A Simple Protein Synthesis Model for the PURE System Operation

Bulletin of Mathematical Biology

Volumn 77, Issue 6, 2015, Pages 1185-1212

  Mavelli, Fabio ^a   Marangoni, Roberto ^b,c   Stano, Pasquale ^d  

^a UNIVERSITY OF BARI   (Italy)

^b UNIVERSITY OF PISA   (Italy)

^c CNR Consiglio Nazionale delle Ricerche   (Italy)

^d ROMA TRE UNIVERSITY   (Italy)

Author keywords

Cell free transcription translation (TX TL); PURE system; Synthetic biology; Synthetic cells

Indexed keywords

LIPOSOME;

ARTIFICIAL CELL; BIOLOGICAL MODEL; COMPUTER SIMULATION; KINETICS; MATHEMATICAL PHENOMENA; METABOLISM; PROTEIN SYNTHESIS; SYNTHETIC BIOLOGY;

ARTIFICIAL CELLS; COMPUTER SIMULATION; KINETICS; LIPOSOMES; MATHEMATICAL CONCEPTS; MODELS, BIOLOGICAL; PROTEIN BIOSYNTHESIS; SYNTHETIC BIOLOGY;

EID: 84931574253     PISSN: 00928240     EISSN: 15229602     Source Type: Journal    
DOI: 10.1007/s11538-015-0082-8     Document Type: Article

References (58)

