Rational Design of Artificial Riboswitches

Chapter

Abstract

A riboswitch is a cis-regulatory RNA element that controls gene expression in response to a specific ligand. This functional RNA is composed of two domains, an aptamer and an expression platform. A ligand binds to the former to induce the latter’s conformational change or alternative folding, which turns on or off the expression of the downstream (or upstream in some cases) gene. Although natural riboswitches are limited in terms of the variation of their ligands, an in vitro-selected aptamer enables us to construct an artificial riboswitch responsive to a user-defined ligand molecule. However, it is difficult to functionally couple such an in vitro-selected aptamer with an expression platform for their efficient communication, which generally requires ligand-dependent hybridization switches of RNA duplexes over a wide range of mRNA. Nonetheless, we have thus far developed several rational methods for designing artificial riboswitches that function in bacterial or eukaryotic translation systems. The methods are described herein in historical order.

Keywords

Riboswitch Aptamer Ribozyme Aptazyme IRES Shunting 

Notes

Acknowledgment

This work was partially supported by JSPS KAKENHI Grant Number 16K05846.

References

  1. Andries O, Kitada T, Bodner K, Sanders NN, Weiss R (2015) Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review. Expert Rev Vaccines 14:313–331CrossRefGoogle Scholar
  2. Berens C, Suess B (2015) Riboswitch engineering – making the all-important second and third steps. Curr Opin Biotechnol 31:10–15CrossRefGoogle Scholar
  3. Berschneider B, Wieland M, Rubini M, Hartig JS (2009) Small-molecule-dependent regulation of transfer RNA in bacteria. Angew Chem Int Ed 48:7564–7567CrossRefGoogle Scholar
  4. Breaker RR (2011) Prospects for riboswitch discovery and analysis. Mol Cell 43:867–879CrossRefGoogle Scholar
  5. Chang AL, Wolf JJ, Smolke CD (2012) Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr Opin Biotechnol 23:679–688CrossRefGoogle Scholar
  6. Chen YY, Jensen MC, Smolke CD (2010) Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc Natl Acad Sci USA 107:8531–8536CrossRefGoogle Scholar
  7. Culler SJ, Hoff KG, Smolke CD (2010) Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330:1251–1255CrossRefGoogle Scholar
  8. Desai SK, Gallivan JP (2004) Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J Am Chem Soc 126:13247–13254CrossRefGoogle Scholar
  9. Endo Y, Sawasaki T (2006) Cell-free expression systems for eukaryotic protein production. Curr Opin Biotechnol 17:373–380CrossRefGoogle Scholar
  10. Endo K, Hayashi K, Inoue T, Saito H (2013) A versatile cis-acting inverter module for synthetic translational switches. Nat Commun 4:2393CrossRefGoogle Scholar
  11. Furukawa K, Gu H, Breaker RR (2014) In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP. In: Ogawa A (ed) Artificial riboswitches. . Methods in molecular biology, vol 1111. Springer, New York, pp 209–220CrossRefGoogle Scholar
  12. Grate D, Wilson C (2001) Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. Bioorg Med Chem 9:2565–2570CrossRefGoogle Scholar
  13. Harvey I, Garneau P, Pelletier J (2002) Inhibition of translation by RNA-small molecule interactions. RNA 8:452–463CrossRefGoogle Scholar
  14. Hayashi G, Nakatani K (2014) Development of photoswitchable RNA aptamer-ligand complexes. In: Ogawa A (ed) Artificial riboswitches. Methods in molecular biology, vol 1111. Springer, New York, pp 29–40CrossRefGoogle Scholar
  15. Hodgman CE, Jewett MC (2012) Cell-free synthetic biology: thinking outside the cell. Metab Eng 14:261–269CrossRefGoogle Scholar
