1
|
Huang X, Du Z. Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs. PLoS One 2024; 19:e0307541. [PMID: 39038036 PMCID: PMC11262651 DOI: 10.1371/journal.pone.0307541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
RNA pseudoknots play a crucial role in various cellular functions. Established pseudoknots show significant variation in both size and structural complexity. Specifically, three-stemmed pseudoknots are characterized by an additional stem-loop embedded in their structure. Recent findings highlight these pseudoknots as bacterial riboswitches and potent stimulators for programmed ribosomal frameshifting in RNA viruses like SARS-CoV2. To investigate the possible presence of functional three-stemmed pseudoknots in human mRNAs, we employed in-house developed computational methods to detect such structures within a dataset comprising 21,780 full-length human mRNA sequences. Numerous three-stemmed pseudoknots were identified. A selected set of 14 potential instances are presented, in which the start codon of the mRNA is found in close proximity either upstream, downstream, or within the identified three-stemmed pseudoknot. These pseudoknots likely play a role in translational initiation regulation. The probability of their existence gains support from their ranking as the most stable pseudoknot identified in the entire mRNA sequence, structural conservation across homologous mRNAs, stereochemical feasibility as demonstrated by structural modeling, and classification as members of the CPK-1 pseudoknot family, which includes many well-established pseudoknots. Furthermore, in four of the mRNAs, two or three closely spaced or tandem three-stemmed pseudoknots were identified. These findings suggest the frequent occurrence of three-stemmed pseudoknots in human mRNAs. A stepwise co-transcriptional folding mechanism is proposed for the formation of a three-stemmed pseudoknot structure. Our results not only provide fresh insights into the structures and functions of pseudoknots but also unveil the potential to target pseudoknots for treating human diseases.
Collapse
Affiliation(s)
- Xiaolan Huang
- School of Computing, Southern Illinois University at Carbondale, IL, United States of America
| | - Zhihua Du
- School of Chemical and Biomolecular Sciences, Southern Illinois University at Carbondale, IL, United States of America
| |
Collapse
|
2
|
Jäger N, Ayyub SA, Peske F, Liedtke D, Bohne J, Hoffmann M, Rodnina MV, Pöhlmann S. The Inhibition of Gag-Pol Expression by the Restriction Factor Shiftless Is Dispensable for the Restriction of HIV-1 Infection. Viruses 2024; 16:583. [PMID: 38675925 PMCID: PMC11055011 DOI: 10.3390/v16040583] [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: 03/01/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
The interferon-induced host cell protein Shiftless (SFL) inhibits -1 programmed ribosomal frameshifting (-1PRF) required for the expression of HIV-1 Gal-Pol and the formation of infectious HIV-1 particles. However, the specific regions in SFL required for antiviral activity and the mechanism by which SFL inhibits -1PRF remain unclear. Employing alanine scanning mutagenesis, we found that basic amino acids in the predicted zinc ribbon motif of SFL are essential for the suppression of Gag-Pol expression but dispensable for anti-HIV-1 activity. We have shown that SFL inhibits the expression of the murine leukemia virus (MLV) Gag-Pol polyprotein and the formation of infectious MLV particles, although Gag-Pol expression of MLV is independent of -1PRF but requires readthrough of a stop codon. These findings indicate that SFL might inhibit HIV-1 infection by more than one mechanism and that SFL might target programmed translational readthrough as well as -1PRF signals, both of which are regulated by mRNA secondary structure elements.
Collapse
Affiliation(s)
- Niklas Jäger
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| | - Shreya Ahana Ayyub
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - Frank Peske
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - David Liedtke
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - Jens Bohne
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany;
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| | - Marina V. Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| |
Collapse
|
3
|
Manjunath LE, Singh A, Devi Kumar S, Vasu K, Kar D, Sellamuthu K, Eswarappa SM. Transcript-specific induction of stop codon readthrough using a CRISPR-dCas13 system. EMBO Rep 2024; 25:2118-2143. [PMID: 38499809 PMCID: PMC11015002 DOI: 10.1038/s44319-024-00115-8] [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: 03/06/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Stop codon readthrough (SCR) is the process where translation continues beyond a stop codon on an mRNA. Here, we describe a strategy to enhance or induce SCR in a transcript-selective manner using a CRISPR-dCas13 system. Using specific guide RNAs, we target dCas13 to the region downstream of canonical stop codons of mammalian AGO1 and VEGFA mRNAs, known to exhibit natural SCR. Readthrough assays reveal enhanced SCR of these mRNAs (both exogenous and endogenous) caused by the dCas13-gRNA complexes. This effect is associated with ribosomal pausing, which has been reported for several SCR events. Our data show that CRISPR-dCas13 can also induce SCR across premature termination codons (PTCs) in the mRNAs of green fluorescent protein and TP53. We demonstrate the utility of this strategy in the induction of readthrough across the thalassemia-causing PTC in HBB mRNA and hereditary spherocytosis-causing PTC in SPTA1 mRNA. Thus, CRISPR-dCas13 can be programmed to enhance or induce SCR in a transcript-selective and stop codon-specific manner.
Collapse
Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sangeetha Devi Kumar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Debaleena Kar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Karthi Sellamuthu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- University of Texas Medical Branch, Galveston, TX, USA
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
| |
Collapse
|
4
|
Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y. High-throughput PRIME-editing screens identify functional DNA variants in the human genome. Mol Cell 2023; 83:4633-4645.e9. [PMID: 38134886 PMCID: PMC10766087 DOI: 10.1016/j.molcel.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/07/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023]
Abstract
Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and single-base resolution manner remains challenging. Here, we develop a pooled prime-editing screen method, PRIME, that can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated single-base resolution analysis. Next, we applied PRIME to functionally characterize 1,304 genome-wide association study (GWAS)-identified non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate that PRIME is capable of characterizing genetic variants at single-base resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.
Collapse
Affiliation(s)
- Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Han Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jovia L Nierenberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Yifan Sun
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cooper Beaman
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Thu Pham
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Mai Nobuhara
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Maya Asami Takagi
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Vivek Narayan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Division of General Internal Medicine, Department of Medicine, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
5
|
Huang X, Du Z. Elaborated pseudoknots that stimulate -1 programmed ribosomal frameshifting or stop codon readthrough in RNA viruses. J Biomol Struct Dyn 2023:1-13. [PMID: 38095458 PMCID: PMC11176267 DOI: 10.1080/07391102.2023.2292296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/25/2023] [Indexed: 05/08/2024]
Abstract
Pseudoknots assume various functions including stimulation of -1 programmed ribosomal frameshifting (PRF) or stop codon readthrough (SCR) in RNA viruses. These pseudoknots vary greatly in sizes and structural complexities. Recent biochemical and structural studies confirm the three-stemmed pseudoknots as the -1 PRF stimulators in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses. We reexamined previously reported -1 PRF or SCR stimulating pseudoknots, especially those containing a relatively long connecting loop between the two pseudoknot-forming stems, for their ability to form elaborated structures. Many potential elaborated pseudoknots were identified that contain one or more of the following extra structural elements: stem-loop, embedded pseudoknot, kissing hairpins, and additional loop-loop interactions. The elaborated pseudoknots are found in several different virus families that utilize either the -1 PRF or SCR recoding mechanisms. Model-building studies were performed to not only establish the structural feasibility of the elaborated pseudoknots but also reveal potential additional structural features that cannot be readily inferred from the predicted secondary structures. Some of the structures, such as embedded double pseudoknots and compact loop-loop pseudoknots mediated by the previously established common pseudoknot motif-1 (CPK-1), represent the first of its kind in the literatures. By advancing discovery of new functional RNA structures, we significantly expand the repertoire of known elaborated pseudoknots that could potentially play a role in -1 PRF and SCR regulation. These results contribute to a better understanding of RNA structures in general, facilitating the design of engineering RNA molecules with certain desired functions.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Xiaolan Huang
- School of Computing, Southern Illinois University at Carbondale, IL 62901, USA
| | - Zhihua Du
- School of Chemical and Biomolecular Sciences, Southern Illinois University at Carbondale, IL 62901, USA
| |
Collapse
|
6
|
Mattioli G, Schürmann R, Nicolafrancesco C, Giuliani A, Milosavljević AR. Effect of Protonation on the Molecular Structure of Adenosine 5'-Triphosphate: A Combined Theoretical and Near Edge X-ray Absorption Fine Structure Study. J Phys Chem Lett 2023; 14:10173-10180. [PMID: 37925744 PMCID: PMC10658619 DOI: 10.1021/acs.jpclett.3c01666] [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: 06/18/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
The present work combines the near edge X-ray absorption mass spectrometry of a protonated adenosine 5'-triphosphate (ATP) molecule isolated in an ion trap with (time-dependent) density functional theory calculations. Our study unravels the effect of protonation on the ATP structure and its spectral properties, providing structure-property relationships at atomistic resolution for protonated ATP (ATPH) isolated in the gas-phase conditions. On the other hand, the present C and N K-edge X-ray absorption spectra of isolated ATPH appear closely like those previously reported for solvated ATP at low pH. Therefore, the present work should be relevant for further investigation and modeling of structure-function properties of protonated adenine and ATP in complex biological environments.
