Protocell design through modular compartmentalization

Journal of the Royal Society Interface

Volumn 10, Issue 87, 2013, Pages

  Miller, David ^a,c   Booth, Paula J ^b   Seddon, John M ^a   Templer, Richard H ^a   Law, Robert V ^a   Woscholski, Rudiger ^a   Ces, Oscar ^a   Barter, Laura M C ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

^c WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

Compartmentalized bioreactors; Signal transduction; Synthetic biology

Indexed keywords

GENE EXPRESSION; MACHINE COMPONENTS; PROTEINS; SIGNAL TRANSDUCTION;

BIOLOGICAL DESIGN; CELLULAR MACHINERY; ENERGY GENERATIONS; EXPRESSION SYSTEM; LIGHT TRANSDUCERS; RESPONSE ELEMENTS; SIGNAL MOLECULES; SYNTHETIC BIOLOGY;

MACHINE DESIGN;

LIPID; PROTEIN;

ARTICLE; CELL COMPARTMENTALIZATION; CELL ORGANELLE; GENE EXPRESSION; PROTOCELL; SIGNAL TRANSDUCTION; ARTIFICIAL CELL; COMPARTMENTALIZED BIOREACTORS; CYTOLOGY; GENETIC ENGINEERING; METABOLISM; PROTEIN ENGINEERING; SYNTHETIC BIOLOGY; ULTRASTRUCTURE;

COMPARTMENTALIZED BIOREACTORS; SIGNAL TRANSDUCTION; SYNTHETIC BIOLOGY;

ARTIFICIAL CELLS; CELL COMPARTMENTATION; GENE EXPRESSION; GENETIC ENGINEERING; PROTEIN ENGINEERING; PROTEINS; SIGNAL TRANSDUCTION;

EID: 84883209391     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2013.0496     Document Type: Article

References (30)