  16. Jenison RD, Gill SC, Pardi A, Polisky B (1994) High-resolution molecular discrimination by RNA. Science 263:1425–1429CrossRefGoogle Scholar
  17. Khvorova A, Lescoute A, Westhof E, Jayasena SD (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 10:708–712CrossRefGoogle Scholar
  18. Kozak M (1987) Effects of intercistronic length on the efficiency of reinitiation by eucaryotic ribosomes. Mol Cell Biol 7:3438–3445CrossRefGoogle Scholar
  19. Lentini R, Martín NY, Mansy SS (2016) Communicating artificial cells. Curr Opin Chem Biol 34:53–61CrossRefGoogle Scholar
  20. Link KH, Guo L, Ames TD, Yen L, Mulligan RC, Breaker RR (2007) Engineering high-speed allosteric hammerhead ribozymes. Biol Chem 388:779–786CrossRefGoogle Scholar
  21. Lynch SA, Gallivan JP (2009) A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res 37:184–192CrossRefGoogle Scholar
  22. Madin K, Sawasaki T, Ogasawara T, Endo Y (2000) A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes. Proc Natl Acad Sci USA 97:559–564CrossRefGoogle Scholar
  23. Martick M, Scott WG (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126:309–320CrossRefGoogle Scholar
  24. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 101:7287–7292CrossRefGoogle Scholar
  25. Mishler DM, Gallivan JP (2014) A family of synthetic riboswitches adopts a kinetic trapping mechanism. Nucleic Acids Res 42:6753–6761CrossRefGoogle Scholar
  26. Muranaka N, Sharma V, Nomura Y, Yokobayashi Y (2009) Efficient design strategy for whole-cell and cell-free biosensors based on engineered riboswitches. Anal Lett 42:108–122CrossRefGoogle Scholar
  27. Murata A, Sato S (2014) In vitro selection of RNA aptamers for a small-molecule dye. In: Ogawa A (ed) Artificial riboswitches. Methods in molecular biology, vol 1111. Springer, New York, pp 17–28CrossRefGoogle Scholar
  28. Murray JB, Arnold JRP (1996) Antibiotic interactions with the hammerhead ribozyme: tetracyclines as a new class of hammerhead inhibitor. Biochem J 317:855–860CrossRefGoogle Scholar
  29. Nakahira Y, Ogawa A, Asano H, Oyama T, Tozawa Y (2013) Theophylline-dependent riboswitch as a novel genetic tool for strict regulation of protein expression in cyanobacterium Synechococcus elongatus PCC 7942. Plant Cell Physiol 54:1724–1735CrossRefGoogle Scholar
  30. Nomura Y, Yokobayashi Y (2014) Dual genetic selection of synthetic riboswitches in Escherichia coli. In: Ogawa A (ed) Artificial riboswitches. Methods in molecular biology, vol 1111. Springer, New York, pp 131–140CrossRefGoogle Scholar
  31. Ogawa A (2009) Biofunction-assisted sensors based on a new method for converting aptazyme activity into reporter protein expression with high efficiency in wheat germ extract. Chembiochem 10:2465–2468CrossRefGoogle Scholar
  32. Ogawa A (2011) Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors. RNA 17:478–488CrossRefGoogle Scholar
  33. Ogawa A (2012) Rational construction of eukaryotic OFF-riboswitches that downregulate internal ribosome entry site-mediated translation in response to their ligands. Bioorg Med Chem Lett 22:1639–1642CrossRefGoogle Scholar
  34. Ogawa A (2013) Ligand-dependent upregulation of ribosomal shunting. Chembiochem 14:1539–1543CrossRefGoogle Scholar
  35. Ogawa A (2014a) Rational design of artificial ON-riboswitches. In: Ogawa A (ed) Artificial riboswitches. . Methods in molecular biology, vol 1111. Springer, New York, pp 165–181CrossRefGoogle Scholar
  36. Ogawa A (ed) (2014b) Artificial riboswitches. Springer, New YorkGoogle Scholar
