Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment

Nature Communications

Volumn 4, Issue , 2013, Pages

  Ichihashi, Norikazu ^a   Usui, Kimihito ^a   Kazuta, Yasuaki ^a   Sunami, Takeshi ^a   Matsuura, Tomoaki ^a   Yomo, Tetsuya ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DOUBLE STRANDED RNA; GENOMIC RNA; RNA DIRECTED RNA POLYMERASE;

BIOCHEMISTRY; ERROR ANALYSIS; EVOLUTIONARY BIOLOGY; EVOLUTIONARY THEORY; EXPERIMENTAL STUDY; GENOME; ORIGIN OF LIFE; PARASITISM; RNA;

ARTICLE; ARTIFICIAL CELL; CELL COMPARTMENTALIZATION; IN VITRO STUDY; MUTATION; NONHUMAN; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA REPLICATION;

ARTIFICIAL CELLS; EVOLUTION, MOLECULAR; GENETIC FITNESS; KINETICS; MUTATION; RNA REPLICASE; RNA, DOUBLE-STRANDED; SELECTION, GENETIC;

EID: 84885092862     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3494     Document Type: Article

References (41)

1. Szostak, J. W., Bartel, D. P. & Luisi, P. L. Synthesizing life. Nature 409, 387-390 (2001).
2. Deamer, D. A giant step towards artificial life? Trends. Biotechnol. 23, 336-338 (2005).
3. Forster, A. C. & Church, G. M. Synthetic biology projects in vitro. Genome Res. 17, 1-6 (2007).
4. Ichihashi, N. et al. Constructing partial models of cells. Cold Spring Harb Perspect Biol. 2, a004945 (2010).
5. Luisi, P. L. & Stano, P. Synthetic biology: Minimal cell mimicry. Nat. Chem. 3, 755-756 (2011).
6. Pohorille, A. & Deamer, D. Artificial cells: Prospects for biotechnology. Trends Biotechnol. 20, 123-128 (2002).
7. Benner, S. A. & Sismour, A. M. Synthetic biology. Nat. Rev. 6, 533-543 (2005).
8. Hanczyc, M. M., Fujikawa, S. M. & Szostak, J. W. Experimental models of primitive cellular compartments: Encapsulation, growth and division. Science 302, 618-622 (2003).
9. Chen, I. A. & Szostak, J. W. Membrane growth can generate a transmembrane pH gradient in fatty acid vesicles. Proc. Natl Acad. Sci. USA 101, 7965-7970 (2004).
10. Chen, I. A., Salehi-ashtiani, K. & Szostak, J. W. RNA catalysis in model protocell vesicles. J. Am. Chem. Soc. 127, 13213-13219 (2005).
11. Zhu, T. F. & Szostak, J. W. Coupled growth and division of model protocell membranes. J. Am. Chem. Soc. 131, 5705-5713 (2009).
12. Mansy, S. S. et al. Template-Directed synthesis of a genetic polymer in a model protocell. Nature 454, 122-125 (2008).
13. Kurihara, K. et al. Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA. Nat. Chem. 3, 775-781 (2011).
14. Noireaux, V., Bar-Ziv, R., Godefroy, J., Salman, H. & Libchaber, A. Toward an artificial cell based on gene expression in vesicles. Phys. Biol. 2, P1-p8 (2005).
15. Zepik, H. H. & Walde, P. Achievements and challenges in generating protocell models. Chembiochem. 9, 2771-2772 (2008).
16. Chiarabelli, C., Stano, P. & Luisi, P. L. Chemical approaches to synthetic biology. Curr. Opin. Biotechnol. 20, 492-497 (2009).
17. Jewett, M. C. & Forster, A. C. Update on designing and building minimal cells. Curr. Opin. Biotechnol. 21, 697-703 (2010).
18. Forlin, M., Lentini, R. & Mansy, S. S. Cellular imitations. Curr. Opin. Chem. Biol. 16, 586-592 (2012).
19. Mills, D. R., Peterson, R. L. & Spiegelman, S. An extracellular Darwinian experiment with a self-Duplicating nucleic acid molecule. Proc. Natl Acad. Sci. USA 58, 217-224 (1967).
20. Wright, M. C. & Joyce, G. F. Continuous in vitro evolution of catalytic function. Science 276, 614-617 (1997).
21. Lincoln, T. A. & Joyce, G. F. Self-sustained replication of an RNA enzyme. Science 323, 1229-1232 (2009).
22. Vaidya, N. et al. Spontaneous network formation among cooperative RNA replicators. Nature 491, 72-77 (2012).
23. Shimizu, Y. et al. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751-755 (2001).
24. Kita, H. et al. Replication of genetic information with self-encoded replicase in liposomes. Chembiochem. 9, 2403-2410 (2008).
25. Tawfik, D. S. & Griffiths, A. D. Man-made cell-Like compartments for molecular evolution. Nat. Biotechnol. 16, 652-656 (1998).
26. Ghadessy, F. J., Ong, J. L. & Holliger, P. Directed evolution of polymerase function by compartmentalized self-replication. Proc. Natl Acad. Sci. USA 98, 4552-4557 (2001).
27. Bansho, Y. et al. Importance of parasite RNA species repression for prolonged translation-coupled RNA self-replication. Chem. Biol. 19, 478-487 (2012).
28. Gerrish, P. J. & Lenski, R. E. The fate of competing beneficial mutations in an asexual population. Genetica 102-103, 127-144 (1998).
29. Kimura, M. The Neutral Theory Of Molecular Evolution (Cambridge University Press, 1983).
30. Inokuchi, Y. & Kajitani, M. Deletion analysis of Qb replicase. Participation of the carboxyl-terminal region of the beta-subunit protein in template recognition. J. Biol. Chem. 272, 15339-15345 (1997).
31. Maynard Smith, J. & Szathmary, E. The Major Transitions in Evolution (Oxford University Press, 1995).
32. Eigen, M. Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58, 465-523 (1971).
33. Bresch, C., Niesert, U. & Harnasch, D. Hypercycles, parasites and packages. J. Theor. Biol. 85, 399-405 (1980).
34. Breaker, R. R. & Joyce, G. F. Emergence of a replicating species from an in vitro RNA evolution reaction. Proc. Natl Acad. Sci. USA 91, 6093-6097 (1994).
35. Ellinger, T., Ehricht, R. & McCaskill, J. S. In vitro evolution of molecular cooperation in CATCH, a cooperatively coupled amplification system. Chem. Biol. 5, 729-741 (1998).
36. Szathmary, E. & Demeter, L. Group selection of early replicators and the origin of life. J. Theor. Biol. 128, 463-486 (1987).
37. Arjan, J. A. et al. Diminishing returns from mutation supply rate in asexual populations. Science 283, 404-406 (1999).
38. Barrick, J. E. et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243-1247 (2009).
39. Rainey, P. B. Evolutionary biology: Arrhythmia of tempo and mode. Nature 461, 1219-1221 (2009).
40. Schatz, D., Leberman, R. & Eckstein, F. Interaction of Escherichia coli tRNA(Ser) with its cognate aminoacyl-tRNA synthetase as determined by footprinting with phosphorothioate-containing tRNA transcripts. Proc. Natl Acad. Sci. USA 88, 6132-6136 (1991).
41. Axelrod, V. D., Brown, E., Priano, C. & Mills, D. R. Coliphage Qb RNA replication: RNA catalytic for single-strand release. Virology 184, 595-608 (1991).