RNA and RNP as new molecular parts in synthetic biology

Journal of Biotechnology

Volumn 132, Issue 1, 2007, Pages 1-7

  Saito, Hirohide ^a,b   Inoue, Tan ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Module; Riboregulator; Ribozyme; RNA; RNP; Synthetic biology

Indexed keywords

RIBONUCLEOPROTEIN (RNP); RIBOREGULATOR; RIBOZYME; SYNTHETIC BIOLOGY; WATSON-CRICK BASE-PAIRS;

BIOMOLECULES; GENE EXPRESSION; RNA;

BIOTECHNOLOGY;

RIBONUCLEOPROTEIN; RNA;

BASE PAIRING; BIOTECHNOLOGY; CELL FUNCTION; COMPLEX FORMATION; GENE EXPRESSION; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN RNA BINDING; REVIEW; RNA STRUCTURE; STRUCTURE ANALYSIS; SYNTHETIC BIOLOGY; WATSON CRICK BASE PAIR;

BIOTECHNOLOGY; DIRECTED MOLECULAR EVOLUTION; DRUG DESIGN; MODELS, MOLECULAR; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; PROTEIN CONFORMATION; RIBONUCLEOPROTEINS; RNA; RNA, CATALYTIC;

EID: 34848895990     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2007.07.952     Document Type: Review

References (53)

