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Narunsky A, Higgs GA, Torres BM, Yu D, de Andrade GB, Kavita K, Breaker RR. The discovery of novel noncoding RNAs in 50 bacterial genomes. Nucleic Acids Res 2024; 52:5152-5165. [PMID: 38647067 PMCID: PMC11109978 DOI: 10.1093/nar/gkae248] [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] [Received: 10/12/2023] [Revised: 03/20/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
Structured noncoding RNAs (ncRNAs) contribute to many important cellular processes involving chemical catalysis, molecular recognition and gene regulation. Few ncRNA classes are broadly distributed among organisms from all three domains of life, but the list of rarer classes that exhibit surprisingly diverse functions is growing. We previously developed a computational pipeline that enables the near-comprehensive identification of structured ncRNAs expressed from individual bacterial genomes. The regions between protein coding genes are first sorted based on length and the fraction of guanosine and cytidine nucleotides. Long, GC-rich intergenic regions are then examined for sequence and structural similarity to other bacterial genomes. Herein, we describe the implementation of this pipeline on 50 bacterial genomes from varied phyla. More than 4700 candidate intergenic regions with the desired characteristics were identified, which yielded 44 novel riboswitch candidates and numerous other putative ncRNA motifs. Although experimental validation studies have yet to be conducted, this rate of riboswitch candidate discovery is consistent with predictions that many hundreds of novel riboswitch classes remain to be discovered among the bacterial species whose genomes have already been sequenced. Thus, many thousands of additional novel ncRNA classes likely remain to be discovered in the bacterial domain of life.
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Affiliation(s)
- Aya Narunsky
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Gadareth A Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Blake M Torres
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Diane Yu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Gabriel Belem de Andrade
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Kumari Kavita
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
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2
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Soares LW, King CG, Fernando CM, Roth A, Breaker RR. Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation. Proc Natl Acad Sci U S A 2024; 121:e2318008121. [PMID: 38306478 PMCID: PMC10861870 DOI: 10.1073/pnas.2318008121] [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: 10/16/2023] [Accepted: 12/02/2023] [Indexed: 02/04/2024] Open
Abstract
Several structured noncoding RNAs in bacteria are essential contributors to fundamental cellular processes. Thus, discoveries of additional ncRNA classes provide opportunities to uncover and explore biochemical mechanisms relevant to other major and potentially ancient processes. A candidate structured ncRNA named the "raiA motif" has been found via bioinformatic analyses in over 2,500 bacterial species. The gene coding for the RNA typically resides between the raiA and comFC genes of many species of Bacillota and Actinomycetota. Structural probing of the raiA motif RNA from the Gram-positive anaerobe Clostridium acetobutylicum confirms key features of its sophisticated secondary structure model. Expression analysis of raiA motif RNA reveals that the RNA is constitutively produced but reaches peak abundance during the transition from exponential growth to stationary phase. The raiA motif RNA becomes the fourth most abundant RNA in C. acetobutylicum, excluding ribosomal RNAs and transfer RNAs. Genetic disruption of the raiA motif RNA causes cells to exhibit substantially decreased spore formation and diminished ability to aggregate. Restoration of normal cellular function in this knock-out strain is achieved by expression of a raiA motif gene from a plasmid. These results demonstrate that raiA motif RNAs normally participate in major cell differentiation processes by operating as a trans-acting factor.
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Affiliation(s)
- Lucas W. Soares
- Department of Microbial Pathogenesis, Yale University, New Haven, CT06536
| | - Christopher G. King
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Chrishan M. Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Adam Roth
- HHMI, Yale University, New Haven, CT06511-8103
| | - Ronald R. Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
- HHMI, Yale University, New Haven, CT06511-8103
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511-8103
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3
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Pavlova N, Traykovska M, Penchovsky R. Targeting FMN, TPP, SAM-I, and glmS Riboswitches with Chimeric Antisense Oligonucleotides for Completely Rational Antibacterial Drug Development. Antibiotics (Basel) 2023; 12:1607. [PMID: 37998809 PMCID: PMC10668854 DOI: 10.3390/antibiotics12111607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Antimicrobial drug resistance has emerged as a significant challenge in contemporary medicine due to the proliferation of numerous bacterial strains resistant to all existing antibiotics. Meanwhile, riboswitches have emerged as promising targets for discovering antibacterial drugs. Riboswitches are regulatory elements in certain bacterial mRNAs that can bind to specific molecules and control gene expression via transcriptional termination, prevention of translation, or mRNA destabilization. By targeting riboswitches, we aim to develop innovative strategies to combat antibiotic-resistant bacteria and enhance the efficacy of antibacterial treatments. This convergence of challenges and opportunities underscores the ongoing quest to revolutionize medical approaches against evolving bacterial threats. For the first time, this innovative review describes the rational design and applications of chimeric antisense oligonucleotides as antibacterial agents targeting four riboswitches selected based on genome-wide bioinformatic analyses. The antisense oligonucleotides are coupled with the cell-penetrating oligopeptide pVEC, which penetrates Gram-positive and Gram-negative bacteria and specifically targets glmS, FMN, TPP, and SAM-I riboswitches in Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli. The average antibiotic dosage of antisense oligonucleotides that inhibits 80% of bacterial growth is around 700 nM (4.5 μg/mL). Antisense oligonucleotides do not exhibit toxicity in human cell lines at this concentration. The results demonstrate that these riboswitches are suitable targets for antibacterial drug development using antisense oligonucleotide technology. The approach is fully rational because selecting suitable riboswitch targets and designing ASOs that target them are based on predefined criteria. The approach can be used to develop narrow or broad-spectrum antibiotics against multidrug-resistant bacterial strains for a short time. The approach is easily adaptive to new resistance using targeting NGS technology.