Collapse
Affiliation(s)
- Giuseppe Mattioli
- Istituto
di Struttura della Materia (ISM), Consiglio
Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, CP 10, 00016 Monterotondo Scalo, Italy
| | - Robin Schürmann
- Synchrotron
SOLEIL, L’Orme
de Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France
- Institute
of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | | | - Alexandre Giuliani
- Synchrotron
SOLEIL, L’Orme
de Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France
- INRAE,
UAR1008, Transform Department, Rue de la Géraudière, BP 71627, 44316 Nantes, France
| | | |
Collapse
|
7
|
Kar D, Manna D, Manjunath LE, Singh A, Som S, Vasu K, Eswarappa SM. Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough. J Mol Biol 2023; 435:168274. [PMID: 37714299 DOI: 10.1016/j.jmb.2023.168274] [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: 03/05/2023] [Revised: 08/15/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
During translation, a stop codon on the mRNA signals the ribosomes to terminate the process. In certain mRNAs, the termination fails due to the recoding of the canonical stop codon, and ribosomes continue translation to generate C-terminally extended protein. This process, termed stop codon readthrough (SCR), regulates several cellular functions. SCR is driven by elements/factors that act immediately downstream of the stop codon. Here, we have analysed the process of SCR using a simple mathematical model to investigate how the kinetics of translating ribosomes influences the efficiency of SCR. Surprisingly, the analysis revealed that the rate of translation inversely regulates the efficiency of SCR. We tested this prediction experimentally in mammalian AGO1 and MTCH2 mRNAs. Reduction in translation either globally by harringtonine or locally by rare codons caused an increase in the efficiency of SCR. Thus, our study has revealed a hitherto unknown mode of regulation of SCR.
Collapse
Affiliation(s)
- Debaleena Kar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/debaleenak8
| | - Debraj Manna
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/DebrajManna27
| | - Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/emlekha
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/Anumehasingh25
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/SaubhikSom
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India.
| |
Collapse
|
8
|
Mikkelsen AA, Gao F, Carino E, Bera S, Simon A. -1 Programmed ribosomal frameshifting in Class 2 umbravirus-like RNAs uses multiple long-distance interactions to shift between active and inactive structures and destabilize the frameshift stimulating element. Nucleic Acids Res 2023; 51:10700-10718. [PMID: 37742076 PMCID: PMC10602861 DOI: 10.1093/nar/gkad744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023] Open
Abstract
Plus-strand RNA viruses frequently employ -1 programmed ribosomal frameshifting (-1 PRF) to maximize their coding capacity. Ribosomes can frameshift at a slippery sequence if progression is impeded by a frameshift stimulating element (FSE), which is generally a stable, complex, dynamic structure with multiple conformations that contribute to the efficiency of -1 PRF. As FSE are usually analyzed separate from the viral genome, little is known about cis-acting long-distance interactions. Using full-length genomic RNA of umbravirus-like (ula)RNA citrus yellow vein associated virus (CY1) and translation in wheat germ extracts, six tertiary interactions were found associated with the CY1 FSE that span nearly three-quarters of the 2.7 kb genomic RNA. All six tertiary interactions are conserved in other Class 2 ulaRNAs and two are conserved in all ulaRNAs. Two sets of interactions comprise local and distal pseudoknots that involve overlapping FSE nucleotides and thus are structurally incompatible, suggesting that Class 2 FSEs assume multiple conformations. Importantly, two long-distance interactions connect with sequences on opposite sides of the critical FSE central stem, which would unzip the stem and destabilize the FSE. These latter interactions could allow a frameshifting ribosome to translate through a structurally disrupted upstream FSE that no longer blocks ribosome progression.
Collapse
Affiliation(s)
- Anna A Mikkelsen
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Feng Gao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Elizabeth Carino
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sayanta Bera
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
9
|
Roy R, Geng A, Shi H, Merriman DK, Dethoff EA, Salmon L, Al-Hashimi HM. Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. J Am Chem Soc 2023; 145:22964-22978. [PMID: 37831584 DOI: 10.1021/jacs.3c04614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Knowing the 3D structures formed by the various conformations populating the RNA free-energy landscape, their relative abundance, and kinetic interconversion rates is required to obtain a quantitative and predictive understanding of how RNAs fold and function at the atomic level. While methods integrating ensemble-averaged experimental data with computational modeling are helping define the most abundant conformations in RNA ensembles, elucidating their kinetic rates of interconversion and determining the 3D structures of sparsely populated short-lived RNA excited conformational states (ESs) remains challenging. Here, we developed an approach integrating Rosetta-FARFAR RNA structure prediction with NMR residual dipolar couplings and relaxation dispersion that simultaneously determines the 3D structures formed by the ground-state (GS) and ES subensembles, their relative abundance, and kinetic rates of interconversion. The approach is demonstrated on HIV-1 TAR, whose six-nucleotide apical loop was previously shown to form a sparsely populated (∼13%) short-lived (lifetime ∼ 45 μs) ES. In the GS, the apical loop forms a broad distribution of open conformations interconverting on the pico-to-nanosecond time scale. Most residues are unpaired and preorganized to bind the Tat-superelongation protein complex. The apical loop zips up in the ES, forming a narrow distribution of closed conformations, which sequester critical residues required for protein recognition. Our work introduces an approach for determining the 3D ensemble models formed by sparsely populated RNA conformational states, provides a rare atomic view of an RNA ES, and kinetically resolves the atomic 3D structures of RNA conformational substates, interchanging on time scales spanning 6 orders of magnitude, from picoseconds to microseconds.
Collapse
Affiliation(s)
- Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Dawn K Merriman
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Elizabeth A Dethoff
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| |
Collapse
|
10
|
Faison EM, Nallathambi A, Zhang Q. Characterizing Protonation-Coupled Conformational Ensembles in RNA via pH-Differential Mutational Profiling with DMS Probing. J Am Chem Soc 2023; 145:18773-18777. [PMID: 37582279 DOI: 10.1021/jacs.3c07736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
RNA molecules undergo conformational transitions in response to cellular and environmental stimuli. Site-specific protonation, a fundamental chemical property, can alter the conformational landscape of RNA to regulate their functions. However, characterizing protonation-coupled RNA conformational ensembles on a large scale remains challenging. Here, we present pH-differential mutational profiling (PD-MaP) with dimethyl sulfate probing for high-throughput detection of protonation-coupled conformational ensembles in RNA. We demonstrated this approach on microRNA-21 precursor (pre-miR-21) and recapitulated a previously discovered A+-G-coupled conformational ensemble. Additionally, we identified a secondary protonation event involving an A+-C mismatch. We validated the occurrence of both protonation-coupled ensembles in pre-miR-21 using NMR relaxation dispersion spectroscopy. Furthermore, the application of PD-MaP on a library of well-annotated human primary microRNAs uncovered widespread protonation-coupled conformational ensembles, suggesting their potentially broad functions in biology.
