Requirements for efficient cotranscriptional regulatory switching in designed variants of the <i>Bacillus subtilis pbuE</i> adenine-responsive riboswitch

Lk, Drogalis; Batey, Robert T.

doi:10.1101/372573

Cited by 5 publications

(4 citation statements)

References 66 publications

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“…This is consistent with a mechanism proposed by LeCuyer and Crothers for interconversion of mutually exclusive helices by nucleating base pairs that seed formation of a new helix while unwinding an existing helix 44,45 . This folding mechanism was also recently reported for the pbuE adenine riboswitch 46 .…”

Section: Discussionsupporting

confidence: 84%

A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control

et al. 2019

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Cotranscriptional folding is an obligate step of RNA biogenesis that can guide RNA structure formation and function through transient intermediate folds. This process is particularly important for transcriptional riboswitches in which the formation of ligand-dependent structures during transcription regulates downstream gene expression. However, the intermediate structures that comprise cotranscriptional RNA folding pathways and the mechanisms that enable transit between them remain largely unknown. Here we determine the series of cotranscriptional folds and rearrangements that mediate antitermination by the Clostridium beijerinckii pfl ZTP riboswitch in response to the purine biosynthetic intermediate ZMP. We uncover sequence and structural determinants that modulate an internal RNA strand displacement process and identify biases within natural ZTP riboswitch sequences that promote on-pathway folding. Our findings establish a mechanism for pfl riboswitch antitermination and suggest general strategies by which nascent RNA molecules navigate cotranscriptional folding pathways.

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Section: Discussionsupporting

confidence: 84%

A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control

et al. 2019

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“…Additionally, the compatibility of CFE reactions for high-throughput screening and the simple format of our DNA expression construct could be used to characterize the thousands of “orphan” riboswitches that have been bioinformatically identified but bind to unknown ligands . We imagine that these strategies could even be used to re-engineer riboswitches to have novel function. − As the rules of riboswitch mechanisms are deciphered at deeper levels, ,− we hope to reach a sufficient understanding to design their functional properties to meet the global needs for field-deployable environmental and health diagnostics.…”

Section: Discussionmentioning

confidence: 99%

Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor

et al. 2019

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Advances in biosensor engineering have enabled the design of programmable molecular systems to detect a range of pathogens, nucleic acids, and chemicals. Here, we engineer and field-test a biosensor for fluoride, a major groundwater contaminant of global concern. The sensor consists of a cell-free system containing a DNA template that encodes a fluoride-responsive riboswitch regulating genes that produce a fluorescent or colorimetric output. Individual reactions can be lyophilized for long-term storage and detect fluoride at levels above 2 ppm, the Environmental Protection Agency's most stringent regulatory standard, in both laboratory and field conditions. Through onsite detection of fluoride in a real-world water source, this work provides a critical proof-ofprinciple for the future engineering of riboswitches and other biosensors to address challenges for global health and the environment.

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“…We imagine that these strategies could even be used to reengineer riboswitches to have novel function (27)(28)(29). As the rules of riboswitch mechanisms are deciphered at deeper levels (11,(30)(31)(32), we hope to reach a sufficient understanding to design their functional properties to meet the global needs for field-deployable environmental and health diagnostics.…”

Section: Discussionmentioning

confidence: 99%

Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor

Thavarajah

Silverman

Verosloff

et al. 2019

Preprint

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Advances in biosensor engineering have enabled the design of programmable molecular systems to detect a range of pathogens, nucleic acids, and chemicals. Here, we engineer and field-test a biosensor for fluoride, a major groundwater contaminant of global concern. The sensor consists of a cell-free system containing a DNA template that encodes a fluoride-responsive riboswitch regulating genes that produce a fluorescent or colorimetric output. Individual reactions can be lyophilized for long-term storage and detect fluoride at levels above 2 parts per million, the EPA's most stringent regulatory standard, in both laboratory and field conditions. Through onsite detection of fluoride in a real-world water source, this work provides a critical proof-of-principle for the future engineering of riboswitches and other biosensors to address challenges for global health and the environment.

show abstract

Requirements for efficient cotranscriptional regulatory switching in designed variants of the Bacillus subtilis pbuE adenine-responsive riboswitch

Cited by 5 publications

References 66 publications

A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control

A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control

Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor

Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor

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