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Affiliation(s)
| | | | - Robert Penchovsky
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
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4
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Hamal Dhakal S, Kavita K, Panchapakesan SSS, Roth A, Breaker RR. 8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage. Proc Natl Acad Sci U S A 2023; 120:e2307854120. [PMID: 37748066 PMCID: PMC10556655 DOI: 10.1073/pnas.2307854120] [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: 05/10/2023] [Accepted: 08/25/2023] [Indexed: 09/27/2023] Open
Abstract
Riboswitches rely on structured aptamer domains to selectively sense their target ligands and regulate gene expression. However, some riboswitch aptamers in bacteria carry mutations in their otherwise strictly conserved binding pockets that change ligand specificities. The aptamer domain of a riboswitch class originally found to selectively sense guanine forms a three-stem junction that has since been observed to exploit numerous alterations in its ligand-binding pocket. These rare variants have modified their ligand specificities to sense other purines or purine derivatives, including adenine, 2'-deoxyguanosine (three classes), and xanthine. Herein, we report the characteristics of a rare variant that is narrowly distributed in the Paenibacillaceae family of bacteria. Known representatives are always associated with genes encoding 8-oxoguanine deaminase. As predicted from this gene association, these variant riboswitches tightly bind 8-oxoguanine (8-oxoG), strongly discriminate against other purine derivatives, and function as genetic "ON" switches. Following exposure of cells to certain oxidative stresses, a representative 8-oxoG riboswitch activates gene expression, likely caused by the accumulation of 8-oxoG due to oxidative damage to G nucleobases in DNA, RNA, and the nucleotide pool. Furthermore, an engineered version of the variant aptamer was prepared that exhibits specificity for 8-oxoadenine, further demonstrating that RNA aptamers can acquire mutations that expand their ability to detect and respond to oxidative damage.
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Affiliation(s)
- Siddhartha Hamal Dhakal
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511-8103
| | - Kumari Kavita
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511-8103
| | | | - Adam Roth
- HHMI, Yale University, New Haven, CT06511-8103
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511-8103
- HHMI, Yale University, New Haven, CT06511-8103
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
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5
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Kumar A, Vashisth H. Mechanism of Ligand Discrimination by the NMT1 Riboswitch. J Chem Inf Model 2023; 63:4864-4874. [PMID: 37486304 PMCID: PMC11088486 DOI: 10.1021/acs.jcim.3c00835] [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: 07/25/2023]
Abstract
Riboswitches are conserved functional domains in mRNA that almost exclusively exist in bacteria. They regulate the biosynthesis and transport of amino acids and essential metabolites such as coenzymes, nucleobases, and their derivatives by specifically binding small molecules. Due to their ability to precisely discriminate between different cognate molecules as well as their common existence in bacteria, riboswitches have become potential antibacterial drug targets that could deliver urgently needed antibiotics with novel mechanisms of action. In this work, we report the recognition mechanisms of four oxidization products (XAN, AZA, UAC, and HPA) generated during purine degradation by an RNA motif termed the NMT1 riboswitch. Specifically, we investigated the physical interactions between the riboswitch and the oxidized metabolites by computing the changes in the free energy on mutating key nucleobases in the ligand binding pocket of the riboswitch. We discovered that the electrostatic interactions are central to ligand discrimination by this riboswitch. The relative binding free energies of the mutations further indicated that some of the mutations can also strengthen the binding affinities of the ligands (AZA, UAC, and HPA). These mechanistic details are also potentially relevant in the design of novel compounds targeting riboswitches.
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Affiliation(s)
- Amit Kumar
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire 03824, United States
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6
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Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. THE PLANT CELL 2023; 35:1671-1707. [PMID: 36747354 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
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Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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7
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Kavita K, Breaker RR. Discovering riboswitches: the past and the future. Trends Biochem Sci 2023; 48:119-141. [PMID: 36150954 PMCID: PMC10043782 DOI: 10.1016/j.tibs.2022.08.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 01/25/2023]
Abstract
Riboswitches are structured noncoding RNA domains used by many bacteria to monitor the concentrations of target ligands and regulate gene expression accordingly. In the past 20 years over 55 distinct classes of natural riboswitches have been discovered that selectively sense small molecules or elemental ions, and thousands more are predicted to exist. Evidence suggests that some riboswitches might be direct descendants of the RNA-based sensors and switches that were likely present in ancient organisms before the evolutionary emergence of proteins. We provide an overview of the current state of riboswitch research, focusing primarily on the discovery of riboswitches, and speculate on the major challenges facing researchers in the field.