Collapse
|
11
|
Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y. High throughput PRIME editing screens identify functional DNA variants in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548736. [PMID: 37502948 PMCID: PMC10370011 DOI: 10.1101/2023.07.12.548736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated saturation mutagenesis. Next, we applied PRIME to functionally characterize 1,304 non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate PRIME capable of characterizing genetic variants at base-pair resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.
Collapse
Affiliation(s)
- Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Han Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jovia L. Nierenberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Yifan Sun
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cooper Beaman
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Thu Pham
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Mai Nobuhara
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Maya Asami Takagi
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Vivek Narayan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Division of General Internal Medicine, Department of Medicine, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
12
|
Taghavi A, Baisden JT, Childs-Disney JL, Yildirim I, Disney M. Conformational dynamics of RNA G4C2 and G2C4 repeat expansions causing ALS/FTD using NMR and molecular dynamics studies. Nucleic Acids Res 2023; 51:5325-5340. [PMID: 37216594 PMCID: PMC10287959 DOI: 10.1093/nar/gkad403] [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: 01/08/2023] [Revised: 04/15/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
G4C2 and G2C4 repeat expansions in chromosome 9 open reading frame 72 (C9orf72) are the most common cause of genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), or c9ALS/FTD. The gene is bidirectionally transcribed, producing G4C2 repeats [r(G4C2)exp] and G2C4 repeats [r(G2C4)exp]. The c9ALS/FTD repeat expansions are highly structured, and structural studies showed that r(G4C2)exp predominantly folds into a hairpin with a periodic array of 1 × 1 G/G internal loops and a G-quadruplex. A small molecule probe revealed that r(G4C2)exp also adopts a hairpin structure with 2 × 2 GG/GG internal loops. We studied the conformational dynamics adopted by 2 × 2 GG/GG loops using temperature replica exchange molecular dynamics (T-REMD) and further characterized the structure and underlying dynamics using traditional 2D NMR techniques. These studies showed that the loop's closing base pairs influence both structure and dynamics, particularly the configuration adopted around the glycosidic bond. Interestingly, r(G2C4) repeats, which fold into an array of 2 × 2 CC/CC internal loops, are not as dynamic. Collectively, these studies emphasize the unique sensitivity of r(G4C2)exp to small changes in stacking interactions, which is not observed in r(G2C4)exp, providing important considerations for further principles in structure-based drug design.
Collapse
Affiliation(s)
- Amirhossein Taghavi
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Jared T Baisden
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| |
Collapse
|
13
|
Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
Collapse
Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| |
Collapse
|
14
|
Liu Y, Munsayac A, Hall I, Keane SC. Solution Structure of NPSL2, A Regulatory Element in the oncomiR-1 RNA. J Mol Biol 2022; 434:167688. [PMID: 35717998 PMCID: PMC9474619 DOI: 10.1016/j.jmb.2022.167688] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/22/2022]
Abstract
The miR-17 ∼ 92a polycistron, also known as oncomiR-1, is commonly overexpressed in multiple cancers and has several oncogenic properties. OncomiR-1 encodes six constituent microRNAs (miRs), each enzymatically processed with different efficiencies. However, the structural mechanism that regulates this differential processing remains unclear. Chemical probing of oncomiR-1 revealed that the Drosha cleavage sites of pri-miR-92a are sequestered in a four-way junction. NPSL2, an independent stem loop element, is positioned just upstream of pri-miR-92a and sequesters a crucial part of the sequence that constitutes the basal helix of pri-miR-92a. Disruption of the NPSL2 hairpin structure could promote the formation of a pri-miR-92a structure that is primed for processing by Drosha. Thus, NPSL2 is predicted to function as a structural switch, regulating pri-miR-92a processing. Here, we determined the solution structure of NPSL2 using solution NMR spectroscopy. This is the first high-resolution structure of an oncomiR-1 element. NPSL2 adopts a hairpin structure with a large, but highly structured, apical and internal loops. The 10-bp apical loop contains a pH-sensitive A+·C mismatch. Additionally, several adenosines within the apical and internal loops have elevated pKa values. The protonation of these adenosines can stabilize the NPSL2 structure through electrostatic interactions. Our study provides fundamental insights into the secondary and tertiary structure of an important RNA hairpin proposed to regulate miR biogenesis.
Collapse
Affiliation(s)
- Yaping Liu
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA. https://twitter.com/YapingLiu5
| | - Aldrex Munsayac
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
| | - Ian Hall
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA. https://twitter.com/ihallu14
| | - Sarah C Keane
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA.
| |
Collapse
|
15
|
Lu B. Translational regulation by ribosome-associated quality control in neurodegenerative disease, cancer, and viral infection. Front Cell Dev Biol 2022; 10:970654. [PMID: 36187485 PMCID: PMC9515510 DOI: 10.3389/fcell.2022.970654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
Translational control at the initiation, elongation, and termination steps exerts immediate effects on the rate as well as the spatiotemporal dynamics of new protein synthesis, shaping the composition of the proteome. Translational control is particularly important for cells under stress as during viral infection or in disease conditions such as cancer and neurodegenerative diseases. Much has been learned about the control mechanisms acting at the translational initiation step under normal or pathological conditions. However, problems during the elongation or termination steps of translation can lead to ribosome stalling and ribosome collision, which will trigger ribosome-associated quality control (RQC) mechanism. Inadequate RQC may lead to the accumulation of faulty translation products that perturb protein homeostasis (proteostasis). Proteostasis signifies a cellular state in which the synthesis, folding, and degradation of proteins are maintained at a homeostatic state such that an intact proteome is preserved. Cellular capacity to preserve proteostasis declines with age, which is thought to contribute to age-related diseases. Proteostasis failure manifested as formation of aberrant protein aggregates, epitomized by the amyloid plaques in Alzheimer’s disease (AD), is a defining feature of neurodegenerative diseases. The root cause of the proteostasis failure and protein aggregation is still enigmatic. Here I will review recent studies supporting that faulty translation products resulting from inadequate RQC of translational stalling and ribosome collision during the translation of problematic mRNAs can be the root cause of proteostasis failure and may represent novel therapeutic targets for neurodegenerative diseases. I will also review evidence that translation regulation by RQC is operative in cancer cells and during viral infection. Better understanding of RQC mechanism may lead to novel therapeutic strategies against neurodegenerative diseases, cancer, and viral infections, including the ongoing COVID-19 pandemic.
Collapse
|
16
|
Stephen C, Mishanina TV. Alkaline pH has an unexpected effect on transcriptional pausing during synthesis of the E. coli pH-responsive riboswitch. J Biol Chem 2022; 298:102302. [PMID: 35934054 PMCID: PMC9472077 DOI: 10.1016/j.jbc.2022.102302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/13/2022] [Accepted: 07/16/2022] [Indexed: 11/17/2022] Open
Abstract
Riboswitches are 5′-untranslated regions of mRNA that change their conformation in response to ligand binding, allowing post-transcriptional gene regulation. This ligand-based model of riboswitch function has been expanded with the discovery of a “pH-responsive element” (PRE) riboswitch in Escherichia coli. At neutral pH, the PRE folds into a translationally inactive structure with an occluded ribosome-binding sequence, whereas at alkaline pH, the PRE adopts a translationally active structure. This unique riboswitch does not rely on ligand binding in a traditional sense to modulate its alternative folding outcomes. Rather, pH controls riboswitch folding by two possible modes that are yet to be distinguished; pH either regulates the transcription rate of RNA polymerase (RNAP) or acts on the RNA itself. Previous work suggested that RNAP pausing is prolonged by alkaline pH at two sites, stimulating PRE folding into the active structure. To date, there has been no rigorous exploration into how pH influences RNAP pausing kinetics during PRE synthesis. To provide that understanding and distinguish between pH acting on RNAP versus RNA, we investigated RNAP pausing kinetics at key sites for PRE folding under different pH conditions. We find that pH influences RNAP pausing but not in the manner proposed previously. Rather, alkaline pH either decreases or has no effect on RNAP pause longevity, suggesting that the modulation of RNAP pausing is not the sole mechanism by which pH affects PRE folding. These findings invite the possibility that the RNA itself actively participates in the sensing of pH.
