JM. 2008. Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes. Microb Cell Fact 7:10.