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Affiliation(s)
- Kumari Kavita
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA.
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8
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Jagodnik J, Tjaden B, Ross W, Gourse R. Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA. Nucleic Acids Res 2023; 51:852-869. [PMID: 36617997 PMCID: PMC9881157 DOI: 10.1093/nar/gkac1224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/30/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Ligand-binding RNAs (RNA aptamers) are widespread in the three domains of life, serving as sensors of metabolites and other small molecules. When aptamers are embedded within RNA transcripts as components of riboswitches, they can regulate gene expression upon binding their ligands. Previous methods for biochemical validation of computationally predicted aptamers are not well-suited for rapid screening of large numbers of RNA aptamers. Therefore, we utilized DRaCALA (Differential Radial Capillary Action of Ligand Assay), a technique designed originally to study protein-ligand interactions, to examine RNA-ligand binding, permitting rapid screening of dozens of RNA aptamer candidates concurrently. Using this method, which we call RNA-DRaCALA, we screened 30 ykkC family subtype 2a RNA aptamers that were computationally predicted to bind (p)ppGpp. Most of the aptamers bound both ppGpp and pppGpp, but some strongly favored only ppGpp or pppGpp, and some bound neither. Expansion of the number of biochemically verified sites allowed construction of more accurate secondary structure models and prediction of key features in the aptamers that distinguish a ppGpp from a pppGpp binding site. To demonstrate that the method works with other ligands, we also used RNA DRaCALA to analyze aptamer binding by thiamine pyrophosphate.
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Affiliation(s)
- Jonathan Jagodnik
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Brian Tjaden
- Department of Computer Science, Wellesley College, Wellesley, MA 02481, USA
| | - Wilma Ross
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
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9
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Zhu Y, Hart GW. Dual-specificity RNA aptamers enable manipulation of target-specific O-GlcNAcylation and unveil functions of O-GlcNAc on β-catenin. Cell 2023; 186:428-445.e27. [PMID: 36626902 PMCID: PMC9868088 DOI: 10.1016/j.cell.2022.12.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 11/02/2022] [Accepted: 12/08/2022] [Indexed: 01/11/2023]
Abstract
O-GlcNAc is a dynamic post-translational modification (PTM) that regulates protein functions. In studying the regulatory roles of O-GlcNAc, a major roadblock is the inability to change O-GlcNAcylation on a single protein at a time. Herein, we developed a dual RNA-aptamer-based approach that simultaneously targeted O-GlcNAc transferase (OGT) and β-catenin, the key transcription factor of the Wnt signaling pathway, to selectively increase O-GlcNAcylation of the latter without affecting other OGT substrates. Using the OGT/β-catenin dual-specificity aptamers, we found that O-GlcNAcylation of β-catenin stabilizes the protein by inhibiting its interaction with β-TrCP. O-GlcNAc also increases β-catenin's interaction with EZH2, recruits EZH2 to promoters, and dramatically alters the transcriptome. Further, by coupling riboswitches or an inducible expression system to aptamers, we enabled inducible regulation of protein-specific O-GlcNAcylation. Together, our findings demonstrate the efficacy and versatility of dual-specificity aptamers for regulating O-GlcNAcylation on individual proteins.
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Affiliation(s)
- Yi Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Gerald W Hart
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
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10
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Lenkeit F, Eckert I, Sinn M, Hauth F, Hartig JS, Weinberg Z. A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity. RNA Biol 2023; 20:10-19. [PMID: 36548032 PMCID: PMC9788692 DOI: 10.1080/15476286.2022.2160562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Riboswitches are regulatory RNAs that specifically bind a small molecule or ion. Like metabolite-binding proteins, riboswitches can evolve new ligand specificities, and some examples of this phenomenon have been validated. As part of work based on comparative genomics to discover novel riboswitches, we encountered a candidate riboswitch with striking similarities to the recently identified guanidine-IV riboswitch. This candidate riboswitch, the Gd4v motif, is predicted in four distinct bacterial phyla, thus almost as widespread as the guanidine-IV riboswitch. Bioinformatic and experimental analysis suggest that the Gd4v motif is a riboswitch that binds a ligand other than guanidine. It is found associated with gene classes that differ from genes regulated by confirmed guanidine riboswitches. In inline-probing assays, we showed that free guanidine binds only weakly to one of the tested sequences of the variant. Further tested compounds did not show binding, attenuation of transcription termination, or activation of a genetic reporter construct. We characterized an N-acetyltransferase frequently associated with the Gd4v motif and compared its substrate preference to an N-acetyltransferase that occurs under control of guanidine-IV riboswitches. The substrates of this Gd4v-motif-associated enzyme did not show activity for Gd4v RNA binding or transcription termination. Hence, the ligand of the candidate riboswitch motif remains unidentified. The variant RNA motif is predominantly found in gut metagenome sequences, hinting at a ligand that is highly relevant in this environment. This finding is a first step to determining the identity of this unknown ligand, and understanding how guanidine-IV-riboswitch-like structures can evolve to bind different ligands.