1. Atkinson DE (1968) The energy charge of the adenylate pool as a regulatory parameter. Interaction with feedback modifiers. Biochemistry 7(11):4030
2. Calviello L, Stano P, Mavelli F, Luisi PL, Marangoni R (2013) Quasi-cellular systems: stochastic simulation analysis at nanoscale range. BMC Bioinform 14(Suppl 7):S7
3. Chiarabelli C, Stano P, Luisi PL (2009) Chemical approaches to synthetic biology. Curr Opin Biotechnol 20(4):492
4. Choudhury A, Hodgman CE, Anderson MJ, Jewett MC (2014) Evaluating fermentation effects on cell growth and crude extract metabolic activity for improved yeast cell-free protein synthesis. Biochem Eng J 91:140
5. Dominak LM, Keating CD (2007) Polymer encapsulation within giant lipid vesicles. Langmuir 23(13):7148
6. Dong H, Nilsson L, Kurland CG (1996) Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol 260(5):649
7. Endy D (2005) Foundations for engineering biology. Nature 438(7067):449
8. Frazier JM, Chushak Y, Foy B (2009) Stochastic simulation and analysis of biomolecular reaction networks. BMC Syst Biol 3:64
9. Harris DC, Jewett MC (2012) Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry. Curr Opin Biotechnol 23(5):672
10. Heinonen JK (2001) Biological role of inorganic pyrophosphate. Kluver Academic Publisher, New York
11. Hockenberry AJ, Jewett MC (2012) Synthetic in vitro circuits. Curr Opin Chem Biol 16(3–4):253
12. Hodgman CE, Jewett MC (2012) Cell-free synthetic biology: thinking outside the cell. Metab Eng 14(3):261
13. Jewett MC, Fritz BR, Timmerman LE, Church GM (2013) In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation. Mol Syst Biol 9(1):678
14. Karzbrun E, Shin J, Bar-Ziv RH, Noireaux V (2011) Coarse-grained dynamics of protein synthesis in a cell-free system. Phys Rev Lett 106(4):048104
15. Kato A, Yanagisawa M, Sato YT, Fujiwara K, Yoshikawa K (2012) Cell-sized confinement in microspheres accelerates the reaction of gene expression. Sci Rep 2:283
16. Kazuta Y, Matsuura T, Ichihashi N, Yomo T (2014) Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system. J Biosci Bioeng 118(5):554
17. Kuruma Y, Stano P, Ueda T, Luisi PL (2009) A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells. Biochim Biophys Acta 1788(2):567
18. Lazzerini-Ospri L, Stano P, Luisi P, Marangoni R (2012) Characterization of the emergent properties of a synthetic quasi-cellular system. BMC Bioinform 13(Suppl 4):S9
19. LeDuc PR, Wong MS, Ferreira PM, Groff RE, Haslinger K, Koonce MP, Lee WY, Love JC, McCammon JA, Monteiro-Riviere NA, Rotello VM, Rubloff GW, Westervelt R, Yoda M (2007) Towards an in vivo biologically inspired nanofactory. Nat Nano 2(1):3
20. Liu AP, Fletcher DA (2009) Biology under construction: in vitro reconstitution of cellular function. Nat Rev Mol Cell Biol 10(9):644
21. Lohse B, Bolinger PY, Stamou D (2008) Encapsulation efficiency measured on single small unilamellar vesicles. J Am Chem Soc 130(44):14372
22. Luisi PL, Ferri F, Stano P (2006) Approaches to semi-synthetic minimal cells: a review. Naturwissenschaften 93(1):1
23. Luisi PL, Allegretti M, Pereira de Souza T, Steiniger F, Fahr A, Stano P (2010) Spontaneous protein crowding in liposomes: a new vista for the origin of cellular metabolism. ChemBioChem 11(14):1989
24. Matsubayashi H, Ueda T (2014) Purified cell-free systems as standard parts for synthetic biology. Curr Opin Chem Biol 22:158
25. Matsubayashi H, Kuruma Y, Ueda T (2014) In vitro synthesis of the E. coli sec translocon from DNA. Angew Chem Int Ed 53(29):7535
26. Matsuura T, Kazuta Y, Aita T, Adachi J, Yomo T (2009) Quantifying epistatic interactions among the components constituting the protein translation system. Mol Syst Biol 5:297
27. Matsuura T, Hosoda K, Kazuta Y, Ichihashi N, Suzuki H, Yomo T (2012) Effects of compartment size on the kinetics of intracompartmental multimeric protein synthesis. ACS Synth Biol 1(9):431
28. Matveev SV, Vinokurov LM, Shaloiko LA, Davies C, Matveeva EA, Alakhov YuB (1996) Effect of the ATP level on the overall protein biosynthesis rate in a wheat germ cell-free system. Biochim Et Biophys Acta 1293(2):207
29. Mavelli F, Altamura E, Cassidei L, Stano P (2014) Recent theoretical approaches to minimal artificial cells. Entropy 16(5):2488–2511
30. Murtas G, Kuruma Y, Bianchini P, Diaspro A, Luisi PL (2007) Protein synthesis in liposomes with a minimal set of enzymes. Biochem Biophys Res Commun 363(1):12
31. NakanoT Moore M, Enomoto A, Suda T (2011) Biological functions for information and communication technologies. In: Sawai H (ed) Studies in computational intelligence, no. 320. Springer, Berlin, pp 49–86
32. Nishimura K, Matsuura T, Nishimura K, Sunami T, Suzuki H, Yomo T (2012) Cell-free protein synthesis inside giant unilamellar vesicles analyzed by flow cytometry. Langmuir 28(22):8426
