1
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Singh K, Reddy G. Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms. J Chem Theory Comput 2024; 20:421-435. [PMID: 38134376 DOI: 10.1021/acs.jctc.3c00999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Riboswitches are mRNA segments that regulate gene expression through conformational changes driven by their cognate ligand binding. The ykkC motif forms a riboswitch class that selectively senses a guanidinium ion (Gdm+) and regulates the downstream expression of proteins which aid in the efflux of excess Gdm+ from the cells. The aptamer domain (AD) of the guanidine-III riboswitch forms an H-type pseudoknot with a triple helical domain that binds a Gdm+. We studied the binding of Gdm+ to the AD of the guanidine (ykkC)-III riboswitch using computer simulations to probe the specificity of the riboswitch to Gdm+ binding. We show that Gdm+ binding is a fast process occurring on the nanosecond time scale, with minimal conformational changes to the AD. Using machine learning and Markov-state models, we identified the excited conformational states of the AD, which have a high Gdm+ binding propensity, making the Gdm+ binding landscape complex exhibiting both conformational selection and induced-fit mechanisms. The proposed apo-AD excited states and their role in the ligand-sensing mechanism are amenable to experimental verification. Further, targeting these excited-state conformations in discovering new antibiotics can be explored.
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Affiliation(s)
- Kushal Singh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012 Karnataka, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012 Karnataka, India
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2
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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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3
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Salvail H, Balaji A, Roth A, Breaker RR. A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine. Cell Rep 2023; 42:113571. [PMID: 38096053 PMCID: PMC10853860 DOI: 10.1016/j.celrep.2023.113571] [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: 09/12/2023] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Natural polyamines such as spermidine and spermine cations have characteristics that make them highly likely to be sensed by riboswitches, such as their general affinity to polyanionic RNA and their broad contributions to cell physiology. Despite previous claims that polyamine riboswitches exist, evidence of their biological functions has remained unconvincing. Here, we report that rare variants of bacterial S-adenosylmethionine-I (SAM-I) riboswitches reject SAM and have adapted to selectively sense spermidine. These spermidine-sensing riboswitch variants are associated with genes whose protein products are directly involved in the production of spermidine and other polyamines. Biochemical and genetic assays demonstrate that representatives of this riboswitch class robustly function as genetic "off" switches, wherein spermidine binding causes premature transcription termination to suppress the expression of polyamine biosynthetic genes. These findings confirm the existence of natural spermidine-sensing riboswitches in bacteria and expand the list of variant riboswitch classes that have adapted to bind different ligands.
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Affiliation(s)
- Hubert Salvail
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Adam Roth
- Howard Hughes Medical Institute, 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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4
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Liao TW, Huang L, Wilson TJ, Ganser LR, Lilley DMJ, Ha T. Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level. Nucleic Acids Res 2023; 51:8957-8969. [PMID: 37522343 PMCID: PMC10516623 DOI: 10.1093/nar/gkad633] [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: 04/19/2023] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
Riboswitches are regulatory elements found in bacterial mRNAs that control downstream gene expression through ligand-induced conformational changes. Here, we used single-molecule FRET to map the conformational landscape of the translational SAM/SAH riboswitch and probe how co-transcriptional ligand-induced conformational changes affect its translation regulation function. Riboswitch folding is highly heterogeneous, suggesting a rugged conformational landscape that allows for sampling of the ligand-bound conformation even in the absence of ligand. The addition of ligand shifts the landscape, favoring the ligand-bound conformation. Mutation studies identified a key structural element, the pseudoknot helix, that is crucial for determining ligand-free conformations and their ligand responsiveness. We also investigated ribosomal binding site accessibility under two scenarios: pre-folding and co-transcriptional folding. The regulatory function of the SAM/SAH riboswitch involves kinetically favoring ligand binding, but co-transcriptional folding reduces this preference with a less compact initial conformation that exposes the Shine-Dalgarno sequence and takes min to redistribute to more compact conformations of the pre-folded riboswitch. Such slow equilibration decreases the effective ligand affinity. Overall, our study provides a deeper understanding of the complex folding process and how the riboswitch adapts its folding pattern in response to ligand, modulates ribosome accessibility and the role of co-transcriptional folding in these processes.
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Affiliation(s)
- Ting-Wei Liao
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Laura R Ganser
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
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5
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Hu G, Zhou HX. Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch. Commun Biol 2023; 6:791. [PMID: 37524918 PMCID: PMC10390503 DOI: 10.1038/s42003-023-05175-5] [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: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023] Open
Abstract
The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) predicted over 10 inner-shell Mg2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminishes the selectivity between SAM and SAH. One Mg2+ ion unique to the apo form maintains the Shine-Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg2+ thus plays vital roles in SAM/SAH riboswitch function.
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Affiliation(s)
- Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, 253023, China
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
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6
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Xue Y, Li J, Chen D, Zhao X, Hong L, Liu Y. Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution. Nat Commun 2023; 14:2320. [PMID: 37087479 PMCID: PMC10122661 DOI: 10.1038/s41467-023-38042-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 04/13/2023] [Indexed: 04/24/2023] Open
Abstract
Growing RNAs fold differently as they are transcribed, which modulates their finally adopted structures. Riboswitches regulate gene expression by structural change, which are sensitive to co-transcriptionally structural biology. Here we develop a strategy to track the structural change of RNAs during transcription at single-nucleotide and single-molecule resolution and use it to monitor individual transcripts of the SAM-VI riboswitch (riboSAM) as transcription proceeds, observing co-existence of five states in riboSAM. We report a bifurcated helix in one newly identified state from NMR and single-molecule FRET (smFRET) results, and its presence directs the translation inhibition in our cellular translation experiments. A model is proposed to illustrate the distinct switch patterns and gene-regulatory outcome of riboSAM when SAM is present or absent. Our strategy enables the precise mapping of RNAs' conformational landscape during transcription, and may combine with detection methods other than smFRET for structural studies of RNAs in general.