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Affiliation(s)
- Felina Lenkeit
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany
| | - Iris Eckert
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107Leipzig, Germany
| | - Malte Sinn
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany
| | - Franziskus Hauth
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany,CONTACT Jörg S. Hartig
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107Leipzig, Germany,Zasha Weinberg Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107Leipzig, Germany
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11
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Childs-Disney JL, Yang X, Gibaut QMR, Tong Y, Batey RT, Disney MD. Targeting RNA structures with small molecules. Nat Rev Drug Discov 2022; 21:736-762. [PMID: 35941229 PMCID: PMC9360655 DOI: 10.1038/s41573-022-00521-4] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
RNA adopts 3D structures that confer varied functional roles in human biology and dysfunction in disease. Approaches to therapeutically target RNA structures with small molecules are being actively pursued, aided by key advances in the field including the development of computational tools that predict evolutionarily conserved RNA structures, as well as strategies that expand mode of action and facilitate interactions with cellular machinery. Existing RNA-targeted small molecules use a range of mechanisms including directing splicing - by acting as molecular glues with cellular proteins (such as branaplam and the FDA-approved risdiplam), inhibition of translation of undruggable proteins and deactivation of functional structures in noncoding RNAs. Here, we describe strategies to identify, validate and optimize small molecules that target the functional transcriptome, laying out a roadmap to advance these agents into the next decade.
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Affiliation(s)
| | - Xueyi Yang
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | | | - Yuquan Tong
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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12
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Pavlova N, Penchovsky R. Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets. Antibiotics (Basel) 2022; 11:antibiotics11091177. [PMID: 36139956 PMCID: PMC9495176 DOI: 10.3390/antibiotics11091177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug targets. Most bacterial riboswitches are located in the 5′-untranslated region of messenger RNAs, act as allosteric cis-acting gene control elements, and have not been found in humans before. Sensing metabolites, the riboswitches regulate the synthesis of vital cellular metabolites in various pathogenic bacteria. The analyses performed in this article represent a complete and informative genome-wide bioinformatics analysis of the adequacy of eight riboswitches as antibacterial drug targets in different pathogenic bacteria based on four criteria. Due to the ability of the riboswitch to control biosynthetic pathways and transport proteins of essential metabolites and the presence/absence of alternative biosynthetic pathways, we classified them into four groups based on their suitability for use as antibacterial drug targets guided by our in silico analyses. We concluded that some of them are promising targets for antibacterial drug discovery, such as the PreQ1, MoCo RNA, cyclic-di-GMP I, and cyclic-di-GMP II riboswitches.
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13
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Waters L. A new class of metal-sensing RNA. Nat Chem Biol 2022; 18:798-799. [PMID: 35879548 DOI: 10.1038/s41589-022-01087-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lauren Waters
- Department of Chemistry, University of Wisconsin Oshkosh, Oshkosh, WI, USA.
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14
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Mahendran G, Jayasinghe OT, Thavakumaran D, Arachchilage GM, Silva GN. Key players in regulatory RNA realm of bacteria. Biochem Biophys Rep 2022; 30:101276. [PMID: 35592614 PMCID: PMC9111926 DOI: 10.1016/j.bbrep.2022.101276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022] Open
Abstract
Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network. The three major classes of prokaryotic ncRNAs and their characterized mechanisms of operation in gene regulation. sRNAs emerging as major players in global gene regulatory networks. Riboswitch mediated gene control mechanisms through on/off switches in response to ligand binding. RNA thermo sensors for temperature-dependent gene expression. Therapeutic importance of ncRNAs and computational approaches involved in the discovery of ncRNAs.
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Affiliation(s)
- Gowthami Mahendran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Oshadhi T. Jayasinghe
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Dhanushika Thavakumaran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Gayan Mirihana Arachchilage
- Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520-8103, USA
- PTC Therapeutics Inc, South Plainfield, NJ, 07080, USA
| | - Gayathri N. Silva
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Corresponding author.