Collapse
|
17
|
Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression. Nat Commun 2022; 13:4284. [PMID: 35879278 PMCID: PMC9310368 DOI: 10.1038/s41467-022-31353-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/10/2022] [Indexed: 12/16/2022] Open
Abstract
The SARS-CoV-2 frameshifting element (FSE), a highly conserved mRNA region required for correct translation of viral polyproteins, defines an excellent therapeutic target against Covid-19. As discovered by our prior graph-theory analysis with SHAPE experiments, the FSE adopts a heterogeneous, length-dependent conformational landscape consisting of an assumed 3-stem H-type pseudoknot (graph motif 3_6), and two alternative motifs (3_3 and 3_5). Here, for the first time, we build and simulate, by microsecond molecular dynamics, 30 models for all three motifs plus motif-stabilizing mutants at different lengths. Our 3_6 pseudoknot systems, which agree with experimental structures, reveal interconvertible L and linear conformations likely related to ribosomal pausing and frameshifting. The 3_6 mutant inhibits this transformation and could hamper frameshifting. Our 3_3 systems exhibit length-dependent stem interactions that point to a potential transition pathway connecting the three motifs during ribosomal elongation. Together, our observations provide new insights into frameshifting mechanisms and anti-viral strategies.
Collapse
|
18
|
Sahoo S, Singh D, Singh A, Pandit M, Vasu K, Som S, Pullagurla NJ, Laha D, Eswarappa SM. Identification and functional characterization of mRNAs that exhibit stop codon readthrough in Arabidopsis thaliana. J Biol Chem 2022; 298:102173. [PMID: 35752360 PMCID: PMC9293766 DOI: 10.1016/j.jbc.2022.102173] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/29/2022] Open
Abstract
Stop codon readthrough (SCR) is the process of continuation of translation beyond the stop codon, generating protein isoforms with C-terminal extensions. SCR has been observed in viruses, fungi, and multicellular organisms, including mammals. However, SCR is largely unexplored in plants. In this study, we have analyzed ribosome profiling datasets to identify mRNAs that exhibit SCR in Arabidopsis thaliana. Analyses of the ribosome density, ribosome coverage, and three-nucleotide periodicity of the ribosome profiling reads in the mRNA region downstream of the stop codon provided strong evidence for SCR in mRNAs of 144 genes. We show that SCR generated putative evolutionarily conserved nuclear localization signals, transmembrane helices, and intrinsically disordered regions in the C-terminal extensions of several of these proteins. Furthermore, gene ontology (GO) functional enrichment analysis revealed that these 144 genes belong to three major functional groups - translation, photosynthesis, and abiotic stress tolerance. Using a luminescence-based readthrough assay, we experimentally demonstrated SCR in representative mRNAs belonging to each of these functional classes. Finally, using microscopy, we show that the SCR product of one gene that contains a nuclear localization signal at the C-terminal extension, CURT1B, localizes to the nucleus as predicted. Based on these observations, we propose that SCR plays an important role in plant physiology by regulating protein localization and function.
Collapse
Affiliation(s)
- Sarthak Sahoo
- Undergraduate Program, Indian Institute of Science, Bengaluru, India; Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Divyoj Singh
- Undergraduate Program, Indian Institute of Science, Bengaluru, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Madhuparna Pandit
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | | | - Debabrata Laha
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | | |
Collapse
|
19
|
Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting. Proc Natl Acad Sci U S A 2022; 119:e2112496119. [PMID: 35671421 PMCID: PMC9214542 DOI: 10.1073/pnas.2112496119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Thermodynamic preferences to form non-native conformations are crucial for understanding how nucleic acids fold and function. However, they are difficult to measure experimentally because this requires accurately determining the population of minor low-abundance (<10%) conformations in a sea of other conformations. Here, we show that melting experiments enable facile measurements of thermodynamic preferences to adopt nonnative conformations in DNA and RNA. The key to this "delta-melt" approach is to use chemical modifications to render specific minor non-native conformations the major state. The validity and robustness of delta-melt is established for four different non-native conformations under various physiological conditions and sequence contexts through independent measurements of thermodynamic preferences using NMR. Delta-melt is faster relative to NMR, simple, and cost-effective and enables thermodynamic preferences to be measured for exceptionally low-populated conformations. Using delta-melt, we obtained rare insights into conformational cooperativity, obtaining evidence for significant cooperativity (1.0 to 2.5 kcal/mol) when simultaneously forming two adjacent Hoogsteen base pairs. We also measured the thermodynamic preferences to form G-C+ and A-T Hoogsteen and A-T base open states for nearly all 16 trinucleotide sequence contexts and found distinct sequence-specific variations on the order of 2 to 3 kcal/mol. This rich landscape of sequence-specific non-native minor conformations in the DNA double helix may help shape the sequence specificity of DNA biochemistry. Thus, melting experiments can now be used to access thermodynamic information regarding regions of the free energy landscape of biomolecules beyond the native folded and unfolded conformations.
Collapse
|
20
|
Nelson JW, Randolph PB, Shen SP, Everette KA, Chen PJ, Anzalone AV, An M, Newby GA, Chen JC, Hsu A, Liu DR. Engineered pegRNAs improve prime editing efficiency. Nat Biotechnol 2022; 40:402-410. [PMID: 34608327 PMCID: PMC8930418 DOI: 10.1038/s41587-021-01039-7] [Citation(s) in RCA: 303] [Impact Index Per Article: 151.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023]
Abstract
Prime editing enables the installation of virtually any combination of point mutations, small insertions or small deletions in the DNA of living cells. A prime editing guide RNA (pegRNA) directs the prime editor protein to the targeted locus and also encodes the desired edit. Here we show that degradation of the 3' region of the pegRNA that contains the reverse transcriptase template and the primer binding site can poison the activity of prime editing systems, impeding editing efficiency. We incorporated structured RNA motifs to the 3' terminus of pegRNAs that enhance their stability and prevent degradation of the 3' extension. The resulting engineered pegRNAs (epegRNAs) improve prime editing efficiency 3-4-fold in HeLa, U2OS and K562 cells and in primary human fibroblasts without increasing off-target editing activity. We optimized the choice of 3' structural motif and developed pegLIT, a computational tool to identify non-interfering nucleotide linkers between pegRNAs and 3' motifs. Finally, we showed that epegRNAs enhance the efficiency of the installation or correction of disease-relevant mutations.
Collapse
Affiliation(s)
- James W Nelson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Peyton B Randolph
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Simon P Shen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Kelcee A Everette
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Peter J Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Andrew V Anzalone
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Meirui An
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan C Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Alvin Hsu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
21
|
Riegger RJ, Caliskan N. Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting. Front Mol Biosci 2022; 9:842261. [PMID: 35281266 PMCID: PMC8915115 DOI: 10.3389/fmolb.2022.842261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/26/2022] [Indexed: 01/08/2023] Open
Abstract
Translation facilitates the transfer of the genetic information stored in the genome via messenger RNAs to a functional protein and is therefore one of the most fundamental cellular processes. Programmed ribosomal frameshifting is a ubiquitous alternative translation event that is extensively used by viruses to regulate gene expression from overlapping open reading frames in a controlled manner. Recent technical advances in the translation field enabled the identification of precise mechanisms as to how and when ribosomes change the reading frame on mRNAs containing cis-acting signals. Several studies began also to illustrate that trans-acting RNA modulators can adjust the timing and efficiency of frameshifting illuminating that frameshifting can be a dynamically regulated process in cells. Here, we intend to summarize these new findings and emphasize how it fits in our current understanding of PRF mechanisms as previously described.