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Affiliation(s)
- Yanyan Xue
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dian Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xizhu Zhao
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200232, China.
| | - Yu Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200232, China.
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7
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Hu G, Zhou HX. Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.532287. [PMID: 36945415 PMCID: PMC10029009 DOI: 10.1101/2023.03.12.532287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg 2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) identified over 10 inner-shell Mg 2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminish the selectivity between SAM and SAH. One Mg 2+ ion unique to the apo form maintains the Shine-Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg 2+ thus plays vital roles in SAM/SAH riboswitch function.
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Affiliation(s)
- Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607
- Department of Physics, University of Illinois Chicago, Chicago, IL 60607
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8
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Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A. Structure-based insights into recognition and regulation of SAM-sensing riboswitches. SCIENCE CHINA. LIFE SCIENCES 2023; 66:31-50. [PMID: 36459353 DOI: 10.1007/s11427-022-2188-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/17/2022] [Indexed: 12/03/2022]
Abstract
Riboswitches are highly conserved RNA elements that located in the 5'-UTR of mRNAs, which undergo real-time structure conformational change to achieve the regulation of downstream gene expression by sensing their cognate ligands. S-adenosylmethionine (SAM) is a ubiquitous methyl donor for transmethylation reactions in all living organisms. SAM riboswitch is one of the most abundant riboswitches that bind to SAM with high affinity and selectivity, serving as regulatory modules in multiple metabolic pathways. To date, seven SAM-specific riboswitch classes that belong to four families, one SAM/SAH riboswitch and one SAH riboswitch have been identified. Each SAM riboswitch family has a well-organized tertiary core scaffold to support their unique ligand-specific binding pocket. In this review, we summarize the current research progress on the distribution, structure, ligand recognition and gene regulation mechanism of these SAM-related riboswitch families, and further discuss their evolutionary prospects and potential applications.
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Affiliation(s)
- Luqian Zheng
- Department of Gastroenterology, Department of Cardiology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.,The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Qianqian Song
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xin Shen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Chunyan Li
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Hongcheng Li
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Aiming Ren
- Department of Gastroenterology, Department of Cardiology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China. .,Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
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9
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Sherlock ME, Higgs G, Yu D, Widner DL, White NA, Sudarsan N, Sadeeshkumar H, Perkins KR, Mirihana Arachchilage G, Malkowski SN, King CG, Harris KA, Gaffield G, Atilho RM, Breaker RR. Architectures and complex functions of tandem riboswitches. RNA Biol 2022; 19:1059-1076. [PMID: 36093908 PMCID: PMC9481103 DOI: 10.1080/15476286.2022.2119017] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Riboswitch architectures that involve the binding of a single ligand to a single RNA aptamer domain result in ordinary dose-response curves that require approximately a 100-fold change in ligand concentration to cover nearly the full dynamic range for gene regulation. However, by using multiple riboswitches or aptamer domains in tandem, these ligand-sensing structures can produce additional, complex gene control outcomes. In the current study, we have computationally searched for tandem riboswitch architectures in bacteria to provide a more complete understanding of the diverse biological and biochemical functions of gene control elements that are made exclusively of RNA. Numerous different arrangements of tandem homologous riboswitch architectures are exploited by bacteria to create more ‘digital’ gene control devices, which operate over a narrower ligand concentration range. Also, two heterologous riboswitch aptamers are sometimes employed to create two-input Boolean logic gates with various types of genetic outputs. These findings illustrate the sophisticated genetic decisions that can be made by using molecular sensors and switches based only on RNA.
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Affiliation(s)
- Madeline E. Sherlock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Research-1S, Aurora, CO, USA
| | - Gadareth Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Diane Yu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Danielle L. Widner
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Neil A. White
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Harini Sadeeshkumar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Kevin R. Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Gayan Mirihana Arachchilage
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
- PTC Therapeutics, Inc, South Plainfield, NJ, USA
| | | | - Christopher G. King
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Glenn Gaffield
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Ruben M. Atilho
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Ronald R. Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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10
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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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11
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Zhang M, Liu G, Zhang Y, Chen T, Feng S, Cai R, Lu C. The Second Class of Tetrahydrofolate (THF-II) Riboswitches Recognizes the Tetrahydrofolic Acid Ligand via Local Conformation Changes. Int J Mol Sci 2022; 23:ijms23115903. [PMID: 35682583 PMCID: PMC9180208 DOI: 10.3390/ijms23115903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 02/05/2023] Open
Abstract
Riboswitches are regulatory noncoding RNAs found in bacteria, fungi and plants, that modulate gene expressions through structural changes in response to ligand binding. Understanding how ligands interact with riboswitches in solution can shed light on the molecular mechanisms of this ancient regulators. Previous studies showed that riboswitches undergo global conformation changes in response to ligand binding to relay information. Here, we report conformation switching models of the recently discovered tetrahydrofolic acid-responsive second class of tetrahydrofolate (THF-II) riboswitches in response to ligand binding. Using a combination of selective 2′-hydroxyl acylation, analyzed by primer extension (SHAPE) assay, 3D modeling and small-angle X-ray scattering (SAXS), we found that the ligand specifically recognizes and reshapes the THF-II riboswitch loop regions, but does not affect the stability of the P3 helix. Our results show that the THF-II riboswitch undergoes only local conformation changes in response to ligand binding, rearranging the Loop1-P3-Loop2 region and rotating Loop1 from a ~120° angle to a ~75° angle. This distinct conformation changes suggest a unique regulatory mechanism of the THF-II riboswitch, previously unseen in other riboswitches. Our findings may contribute to the fields of RNA sensors and drug design.