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15
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Iron-responsive riboswitches. Curr Opin Chem Biol 2022; 68:102135. [DOI: 10.1016/j.cbpa.2022.102135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/23/2022]
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16
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Hamal Dhakal S, Panchapakesan SSS, Slattery P, Roth A, Breaker RR. Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine. Proc Natl Acad Sci U S A 2022; 119:e2120246119. [PMID: 35622895 PMCID: PMC9295807 DOI: 10.1073/pnas.2120246119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/12/2022] [Indexed: 12/30/2022] Open
Abstract
The aptamer portions of previously reported riboswitch classes that sense guanine, adenine, or 2′-deoxyguanosine are formed by a highly similar three-stem junction with distinct nucleotide sequences in the regions joining the stems. The nucleotides in these joining regions form the major features of the selective ligand-binding pocket for each aptamer. Previously, we reported the existence of additional, rare variants of the predominant guanine-sensing riboswitch class that carry nucleotide differences in the ligand-binding pocket, suggesting that these RNAs have further diversified their structures and functions. Herein, we report the discovery and analysis of three naturally occurring variants of guanine riboswitches that are narrowly distributed across Firmicutes. These RNAs were identified using comparative sequence analysis methods, which also revealed that some of the gene associations for these variants are atypical for guanine riboswitches or their previously known natural variants. Binding assays demonstrate that the newfound variant riboswitch representatives recognize xanthine, guanine, or 2′-deoxyguanosine, with the guanine class exhibiting greater discrimination against related purines than the more common guanine riboswitch class reported previously. These three additional variant classes, together with the four previously discovered riboswitch classes that employ the same three-stem junction architecture, reveal how a simple structural framework can be diversified to expand the range of purine-based ligands sensed by RNA.
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Affiliation(s)
- Siddhartha Hamal Dhakal
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
| | | | - Paul Slattery
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
| | - Adam Roth
- HHMI, Yale University, New Haven, CT 06520-8103
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
- HHMI, Yale University, New Haven, CT 06520-8103
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103
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17
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Yadav R, Widom JR, Chauvier A, Walter NG. An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch. Nat Commun 2022; 13:207. [PMID: 35017489 PMCID: PMC8752731 DOI: 10.1038/s41467-021-27827-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 12/02/2021] [Indexed: 01/22/2023] Open
Abstract
The archetypical transcriptional crcB fluoride riboswitch from Bacillus cereus is an intricately structured non-coding RNA element enhancing gene expression in response to toxic levels of fluoride. Here, we used single molecule FRET to uncover three dynamically interconverting conformations appearing along the transcription process: two distinct undocked states and one pseudoknotted docked state. We find that the fluoride anion specifically snap-locks the magnesium-induced, dynamically docked state. The long-range, nesting, single base pair A40-U48 acts as the main linchpin, rather than the multiple base pairs comprising the pseudoknot. We observe that the proximally paused RNA polymerase further fine-tunes the free energy to promote riboswitch docking. Finally, we show that fluoride binding at short transcript lengths is an early step toward partitioning folding into the docked conformation. These results reveal how the anionic fluoride ion cooperates with the magnesium-associated RNA to govern regulation of downstream genes needed for fluoride detoxification of the cell.
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Affiliation(s)
- Rajeev Yadav
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Physics and Astronomy, Michigan State University, East Lansing, MI, 48824, USA
| | - Julia R Widom
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, 97403, USA
| | - Adrien Chauvier
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, USA.
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18
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Evguenieva-Hackenberg E. Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1696. [PMID: 34651439 DOI: 10.1002/wrna.1696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022]
Abstract
Gene expression strategies ensuring bacterial survival and competitiveness rely on cis- and trans-acting RNA-regulators (riboregulators). Among the cis-acting riboregulators are transcriptional and translational attenuators, and antisense RNAs (asRNAs). The trans-acting riboregulators are small RNAs (sRNAs) that bind proteins or base pairs with other RNAs. This classification is artificial since some regulatory RNAs act both in cis and in trans, or function in addition as small mRNAs. A prominent example is the archetypical, ribosome-dependent attenuator of tryptophan (Trp) biosynthesis genes. It responds by transcription attenuation to two signals, Trp availability and inhibition of translation, and gives rise to two trans-acting products, the attenuator sRNA rnTrpL and the leader peptide peTrpL. In Escherichia coli, rnTrpL links Trp availability to initiation of chromosome replication and in Sinorhizobium meliloti, it coordinates regulation of split tryptophan biosynthesis operons. Furthermore, in S. meliloti, peTrpL is involved in mRNA destabilization in response to antibiotic exposure. It forms two types of asRNA-containing, antibiotic-dependent ribonucleoprotein complexes (ARNPs), one of them changing the target specificity of rnTrpL. The posttranscriptional role of peTrpL indicates two emerging paradigms: (1) sRNA reprograming by small molecules and (2) direct involvement of antibiotics in regulatory RNPs. They broaden our view on RNA-based mechanisms and may inspire new approaches for studying, detecting, and using antibacterial compounds. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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19
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Pandey M, Ojha D, Bansal S, Rode AB, Chawla G. From bench side to clinic: Potential and challenges of RNA vaccines and therapeutics in infectious diseases. Mol Aspects Med 2021; 81:101003. [PMID: 34332771 DOI: 10.1016/j.mam.2021.101003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/27/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022]
Abstract
The functional and structural versatility of Ribonucleic acids (RNAs) makes them ideal candidates for overcoming the limitations imposed by small molecule-based drugs. Hence, RNA-based biopharmaceuticals such as messenger RNA (mRNA) vaccines, antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), microRNA mimics, anti-miRNA oligonucleotides (AMOs), aptamers, riboswitches, and CRISPR-Cas9 are emerging as vital tools for the treatment and prophylaxis of many infectious diseases. Some of the major challenges to overcome in the area of RNA-based therapeutics have been the instability of single-stranded RNAs, delivery to the diseased cell, and immunogenicity. However, recent advancements in the delivery systems of in vitro transcribed mRNA and chemical modifications for protection against nucleases and reducing the toxicity of RNA have facilitated the entry of several exogenous RNAs into clinical trials. In this review, we provide an overview of RNA-based vaccines and therapeutics, their production, delivery, current advancements, and future translational potential in treating infectious diseases.