Collapse
Affiliation(s)
- Ricarda J. Riegger
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Graduate School of Life Sciences (GSLS), University of Würzburg, Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
- *Correspondence: Neva Caliskan,
| |
Collapse
|
22
|
Jones CP, Ferré-D'Amaré AR. Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot. RNA (NEW YORK, N.Y.) 2022; 28:239-249. [PMID: 34845084 PMCID: PMC8906546 DOI: 10.1261/rna.078825.121] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 11/04/2021] [Indexed: 05/30/2023]
Abstract
SARS-CoV-2 produces two long viral protein precursors from one open reading frame using a highly conserved RNA pseudoknot that enhances programmed -1 ribosomal frameshifting. The 1.3 Å-resolution X-ray structure of the pseudoknot reveals three coaxially stacked helices buttressed by idiosyncratic base triples from loop residues. This structure represents a frameshift-stimulating state that must be deformed by the ribosome and exhibits base-triple-adjacent pockets that could be targeted by future small-molecule therapeutics.
Collapse
Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| |
Collapse
|
23
|
Yan S, Zhu Q, Jain S, Schlick T. Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression. RESEARCH SQUARE 2022:rs.3.rs-1160075. [PMID: 35018371 PMCID: PMC8750709 DOI: 10.21203/rs.3.rs-1160075/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Conserved SARS-CoV-2 RNA regions of critical biological functions define excellent targets for anti-viral therapeutics against Covid-19 variants. One such region is the frameshifting element (FSE), responsible for correct translation of viral polyproteins. Here, we analyze molecular-dynamics motions of three FSE conformations, discovered by graph-theory analysis, and associated mutants designed by graph-based inverse folding: two distinct 3-stem H-type pseudoknots and a 3-way junction. We find that the prevalent H-type pseudoknot in literature adopts ring-like conformations, which in combination with 5' end threading could promote ribosomal pausing. An inherent shape switch from "L" to linear that may help trigger the frameshifting is suppressed in our designed mutant. The alternative conformation trajectories suggest a stable intermediate structure with mixed stem interactions of all three conformations, pointing to a possible transition pathway during ribosomal translation. These observations provide new insights into anti-viral strategies and frameshifting mechanisms.
Collapse
Affiliation(s)
- Shuting Yan
- Department of Chemistry, New York University, New York, NY 10003 U.S.A
| | - Qiyao Zhu
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 U.S.A
| | - Swati Jain
- Department of Chemistry, New York University, New York, NY 10003 U.S.A
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, NY 10003 U.S.A
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 U.S.A
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, P.R. China
| |
Collapse
|
24
|
Kotar A, Ma S, Keane SC. pH dependence of C•A, G•A and A•A mismatches in the stem of precursor microRNA-31. Biophys Chem 2022; 283:106763. [DOI: 10.1016/j.bpc.2022.106763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022]
|
25
|
Fang X, Gallego J, Wang YX. Deriving RNA topological structure from SAXS. Methods Enzymol 2022; 677:479-529. [DOI: 10.1016/bs.mie.2022.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
26
|
Del Toro N, Lessard F, Bouchard J, Mobasheri N, Guillon J, Igelmann S, Tardif S, Buffard T, Bourdeau V, Brakier-Gingras L, Ferbeyre G. Cellular Senescence limits Translational Readthrough. Biol Open 2021; 10:272574. [PMID: 34676390 PMCID: PMC8649927 DOI: 10.1242/bio.058688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/14/2021] [Indexed: 11/20/2022] Open
Abstract
The origin and evolution of cancer cells is considered to be mainly fueled by DNA mutations. Although translation errors could also expand the cellular proteome, their role in cancer biology remains poorly understood. Tumor suppressors called caretakers block cancer initiation and progression by preventing DNA mutations and/or stimulating DNA repair. If translational errors contribute to tumorigenesis, then caretaker genes should prevent such errors in normal cells in response to oncogenic stimuli. Here, we show that the process of cellular senescence induced by oncogenes, tumor suppressors or chemotherapeutic drugs is associated with a reduction in translational readthrough (TR) measured using reporters containing termination codons withing the context of both normal translation termination or programmed TR. Senescence reduced both basal TR and TR stimulated by aminoglycosides. Mechanistically, the reduction of TR during senescence is controlled by the RB tumor suppressor pathway. Cells that escape from cellular senescence either induced by oncogenes or chemotherapy have an increased TR. Also, breast cancer cells that escape from therapy-induced senescence express high levels of AGO1x, a TR isoform of AGO1 linked to breast cancer progression. We propose that senescence and the RB pathway reduce TR limiting proteome diversity and the expression of TR proteins required for cancer cell proliferation. Summary: We report that senescence and the RB pathway reduce translational readthrough (TR) limiting proteome diversity and the expression of TR proteins such as Ago1X required for cancer cell proliferation.
Collapse
Affiliation(s)
- Neylen Del Toro
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Frédéric Lessard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Jacob Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Nasrin Mobasheri
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Jordan Guillon
- CRCHUM, 900 Saint-Denis, bureau R10.432, Montréal, Québec, H2X 0A9, Canada
| | - Sebastian Igelmann
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada.,CRCHUM, 900 Saint-Denis, bureau R10.432, Montréal, Québec, H2X 0A9, Canada
| | - Sarah Tardif
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Tony Buffard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Véronique Bourdeau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Léa Brakier-Gingras
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada.,CRCHUM, 900 Saint-Denis, bureau R10.432, Montréal, Québec, H2X 0A9, Canada
| |
Collapse
|
27
|
Karasik A, Jones GD, DePass AV, Guydosh NR. Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences. Nucleic Acids Res 2021; 49:6007-6026. [PMID: 33556964 DOI: 10.1093/nar/gkab036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/06/2021] [Accepted: 02/03/2021] [Indexed: 11/15/2022] Open
Abstract
Ribonuclease L (RNase L) is activated as part of the innate immune response and plays an important role in the clearance of viral infections. When activated, it endonucleolytically cleaves both viral and host RNAs, leading to a global reduction in protein synthesis. However, it remains unknown how widespread RNA decay, and consequent changes in the translatome, promote the elimination of viruses. To study how this altered transcriptome is translated, we assayed the global distribution of ribosomes in RNase L activated human cells with ribosome profiling. We found that RNase L activation leads to a substantial increase in the fraction of translating ribosomes in ORFs internal to coding sequences (iORFs) and ORFs within 5' and 3' UTRs (uORFs and dORFs). Translation of these alternative ORFs was dependent on RNase L's cleavage activity, suggesting that mRNA decay fragments are translated to produce short peptides that may be important for antiviral activity.
Collapse
Affiliation(s)
- Agnes Karasik
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grant D Jones
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew V DePass
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
28
|
Atkins JF, O’Connor KM, Bhatt PR, Loughran G. From Recoding to Peptides for MHC Class I Immune Display: Enriching Viral Expression, Virus Vulnerability and Virus Evasion. Viruses 2021; 13:1251. [PMID: 34199077 PMCID: PMC8310308 DOI: 10.3390/v13071251] [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: 05/04/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 01/02/2023] Open
Abstract
Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined.
Collapse
Affiliation(s)
- John F. Atkins
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Kate M. O’Connor
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Pramod R. Bhatt
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Gary Loughran
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| |
Collapse
|
29
|
Tissue-specific dynamic codon redefinition in Drosophila. Proc Natl Acad Sci U S A 2021; 118:2012793118. [PMID: 33500350 DOI: 10.1073/pnas.2012793118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Translational stop codon readthrough occurs in organisms ranging from viruses to mammals and is especially prevalent in decoding Drosophila and viral mRNAs. Recoding of UGA, UAG, or UAA to specify an amino acid allows a proportion of the protein encoded by a single gene to be C-terminally extended. The extended product from Drosophila kelch mRNA is 160 kDa, whereas unextended Kelch protein, a subunit of a Cullin3-RING ubiquitin ligase, is 76 kDa. Previously we reported tissue-specific regulation of readthrough of the first kelch stop codon. Here, we characterize major efficiency differences in a variety of cell types. Immunoblotting revealed low levels of readthrough in malpighian tubules, ovary, and testis but abundant readthrough product in lysates of larval and adult central nervous system (CNS) tissue. Reporters of readthrough demonstrated greater than 30% readthrough in adult brains, and imaging in larval and adult brains showed that readthrough occurred in neurons but not glia. The extent of readthrough stimulatory sequences flanking the readthrough stop codon was assessed in transgenic Drosophila and in human tissue culture cells where inefficient readthrough occurs. A 99-nucleotide sequence with potential to form an mRNA stem-loop 3' of the readthrough stop codon stimulated readthrough efficiency. However, even with just six nucleotides of kelch mRNA sequence 3' of the stop codon, readthrough efficiency only dropped to 6% in adult neurons. Finally, we show that high-efficiency readthrough in the Drosophila CNS is common; for many neuronal proteins, C-terminal extended forms of individual proteins are likely relatively abundant.
