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Rational Design of Artificial Riboswitches

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Applied RNA Bioscience

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.

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Notes

  1. 1.

    Recently, a versatile cis-acting inverter module has been developed for eukaryotic ON-riboswitches (Endo et al. 2013).

  2. 2.

    We also succeeded in the rational design of a trans-acting gene regulator using an aptazyme/suppressor-tRNA conjugate (Ogawa and Maeda 2008b). Although this regulator is suited for a cell-free translation system, another group improved it so as to function in living cells (E. coli) (Berschneider et al. 2009).

  3. 3.

    This cascade strategy would be available for enhancing the overall switching efficiency in any riboswitch, regardless of the type of organisms.

  4. 4.

    The low cultivation temperature probably contributed also to the active ribozyme folding.

  5. 5.

    This is my current view, though at that time we thought that the magnesium ion concentration was sufficiently increased but the efficiency remained low for other reasons (Ogawa and Maeda 2008a).

  6. 6.

    In particular, a high-quality WGE provides more cell-like conditions because it has almost no contamination of the suicide system directed against ribosomes, which usually does not exist in cells but invades when a cell wall is damaged (Madin et al. 2000).

  7. 7.

    OFF-riboswitches had also been constructed by using ON-type self-cleaving aptazymes and the opposite signal inversion (ON–OFF) (Win and Smolke 2007).

  8. 8.

    The hybridization switches had been designed for responding to theophylline by using its aptamer. Although the paper reported that these switches could also be used for tetracycline, tetracycline is known to inhibit the hammerhead ribozyme itself (Murray and Arnold 1996).

  9. 9.

    Afterward, I succeeded in constructing hybridization switch-free eukaryotic ON-riboswitches (Ogawa 2013).

  10. 10.

    A ΔG value was used as an index of the MS-SL stability. This value can be calculated using only the sequence information of the implanted aptamer and a standard personal computer (Mathews et al. 2004).

  11. 11.

    In bacterial expression systems, translation rapidly proceeds in synchrony with transcription, so that thermodynamically controlled riboswitches may function less efficiently than kinetically controlled ones (Mishler and Gallivan 2014).

  12. 12.

    It is known that a large population of eukaryotic 40S ribosomal subunits remains on mRNA even after the translation of a relatively short ORF and scans the downstream region (Kozak 1987).

  13. 13.

    Recently, I edited a book that covers various detailed methods for constructing artificial riboswitches (including IRES-based one) and ligand-responsive gene regulators (Ogawa 2014b).

  14. 14.

    In the case that there has been no report on an appropriate aptamer (or aptazyme), it is first necessary to obtain one using an in vitro selection method (under conditions suited to the expression system to be used, if possible). In addition, the selected aptamer should be minimized by eliminating extra sequences.

  15. 15.

    We have recently constructed a novel regulation type of eukaryotic ON-riboswitch that ligand-dose-dependently upregulates translation initiation mediated by a 3′ cap-independent translation element (3′ CITE) with no major hybridization switches (Ogawa et al. 2017).

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Acknowledgment

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

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Authors and Affiliations

  1. Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan

    Atsushi Ogawa

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  1. Atsushi Ogawa
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Correspondence to Atsushi Ogawa .

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Editors and Affiliations

  1. Graduate School of Biostudies, Kyoto University, Kyoto, Japan

    Seiji Masuda

  2. Applied Biology, Kyoto Institute of Technology, Kyoto, Japan

    Shingo Izawa

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Ogawa, A. (2018). Rational Design of Artificial Riboswitches. In: Masuda, S., Izawa, S. (eds) Applied RNA Bioscience. Springer, Singapore. https://doi.org/10.1007/978-981-10-8372-3_6

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