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Olenginski LT, Spradlin SF, Batey RT. Flipping the script: Understanding riboswitches from an alternative perspective. J Biol Chem 2024; 300:105730. [PMID: 38336293 PMCID: PMC10907184 DOI: 10.1016/j.jbc.2024.105730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Riboswitches are broadly distributed regulatory elements most frequently found in the 5'-leader sequence of bacterial mRNAs that regulate gene expression in response to the binding of a small molecule effector. The occupancy status of the ligand-binding aptamer domain manipulates downstream information in the message that instructs the expression machinery. Currently, there are over 55 validated riboswitch classes, where each class is defined based on the identity of the ligand it binds and/or sequence and structure conservation patterns within the aptamer domain. This classification reflects an "aptamer-centric" perspective that dominates our understanding of riboswitches. In this review, we propose a conceptual framework that groups riboswitches based on the mechanism by which RNA manipulates information directly instructing the expression machinery. This scheme does not replace the established aptamer domain-based classification of riboswitches but rather serves to facilitate hypothesis-driven investigation of riboswitch regulatory mechanisms. Based on current bioinformatic, structural, and biochemical studies of a broad spectrum of riboswitches, we propose three major mechanistic groups: (1) "direct occlusion", (2) "interdomain docking", and (3) "strand exchange". We discuss the defining features of each group, present representative examples of riboswitches from each group, and illustrate how these RNAs couple small molecule binding to gene regulation. While mechanistic studies of the occlusion and docking groups have yielded compelling models for how these riboswitches function, much less is known about strand exchange processes. To conclude, we outline the limitations of our mechanism-based conceptual framework and discuss how critical information within riboswitch expression platforms can inform gene regulation.
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Affiliation(s)
| | | | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA.
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Wu Y, Zhu L, Zhang Y, Xu W. Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304852. [PMID: 37658499 DOI: 10.1002/smll.202304852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/15/2023] [Indexed: 09/03/2023]
Abstract
Riboswitches have received significant attention over the last two decades for their multiple functionalities and great potential for applications in various fields. This article highlights and reviews the recent advances in biosensing and biotherapy. These fields involve a wide range of applications, such as food safety detection, environmental monitoring, metabolic engineering, live cell imaging, wearable biosensors, antibacterial drug targets, and gene therapy. The discovery, origin, and optimization of riboswitches are summarized to help readers better understand their multidimensional applications. Finally, this review discusses the multidimensional challenges and development of riboswitches in order to further expand their potential for novel applications.
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Affiliation(s)
- Yifan Wu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Yangzi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
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Procknow RR, Kennedy KJ, Kluba M, Rodriguez LJ, Taga ME. Genetic dissection of regulation by a repressing and novel activating corrinoid riboswitch enables engineering of synthetic riboswitches. mBio 2023; 14:e0158823. [PMID: 37823641 PMCID: PMC10653944 DOI: 10.1128/mbio.01588-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE In addition to proteins, microbes can use structured RNAs such as riboswitches for the important task of regulating gene expression. Riboswitches control gene expression by changing their structure in response to binding a small molecule and are widespread among bacteria. Here we determine the mechanism of regulation in a riboswitch that responds to corrinoids-a family of coenzymes related to vitamin B12. We report the alternative RNA secondary structures that couple corrinoid sensing with response in a repressing and novel activating corrinoid riboswitch. We then applied this knowledge to flipping the regulatory sign by constructing synthetic riboswitches that activate expression to a higher level than the natural one. In the process, we observed patterns in which sequence, in addition to structure, impacts function in paired RNA regions. The synthetic riboswitches we describe here have potential applications as biosensors.
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Affiliation(s)
- Rebecca R. Procknow
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kristopher J. Kennedy
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Maxwell Kluba
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Lesley J. Rodriguez
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Michiko E. Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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Khorkova O, Stahl J, Joji A, Volmar CH, Wahlestedt C. Amplifying gene expression with RNA-targeted therapeutics. Nat Rev Drug Discov 2023; 22:539-561. [PMID: 37253858 PMCID: PMC10227815 DOI: 10.1038/s41573-023-00704-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 06/01/2023]
Abstract
Many diseases are caused by insufficient expression of mutated genes and would benefit from increased expression of the corresponding protein. However, in drug development, it has been historically easier to develop drugs with inhibitory or antagonistic effects. Protein replacement and gene therapy can achieve the goal of increased protein expression but have limitations. Recent discoveries of the extensive regulatory networks formed by non-coding RNAs offer alternative targets and strategies to amplify the production of a specific protein. In addition to RNA-targeting small molecules, new nucleic acid-based therapeutic modalities that allow highly specific modulation of RNA-based regulatory networks are being developed. Such approaches can directly target the stability of mRNAs or modulate non-coding RNA-mediated regulation of transcription and translation. This Review highlights emerging RNA-targeted therapeutics for gene activation, focusing on opportunities and challenges for translation to the clinic.