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Affiliation(s)
- Minmin Zhang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China;
| | - Yunlong Zhang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Ting Chen
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Shanshan Feng
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Rujie Cai
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Correspondence: (R.C.); (C.L.); Tel.: +86-21-6779-2740 (C.L.)
| | - Changrui Lu
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
- Correspondence: (R.C.); (C.L.); Tel.: +86-21-6779-2740 (C.L.)
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12
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Abstract
More than 55 distinct classes of riboswitches that respond to small metabolites or elemental ions have been experimentally validated to date. The ligands sensed by these riboswitches are biased in favor of fundamental compounds or ions that are likely to have been relevant to ancient forms of life, including those that might have populated the "RNA World", which is a proposed biochemical era that predates the evolutionary emergence of DNA and proteins. In the following text, I discuss the various types of ligands sensed by some of the most common riboswitches present in modern bacterial cells and consider implications for ancient biological processes centered on the proven capabilities of these RNA-based sensors. Although most major biochemical aspects of metabolism are represented by known riboswitch classes, there are striking sensory gaps in some key areas. These gaps could reveal weaknesses in the performance capabilities of RNA that might have hampered RNA World evolution, or these could highlight opportunities to discover additional riboswitch classes that sense essential metabolites.
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Affiliation(s)
- Ronald R. Breaker
- Corresponding Author: Ronald R. Breaker - Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, United States; Phone: 203-432-9389; , Twitter: @RonBreaker
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13
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Scheuer R, Dietz T, Kretz J, Hadjeras L, McIntosh M, Evguenieva-Hackenberg E. Incoherent dual regulation by a SAM-II riboswitch controlling translation at a distance. RNA Biol 2022; 19:980-995. [PMID: 35950733 PMCID: PMC9373788 DOI: 10.1080/15476286.2022.2110380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Sinorhizobium meliloti, the methionine biosynthesis genes metA and metZ are preceded by S-adenosyl-L-methionine (SAM) riboswitches of the SAM-II class. Upon SAM binding, structural changes in the metZ riboswitch were predicted to cause transcriptional termination, generating the sRNA RZ. By contrast, the metA riboswitch was predicted to regulate translation from an AUG1 codon. However, downstream of the metA riboswitch, we found a putative Rho-independent terminator and an in-frame AUG2 codon, which may contribute to metA regulation. We validated the terminator between AUG1 and AUG2, which generates the sRNA RA1 that is processed to RA2. Under high SAM conditions, the activities of the metA and metZ promoters and the steady-state levels of the read-through metA and metZ mRNAs were decreased, while the levels of the RZ and RA2 sRNAs were increased. Under these conditions, the sRNAs and the mRNAs were stabilized. Reporter fusion experiments revealed that the Shine–Dalgarno (SD) sequence in the metA riboswitch is required for translation, which, however, starts 74 nucleotides downstream at AUG2, suggesting a novel translation initiation mechanism. Further, the reporter fusion data supported the following model of RNA-based regulation: Upon SAM binding by the riboswitch, the SD sequence is sequestered to downregulate metA translation, while the mRNA is stabilized. Thus, the SAM-II riboswitches fulfil incoherent, dual regulation, which probably serves to ensure basal metA and metZ mRNA levels under high SAM conditions. This probably helps to adapt to changing conditions and maintain SAM homoeostasis.
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Affiliation(s)
- Robina Scheuer
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Theresa Dietz
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Jonas Kretz
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Lydia Hadjeras
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
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14
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Bendre AD, Peters PJ, Kumar J. Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM. J Membr Biol 2021; 254:321-341. [PMID: 33954837 PMCID: PMC8099146 DOI: 10.1007/s00232-021-00179-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 03/23/2021] [Indexed: 12/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the deadliest pathogens encountered by humanity. Over the decades, its characteristic membrane organization and composition have been understood. However, there is still limited structural information and mechanistic understanding of the constituent membrane proteins critical for drug discovery pipelines. Recent advances in single-particle cryo-electron microscopy and cryo-electron tomography have provided the much-needed impetus towards structure determination of several vital Mtb membrane proteins whose structures were inaccessible via X-ray crystallography and NMR. Important insights into membrane composition and organization have been gained via a combination of electron tomography and biochemical and biophysical assays. In addition, till the time of writing this review, 75 new structures of various Mtb proteins have been reported via single-particle cryo-EM. The information obtained from these structures has improved our understanding of the mechanisms of action of these proteins and the physiological pathways they are associated with. These structures have opened avenues for structure-based drug design and vaccine discovery programs that might help achieve global-TB control. This review describes the structural features of selected membrane proteins (type VII secretion systems, Rv1819c, Arabinosyltransferase, Fatty Acid Synthase, F-type ATP synthase, respiratory supercomplex, ClpP1P2 protease, ClpB disaggregase and SAM riboswitch), their involvement in physiological pathways, and possible use as a drug target. Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. The Cryo-EM and tomography have simplified the understanding of the mycobacterial membrane organization. Some proteins are located in the plasma membrane; some span the entire envelope, while some, like MspA, are located in the mycomembrane. Cryo-EM has made the study of such membrane proteins feasible.
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Affiliation(s)
- Ameya D Bendre
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India.
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15
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Brewer KI, Greenlee EB, Higgs G, Yu D, Mirihana Arachchilage G, Chen X, King N, White N, Breaker RR. Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes. RNA Biol 2021; 18:2417-2432. [PMID: 33970790 PMCID: PMC8632094 DOI: 10.1080/15476286.2021.1917891] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding 'intergenic regions' (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel ribo-switch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.