Collapse
|
30
|
Abstract
I was fortunate to be associated with the lab of Stephen Oroszlan at the US National Cancer Institute from ~1982 until his conversion to Emeritus status in 1995. His lab made groundbreaking discoveries on retroviral proteins during that time, including many features that could not have been inferred or anticipated from straightforward sequence information. Building on the Oroszlan lab results, my colleagues and I demonstrated that the zinc fingers in nucleocapsid proteins play a crucial role in genomic RNA encapsidation; that the N-terminal myristylation of the Gag proteins of many retroviruses is important for their association with the plasma membrane before particle assembly is completed; and that gammaretroviruses initially synthesize their Env protein as an inactive precursor and then truncate the cytoplasmic tail of the transmembrane protein, activating Env fusogenicity, during virus maturation. We also elucidated several aspects of the mechanism of translational suppression in pol gene expression in gammaretroviruses; amazingly, this is a fundamentally different mechanism of suppression from that in most other retroviral genera.
Collapse
Affiliation(s)
- Alan Rein
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| |
Collapse
|
31
|
Manjunath LE, Singh A, Sahoo S, Mishra A, Padmarajan J, Basavaraju CG, Eswarappa SM. Stop codon read-through of mammalian MTCH2 leading to an unstable isoform regulates mitochondrial membrane potential. J Biol Chem 2020; 295:17009-17026. [PMID: 33028634 PMCID: PMC7863902 DOI: 10.1074/jbc.ra120.014253] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Stop codon read-through (SCR) is a process of continuation of translation beyond a stop codon. This phenomenon, which occurs only in certain mRNAs under specific conditions, leads to a longer isoform with properties different from that of the canonical isoform. MTCH2, which encodes a mitochondrial protein that regulates mitochondrial metabolism, was selected as a potential read-through candidate based on evolutionary conservation observed in the proximal region of its 3' UTR. Here, we demonstrate translational read-through across two evolutionarily conserved, in-frame stop codons of MTCH2 using luminescence- and fluorescence-based assays, and by analyzing ribosome-profiling and mass spectrometry (MS) data. This phenomenon generates two isoforms, MTCH2x and MTCH2xx (single- and double-SCR products, respectively), in addition to the canonical isoform MTCH2, from the same mRNA. Our experiments revealed that a cis-acting 12-nucleotide sequence in the proximal 3' UTR of MTCH2 is the necessary signal for SCR. Functional characterization showed that MTCH2 and MTCH2x were localized to mitochondria with a long t1/2 (>36 h). However, MTCH2xx was found predominantly in the cytoplasm. This mislocalization and its unique C terminus led to increased degradation, as shown by greatly reduced t1/2 (<1 h). MTCH2 read-through-deficient cells, generated using CRISPR-Cas9, showed increased MTCH2 expression and, consistent with this, decreased mitochondrial membrane potential. Thus, double-SCR of MTCH2 regulates its own expression levels contributing toward the maintenance of normal mitochondrial membrane potential.
Collapse
Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sarthak Sahoo
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Ashutosh Mishra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Jinsha Padmarajan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India.
| |
Collapse
|
32
|
Zhang H, Hall I, Nissley AJ, Abdallah K, Keane SC. A Tale of Two Transitions: The Unfolding Mechanism of the prfA RNA Thermosensor. Biochemistry 2020; 59:4533-4545. [PMID: 33231432 DOI: 10.1021/acs.biochem.0c00588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA thermosensors (RNATs), found in the 5' untranslated region (UTR) of some bacterial messenger RNAs (mRNAs), control the translation of the downstream gene in a temperature-dependent manner. In Listeria monocytogenes, the expression of a key transcription factor, PrfA, is mediated by an RNAT in its 5' UTR. PrfA functions as a master regulator of virulence in L. monocytogenes, controlling the expression of many virulence factors. The temperature-regulated expression of PrfA by its RNAT element serves as a signal of successful host invasion for the bacteria. Structurally, the prfA RNAT bears little resemblance to known families of RNATs, and prior studies demonstrated that the prfA RNAT is highly responsive over a narrow temperature range. Herein, we have undertaken a comprehensive mutational and thermodynamic analysis to ascertain the molecular determinants of temperature sensitivity. We provide evidence to support the idea that the prfA RNAT unfolding is different from that of cssA, a well-characterized RNAT, suggesting that these RNATs function via distinct mechanisms. Our data show that the unfolding of the prfA RNAT occurs in two distinct events and that the internal loops play an important role in mediating the cooperativity of RNAT unfolding. We further demonstrated that regions distal to the ribosome binding site (RBS) not only contribute to RNAT structural stability but also impact translation of the downstream message. Our collective results provide insight connecting the thermal stability of the prfA RNAT structure, unfolding energetics, and translational control.
Collapse
Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ian Hall
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amos J Nissley
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kyrillos Abdallah
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
33
|
Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
|
34
|
Baisden JT, Boyer JA, Zhao B, Hammond SM, Zhang Q. Visualizing a protonated RNA state that modulates microRNA-21 maturation. Nat Chem Biol 2020; 17:80-88. [PMID: 33106660 DOI: 10.1038/s41589-020-00667-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 08/02/2020] [Accepted: 09/02/2020] [Indexed: 01/09/2023]
Abstract
MicroRNAs are evolutionarily conserved small, noncoding RNAs that regulate diverse biological processes. Due to their essential regulatory roles, microRNA biogenesis is tightly regulated, where protein factors are often found to interact with specific primary and precursor microRNAs for regulation. Here, using NMR relaxation dispersion spectroscopy and mutagenesis, we reveal that the precursor of oncogenic microRNA-21 exists as a pH-dependent ensemble that spontaneously reshuffles the secondary structure of the entire apical stem-loop region, including the Dicer cleavage site. We show that the alternative excited conformation transiently sequesters the bulged adenine into a noncanonical protonated A+-G mismatch, conferring a substantial enhancement in Dicer processing over its ground conformational state. These results indicate that microRNA maturation efficiency may be encoded in the intrinsic dynamic ensemble of primary and precursor microRNAs, providing a potential means of regulating microRNA biogenesis in response to environmental and cellular stimuli.
Collapse
Affiliation(s)
- Jared T Baisden
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joshua A Boyer
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bo Zhao
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott M Hammond
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
35
|
Palma M, Lejeune F. Deciphering the molecular mechanism of stop codon readthrough. Biol Rev Camb Philos Soc 2020; 96:310-329. [PMID: 33089614 DOI: 10.1111/brv.12657] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/11/2022]
Abstract
Recognition of the stop codon by the translation machinery is essential to terminating translation at the right position and to synthesizing a protein of the correct size. Under certain conditions, the stop codon can be recognized as a coding codon promoting translation, which then terminates at a later stop codon. This event, called stop codon readthrough, occurs either by error, due to a dedicated regulatory environment leading to generation of different protein isoforms, or through the action of a readthrough compound. This review focuses on the mechanisms of stop codon readthrough, the nucleotide and protein environments that facilitate or inhibit it, and the therapeutic interest of stop codon readthrough in the treatment of genetic diseases caused by nonsense mutations.