  37. Ogawa A (2015) Engineering of ribosomal shunt-modulating eukaryotic ON riboswitches by using a cell-free translation system. In: Burke-Aguero DH (ed) Riboswitches as targets and tools. Methods in enzymology, vol 550. Springer, New York, pp 109–128CrossRefGoogle Scholar
  38. Ogawa A, Maeda M (2007) Aptazyme-based riboswitches as label-free and detector-free sensors for cofactors. Bioorg Med Chem Lett 17:3156–3160CrossRefGoogle Scholar
  39. Ogawa A, Maeda M (2008a) An artificial aptazyme-based riboswitch and its cascading system in E. coli. Chembiochem 9:206–209CrossRefGoogle Scholar
  40. Ogawa A, Maeda M (2008b) A novel label-free biosensor using an aptazyme-suppressor-tRNA conjugate and an amber-mutated reporter gene. Chembiochem 9:2204–2208CrossRefGoogle Scholar
  41. Ogawa A, Murashige Y, Tabuchi J, Omatsu T (2017) Ligand-responsive upregulation of 3’ CITE-mediated translation in a wheat germ cell-free expression system. Mol BioSyst 13:314–319CrossRefGoogle Scholar
  42. Ohuchi S (2014) Identification of RNA aptamers against recombinant proteins with a hexa-histidine tag. In: Ogawa A (ed) Artificial riboswitches. Methods in molecular biology, vol 1111. Springer, New York, pp 41–56CrossRefGoogle Scholar
  43. Pooggin MM, Hohn T, Fütterer J (2000) Role of a short open reading frame in ribosome shunt on the Cauliflower mosaic virus RNA leader. J Biol Chem 275:17288–17296CrossRefGoogle Scholar
  44. Roth A, Breaker RR (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78:305–334CrossRefGoogle Scholar
  45. Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T (2001) Cell-free translation reconstituted with purified components. Nat Biotechnol 19:751–755CrossRefGoogle Scholar
  46. Soukup GA, Breaker RR (1999) Engineering precision RNA molecular switches. Proc Natl Acad Sci USA 96:3584–3589CrossRefGoogle Scholar
  47. Soukup GA, Emilsson GAM, Breaker RR (2000) Altering molecular recognition of RNA aptamers by allosteric selection. J Mol Biol 298:623–632CrossRefGoogle Scholar
  48. Soukup GA, DeRose EC, Koizumi M, Breaker RR (2001) Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. RNA 7:524–536CrossRefGoogle Scholar
  49. Suess B, Hanson S, Berens C, Fink B, Schroeder R, Hillen W (2003) Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res 31:1853–1858CrossRefGoogle Scholar
  50. Suess B, Fink B, Berens C, Stentz R, Hillen W (2004) A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res 32:1610–1614CrossRefGoogle Scholar
  51. Topp S, Gallivan JP (2007) Guiding bacteria with small molecules and RNA. J Am Chem Soc 129:6807–6811CrossRefGoogle Scholar
  52. Topp S, Gallivan JP (2010) Emerging applications of riboswitches in chemical biology. ACS Chem Biol 5:139–148CrossRefGoogle Scholar
  53. Topp S, Reynoso CM, Seeliger JC, Goldlust IS, Desai SK, Murat D, Shen A, Puri AW, Komeili A, Bertozzi CR, Scott JR, Gallivan JP (2010) Synthetic riboswitches that induce gene expression in diverse bacterial species. Appl Environ Microbiol 76:7881–7884CrossRefGoogle Scholar
  54. Walsh S, Gardner L, Deiters A, Williams GJ (2014) Intracellular light-activation of riboswitch activity. Chembiochem 15:1346–1351CrossRefGoogle Scholar
  55. Werstuck G, Green MR (1998) Controlling gene expression in living cells through small molecule-RNA interactions. Science 282:296–298CrossRefGoogle Scholar
  56. Wieland M, Hartig JS (2008) Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew Chem Int Ed 47:2604–2607CrossRefGoogle Scholar
  57. Win MN, Smolke CD (2007) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci USA 104:14283–14288CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Proteo-Science CenterEhime UniversityMatsuyamaJapan

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