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Affiliation(s)
- Kenneth I Brewer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Etienne B Greenlee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Gadareth Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Diane Yu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Xi Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Nicholas King
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Neil White
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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16
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Panchapakesan SSS, Corey L, Malkowski SN, Higgs G, Breaker RR. A second riboswitch class for the enzyme cofactor NAD . RNA (NEW YORK, N.Y.) 2021; 27:99-105. [PMID: 33087526 PMCID: PMC7749635 DOI: 10.1261/rna.077891.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/19/2020] [Indexed: 06/01/2023]
Abstract
A bacterial noncoding RNA motif almost exclusively associated with pnuC genes was uncovered using comparative sequence analysis. Some PnuC proteins are known to transport nicotinamide riboside (NR), which is a component of the ubiquitous and abundant enzyme cofactor nicotinamide adenine dinucleotide (NAD+). Thus, we speculated that the newly found "pnuC motif" RNAs might function as aptamers for a novel class of NAD+-sensing riboswitches. RNA constructs that encompass the conserved nucleotides and secondary structure features that define the motif indeed selectively bind NAD+, nicotinamide mononucleotide (NMN), and NR. Mutations that disrupt strictly conserved nucleotides of the aptamer also disrupt ligand binding. These bioinformatic and biochemical findings indicate that pnuC motif RNAs are likely members of a second riboswitch class that regulates gene expression in response to NAD+ binding.
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Affiliation(s)
- Shanker S S Panchapakesan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Lukas Corey
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Sarah N Malkowski
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Gadareth Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
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17
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Malkowski SN, Atilho RM, Greenlee EB, Weinberg CE, Breaker RR. A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine. RNA (NEW YORK, N.Y.) 2020; 26:1838-1846. [PMID: 32843366 PMCID: PMC7668255 DOI: 10.1261/rna.077313.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/14/2020] [Indexed: 05/31/2023]
Abstract
The Fibro-purF motif is a putative structured noncoding RNA domain that was discovered previously in species of Fibrobacter by using comparative sequence analysis methods. An updated bioinformatics search yielded a total of only 30 unique-sequence representatives, exclusively found upstream of the purF gene that codes for the enzyme amidophosphoribosyltransferase. This enzyme synthesizes the compound 5-phospho-D-ribosylamine (PRA), which is the first committed step in purine biosynthesis. The consensus model for Fibro-purF motif RNAs includes a predicted three-stem junction that carries numerous conserved nucleotide positions within the regions joining the stems. This architecture appears to be of sufficient size and complexity for the formation of the ligand-binding aptamer portion of a riboswitch. In this study, we conducted biochemical analyses of a representative Fibro-purF motif RNA to confirm that the RNA generally folds according to the predicted consensus model. However, due to the instability of PRA, binding of this ligand candidate by the RNA could not be directly assessed. Genetic analyses were used to demonstrate that Fibro-purF motif RNAs regulate gene expression in accordance with predicted PRA concentrations. These findings indicate that Fibro-purF motif RNAs are genetic regulation elements that likely suppress PRA biosynthesis when sufficient levels of this purine precursor are present.
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Affiliation(s)
- Sarah N Malkowski
- Department of Chemistry, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ruben M Atilho
- Department of Molecular Biophysics and Biochemistry, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Etienne B Greenlee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Christina E Weinberg
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
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18
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Nußbaumer F, Plangger R, Roeck M, Kreutz C. Aromatic
19
F–
13
C TROSY—[
19
F,
13
C]‐Pyrimidine Labeling for NMR Spectroscopy of RNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Felix Nußbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Manuel Roeck
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
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19
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Nußbaumer F, Plangger R, Roeck M, Kreutz C. Aromatic 19 F- 13 C TROSY-[ 19 F, 13 C]-Pyrimidine Labeling for NMR Spectroscopy of RNA. Angew Chem Int Ed Engl 2020; 59:17062-17069. [PMID: 32558232 PMCID: PMC7540360 DOI: 10.1002/anie.202006577] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 12/22/2022]
Abstract
We present the access to [5-19 F, 5-13 C]-uridine and -cytidine phosphoramidites for the production of site-specifically modified RNAs up to 65 nucleotides (nts). The amidites were used to introduce [5-19 F, 5-13 C]-pyrimidine labels into five RNAs-the 30 nt human immunodeficiency virus trans activation response (HIV TAR) 2 RNA, the 61 nt human hepatitis B virus ϵ (hHBV ϵ) RNA, the 49 nt SAM VI riboswitch aptamer domain from B. angulatum, the 29 nt apical stem loop of the pre-microRNA (miRNA) 21 and the 59 nt full length pre-miRNA 21. The main stimulus to introduce the aromatic 19 F-13 C-spin topology into RNA comes from a work of Boeszoermenyi et al., in which the dipole-dipole interaction and the chemical shift anisotropy relaxation mechanisms cancel each other leading to advantageous TROSY properties shown for aromatic protein sidechains. This aromatic 13 C-19 F labeling scheme is now transferred to RNA. We provide a protocol for the resonance assignment by solid phase synthesis based on diluted [5-19 F, 5-13 C]/[5-19 F] pyrimidine labeling. For the 61 nt hHBV ϵ we find a beneficial 19 F-13 C TROSY enhancement, which should be even more pronounced in larger RNAs and will facilitate the NMR studies of larger RNAs. The [19 F, 13 C]-labeling of the SAM VI aptamer domain and the pre-miRNA 21 further opens the possibility to use the biorthogonal stable isotope reporter nuclei in in vivo NMR to observe ligand binding and microRNA processing in a biological relevant setting.
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Affiliation(s)
- Felix Nußbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Manuel Roeck
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
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20
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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21
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Abstract
Biocatalysis is dominated by protein enzymes, and only a few classes of ribozymes are known to contribute to the task of promoting biochemical transformations. The RNA World theory encompasses the notion that earlier forms of life made use of a much greater diversity of ribozymes and other functional RNAs to guide complex metabolic states long before proteins had emerged in evolution. In recent years, the discoveries of various classes of ribozymes, riboswitches, and other noncoding RNAs in bacteria have provided additional support for the hypothesis that RNA molecules indeed have the catalytic competence to promote diverse chemical reactions without the aid of protein enzymes. Herein, some of the most striking observations made from examinations of natural riboswitches that bind small ligands are highlighted and used as a basis to imagine the characteristics and functions of long-extinct ribozymes from the RNA World.