1. Martin VJJ, Pitera DJ, Withers ST, Newman JD, Keasling JD. 2003 Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21, 796-802. (doi:10. 1038/nbt833)
2. Jiang Y, Morgan-Kiss RM, Campbell JW, Chan CH, Cronan JE. 2010 Expression of Vibrio harveyi acyl-ACP synthetase allows efficient entry of exogenous fatty acids into the Escherichia coli fatty acid and lipid A synthetic pathways. Biochemistry 49, 718-726. (doi:10.1021/bi901890a)
3. Ro D-K et al. 2006 Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440, 940-943. (doi:10.1038/ nature04640)
4. Steen EJ, Chan R, Prasad N, Myers S, Petzold CJ, Redding A, Ouellet M, Keasling JD. 2008 Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb. Cell Fact. 7, 36. (doi:10.1186/1475-2859-7-36)
5. Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A, Del Cardayre SB, Keasling JD. 2010 Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463, 559-562. (doi:10.1038/nature08721)
6. Atsumi S, Hanai T, Liao JC. 2008 Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451, 86-89. (doi:10. 1038/nature06450)
7. Conrado RJ et al. 2012 DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res. 40, 1879-1889. (doi:10.1093/nar/gkr888)
8. Delebecque CJ, Lindner AB, Silver Pa, Aldaye FA. 2011 Organization of intracellular reactions with rationally designed RNA assemblies. Science 333, 470-474. (doi:10.1126/science.1206938)
9. Levskaya A et al. 2005 Synthetic biology: engineering Escherichia coli to see light. Nature 438, 441-442. (doi:10.1038/nature04405)
10. Callura JM, Cantor CR, Collins JJ. 2012 Genetic switchboard for synthetic biology applications. Proc. Natl Acad. Sci. USA 109, 5850-5855. (doi:10.1073/pnas.1203808109)
11. 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, 24-34. (doi:10.1016/j.biosystems.2012.01.002)
12. Noireaux V, Maeda YT, Libchaber A. 2011 Inaugural article: development of an artificial cell, from selforganization to computation and self-reproduction. Proc. Natl Acad. Sci. USA 108, 3473-3480. (doi:10. 1073/pnas.1017075108)
13. Stano P, Luisi PL. 2010 Achievements and open questions in the self-reproduction of vesicles and synthetic minimal cells. Chem. Commun. 46, 3639-3653. (doi:10.1039/b913997d)
14. Knight T. 2012 Idempotent vector design for standard assembly of biobricks. See http://hdl. handle.net/1721.1/21168.
15. Tan C, Marguet P, You L. 2009 Emergent bistability by a growth-modulating positive feedback circuit. Nat. Chem. Biol. 5, 842-848. (doi:10.1038/nchembio. 218)
16. Lee TI et al. 2002 Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804. (doi:10.1126/science.1075090)
17. Schwille P. 2011 Bottom-up synthetic biology: engineering in a tinkerer's world. Science 333, 1252-1254. (doi:10.1126/science.1211701)
18. Baker SE et al. 2009 Hydrogen production by a hyperthermophilic membrane-bound hydrogenase in water-soluble nanolipoprotein particles. J. Am. Chem. Soc. 131, 7508-7509. (doi:10.1021/ja809251f)
19. Kovacic J, Bozic B, Svetina S. 2010 Budding of giant unilamellar vesicles induced by an amphitropic protein b2-glycoprotein I. Biophys. Chem. 152, 46-54. (doi:10.1016/j.bpc.2010.07.005)
20. Mavelli F, Ruiz-Mirazo K. 2013 Theoretical conditions for the stationary reproduction of model protocells. Integr. Biol. 5, 324-341. (doi:10.1039/ C2IB20222K)
21. Tsai F-C, Stuhrmann B, Koenderink GH. 2011 Encapsulation of active cytoskeletal protein networks in cell-sized liposomes. Langmuir 27, 10 061-10 071. (doi:10.1021/la201604z)
22. Charalambous K, Booth PJ, Woscholski R, Seddon JM, Templer RH, Law RV, Barter LMC, Ces O. 2012 Engineering de novo membrane-mediated protein-protein communication networks. J. Am. Chem. Soc. 134, 5746-5749. (doi:10.1021/ ja300523q)
23. Freisleben HJ, Zwicker K, Jezek P, John G, Bettin-Bogutzki A, Ring K, Nawroth T. 1995 Reconstitution of bacteriorhodopsin and ATP synthase from Micrococcus luteus into liposomes of the purified main tetraether lipid from Thermoplasma acidophilum: proton conductance and light-driven ATP synthesis. Chem. Phys. Lipids 78, 137-147. (doi:10.1016/0009-3084(95)02491-Z)
24. Guatelli JC, Whitfield KM, Kwoh DY, Barringer KJ, Richman DD, Gingeras TR. 1990 Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc. Natl Acad. Sci. USA 87, 7797. (doi:10.1073/pnas.87. 19.7797-a)
25. Avnir Y, Barenholz Y. 2005 pH determination by pyranine: medium-related artifacts and their correction. Anal. Biochem. 347, 34-41. (doi:10. 1016/j.ab.2005.09.026)
26. Clement NR, Gould JM. 1981 Pyranine (8-hydroxy-1,3,6-pyrenetrisulfonate) as a probe of internal aqueous hydrogen ion concentration in phospholipid vesicles. Biochemistry 20, 1534-1538. (doi:10.1021/bi00509a019)
27. Ba'ez-Viveros JL, Flores N, Jua'rez K, Castillo-Espana P, Bolivar F, Gosset G. 2007 Metabolic transcription analysis of engineered Escherichia coli strains that overproduce L-phenylalanine. Microb. Cell Fact. 6, 30. (doi:10.1186/1475-2859-6-30)
28. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, Van Oudenaarden A. 2002 Regulation of noise in the expression of a single gene. Nat. Genet. 31, 69-73. (doi:10.1038/ng869)
29. Elowitz MB, Levine AJ, Siggia ED, Swain PS. 2002 Stochastic gene expression in a single cell. Science 297, 1183-1186. (doi:10.1126/science. 1070919)
30. 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, 1056-1063. (doi:10.1002/cbic.200800810)