1. Atsumi S., Ikawa Y., Shiraishi H., and Inoue T. Design and development of a catalytic ribonucleoprotein. EMBO J. 20 (2001) 5453-5460
2. Atsumi S., Ikawa Y., Shiraishi H., and Inoue T. Selections for constituting new RNA-protein interactions in catalytic RNP. Nucleic Acids Res. 31 (2003) 661-669
3. Batey R.T., Rambo R.P., and Doudna J.A. Tertiary motifs in RNA structure and folding. Angew. Chem. Int. Ed. Engl. 38 (1999) 2326-2343
4. Battiste J.L., Mao H., Rao N.S., Tan R., Muhandiram D.R., Kay L.E., Frankel A.D., and Williamson J.R. Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex. Science 273 (1996) 1547-1551
5. Bauer G., and Suess B. Engineered riboswitches as novel tools in molecular biology. J. Biotechnol. 124 (2006) 4-11
6. Bayer T.S., and Smolke C.D. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 23 (2005) 337-343
7. Becskei A., Seraphin B., and Serrano L. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 20 (2001) 2528-2535
8. Benner S.A., and Sismour A.M. Synthetic biology. Nat. Rev. Genet. 6 (2005) 533-543
9. Bio F.A.B.G., Baker D., Church G., Collins J., Endy D., Jacobson J., Keasling J., Modrich P., Smolke C., and Weiss R. Engineering life: building a fab for biology. Sci. Am. 294 (2006) 44-51
10. Campisi D.M., Calabro V., and Frankel A.D. Structure-based design of a dimeric RNA-peptide complex. EMBO J. 20 (2001) 178-186
11. Caprara M.G., Lehnert V., Lambowitz A.M., and Westhof E. A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core. Cell 87 (1996) 1135-1145
12. Chworos A., Severcan I., Koyfman A.Y., Weinkam P., Oroudjev E., Hansma H.G., and Jaeger L. Building programmable jigsaw puzzles with RNA. Science 306 (2004) 2068-2072
13. Davidson E.A., and Ellington A.D. Synthetic RNA circuits. Nat. Chem. Biol. 3 (2007) 23-28
14. Elowitz M.B., and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 403 (2000) 335-338
15. Endy D. Foundations for engineering biology. Nature 438 (2005) 449-453
16. Gardner T.S., Cantor C.R., and Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403 (2000) 339-342
17. Guo P. RNA nanotechnology: engineering, assembly and applications in detection, gene delivery and therapy. J. Nanosci. Nanotechnol. 5 (2005) 1964-1982
18. Hartig J.S., Najafi-Shoushtari S.H., Grune I., Yan A., Ellington A.D., and Famulok M. Protein-dependent ribozymes report molecular interactions in real time. Nat. Biotechnol. 20 (2002) 717-722
19. Ikawa Y., Fukada K., Watanabe S., Shiraishi H., and Inoue T. Design, construction, and analysis of a novel class of self-folding RNA. Structure 10 (2002) 527-534
20. Ikawa Y., and Inoue T. Ribozymes switched by proteins. In: Silverman S.K. (Ed). Nucleic Acid Switches Sens. (2006) 37-47
21. Ikawa Y., Tsuda K., Matsumura S., Atsumi S., and Inoue T. Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP. Nucleic Acids Res. 31 (2003) 1488-1496
22. Ikawa Y., Tsuda K., Matsumura S., and Inoue T. De novo synthesis and development of an RNA enzyme. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 13750-13755
23. Isaacs F.J., Dwyer D.J., and Collins J.J. RNA synthetic biology. Nat. Biotechnol. 24 (2006) 545-554
24. Isaacs F.J., Dwyer D.J., Ding C., Pervouchine D.D., Cantor C.R., and Collins J.J. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22 (2004) 841-847
25. Jaeger L., and Chworos A. The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol. 16 (2006) 531-543
26. Jaeger L., and Leontis N.B. Tecto-RNA: one-dimensional self-assembly through tertiary interactions. Angew. Chem. Int. Ed. Engl. 39 (2000) 2521-2524
27. Jaeger L., Westhof E., and Leontis N.B. TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res. 29 (2001) 455-463
28. Johnston W.K., Unrau P.J., Lawrence M.S., Glasner M.E., and Bartel D.P. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292 (2001) 1319-1325
29. Joyce G.F., van der Horst G., and Inoue T. Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5. Nucleic Acids Res. 17 (1989) 7879-7889
30. Klein D.J., Schmeing T.M., Moore P.B., and Steitz T.A. The kink-turn: a new RNA secondary structure motif. EMBO J. 20 (2001) 4214-4221
31. Kramer B.P., Viretta A.U., Daoud-El-Baba M., Aubel D., Weber W., and Fussenegger M. An engineered epigenetic transgene switch in mammalian cells. Nat. Biotechnol. 22 (2004) 867-870
32. Legault P., Li J., Mogridge J., Kay L.E., and Greenblatt J. NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell 93 (1998) 289-299
33. Lescoute A., and Westhof E. The interaction networks of structured RNAs. Nucleic Acids Res. 34 (2006) 6587-6604
34. Li X., Horiya S., and Harada K. An efficient thermally induced RNA conformational switch as a framework for the functionalization of RNA nanostructures. J. Am. Chem. Soc. 128 (2006) 4035-4040
35. Liu B., Baudrey S., Jaeger L., and Bazan G.C. Characterization of tectoRNA assembly with cationic conjugated polymers. J. Am. Chem. Soc. 126 (2004) 4076-4077
36. Matsumura S., Ikawa Y., and Inoue T. Biochemical characterization of the kink-turn RNA motif. Nucleic Acids Res. 31 (2003) 5544-5551
37. Mayer O., Windbichler N., Wank H., and Schroeder R. Protein-induced RNA switches in nature. In: Silverman S.K. (Ed). Nucleic Acid Switches Sens. (2006) 75-88
38. Mohr G., Caprara M.G., Guo Q., and Lambowitz A.M. A tyrosyl-tRNA synthetase can function similarly to an RNA structure in the Tetrahymena ribozyme. Nature 370 (1994) 147-150
39. Murphy F.L., and Cech T.R. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. J. Mol. Biol. 236 (1994) 49-63
40. Nahvi A., Sudarsan N., Ebert M.S., Zou X., Brown K.L., and Breaker R.R. Genetic control by a metabolite binding mRNA. Chem. Biol. 9 (2002) 1043
41. Nasalean L., Baudrey S., Leontis N.B., and Jaeger L. Controlling RNA self-assembly to form filaments. Nucleic Acids Res. 34 (2006) 1381-1392
42. Nissen P., Ippolito J.A., Ban N., Moore P.B., and Steitz T.A. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 4899-4903
43. Saito H., Kourouklis D., and Suga H. An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J 20 (2001) 1797-1806
44. Sando S., Narita A., Abe K., and Aoyama Y. Doubly catalytic sensing of HIV-1-related CCR5 sequence in prokaryotic cell-free translation system using riboregulator-controlled luciferase activity. J. Am. Chem. Soc. 127 (2005) 5300-5301
45. Scarabino D., Crisari A., Lorenzini S., Williams K., and Tocchini-Valentini G.P. tRNA prefers to kiss. EMBO J. 18 (1999) 4571-4578
46. Seelig G., Soloveichik D., Zhang D.Y., and Winfree E. Enzyme-free nucleic acid logic circuits. Science 314 (2006) 1585-1588
47. Sprinzak D., and Elowitz M.B. Reconstruction of genetic circuits. Nature 438 (2005) 443-448
48. Szostak J.W., Bartel D.P., and Luisi P.L. Synthesizing life. Nature 409 (2001) 387-390
49. Tanner M.A., and Cech T.R. An important RNA tertiary interaction of group I and group II introns is implicated in gram-positive RNase P RNAs. RNA 1 (1995) 349-350
50. van der Horst G., Christian A., and Inoue T. Reconstitution of a group I intron self-splicing reaction with an activator RNA. Proc. Natl. Acad. Sci. U.S.A. 88 (1991) 184-188
51. Wang D.Y., and Sen D. Rationally designed allosteric variants of hammerhead ribozymes responsive to the HIV-1 Tat protein. Comb. Chem. High Throughput Screen 5 (2002) 301-312
52. Wilson D.S., and Szostak J.W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68 (1999) 611-647
53. Winkler W.C. Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr. Opin. Chem. Biol. 9 (2005) 594-602