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Affiliation(s)
- Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Department of Chemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, United States
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22
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Huang L, Liao TW, Wang J, Ha T, Lilley DMJ. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch. Nucleic Acids Res 2020; 48:7545-7556. [PMID: 32520325 PMCID: PMC7367207 DOI: 10.1093/nar/gkaa493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/25/2020] [Accepted: 05/30/2020] [Indexed: 01/09/2023] Open
Abstract
While most SAM riboswitches strongly discriminate between SAM and SAH, the SAM/SAH riboswitch responds to both ligands with similar apparent affinities. We have determined crystal structures of the SAM/SAH riboswitch bound to SAH, SAM and other variant ligands at high resolution. The riboswitch forms an H-type pseudoknot structure with coaxial alignment of the stem–loop helix (P1) and the pseudoknot helix (PK). An additional three base pairs form at the non-open end of P1, and the ligand is bound at the interface between the P1 extension and the PK helix. The adenine nucleobase is stacked into the helix and forms a trans Hoogsteen–Watson–Crick base pair with a uridine, thus becoming an integral part of the helical structure. The majority of the specific interactions are formed with the adenosine. The methionine or homocysteine chain lies in the groove making a single hydrogen bond, and there is no discrimination between the sulfonium of SAM or the thioether of SAH. Single-molecule FRET analysis reveals that the riboswitch exists in two distinct conformations, and that addition of SAM or SAH shifts the population into a stable state that likely corresponds to the form observed in the crystal. A model for translational regulation is presented whereby in the absence of ligand the riboswitch is largely unfolded, lacking the PK helix so that translation can be initiated at the ribosome binding site. But the presence of ligand stabilizes the folded conformation that includes the PK helix, so occluding the ribosome binding site and thus preventing the initiation of translation.
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Affiliation(s)
- Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China.,Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | | | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Taekjip Ha
- Department of Biophysics.,Department of Biophysics and Biophysical Chemistry.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.,Howard Hughes Medical Institute, Baltimore, MD, USA
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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23
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Zhang J. Unboxing the T-box riboswitches-A glimpse into multivalent and multimodal RNA-RNA interactions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1600. [PMID: 32633085 PMCID: PMC7583486 DOI: 10.1002/wrna.1600] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022]
Abstract
The T-box riboswitches are widespread bacterial noncoding RNAs that directly bind specific tRNAs, sense aminoacylation on bound tRNAs, and switch conformations to control amino-acid metabolism and to maintain nutritional homeostasis. The core mechanisms of tRNA recognition, amino acid sensing, and conformational switching by the T-boxes have been recently elucidated, providing a wealth of new insights into multivalent and multimodal RNA-RNA interactions. This review dissects the structures and tRNA-recognition mechanisms by the Stem I, Stem II, and Discriminator domains, which collectively compose the T-box riboswitches. It further compares and contrasts the two classes of T-boxes that regulate transcription and translation, respectively, and integrates recent findings to derive general themes, trends, and insights into complex RNA-RNA interactions. Specifically, the T-box paradigm reveals that noncoding RNAs can interact with each other through multiple coordinated contacts, concatenation of stacked helices, and mutually induced fit. Numerous tertiary contacts, especially those emanating from strings of single-stranded purines, act in concert to reinforce long-range base-pairing and stacking interactions. These coordinated, mixed-mode contacts allow the T-box RNA to sterically sense aminoacylation on the tRNA using a bipartite steric sieve, and to couple this readout to a conformational switch mediated by tRNA-T-box stacking. Together, the insights gleaned from the T-box riboswitches inform investigations into other complex RNA structures and assemblies, development of T-box-targeted antimicrobials, and may inspire design and engineering of novel RNA sensors, regulators, and interfaces. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Riboswitches.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
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24
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Sherlock ME, Breaker RR. Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes. RNA (NEW YORK, N.Y.) 2020; 26:675-693. [PMID: 32165489 PMCID: PMC7266159 DOI: 10.1261/rna.074997.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Comparative sequence analyses have been used to discover numerous classes of structured noncoding RNAs, some of which are riboswitches that specifically recognize small-molecule or elemental ion ligands and influence expression of adjacent downstream genes. Determining the correct identity of the ligand for a riboswitch candidate typically is aided by an understanding of the genes under its regulatory control. Riboswitches whose ligands were straightforward to identify have largely been associated with well-characterized metabolic pathways, such as coenzyme or amino acid biosynthesis. Riboswitch candidates whose ligands resist identification, collectively known as orphan riboswitches, are often associated with genes coding for proteins of unknown function, or genes for various proteins with no established link to one another. The cognate ligands for 16 former orphan riboswitch motifs have been identified to date. The successful pursuit of the ligands for these classes has provided insight into areas of biology that are not yet fully explored, such as ion homeostasis, signaling networks, and other previously underappreciated biochemical or physiological processes. Herein we discuss the strategies and methods used to match ligands with orphan riboswitch classes, and overview the lessons learned to inform and motivate ongoing efforts to identify ligands for the many remaining candidates.
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Affiliation(s)
- Madeline E Sherlock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
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25
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Zhang X, Sun W, Chen D, Murchie AIH. Interactions between SAM and the 5' UTR mRNA of the sam1 gene regulate translation in S. pombe. RNA (NEW YORK, N.Y.) 2020; 26:150-161. [PMID: 31767786 PMCID: PMC6961541 DOI: 10.1261/rna.072983.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/14/2019] [Indexed: 05/03/2023]
Abstract
The 5' untranslated region (5' UTR) of eukaryotic mRNA plays an important role in translation. Here we report the function of the 5' UTR mRNA of S-adenosylmethionine synthetase (sam1) in translational modulation in the presence of SAM in fission yeast Schizosaccharomyces pombe Reporter assays, binding and chemical probing experiments, and mutational analysis show that the 5' UTR mRNA of sam1 binds to SAM to effect translation. Translational modulation is dependent on a tertiary structure transition in the RNA upon SAM binding. The characterization of such an RNA that is directly associated with an essential metabolic process in eukaryotes provides additional evidence that ligand binding by RNAs plays an important role in eukaryotic gene regulation.
