A new frontier in synthetic biology: Automated design of small RNA devices in bacteria

Trends in Genetics

Volumn 29, Issue 9, 2013, Pages 529-536

  Rodrigo, Guillermo ^a,b   Landrain, Thomas E ^a,b   Shen, Shensi ^a,b   Jaramillo, Alfonso ^a,b  

^a CNRS   (France)

^b UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

Author keywords

Computational design; Post transcriptional regulation; RNA folding; Synthetic biology

Indexed keywords

BACTERIAL RNA; MESSENGER RNA;

5' UNTRANSLATED REGION; AUTOMATION; CONFORMATIONAL TRANSITION; CYTOPLASM; EVOLUTIONARY ALGORITHM; GENE CONTROL; GENE EXPRESSION; GENE MUTATION; GENE REPRESSION; GENETIC ENGINEERING; GENETIC VARIABILITY; INTERACTIONS WITH RNA; NONHUMAN; OPEN READING FRAME; PHYSICOCHEMICAL MODEL; PRIORITY JOURNAL; PROTEIN EXPRESSION; REVIEW; RNA SEQUENCE; SITE DIRECTED MUTAGENESIS; SYNTHETIC BIOLOGY; TRANSLATION INITIATION;

PROKARYOTA;

EID: 84882645053     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2013.06.005     Document Type: Review

References (58)

