A synthetic riboswitch with chemical band-pass response

Muranaka, Norihito; Yokobayashi, Yohei

doi:10.1039/c0cc01438a

Cited by 33 publications

(32 citation statements)

References 16 publications

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“…transcription termination and translation initiation) could function as a natural “band-pass” switch, wherein activation demands a certain window of ligand concentration. Such band-pass RNA switches have been successfully engineered to activate expression at a median ligand concentration, while suppressing expression when concentrations become either too low or too high (Muranaka and Yokobayashi, 2010). …”

Section: Tandem Riboswitches Increase Functional Complexitymentioning

confidence: 99%

Prospects for Riboswitch Discovery and Analysis

2011

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An expanding number of metabolite-binding riboswitch classes are being discovered in the non-coding portions of bacterial genomes. Findings over the last decade indicate that bacteria commonly use these RNA genetic elements as regulators of metabolic pathways and as mediators of changes in cell physiology. Some riboswitches are surprisingly complex, and they rival protein factors in their structural and functional sophistication. Each new riboswitch discovery expands our knowledge of the biochemical capabilities of RNA and some give rise to new questions that require additional study to be addressed. Some of the greatest prospects for riboswitch research and some of the more interesting mysteries are discussed in this review.

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Section: Tandem Riboswitches Increase Functional Complexitymentioning

confidence: 99%

Prospects for Riboswitch Discovery and Analysis

2011

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“…The question of how gene regulatory networks can achieve concentration-dependent responses in a morphogen gradient is a pivotal one in developmental biology and several different mechanisms have been suggested24. Isolated networks achieving this function have been built previously262728293031323334, but never with the explicit intention of covering and comparing all possible dynamical mechanisms.…”

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confidence: 99%

A unified design space of synthetic stripe-forming networks

et al. 2014

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Synthetic biology is a promising tool to study the function and properties of gene regulatory networks. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. Here we go beyond individual networks and explore both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally test every possible 3-node network for stripe formation in a morphogen gradient. We discover four different dynamical mechanisms to form a stripe and identify the minimal network of each group. Next, with the help of newly established engineering criteria we build these four networks synthetically and show that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allows us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.

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“…Finally, in a series of attempts to mimic natural systems, small-molecule riboswitches have been arrayed in tandem to constitute logic gates ( Table 5) (e.g., NOR, NAND, AND, etc.). 61,62,82,83 This is another way by which the power of turning simple riboswitch-like RNA devices into complex translational and transcriptional control systems has been showcased.…”

Section: Engineering Dual and Chimeric Riboregulatorsmentioning

confidence: 99%