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Affiliation(s)
- Xuhui Zhang
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenxia Sun
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dongrong Chen
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Alastair I H Murchie
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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26
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Sun A, Gasser C, Li F, Chen H, Mair S, Krasheninina O, Micura R, Ren A. SAM-VI riboswitch structure and signature for ligand discrimination. Nat Commun 2019; 10:5728. [PMID: 31844059 PMCID: PMC6914780 DOI: 10.1038/s41467-019-13600-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022] Open
Abstract
Riboswitches are metabolite-sensing, conserved domains located in non-coding regions of mRNA that are central to regulation of gene expression. Here we report the first three-dimensional structure of the recently discovered S-adenosyl-L-methionine responsive SAM-VI riboswitch. SAM-VI adopts a unique fold and ligand pocket that are distinct from all other known SAM riboswitch classes. The ligand binds to the junctional region with its adenine tightly intercalated and Hoogsteen base-paired. Furthermore, we reveal the ligand discrimination mode of SAM-VI by additional X-ray structures of this riboswitch bound to S-adenosyl-L-homocysteine and a synthetic ligand mimic, in combination with isothermal titration calorimetry and fluorescence spectroscopy to explore binding thermodynamics and kinetics. The structure is further evaluated by analysis of ligand binding to SAM-VI mutants. It thus provides a thorough basis for developing synthetic SAM cofactors for applications in chemical and synthetic RNA biology.
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Affiliation(s)
- Aiai Sun
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Catherina Gasser
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria
| | - Fudong Li
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics and School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Stefan Mair
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria
| | - Olga Krasheninina
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
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27
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Zhang K, Li S, Kappel K, Pintilie G, Su Z, Mou TC, Schmid MF, Das R, Chiu W. Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Nat Commun 2019; 10:5511. [PMID: 31796736 PMCID: PMC6890682 DOI: 10.1038/s41467-019-13494-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/03/2019] [Indexed: 01/17/2023] Open
Abstract
Specimens below 50 kDa have generally been considered too small to be analyzed by single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it difficult to obtain high-resolution structures by cryo-EM. In bacteria, riboswitches regulate sulfur metabolism through binding to the S-adenosylmethionine (SAM) ligand and offer compelling targets for new antibiotics. SAM-I, SAM-I/IV, and SAM-IV are the three most commonly found SAM riboswitches, but the structure of SAM-IV is still unknown. Here, we report the structures of apo and SAM-bound SAM-IV riboswitches (119-nt, ~40 kDa) to 3.7 Å and 4.1 Å resolution, respectively, using cryo-EM. The structures illustrate homologies in the ligand-binding core but distinct peripheral tertiary contacts in SAM-IV compared to SAM-I and SAM-I/IV. Our results demonstrate the feasibility of resolving small RNAs with enough detail to enable detection of their ligand-binding pockets and suggest that cryo-EM could play a role in structure-assisted drug design for RNA.
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Affiliation(s)
- Kaiming Zhang
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Shanshan Li
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Grigore Pintilie
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Zhaoming Su
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Tung-Chung Mou
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, 59812, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Department of Physics, Stanford University, Stanford, CA, 94305, USA.
| | - Wah Chiu
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA.
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
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28
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Malkowski SN, Spencer TCJ, Breaker RR. Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD . RNA (NEW YORK, N.Y.) 2019; 25:1616-1627. [PMID: 31467147 PMCID: PMC6859854 DOI: 10.1261/rna.072538.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 07/29/2019] [Indexed: 05/04/2023]
Abstract
The nadA motif is a riboswitch candidate present in various Acidobacteria species that was previously identified by bioinformatic analysis of bacterial DNA data sets. More than 100 unique representatives have been identified exclusively upstream of nadA genes, which code for an enzyme in the biosynthetic pathway of the ubiquitous coenzyme NAD+ The architecture of nadA motif RNAs suggests they use structurally similar tandem ligand-binding aptamer domains to control translation initiation. Biochemical analyses reveal that the first domain selectively binds ligands carrying an adenosine 5'-diphosphate (5' ADP) moiety, including NAD+ and its reduced form, NADH. Genetic analyses indicate that a tandem nadA motif RNA suppresses gene expression when NAD+ is abundant, and that both aptamer domains are required for maximal gene regulation. However, we have not observed selective binding of the nicotinamide moiety of NAD+ or binding by the second putative aptamer in vitro, despite sequence and structural similarities between the tandem domains.
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Affiliation(s)
- Sarah N Malkowski
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Tara C J Spencer
- Department of Biology, Howard University, Washington, D.C. 20059, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
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29
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Crum M, Ram-Mohan N, Meyer MM. Regulatory context drives conservation of glycine riboswitch aptamers. PLoS Comput Biol 2019; 15:e1007564. [PMID: 31860665 PMCID: PMC6944388 DOI: 10.1371/journal.pcbi.1007564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/06/2020] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
In comparison to protein coding sequences, the impact of mutation and natural selection on the sequence and function of non-coding (ncRNA) genes is not well understood. Many ncRNA genes are narrowly distributed to only a few organisms, and appear to be rapidly evolving. Compared to protein coding sequences, there are many challenges associated with assessment of ncRNAs that are not well addressed by conventional phylogenetic approaches, including: short sequence length, lack of primary sequence conservation, and the importance of secondary structure for biological function. Riboswitches are structured ncRNAs that directly interact with small molecules to regulate gene expression in bacteria. They typically consist of a ligand-binding domain (aptamer) whose folding changes drive changes in gene expression. The glycine riboswitch is among the most well-studied due to the widespread occurrence of a tandem aptamer arrangement (tandem), wherein two homologous aptamers interact with glycine and each other to regulate gene expression. However, a significant proportion of glycine riboswitches are comprised of single aptamers (singleton). Here we use graph clustering to circumvent the limitations of traditional phylogenetic analysis when studying the relationship between the tandem and singleton glycine aptamers. Graph clustering enables a broader range of pairwise comparison measures to be used to assess aptamer similarity. Using this approach, we show that one aptamer of the tandem glycine riboswitch pair is typically much more highly conserved, and that which aptamer is conserved depends on the regulated gene. Furthermore, our analysis also reveals that singleton aptamers are more similar to either the first or second tandem aptamer, again based on the regulated gene. Taken together, our findings suggest that tandem glycine riboswitches degrade into functional singletons, with the regulated gene(s) dictating which glycine-binding aptamer is conserved.