1. Khalil A.S., Collins J.J. Synthetic biology: applications come of age. Nat. Rev. Genet. 2012, 11:367-379.
2. Cardinale S., Arkin A.P. Contextualizing context for synthetic biology: identifying causes of failure of synthetic biological system. Biotechnol. J. 2012, 7:856-866.
3. Waters L.S., Storz G. Regulatory RNAs in bacteria. Cell 2009, 136:615-628.
4. Mercer T.R., et al. Long non-coding RNAs: insights into functions. Nat. Rev. Genet. 2009, 10:155-159.
5. Salis H.M., et al. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 2009, 27:946-950.
6. Rodrigo G., et al. De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:15271-15276.
7. Mutalik V.K., et al. Rationally designed families of orthogonal RNA regulators of translation. Nat. Chem. Biol. 2012, 8:447-454.
8. Carothers J.M., et al. Model-driven engineering of RNA devices to quantitatively program gene expression. Science 2011, 334:1716-1719.
9. Isaacs F.J., et al. RNA synthetic biology. Nat. Biotechnol. 2006, 24:545-554.
10. Liang J.C., et al. Engineering biological systems with synthetic RNA molecules. Mol. Cell 2011, 43:915-926.
11. Bida J.P., Das R. Squaring theory with practice in RNA design. Curr. Opin. Struct. Biol. 2012, 22:457-466.
12. Hofacker I.L., et al. Fast folding and comparison of RNA secondary structures. Monatsch. Chem. 1994, 125:167-188.
13. Laing C., Schlick T. Computational approaches to RNA structure prediction, analysis and design. Curr. Opin. Struct. Biol. 2011, 21:306-318.
14. Rodrigo G., et al. Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Lett. 2012, 586:2037-2042.
15. Lux M.W., et al. Genetic design automation: engineering fantasy or scientific renewal?. Trends Biotechnol. 2012, 30:120-126.
16. Krishnan Y., Bathe M. Designer nucleic acids to probe and program the cell. Trends Cell Biol. 2012, 22:624-633.
17. Koga N., et al. Principles for designing ideal protein structures. Nature 2012, 491:222-227.
18. Mathews D.H., et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 1999, 288:911-940.
19. Mathews D.H., et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:7287-7292.
20. Dirks R.M., et al. Paradigms for computational nucleic acid design. Nucleic Acids Res. 2004, 32:1392-1403.
21. Penchovsky R., Breaker R.R. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat. Biotechnol. 2005, 23:1424-1433.
22. Isaacs F.J., et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 2004, 22:841-847.
23. Muckstein U., et al. Thermodynamics of RNA-RNA binding. Bioinformatics 2006, 22:1177-1182.
24. Wilson D.S., Szostak J.W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 1999, 68:611-647.
25. Hatfield G.W., Roth D.A. Optimizing scaleup yield for protein production: Computationally Optimized DNA Assembly (CODA) and translation engineering. Biotechnol. Annu. Rev. 2007, 13:27-42.
26. Pfleger B.F., et al. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 2006, 24:1027-1032.
27. Anderson J.C., et al. Environmental signal integration by a modular AND gate. Mol. Syst. Biol. 2007, 3:133.
28. Egbert R.G., Klavins E. Fine-tuning gene networks using simple sequence repeats. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:16817-16822.
29. Na D., et al. Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. BMC Syst. Biol. 2010, 4:71.
30. Lou C., et al. Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat. Biotechnol. 2012, 30:1137-1142.
31. Chen X., Ellington A.D. Design principles for ligand-sensing, conformation-switching ribozymes. PLoS Comput. Biol. 2009, 5:e1000620.
32. Deana A., et al. The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Nature 2008, 451:355-358.
33. Wang B., et al. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat. Commun. 2011, 2:508.
34. Davis J.H., et al. Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res. 2011, 39:1131-1141.
35. Güell M., et al. Bacterial transcriptomics: what is beyond the RNA horiz-ome?. Nat. Rev. Microbiol. 2011, 9:658-669.
36. Rodrigo G., et al. Full design automation of multi-state RNA devices to program gene expression using energy-based optimization. PLoS Comput. Biol. 2013, 10.1371/journal.pcbi.1003172.
37. Lucks J.B., et al. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:8617-8622.
38. Westhof E., Jaeger L. RNA pseudoknots. Curr. Opin. Struct. Biol. 1992, 2:327-333.
39. Bindewald E., et al. Multi-strand RNA secondary structure prediction and nanostructure design including pseudoknots. ACS Nano 2011, 5:9542-9551.
40. Chworos A., et al. Building programmable jigsaw puzzles with RNA. Science 2004, 306:2068-2072.
41. Afonin K.A., et al. In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat. Nanotechnol. 2010, 5:676-682.
42. Severcan I., et al. A polyhedron made of tRNAs. Nat. Chem. 2010, 2:772-779.
43. Delebecque C.J., et al. Organization of intracellular reactions with rationally designed RNA assemblies. Science 2011, 333:470-474.
44. Leontis N.B., et al. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 2002, 30:3497-3531.
45. Das R., et al. Atomic accuracy in predicting and designing noncanonical RNA structure. Nat. Methods 2010, 7:291-294.
46. Clancy K., Voigt C.A. Programming cells: towards an automated 'Genetic Compiler'. Curr. Opin. Biotechnol. 2010, 21:572-581.
47. Callura J.M., et al. Genetic switchboard for synthetic biology applications. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:5850-5855.
48. Na D., et al. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat. Biotechnol. 2013, 31:170-174.
49. Qi L., et al. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res. 2012, 40:5775-5786.
50. Bayer T.S., Smolke C.D. Programmable, ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 2005, 23:337-343.
51. Haseltine E.L., Arnold F.H. Synthetic gene circuits: design with directed evolution. Annu. Rev. Biophys. Biomol. Struct. 2007, 36:1-19.
52. Esvelt K.M., et al. A system for the continuous directed evolution of biomolecules. Nature 2011, 472:499-503.
53. Dreier B., Plückthun A. Ribosome display: a technology for selecting and evolving proteins from large libraries. Methods Mol. Biol. 2011, 687:283-306.
54. Bartel D.P., Szostak J.W. Isolation of new ribozymes from a large pool of random sequences. Science 1993, 261:1411-1418.
55. Voigt C.A., et al. Rational evolutionary design: the theory of in vitro protein evolution. Adv. Protein Chem. 2000, 55:79-160.
56. Ladani S.T., Hamelberg D. Entropic and surprisingly small intramolecular polarization effects in the mechanism of cyclophilin A. J. Phys. Chem. B 2012, 116:10771-10778.
57. Kirkpatrick S., et al. Optimization by simulated annealing. Science 1983, 220:671-680.
58. Callura J.M., et al. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:15898-15903.