Abstract
The recent description of a new class of small endonucleolytic ribozymes termed twister opened new avenues into the development of artificial riboswitches, providing new tools for the development of artificial genetic circuits in bacteria. Here we present a method to develop new ligand-dependent riboswitches, employing the newly described catalytic motif as an expression platform in conjugation with naturally occurring or in vitro-selected aptameric domains. The twister motif is an outstandingly flexible tool for the development of highly active ribozyme-based riboswitches able to control gene expression in a ligand-dependent manner in Escherichia coli.
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References
Ferre-D'Amare AR, Scott WG (2010) Small self-cleaving ribozymes. Cold Spring Harb Perspect Biol 2(10):a003574
Prody GA, Bakos JT, Buzayan JM, Schneider IR, Bruening G (1986) Autolytic processing of dimeric plant virus satellite RNA. Science 231(4745):1577–1580
Buzayan JM, Hampel A, Bruening G (1986) Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res 14(24):9729–9743
Sharmeen L, Kuo MY, Dinter-Gottlieb G, Taylor J (1988) Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol 62(8):2674–2679
Saville BJ, Collins RA (1990) A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell 61(4):685–696
Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428(6980):281–286. doi:10.1038/nature02362 nature02362 (pii)
Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR (2014) A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat Chem Biol 10(1):56–60
Liu Y, Wilson TJ, McPhee SA, Lilley DM (2014) Crystal structure and mechanistic investigation of the twister ribozyme. Nat Chem Biol 10:739–744
Eiler D, Wang J, Steitz TA (2014) Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme. Proc Natl Acad Sci U S A 111(36):13028–13033
Ren A, Kosutic M, Rajashankar KR, Frener M, Santner T, Westhof E, Micura R, Patel DJ (2014) In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme. Nat Commun 5:5534
Vinkenborg JL, Karnowski N, Famulok M (2011) Aptamers for allosteric regulation. Nat Chem Biol 7(8):519–527
Frommer J, Appel B, Muller S (2015) Ribozymes that can be regulated by external stimuli. Curr Opin Biotechnol 31:35–41
Berens C, Groher F, Suess B (2015) RNA aptamers as genetic control devices: the potential of riboswitches as synthetic elements for regulating gene expression. Biotechnol J 10(2):246–257. doi:10.1002/biot.201300498
Klauser B, Atanasov J, Siewert LK, Hartig JS (2014) Ribozyme-based aminoglycoside switches of gene expression engineered by genetic selection in S. cerevisiae. ACS Synth Biol 4(5):516–525
Wieland M, Benz A, Klauser B, Hartig JS (2009) Artificial ribozyme switches containing natural riboswitch aptamer domains. Angew Chem Int Ed Engl 48(15):2715–2718. doi:10.1002/anie.200805311
Wieland M, Auslander D, Fussenegger M (2012) Engineering of ribozyme-based riboswitches for mammalian cells. Methods 56(3):351–357
Gu H, Furukawa K, Breaker RR (2012) Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5′-monophosphate. Anal Chem 84(11):4935–4941. doi:10.1021/ac300415k
Klauser B, Hartig JS (2013) An engineered small RNA-mediated genetic switch based on a ribozyme expression platform. Nucleic Acids Res 41(10):5542–5552
Nomura Y, Zhou L, Miu A, Yokobayashi Y (2013) Controlling mammalian gene expression by allosteric hepatitis delta virus ribozymes. ACS Synth Biol 2(12):684–689. doi:10.1021/sb400037a
Saragliadis A, Hartig JS (2013) Ribozyme-based transfer RNA switches for post-transcriptional control of amino acid identity in protein synthesis. J Am Chem Soc 135(22):8222–8226. doi:10.1021/ja311107p
Klauser B, Saragliadis A, Auslander S, Wieland M, Berthold MR, Hartig JS (2012) Post-transcriptional Boolean computation by combining aptazymes controlling mRNA translation initiation and tRNA activation. Mol Biosyst 8(9):2242–2248. doi:10.1039/c2mb25091h
Win MN, Smolke CD (2008) Higher-order cellular information processing with synthetic RNA devices. Science 322(5900):456–460
Wieland M, Hartig JS (2008) Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew Chem Int Ed Engl 47(14):2604–2607. doi:10.1002/anie.200703700
Sambrook J, Russel DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Reetz MT, Kahakeaw D, Lohmer R (2008) Addressing the numbers problem in directed evolution. Chembiochem 9(11):1797–1804. doi:10.1002/cbic.200800298
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Felletti, M., Klauser, B., Hartig, J.S. (2016). Screening of Genetic Switches Based on the Twister Ribozyme Motif. In: Mayer, G. (eds) Nucleic Acid Aptamers. Methods in Molecular Biology, vol 1380. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3197-2_19
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DOI: https://doi.org/10.1007/978-1-4939-3197-2_19
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