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Affiliation(s)
- Matt Crum
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Nikhil Ram-Mohan
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Michelle M. Meyer
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
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30
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Weickhmann AK, Keller H, Wurm JP, Strebitzer E, Juen MA, Kremser J, Weinberg Z, Kreutz C, Duchardt-Ferner E, Wöhnert J. The structure of the SAM/SAH-binding riboswitch. Nucleic Acids Res 2019; 47:2654-2665. [PMID: 30590743 PMCID: PMC6411933 DOI: 10.1093/nar/gky1283] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/12/2018] [Accepted: 12/26/2018] [Indexed: 12/16/2022] Open
Abstract
S-adenosylmethionine (SAM) is a central metabolite since it is used as a methyl group donor in many different biochemical reactions. Many bacteria control intracellular SAM concentrations using riboswitch-based mechanisms. A number of structurally different riboswitch families specifically bind to SAM and mainly regulate the transcription or the translation of SAM-biosynthetic enzymes. In addition, a highly specific riboswitch class recognizes S-adenosylhomocysteine (SAH)—the product of SAM-dependent methyl group transfer reactions—and regulates enzymes responsible for SAH hydrolysis. High-resolution structures are available for many of these riboswitch classes and illustrate how they discriminate between the two structurally similar ligands SAM and SAH. The so-called SAM/SAH riboswitch class binds both ligands with similar affinities and is structurally not yet characterized. Here, we present a high-resolution nuclear magnetic resonance structure of a member of the SAM/SAH-riboswitch class in complex with SAH. Ligand binding induces pseudoknot formation and sequestration of the ribosome binding site. Thus, the SAM/SAH-riboswitches are translational ‘OFF’-switches. Our results establish a structural basis for the unusual bispecificity of this riboswitch class. In conjunction with genomic data our structure suggests that the SAM/SAH-riboswitches might be an evolutionary late invention and not a remnant of a primordial RNA-world as suggested for other riboswitches.
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Affiliation(s)
- A Katharina Weickhmann
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
| | - Heiko Keller
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
| | - Jan P Wurm
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Bavaria, Germany
| | - Elisabeth Strebitzer
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Michael A Juen
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Johannes Kremser
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Institute of Informatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
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31
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Harris KA, Odzer NB, Breaker RR. Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans. Mol Microbiol 2019; 112:1552-1563. [PMID: 31461569 DOI: 10.1111/mmi.14379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2019] [Indexed: 12/26/2022]
Abstract
OLE RNAs represent an unusual class of bacterial noncoding RNAs common in Gram-positive anaerobes. The OLE RNA of the alkaliphile Bacillus halodurans is highly expressed and naturally interacts with at least two RNA-binding proteins called OapA and OapB. The phenotypes of the corresponding knockouts include growth inhibition when exposed to ethanol or other short-chain alcohols or when incubated at modestly reduced temperatures (e.g. 20°C). Intriguingly, the OapA 'PM1' mutant, which carries two amino acid changes to a highly conserved region, yields a dominant-negative phenotype that causes more severe growth defects under these same stress conditions. Herein, we report that the PM1 strain also exhibits extreme sensitivity to elevated Mg2+ concentrations, beginning as low as 2 mM. Suppressor mutants predominantly map to genes for aconitate hydratase and isocitrate dehydrogenase, which are expected to alter cellular citrate concentrations. Citrate reduces the severity of the Mg2+ toxicity phenotype, but neither the genomic mutations nor the addition of citrate to the medium overcomes ethanol toxicity or temperature sensitivity. These findings reveal that OLE RNA and its protein partners are involved in biochemical responses under several stress conditions, wherein the unusual sensitivity to Mg2+ can be independently suppressed by specific genomic mutations.
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Affiliation(s)
- Kimberly A Harris
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Nicole B Odzer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Ronald R Breaker
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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32
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Chen X, Mirihana Arachchilage G, Breaker RR. Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria. RNA (NEW YORK, N.Y.) 2019; 25:1091-1097. [PMID: 31186369 PMCID: PMC6800512 DOI: 10.1261/rna.071829.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/07/2019] [Indexed: 05/10/2023]
Abstract
We previously reported a large collection of structured noncoding RNAs (ncRNAs) that includes many riboswitch candidates identified through comparative sequence analysis of bacterial intergenic regions. One of these candidates, initially named the "folE motif," adopts a simple architecture commonly found upstream of folE genes. FolE enzymes catalyze the first enzyme in the de novo folate biosynthesis pathway. Herein, we demonstrate that folE motif RNAs selectively bind the enzyme cofactor tetrahydrofolate (THF) and several of its close derivatives. These aptamers, commonly found in Gram-negative bacteria, are distinct from aptamers of the previous validated THF riboswitch class found in Gram-positive bacteria. Our findings indicate that folE motif RNAs are aptamer domains for a second THF riboswitch class, named THF-II. The biochemical validation of THF-II riboswitches further highlights the ability of bacteria to utilize diverse RNA structures to sense universal enzyme cofactors that are predicted to be of ancient origin.
