Small‐Molecule‐Dependent Regulation of Transfer RNA in Bacteria

Berschneider, Barbara; Wieland, Markus; Rubini, Marina; Hartig, Jörg S.

doi:10.1002/anie.200900851

Cited by 43 publications

(38 citation statements)

References 30 publications

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“…However, protein-responsive ribozymes have been validated only in vitro and could not be used to control target-gene expression in living cells 31,32 . Ligandcontrolled ribozymes were also successfully used to modulate the activity of other functional RNAs such as tRNA 33 , rRNA 34 and short hairpin RNA 35 , as well as for the control of T-cell proliferation 36 and transgene expression in oncolytic viruses 37 . Nevertheless, the design of trigger-responsive ribozymes remains challenging because the integration of aptamers into ribozymes often impairs critical tertiary interloop structures, which results in moderate switching capacities 38,39 .…”

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confidence: 99%

A general design strategy for protein-responsive riboswitches in mammalian cells

et al. 2014

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RNAs are ideal for the design of gene switches that can monitor and program cellular behavior because of their high modularity and predictable structure-function relationship. We have assembled an expression platform with an embedded modular ribozyme scaffold that correlates self-cleavage activity of designer ribozymes with transgene translation in bacteria and mammalian cells. A design approach devised to screen ribozyme libraries in bacteria and validate variants with functional tertiary stem-loop structures in mammalian cells resulted in a designer ribozyme with a protein-binding nutR-boxB stem II and a selected matching stem I. In a mammalian expression context, this designer ribozyme exhibited dose-dependent translation control by the N-peptide, had rapid induction kinetics and could be combined with classic small molecule-responsive transcription control modalities to construct complex, programmable genetic circuits.

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confidence: 99%

A general design strategy for protein-responsive riboswitches in mammalian cells

et al. 2014

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“…So far, aptamers binding several ligands were combined with HHRs functioning as expression platforms in order to control mRNAs, tRNAs, 16S rRNA as well as RNAi in organisms as diverse as bacteria and mammalian cells. 11,15,16,21,[23][24][25]41 The present work shows that a physical stimulus such as a change in temperature can also be used in order to regulate gene expression via a hammerhead-mediated mRNA cleavage reaction. Importantly, most natural RNAT and all previously engineered RNAT are composed of secondary structures that mask the SD sequence.…”

Section: Discussionmentioning

confidence: 81%

“…[18][19][20] In our opinion, ribozyme-based devices have the advantage of almost universal applicability for controlling RNA functions. Apart from regulating mRNA translation in bacteria and mRNA integrity in mammalian cells, 21,22 they can be utilized in order to control the activity of tRNAs, 23 16S rRNA, 24 as well as RNAi in mammalia. 21 In addition, they can be combined in a modular fashion in order to yield two-input Boolean logic operators.…”

Section: Thermozymesmentioning

confidence: 99%

Thermozymes

et al. 2013

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“…The reprogramming of ligand selectivity yielded switches that are triggered by theophylline, thiamine pyrophosphate, p -aminophenylalanine, tetracycline and guanine (8,21,23–25). Besides controlling translation initiation through the insertion of the aptazyme within the UTR of an mRNA (8,22,26), allosteric HHRs can also be attached to other functional RNA classes to control tRNA (27), 16S ribosomal subunit (28) and pri-miRNA function (12). Our group recently demonstrated that the combination of aptazyme-based genetic switches for mRNAs and tRNAs enables the construction of Boolean logic operators inside cells (29).…”

Section: Introductionmentioning

confidence: 99%

An engineered small RNA-mediated genetic switch based on a ribozyme expression platform

Klauser

Hartig

2013

Nucleic Acids Research

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An important requirement for achieving many goals of synthetic biology is the availability of a large repertoire of reprogrammable genetic switches and appropriate transmitter molecules. In addition to engineering genetic switches, the interconnection of individual switches becomes increasingly important for the construction of more complex genetic networks. In particular, RNA-based switches of gene expression have become a powerful tool to post-transcriptionally program genetic circuits. RNAs used for regulatory purposes have the advantage to transmit, sense, process and execute information. We have recently used the hammerhead ribozyme to control translation initiation in a small molecule-dependent fashion. In addition, riboregulators have been constructed in which a small RNA acts as transmitter molecule to control translation of a target mRNA. In this study, we combine both concepts and redesign the hammerhead ribozyme to sense small trans-acting RNAs (taRNAs) as input molecules resulting in repression of translation initiation in Escherichia coli. Importantly, our ribozyme-based expression platform is compatible with previously reported artificial taRNAs, which were reported to act as inducers of gene expression. In addition, we provide several insights into key requirements of riboregulatory systems, including the influences of varying transcriptional induction of the taRNA and mRNA transcripts, 5′-processing of taRNAs, as well as altering the secondary structure of the taRNA. In conclusion, we introduce an RNA-responsive ribozyme-based expression system to the field of artificial riboregulators that can serve as reprogrammable platform for engineering higher-order genetic circuits.

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Small‐Molecule‐Dependent Regulation of Transfer RNA in Bacteria

Cited by 43 publications

References 30 publications

A general design strategy for protein-responsive riboswitches in mammalian cells

A general design strategy for protein-responsive riboswitches in mammalian cells

Thermozymes

An engineered small RNA-mediated genetic switch based on a ribozyme expression platform

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