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Affiliation(s)
- Manish Pandey
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Divya Ojha
- Laboratory of Synthetic Biology, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Sakshi Bansal
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Ambadas B Rode
- Laboratory of Synthetic Biology, Regional Centre for Biotechnology, Faridabad, 121001, India.
| | - Geetanjali Chawla
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India.
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20
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Siblings or doppelgängers? Deciphering the evolution of structured cis-regulatory RNAs beyond homology. Biochem Soc Trans 2021; 48:1941-1951. [PMID: 32869842 PMCID: PMC7609027 DOI: 10.1042/bst20191060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 11/21/2022]
Abstract
Structured cis-regulatory RNAs have evolved across all domains of life, highlighting the utility and plasticity of RNA as a regulatory molecule. Homologous RNA sequences and structures often have similar functions, but homology may also be deceiving. The challenges that derive from trying to assign function to structure and vice versa are not trivial. Bacterial riboswitches, viral and eukaryotic IRESes, CITEs, and 3′ UTR elements employ an array of mechanisms to exert their effects. Bioinformatic searches coupled with biochemical and functional validation have elucidated some shared and many unique ways cis-regulators are employed in mRNA transcripts. As cis-regulatory RNAs are resolved in greater detail, it is increasingly apparent that shared homology can mask the full spectrum of mRNA cis-regulator functional diversity. Furthermore, similar functions may be obscured by lack of obvious sequence similarity. Thus looking beyond homology is crucial for furthering our understanding of RNA-based regulation.
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21
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Bange G, Brodersen DE, Liuzzi A, Steinchen W. Two P or Not Two P: Understanding Regulation by the Bacterial Second Messengers (p)ppGpp. Annu Rev Microbiol 2021; 75:383-406. [PMID: 34343020 DOI: 10.1146/annurev-micro-042621-122343] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Under stressful growth conditions and nutrient starvation, bacteria adapt by synthesizing signaling molecules that profoundly reprogram cellular physiology. At the onset of this process, called the stringent response, members of the RelA/SpoT homolog (RSH) protein superfamily are activated by specific stress stimuli to produce several hyperphosphorylated forms of guanine nucleotides, commonly referred to as (p)ppGpp. Some bifunctional RSH enzymes also harbor domains that allow for degradation of (p)ppGpp by hydrolysis. (p)ppGpp synthesis or hydrolysis may further be executed by single-domain alarmone synthetases or hydrolases, respectively. The downstream effects of (p)ppGpp rely mainly on direct interaction with specific intracellular effectors, which are widely used throughout most cellular processes. The growing number of identified (p)ppGpp targets allows us to deduce both common features of and differences between gram-negative and gram-positive bacteria. In this review, we give an overview of (p)ppGpp metabolism with a focus on the functional and structural aspects of the enzymes involved and discuss recent findings on alarmone-regulated cellular effectors. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gert Bange
- SYNMIKRO Research Center, Philipps-University Marburg, 35043 Marburg, Germany; .,Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Centre for Bacterial Stress Response and Persistence, Aarhus University, 8000 Aarhus C, Denmark
| | - Anastasia Liuzzi
- Department of Molecular Biology and Genetics, Centre for Bacterial Stress Response and Persistence, Aarhus University, 8000 Aarhus C, Denmark
| | - Wieland Steinchen
- SYNMIKRO Research Center, Philipps-University Marburg, 35043 Marburg, Germany; .,Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
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22
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Xu X, Egger M, Chen H, Bartosik K, Micura R, Ren A. Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition. Nucleic Acids Res 2021; 49:7139-7153. [PMID: 34125892 PMCID: PMC8266621 DOI: 10.1093/nar/gkab486] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/29/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson–Crick base pair to junction J2. Xanthine inserts between a G–U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.