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Affiliation(s)
- Xi Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | | | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
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33
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Abstract
The three-dimensional structures of RNA molecules provide rich and often critical information for understanding their functions, including how they recognize small molecule and protein partners. Computational modeling of RNA 3D structure is becoming increasingly accurate, particularly with the availability of growing numbers of template structures already solved experimentally and the development of sequence alignment and 3D modeling tools to take advantage of this database. For several recent "RNA puzzle" blind modeling challenges, we have successfully identified useful template structures and achieved accurate structure predictions through homology modeling tools developed in the Rosetta software suite. We describe our semi-automated methodology here and walk through two illustrative examples: an adenine riboswitch aptamer, modeled from a template guanine riboswitch structure, and a SAM I/IV riboswitch aptamer, modeled from a template SAM I riboswitch structure.
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Affiliation(s)
- Andrew M Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, United States
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States; Biophysics Program, Stanford University, Stanford, CA, United States.
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34
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Atilho RM, Mirihana Arachchilage G, Greenlee EB, Knecht KM, Breaker RR. A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer. eLife 2019; 8:45210. [PMID: 30950790 PMCID: PMC6478431 DOI: 10.7554/elife.45210] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/04/2019] [Indexed: 12/29/2022] Open
Abstract
We recently implemented a bioinformatics pipeline that can uncover novel, but rare, riboswitch candidates as well as other noncoding RNA structures in bacteria. A prominent candidate revealed by our initial search efforts was called the ‘thiS motif’ because of its frequent association with a gene coding for the ThiS protein, which delivers sulfur to form the thiazole moiety of the thiamin precursor HET-P. In the current report, we describe biochemical and genetic data demonstrating that thiS motif RNAs function as sensors of the thiamin precursor HMP-PP, which is fused with HET-P ultimately to form the final active coenzyme thiamin pyrophosphate (TPP). HMP-PP riboswitches exhibit a distinctive architecture wherein an unusually small ligand-sensing aptamer is almost entirely embedded within an otherwise classic intrinsic transcription terminator stem. This arrangement yields remarkably compact genetic switches that bacteria use to tune the levels of thiamin precursors during the biosynthesis of this universally distributed coenzyme. Many bacteria use small genetic devices called riboswitches to sense molecules that are essential for life and regulate the genes necessary to make, break or move these molecules. Riboswitches are made of molecules of RNA and appear to have ancient origins that predate the evolution of bacteria and other lifeforms made of cells. Inside modern bacteria, chunks of DNA in the genome provide the instructions to make riboswitches and around 40 different types of riboswitch have been identified so far. However, it has been proposed that the instructions for thousands more riboswitches may remain hidden in the DNA of bacteria. All of the currently known riboswitches contain a region called an aptamer that binds to a target molecule. This binding causes another structure in the riboswitch RNA to switch a specific gene on or off. For example, the aptamer binding might cause a hairpin-like structure called a terminator to form, which stops a gene being used to make new RNA molecules. In 2019 a team of researchers reported using a computational approach to identify new riboswitches in bacteria. This approach identified many different chunks of DNA that might code for a riboswitch, including one known as the thiS motif. This potential new riboswitch appeared to be associated with a gene that encodes a protein required to make a vitamin called thiamin (also known as vitamin B1). To test the new computational approach, Atilho et al. including several of the researchers involved in the earlier work used genetic and biochemical techniques to study the thiS motif. The experiments revealed that the motif binds to a molecule called HMP-PP, which bacteria use to make thiamin. Unexpectedly, the aptamer of the riboswitch was nested within a terminator, rather than being a separate entity. The findings of Atilho et al. reveal that riboswitches can be even more compact than previously thought. Furthermore, these findings reveal new insights into how bacteria use riboswitches to manage their vitamin levels. In the future it may be possible to develop drugs that target such riboswitches to starve bacteria of these essential molecules.
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Affiliation(s)
- Ruben M Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | | | - Etienne B Greenlee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Kirsten M Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
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35
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Atilho RM, Perkins KR, Breaker RR. Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity. RNA (NEW YORK, N.Y.) 2019; 25:23-34. [PMID: 30287481 PMCID: PMC6298564 DOI: 10.1261/rna.067975.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/02/2018] [Indexed: 05/10/2023]
Abstract
Many bacteria use flavin mononucleotide (FMN) riboswitches to control the expression of genes responsible for the biosynthesis and transport of this enzyme cofactor or its precursor, riboflavin. Rare variants of FMN riboswitches found in strains of Clostridium difficile and some other bacteria typically control the expression of proteins annotated as transporters, including multidrug efflux pumps. These RNAs no longer recognize FMN, and differ from the original riboswitch consensus sequence at nucleotide positions normally involved in binding of the ribityl and phosphate moieties of the cofactor. Representatives of one of the two variant subtypes were found to bind the FMN precursor riboflavin and the FMN degradation products lumiflavin and lumichrome. Although the biologically relevant ligand sensed by these variant FMN riboswitches remains uncertain, our findings suggest that many strains of C. difficile might use rare riboswitches to sense flavin degradation products and activate transporters for their detoxification.
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Affiliation(s)
- Ruben M Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Kevin R Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
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36
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Abstract
A growing collection of bacterial riboswitch classes is being discovered that sense central metabolites, coenzymes, and signaling molecules. Included among the various mechanisms of gene regulation exploited by these RNA regulatory elements are several that modulate messenger RNA (mRNA) translation. In this review, the mechanisms of riboswitch-mediated translation control are summarized to highlight both their diversity and potential ancient origins. These mechanisms include ligand-gated presentation or occlusion of ribosome-binding sites, control of alternative splicing of mRNAs, and the regulation of mRNA stability. Moreover, speculation on the potential for novel riboswitch discoveries is presented, including a discussion on the potential for the discovery of a greater diversity of mechanisms for translation control.
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Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103
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