Collapse
Affiliation(s)
- Martine Palma
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| |
Collapse
|
36
|
Penn WD, Harrington HR, Schlebach JP, Mukhopadhyay S. Regulators of Viral Frameshifting: More Than RNA Influences Translation Events. Annu Rev Virol 2020; 7:219-238. [PMID: 32600156 DOI: 10.1146/annurev-virology-012120-101548] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Programmed ribosomal frameshifting (PRF) is a conserved translational recoding mechanism found in all branches of life and viruses. In bacteria, archaea, and eukaryotes PRF is used to downregulate protein production by inducing a premature termination of translation, which triggers messenger RNA (mRNA) decay. In viruses, PRF is used to drive the production of a new protein while downregulating the production of another protein, thus maintaining a stoichiometry optimal for productive infection. Traditionally, PRF motifs have been defined by the characteristics of two cis elements: a slippery heptanucleotide sequence followed by an RNA pseudoknot or stem-loop within the mRNA. Recently, additional cis and new trans elements have been identified that regulate PRF in both host and viral translation. These additional factors suggest PRF is an evolutionarily conserved process whose function and regulation we are just beginning to understand.
Collapse
Affiliation(s)
- Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Haley R Harrington
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | | | | |
Collapse
|
37
|
Murphy RE, Saad JS. The Interplay between HIV-1 Gag Binding to the Plasma Membrane and Env Incorporation. Viruses 2020; 12:E548. [PMID: 32429351 PMCID: PMC7291237 DOI: 10.3390/v12050548] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/21/2022] Open
Abstract
Advancement in drug therapies and patient care have drastically improved the mortality rates of HIV-1 infected individuals. Many of these therapies were developed or improved upon by using structure-based techniques, which underscore the importance of understanding essential mechanisms in the replication cycle of HIV-1 at the structural level. One such process which remains poorly understood is the incorporation of the envelope glycoprotein (Env) into budding virus particles. Assembly of HIV particles is initiated by targeting of the Gag polyproteins to the inner leaflet of the plasma membrane (PM), a process mediated by the N-terminally myristoylated matrix (MA) domain and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). There is strong evidence that formation of the Gag lattice on the PM is a prerequisite for the incorporation of Env into budding particles. It is also suggested that Env incorporation is mediated by an interaction between its cytoplasmic tail (gp41CT) and the MA domain of Gag. In this review, we highlight the latest developments and current efforts to understand the interplay between gp41CT, MA, and the membrane during assembly. Elucidation of the molecular determinants of Gag-Env-membrane interactions may help in the development of new antiviral therapeutic agents that inhibit particle assembly, Env incorporation and ultimately virus production.
Collapse
Affiliation(s)
| | - Jamil S. Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| |
Collapse
|
38
|
Abstract
Viruses must co-opt the cellular translation machinery to produce progeny virions. Eukaryotic viruses have evolved a variety of ways to manipulate the cellular translation apparatus, in many cases using elegant RNA-centred strategies. Viral RNAs can alter or control every phase of protein synthesis and have diverse targets, mechanisms and structures. In addition, as cells attempt to limit infection by downregulating translation, some of these viral RNAs enable the virus to overcome this response or even take advantage of it to promote viral translation over cellular translation. In this Review, we present important examples of viral RNA-based strategies to exploit the cellular translation machinery. We describe what is understood of the structures and mechanisms of diverse viral RNA elements that alter or regulate translation, the advantages that are conferred to the virus and some of the major unknowns that provide motivation for further exploration. Eukaryotic viruses have evolved a variety of ways to manipulate the cellular translation apparatus. In this Review, Jaafar and Kieft present important examples of viral RNA-based strategies to exploit the cellular translation machinery.
Collapse
Affiliation(s)
- Zane A Jaafar
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO, USA.
| |
Collapse
|
39
|
Abstract
RNA molecules fold into complex three-dimensional structures that sample alternate conformations ranging from minor differences in tertiary structure dynamics to major differences in secondary structure. This allows them to form entirely different substructures with each population potentially giving rise to a distinct biological outcome. The substructures can be partitioned along an existing energy landscape given a particular static cellular cue or can be shifted in response to dynamic cues such as ligand binding. We review a few key examples of RNA molecules that sample alternate conformations and how these are capitalized on for control of critical regulatory functions.
Collapse
Affiliation(s)
- Marie Teng-Pei Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Victoria D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| |
Collapse
|
40
|
Michorowska S, Giebułtowicz J, Wolinowska R, Konopka A, Wilkaniec A, Krajewski P, Bulska E, Wroczyński P. Detection of ALDH3B2 in Human Placenta. Int J Mol Sci 2019; 20:E6292. [PMID: 31847104 PMCID: PMC6941052 DOI: 10.3390/ijms20246292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 01/28/2023] Open
Abstract
Aldehyde dehydrogenase 3B2 (ALDH3B2) gene contains a premature termination codon, which can be skipped or suppressed resulting in full-length protein expression. Alternatively, the longest putative open reading frame starting with the second in-frame start codon would encode short isoform. No unequivocal evidence of ALDH3B2 expression in healthy human tissues is available. The aim of this study was to confirm its expression in human placenta characterized by the highest ALDH3B2 mRNA abundance. ALDH3B2 DNA and mRNA were sequenced. The expression was investigated using western blot. The identity of the protein was confirmed using mass spectrometry (MS). The predicted tertiary and quaternary structures, subcellular localization, and phosphorylation sites were assessed using bioinformatic analyses. All DNA and mRNA isolates contained the premature stop codon. In western blot analyses, bands corresponding to the mass of full-length protein were detected. MS analysis led to the identification of two unique peptides, one of which is encoded by the nucleotide sequence located upstream the second start codon. Bioinformatic analyses suggest cytoplasmic localization and several phosphorylation sites. Despite premature stop codon in DNA and mRNA sequences, full-length ALDH3B2 was found. It can be formed as a result of premature stop codon readthrough, complex phenomenon enabling stop codon circumvention.
Collapse
Affiliation(s)
- Sylwia Michorowska
- Department of Bioanalysis and Drug Analysis, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.G.); (P.W.)
| | - Joanna Giebułtowicz
- Department of Bioanalysis and Drug Analysis, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.G.); (P.W.)
| | - Renata Wolinowska
- Department of Pharmaceutical Microbiology, Centre for Preclinical Research and Technology (CePT), Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland;
| | - Anna Konopka
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 02-097 Warsaw, Poland; (A.K.); (E.B.)
| | - Anna Wilkaniec
- Department of Cellular Signaling, Mossakowski Research Centre, Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland;
| | - Paweł Krajewski
- Forensic Medicine Department, First Faculty of Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland;
| | - Ewa Bulska
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 02-097 Warsaw, Poland; (A.K.); (E.B.)
| | - Piotr Wroczyński
- Department of Bioanalysis and Drug Analysis, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.G.); (P.W.)
| |
Collapse
|
41
|
Kar D, Sellamuthu K, Kumar SD, Eswarappa SM. Induction of Translational Readthrough across the Thalassemia-Causing Premature Stop Codon in β-Globin-Encoding mRNA. Biochemistry 2019; 59:80-84. [PMID: 31577420 DOI: 10.1021/acs.biochem.9b00761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonsense mutations that result in premature stop codons in the HBB gene cause β-thalassemia. This disease is characterized by a reduced hemoglobin level due to the lack of β-globin. Compounds that induce translational readthrough across the thalassemia-causing premature stop codon will have therapeutic benefits. Currently available molecules that induce translational readthrough lack specificity, and some of them show toxicity after prolonged use. In this study, we have developed an oligonucleotide-based approach to induce translational readthrough across the thalassemia-causing premature stop codon. Oligonucleotides that target HBB mRNA downstream of the premature stop codon could induce translational readthrough, generating a full-length β-globin protein. We show this effect using fluorescence- and luminescence-based readthrough assays and by Western blot. Remarkably, the amount of oligonucleotide-induced translational readthrough product is comparable to that of the protein generated by normal translation when there was no premature stop codon. Thus, these oligonucleotides, with certain modifications, have the potential to be used as drugs for the treatment of β-thalassemia. Also, this strategy can be extended to treat other genetic diseases caused by premature stop codons.