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Affiliation(s)
- Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Michaela Egger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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23
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Cubi R, Bouhedda F, Collot M, Klymchenko AS, Ryckelynck M. µIVC-Useq: a microfluidic-assisted high-throughput functionnal screening in tandem with next generation sequencing and artificial neural network to rapidly characterize RNA molecules. RNA (NEW YORK, N.Y.) 2021; 27:rna.077586.120. [PMID: 33952671 PMCID: PMC8208054 DOI: 10.1261/rna.077586.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 05/01/2021] [Indexed: 05/10/2023]
Abstract
The function of an RNA is intimately linked to its three-dimensional structure. X-ray crystallography or NMR allow the fine structural characterization of small RNA (e.g., aptamers) with a precision down to atomic resolution. Yet, these technics are time consuming, laborious and do not inform on mutational robustness and the extent to which a sequence can be modified without altering RNA function, an important set of information to assist RNA engineering. On another hand, thought powerful, in silico predictions still lack the required accuracy. These limitations can be overcome by using high-throughput microfluidic-assisted functional screening technologies, as they allow exploring large mutant libraries in a rapid and cost-effective manner. Among them, we recently introduced the microfluidic-assisted In Vitro Compartmentalization (µIVC), an efficient screening strategy in which reactions are performed in picoliter droplets at rates of several thousand per second. We later improved µIVC efficiency by using in tandem with high throughput sequencing, thought a laborious bioinformatic step was still required at the end of the process. In the present work, we strongly increased the automation level of the pipeline by implementing an artificial neural network enabling unsupervised bioinformatic analysis. We demonstrate the efficiency of this "µIVC-Useq" technology by rapidly identifying a set of sequences readily accepted by a key domain of the light-up RNA aptamer SRB-2. This work not only shed some new light on the way this aptamer can be engineered, but it also allowed us to easily identify new variants with an up-to 10-fold improved performance.
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24
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Sinn M, Hauth F, Lenkeit F, Weinberg Z, Hartig JS. Widespread bacterial utilization of guanidine as nitrogen source. Mol Microbiol 2021; 116:200-210. [PMID: 33590553 DOI: 10.1111/mmi.14702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/30/2022]
Abstract
Guanidine is sensed by at least four different classes of riboswitches that are widespread in bacteria. However, only very few insights into physiological roles of guanidine exist. Genes predominantly regulated by guanidine riboswitches are Gdx transporters exporting the compound from the bacterial cell. In addition, urea/guanidine carboxylases and associated hydrolases and ABC transporters are often found combined in guanidine-inducible operons. We noted that the associated ABC transporters are configured to function as importers, challenging the current view that riboswitches solely control the detoxification of guanidine in bacteria. We demonstrate that the carboxylase pathway enables utilization of guanidine as sole nitrogen source. We isolated three enterobacteria (Raoultella terrigena, Klebsiella michiganensis, and Erwinia rhapontici) that utilize guanidine efficiently as N-source. Proteome analyses show that the expression of a carboxylase, associated hydrolases and transport genes is strongly induced by guanidine. Finding two urea/guanidine carboxylase enzymes in E. rhapontici, we demonstrate that the riboswitch-controlled carboxylase displays specificity toward guanidine, whereas the other enzyme prefers urea. We characterize the distribution of riboswitch-associated carboxylases and Gdx exporters in bacterial habitats by analyzing available metagenome data. The findings represent a paradigm shift from riboswitch-controlled detoxification of guanidine to the uptake and assimilation of this enigmatic nitrogen-rich compound.
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Affiliation(s)
- Malte Sinn
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Franziskus Hauth
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Felina Lenkeit
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
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25
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Goldman AD, Kacar B. Cofactors are Remnants of Life's Origin and Early Evolution. J Mol Evol 2021; 89:127-133. [PMID: 33547911 PMCID: PMC7982383 DOI: 10.1007/s00239-020-09988-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/21/2020] [Indexed: 12/22/2022]
Abstract
The RNA World is one of the most widely accepted hypotheses explaining the origin of the genetic system used by all organisms today. It proposes that the tripartite system of DNA, RNA, and proteins was preceded by one consisting solely of RNA, which both stored genetic information and performed the molecular functions encoded by that genetic information. Current research into a potential RNA World revolves around the catalytic properties of RNA-based enzymes, or ribozymes. Well before the discovery of ribozymes, Harold White proposed that evidence for a precursor RNA world could be found within modern proteins in the form of coenzymes, the majority of which contain nucleobases or nucleoside moieties, such as Coenzyme A and S-adenosyl methionine, or are themselves nucleotides, such as ATP and NADH (a dinucleotide). These coenzymes, White suggested, had been the catalytic active sites of ancient ribozymes, which transitioned to their current forms after the surrounding ribozyme scaffolds had been replaced by protein apoenzymes during the evolution of translation. Since its proposal four decades ago, this groundbreaking hypothesis has garnered support from several different research disciplines and motivated similar hypotheses about other classes of cofactors, most notably iron-sulfur cluster cofactors as remnants of the geochemical setting of the origin of life. Evidence from prebiotic geochemistry, ribozyme biochemistry, and evolutionary biology, increasingly supports these hypotheses. Certain coenzymes and cofactors may bridge modern biology with the past and can thus provide insights into the elusive and poorly-recorded period of the origin and early evolution of life.