33. Niwa T, Kanamori T, Ueda T, Taguchi H (2012) Global analysis of chaperone effects using a reconstituted cell-free translation system. Proc Nat Acad Sci 109(23):8937
34. Noireaux V, Bar-Ziv R, Libchaber A (2003) Principles of cell-free genetic circuit assembly. Proc Natl Acad Sci USA 100(22):12672
35. Okano T, Matsuura T, Suzuki H, Yomo T (2014) Cell-free protein synthesis in a microchamber revealed the presence of an optimum compartment volume for high-order reactions. ACS Synth Biol 3(6):347
36. Pereira de Souza T, Stano P, Luisi PL (2009) The minimal size of liposome-based model cells brings about a remarkably enhanced entrapment and protein synthesis. ChemBioChem 10(6):1056
37. Pereira de Souza T, Steiniger F, Stano P, Fahr A, Luisi PL (2011) Spontaneous crowding of ribosomes and proteins inside vesicles: a possible mechanism for the origin of cell metabolism. ChemBioChem 12(15):2325
38. Rampioni G, Mavelli F, Damiano L, DAngelo F, Messina M, Leoni L, Stano P (2014) A synthetic biology approach to bio-chem-ICT: first moves towards chemical communication between synthetic and natural cells. Nat Comput 13:333–349
39. Saito H, Kato Y, Le Berre M, Yamada A, Inoue T, Yosikawa K, Baigl D (2009) Time-resolved tracking of a minimum gene expression system reconstituted in giant liposomes. ChemBioChem 10(10):1640
40. Schoborg JA, Hodgman CE, Anderson MJ, Jewett MC (2014) Substrate replenishment and byproduct removal improve yeast cell-free protein synthesis. Biotechnol J 9(5):630
41. Seo SW, Yang J, Min BE, Jang S, Lim JH, Lim HG, Kim SC, Kim SY, Jeong JH, Jung GY (2013) Synthetic biology: tools to design microbes for the production of chemicals and fuels. Biotechnol Adv 31(6):811
42. Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T (2001) Cell-free translation reconstituted with purified components. Nat Biotechnol 19(8):751. doi:10.1038/90802
43. Shimizu Y, Kanamori T, Ueda T (2005) Protein synthesis by pure translation systems. Methods 36(3):299
44. Shin J, Jardine P, Noireaux V (2012) Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS Synth Biol 1(9):408
45. Siegal-Gaskins D, Tuza ZA, Kim J, Noireaux V, Murray RM (2014) Gene circuit performance characterization and resource usage in a cell-free “breadboard”. ACS Synth Biol 3(6):416
46. Soga H, Fujii S, Yomo T, Kato Y, Watanabe H, Matsuura T (2014) In vitro membrane protein synthesis inside cell-sized vesicles reveals the dependence of membrane protein integration on vesicle volume. ACS Synth Biol 3:372–379
47. Stano P, Carrara P, Kuruma Y, de Souza TP, Luisi PL (2011) Compartmentalized reactions as a case of soft-matter biotechnology: synthesis of proteins and nucleic acids inside lipid vesicles. J Mater Chem 21(47):18887
48. Stano P, Rampioni G, Carrara P, Damiano L, Leoni L, Luisi PL (2012) Semi-synthetic minimal cells as a tool for biochemical ICT. BioSystems 109(1):24
49. Stano P, Luisi PL (2013) Semi-synthetic minimal cells: origin and recent developments. Curr Opin Biotechnol 24:633–638
50. Stano P, D’Aguanno E, Bolz J, Fahr A, Luisi PL (2013) A remarkable self-organization process as the origin of primitive functional cells. Angew Chem Int Ed Engl 52(50):13397
51. Stano P, Souza T, Carrara P, Altamura E, D’Aguanno E, Caputo M, Luisi PL, Mavelli F (2015) Recent biophysical issues about the preparation of solute-filled lipid vesicles. Mech Adv Mater Struct 22:748–759
52. Stögbauer T, Windhager L, Zimmer R, Rädler JO (2012) Experiment and mathematical modeling of gene expression dynamics in a cell-free system. Integr Biol 4(5):494
53. Sun BY, Chiu DT (2005) Determination of the encapsulation efficiency of individual vesicles using single-vesicle photolysis and confocal single-molecule detection. Anal Chem 77(9):2770
54. Sunami T, Hosoda K, Suzuki H, Matsuura T, Yomo T (2010) Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions. Langmuir 26(11):8544
55. van Nies P, Nourian Z, Kok M, van Wijk R, Moeskops J, Westerlaken I, Poolman JM, Eelkema R, van Esch JH, Kuruma Y, Ueda T, Danelon C (1963) Unbiased tracking of the progression of mRNA and protein synthesis in bulk and in liposome-confined reactions. ChemBioChem 14(15):1963–1966
56. Walde P, Umakoshi H, Stano P, Mavelli F (2014) Emergent properties arising from the assembly of amphiphiles. Artificial vesicle membranes as reaction promoters and regulators. Chem Comm 50:10177–10197
57. Yarchuk O, Jacques N, Guillerez J, Dreyfus M (1992) Interdependence of translation, transcription and mRNA degradation in the lacZ gene. J Mol Biol 226(3):581
58. Zhao H (ed) (2013) Synthetic Biology. Tools and applications. Academic Press-Elsevier, Amsterdam