title: Engineering and In Vivo Applications of Riboswitches.
abstract: Riboswitches are common gene regulatory units mostly found in bacteria that are capable of altering gene expression in response to a small molecule. These structured RNA elements consist of two modular subunits: an aptamer domain that binds with high specificity and affinity to a target ligand and an expression platform that transduces ligand binding to a gene expression output. Significant progress has been made in engineering novel aptamer domains for new small molecule inducers of gene expression. Modified expression platforms have also been optimized to function when fused with both natural and synthetic aptamer domains. As this field expands, the use of these privileged scaffolds has permitted the development of tools such as RNA-based fluorescent biosensors. In this review, we summarize the methods that have been developed to engineer new riboswitches and highlight applications of natural and synthetic riboswitches in enzyme and strain engineering, in controlling gene expression and cellular physiology, and in real-time imaging of cellular metabolites and signals.
authors.affiliation: Department of Chemistry, University of California, Berkeley, California 94720; email: mingch@berkeley.edu.
authors.forename: Zachary F
authors.initials: ZF
authors.lastname: Hallberg
authors.affiliation: Department of Chemistry, University of California, Berkeley, California 94720; email: mingch@berkeley.edu.
authors.forename: Yichi
authors.initials: Y
authors.lastname: Su
authors.affiliation: Department of Chemistry, University of California, Berkeley, California 94720; email: mingch@berkeley.edu.
authors.forename: Rebekah Z
authors.initials: RZ
authors.lastname: Kitto
authors.affiliation: Department of Chemistry, University of California, Berkeley, California 94720; email: mingch@berkeley.edu.|Department of Molecular and Cell Biology, University of California, Berkeley, California 94720.
authors.forename: Ming C
authors.initials: MC
authors.lastname: Hammond
mesh_terms: D052157:Aptamers, Nucleotide / Q000138:chemical synthesis / Q000378:metabolism*; D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D015374:Biosensing Techniques / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005818:Genetic Engineering / Q000379:methods*; D008024:Ligands; D057054:Molecular Imaging / Q000379:methods; D043362:Rhodocyclaceae / Q000235:genetics / Q000378:metabolism; D058928:Riboswitch
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D058928:Riboswitch
keywords: RNA; aptamer; biosensor; metabolite sensing; riboswitch