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Affiliation(s)
- Olga Khorkova
- OPKO Health, Miami, FL, USA
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Chemistry, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA.
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA.
- Department of Chemistry, University of Miami, Miami, FL, USA.
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Procknow RR, Kennedy KJ, Kluba M, Rodriguez LJ, Taga ME. Genetic dissection of regulation by a repressing and novel activating corrinoid riboswitch enables engineering of synthetic riboswitches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546531. [PMID: 37425860 PMCID: PMC10327014 DOI: 10.1101/2023.06.26.546531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The ability to sense and respond to intracellular metabolite levels enables cells to adapt to environmental conditions. Many prokaryotes use riboswitches - structured RNA elements usually located in the 5' untranslated region of mRNAs - to sense intracellular metabolites and respond by modulating gene expression. The corrinoid riboswitch class, which responds to adenosylcobalamin (coenzyme B12) and related metabolites, is among the most widespread in bacteria. The structural elements for corrinoid binding and the requirement for a kissing loop interaction between the aptamer and expression platform domains have been established for several corrinoid riboswitches. However, the conformational changes in the expression platform that modulate gene expression in response to corrinoid binding remain unknown. Here, we employ an in vivo GFP reporter system in Bacillus subtilis to define alternative secondary structures in the expression platform of a corrinoid riboswitch from Priestia megaterium by disrupting and restoring base-pairing interactions. Moreover, we report the discovery and characterization of the first riboswitch known to activate gene expression in response to corrinoids. In both cases, mutually exclusive RNA secondary structures are responsible for promoting or preventing the formation of an intrinsic transcription terminator in response to the corrinoid binding state of the aptamer domain. Knowledge of these regulatory mechanisms allowed us to develop synthetic corrinoid riboswitches that convert repressing riboswitches to riboswitches that robustly induce gene expression in response to corrinoids. Due to their high expression levels, low background, and over 100-fold level of induction, these synthetic riboswitches have potential use as biosensors or genetic tools.
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Affiliation(s)
- Rebecca R. Procknow
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | - Kristopher J. Kennedy
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | - Maxwell Kluba
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | - Lesley J. Rodriguez
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | - Michiko E. Taga
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA USA
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Lennon SR, Wierzba AJ, Siwik SH, Gryko D, Palmer AE, Batey RT. Targeting Riboswitches with Beta-Axial-Substituted Cobalamins. ACS Chem Biol 2023; 18:1136-1147. [PMID: 37094176 PMCID: PMC10395008 DOI: 10.1021/acschembio.2c00939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
RNA-targeting small-molecule therapeutics is an emerging field hindered by an incomplete understanding of the basic principles governing RNA-ligand interactions. One way to advance our knowledge in this area is to study model systems where these interactions are better understood, such as riboswitches. Riboswitches bind a wide array of small molecules with high affinity and selectivity, providing a wealth of information on how RNA recognizes ligands through diverse structures. The cobalamin-sensing riboswitch is a particularly useful model system, as similar sequences show highly specialized binding preferences for different biological forms of cobalamin. This riboswitch is also widely dispersed across bacteria and therefore holds strong potential as an antibiotic target. Many synthetic cobalamin forms have been developed for various purposes including therapeutics, but their interaction with cobalamin riboswitches is yet to be explored. In this study, we characterize the interactions of 11 cobalamin derivatives with three representative cobalamin riboswitches using in vitro binding experiments (both chemical footprinting and a fluorescence-based assay) and a cell-based reporter assay. The derivatives show productive interactions with two of the three riboswitches, demonstrating simultaneous plasticity and selectivity within these RNAs. The observed plasticity is partially achieved through a novel structural rearrangement within the ligand binding pocket, providing insight into how similar RNA structures can be targeted. As the derivatives also show in vivo functionality, they serve as several potential lead compounds for further drug development.
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Affiliation(s)
- Shelby R. Lennon
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Aleksandra J. Wierzba
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303 – 0596, USA
| | - Shea H. Siwik
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Dorota Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303 – 0596, USA
| | - Robert T. Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
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Bevilacqua PC, Tolbert BS. Regulatory Mechanisms through RNA Conformational Switching and Dynamics. J Mol Biol 2022; 434:167794. [PMID: 35988750 PMCID: PMC9484478 DOI: 10.1016/j.jmb.2022.167794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Philip C Bevilacqua
- Department of Chemistry and of Biochemistry & Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Blanton S Tolbert
- Department of Chemistry, Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.
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