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Affiliation(s)
- Aaron D Goldman
- Department of Biology, Oberlin College and Conservatory, Oberlin, OH, 44074, USA. .,Blue Marble Space Institute of Science, Seattle, WA, 98154, USA.
| | - Betul Kacar
- Blue Marble Space Institute of Science, Seattle, WA, 98154, USA. .,Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA. .,Lunar and Planetary Laboratory and Department of Astronomy, University of Arizona, Tucson, AZ, 85721, USA. .,Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan.
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26
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Abstract
Microorganisms contend with numerous and unusual chemical threats and have evolved a catalog of resistance mechanisms in response. One particularly ancient, pernicious threat is posed by fluoride ion (F-), a common xenobiotic in natural environments that causes broad-spectrum harm to metabolic pathways. This review focuses on advances in the last ten years toward understanding the microbial response to cytoplasmic accumulation of F-, with a special emphasis on the structure and mechanisms of the proteins that microbes use to export fluoride: the CLCF family of F-/H+ antiporters and the Fluc/FEX family of F- channels.
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Affiliation(s)
- Benjamin C McIlwain
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Michal T Ruprecht
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; .,Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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27
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Lenkeit F, Eckert I, Hartig JS, Weinberg Z. Discovery and characterization of a fourth class of guanidine riboswitches. Nucleic Acids Res 2021; 48:12889-12899. [PMID: 33237283 PMCID: PMC7736828 DOI: 10.1093/nar/gkaa1102] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022] Open
Abstract
Riboswitches are RNAs that specifically sense a small molecule and regulate genes accordingly. The recent discovery of guanidine-binding riboswitches revealed the biological significance of this compound, and uncovered genes related to its biology. For example, certain sugE genes encode guanidine exporters and are activated by the riboswitches to reduce toxic levels of guanidine in the cell. In order to study guanidine biology and riboswitches, we applied a bioinformatics strategy for discovering additional guanidine riboswitches by searching for new candidate motifs associated with sugE genes. Based on in vitro and in vivo experiments, we determined that one of our six best candidates is a new structural class of guanidine riboswitches. The expression of a genetic reporter was induced 80-fold in response to addition of 5 mM guanidine in Staphylococcus aureus. This new class, called the guanidine-IV riboswitch, reveals additional guanidine-associated protein domains that are extremely rarely or never associated with previously established guanidine riboswitches. Among these protein domains are two transporter families that are structurally distinct from SugE, and could represent novel types of guanidine exporters. These results establish a new metabolite-binding RNA, further validate a bioinformatics method for finding riboswitches and suggest substrate specificities for as-yet uncharacterized transporter proteins.
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Affiliation(s)
- Felina Lenkeit
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Iris Eckert
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
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28
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Riboswitch-Mediated Detection of Metabolite Fluctuations During Live Cell Imaging of Bacteria. Methods Mol Biol 2021; 2323:153-170. [PMID: 34086280 DOI: 10.1007/978-1-0716-1499-0_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Riboswitches are a class of noncoding RNAs that regulate gene expression in response to changes in intracellular metabolite concentrations. When riboswitches are placed upstream of genetic reporters, the degree of reporter activity reflects the relative abundance of the metabolite that is sensed by the riboswitch. This method describes how reporters for live cell imaging, such as yellow fluorescent protein (YFP), can be placed under genetic control by metabolite-sensing riboswitches in the bacterium Bacillus subtilis. Specifically, a protocol for generating a fluorescent YFP reporter, based on a c-di-GMP responsive riboswitch, is outlined below.
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29
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Jain S, Kaur J, Prasad S, Roy I. Nucleic acid therapeutics: a focus on the development of aptamers. Expert Opin Drug Discov 2020; 16:255-274. [PMID: 32990095 DOI: 10.1080/17460441.2021.1829587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Aptamers provide exciting opportunities for the development of specific and targeted therapeutic approaches. AREAS COVERED In this review, the authors discuss different therapeutic options available with nucleic acids, including aptamers, focussing on similarities and differences between them. The authors concentrate on case studies with specific aptamers, which exemplify their distinct advantages. The reasons for failure, wherever available, are deliberated upon. Attempts to accelerate the in vitro selection process have been discussed. Challenges with aptamers in terms of their specificity and targeted delivery and strategies to overcome these are described. Examples of precise regulation of systemic half-life of aptamers using antidotes are discussed. EXPERT OPINION Despite their nontoxic nature, a variety of reasons limit the therapeutic potential of aptamers in the clinic. The analysis of adverse effects observed with the pegnivacogin/anivamersen pair has highlighted the need to screen for preexisting PEG antibodies in any clinical trial involving pegylated molecules. Surprisingly, and promisingly, the ability of nucleic acid therapeutics to breach the blood brain barrier seems achievable. The recognition of specific motifs, e.g. G-quadruplex in thrombin-binding aptamers, or a 'nucleation' zone while designing aptamer-antidote pairs, is likely to accelerate the discovery of therapeutically efficacious molecules.
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Affiliation(s)
- Swati Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Jaskirat Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
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Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 2020; 25:molecules25122881. [PMID: 32585844 PMCID: PMC7357161 DOI: 10.3390/molecules25122881] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.
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