Collapse
Affiliation(s)
- Debaleena Kar
- Department of Biochemistry , Indian Institute of Science , Bengaluru , Karnataka 560012 , India
| | - Karthi Sellamuthu
- Department of Biochemistry , Indian Institute of Science , Bengaluru , Karnataka 560012 , India
| | - Sangeetha Devi Kumar
- Department of Biochemistry , Indian Institute of Science , Bengaluru , Karnataka 560012 , India
| | - Sandeep M Eswarappa
- Department of Biochemistry , Indian Institute of Science , Bengaluru , Karnataka 560012 , India
| |
Collapse
|
42
|
Singh A, Manjunath LE, Kundu P, Sahoo S, Das A, Suma HR, Fox PL, Eswarappa SM. Let-7a-regulated translational readthrough of mammalian AGO1 generates a microRNA pathway inhibitor. EMBO J 2019; 38:e100727. [PMID: 31330067 PMCID: PMC6694283 DOI: 10.15252/embj.2018100727] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 01/01/2023] Open
Abstract
Translational readthrough generates proteins with extended C-termini, which often possess distinct properties. Here, we have used various reporter assays to demonstrate translational readthrough of AGO1 mRNA. Analysis of ribosome profiling data and mass spectrometry data provided additional evidence for translational readthrough of AGO1. The endogenous readthrough product, Ago1x, could be detected by a specific antibody both in vitro and in vivo. This readthrough process is directed by a cis sequence downstream of the canonical AGO1 stop codon, which is sufficient to drive readthrough even in a heterologous context. This cis sequence has a let-7a miRNA-binding site, and readthrough is promoted by let-7a miRNA. Interestingly, Ago1x can load miRNAs on target mRNAs without causing post-transcriptional gene silencing, due to its inability to interact with GW182. Because of these properties, Ago1x can serve as a competitive inhibitor of miRNA pathway. In support of this, we observed increased global translation in cells overexpressing Ago1x. Overall, our results reveal a negative feedback loop in the miRNA pathway mediated by the translational readthrough product of AGO1.
Collapse
Affiliation(s)
- Anumeha Singh
- Department of BiochemistryIndian Institute of ScienceBengaluruKarnatakaIndia
| | - Lekha E Manjunath
- Department of BiochemistryIndian Institute of ScienceBengaluruKarnatakaIndia
| | - Pradipta Kundu
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBengaluruKarnatakaIndia
| | - Sarthak Sahoo
- Department of BiochemistryIndian Institute of ScienceBengaluruKarnatakaIndia
| | - Arpan Das
- Department of BiochemistryIndian Institute of ScienceBengaluruKarnatakaIndia
- Present address:
Department of Molecular, Cellular and Developmental BiologyUniversity of ColoradoBoulderCOUSA
| | - Harikumar R Suma
- Department of BiochemistryIndian Institute of ScienceBengaluruKarnatakaIndia
| | - Paul L Fox
- Department of Cellular and Molecular MedicineThe Lerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Sandeep M Eswarappa
- Department of BiochemistryIndian Institute of ScienceBengaluruKarnatakaIndia
| |
Collapse
|
43
|
Complex dynamics under tension in a high-efficiency frameshift stimulatory structure. Proc Natl Acad Sci U S A 2019; 116:19500-19505. [PMID: 31409714 DOI: 10.1073/pnas.1905258116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Specific structures in mRNA can stimulate programmed ribosomal frameshifting (PRF). PRF efficiency can vary enormously between different stimulatory structures, but the features that lead to efficient PRF stimulation remain uncertain. To address this question, we studied the structural dynamics of the frameshift signal from West Nile virus (WNV), which stimulates -1 PRF at very high levels and has been proposed to form several different structures, including mutually incompatible pseudoknots and a double hairpin. Using optical tweezers to apply tension to single mRNA molecules, mimicking the tension applied by the ribosome during PRF, we found that the WNV frameshift signal formed an unusually large number of different metastable structures, including all of those previously proposed. From force-extension curve measurements, we mapped 2 mutually exclusive pathways for the folding, each encompassing multiple intermediates. We identified the intermediates in each pathway from length changes and the effects of antisense oligomers blocking formation of specific contacts. Intriguingly, the number of transitions between the different conformers of the WNV frameshift signal was maximal in the range of forces applied by the ribosome during -1 PRF. Furthermore, the occupancy of the pseudoknotted conformations was far too low for static pseudoknots to account for the high levels of -1 PRF. These results support the hypothesis that conformational heterogeneity plays a key role in frameshifting and suggest that transitions between different conformers under tension are linked to efficient PRF stimulation.
Collapse
|
44
|
Lyon K, Aguilera LU, Morisaki T, Munsky B, Stasevich TJ. Live-Cell Single RNA Imaging Reveals Bursts of Translational Frameshifting. Mol Cell 2019; 75:172-183.e9. [PMID: 31178355 DOI: 10.1016/j.molcel.2019.05.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/14/2019] [Accepted: 04/30/2019] [Indexed: 11/25/2022]
Abstract
Ribosomal frameshifting during the translation of RNA is implicated in human disease and viral infection. While previous work has uncovered many details about single RNA frameshifting kinetics in vitro, little is known about how single RNA frameshift in living systems. To confront this problem, we have developed technology to quantify live-cell single RNA translation dynamics in frameshifted open reading frames. Applying this technology to RNA encoding the HIV-1 frameshift sequence reveals a small subset (∼8%) of the translating pool robustly frameshift. Frameshifting RNA are translated at similar rates as non-frameshifting RNA (∼3 aa/s) and can continuously frameshift for more than four rounds of translation. Fits to a bursty model of frameshifting constrain frameshifting kinetic rates and demonstrate how ribosomal traffic jams contribute to the persistence of the frameshifting state. These data provide insight into retroviral frameshifting and could lead to alternative strategies to perturb the process in living cells.
Collapse
Affiliation(s)
- Kenneth Lyon
- Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA
| | - Luis U Aguilera
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian Munsky
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA; World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan.
| |
Collapse
|
45
|
Rangadurai A, Szymaski ES, Kimsey IJ, Shi H, Al-Hashimi HM. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R 1ρ relaxation dispersion. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 112-113:55-102. [PMID: 31481159 PMCID: PMC6727989 DOI: 10.1016/j.pnmrs.2019.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 05/10/2023]
Abstract
This review describes off-resonance R1ρ relaxation dispersion NMR methods for characterizing microsecond-to-millisecond chemical exchange in uniformly 13C/15N labeled nucleic acids in solution. The review opens with a historical account of key developments that formed the basis for modern R1ρ techniques used to study chemical exchange in biomolecules. A vector model is then used to describe the R1ρ relaxation dispersion experiment, and how the exchange contribution to relaxation varies with the amplitude and frequency offset of an applied spin-locking field, as well as the population, exchange rate, and differences in chemical shifts of two exchanging species. Mathematical treatment of chemical exchange based on the Bloch-McConnell equations is then presented and used to examine relaxation dispersion profiles for more complex exchange scenarios including three-state exchange. Pulse sequences that employ selective Hartmann-Hahn cross-polarization transfers to excite individual 13C or 15N spins are then described for measuring off-resonance R1ρ(13C) and R1ρ(15N) in uniformly 13C/15N labeled DNA and RNA samples prepared using commercially available 13C/15N labeled nucleotide triphosphates. Approaches for analyzing R1ρ data measured at a single static magnetic field to extract a full set of exchange parameters are then presented that rely on numerical integration of the Bloch-McConnell equations or the use of algebraic expressions. Methods for determining structures of nucleic acid excited states are then reviewed that rely on mutations and chemical modifications to bias conformational equilibria, as well as structure-based approaches to calculate chemical shifts. Applications of the methodology to the study of DNA and RNA conformational dynamics are reviewed and the biological significance of the exchange processes is briefly discussed.
Collapse
Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eric S Szymaski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Nymirum, 4324 S. Alston Avenue, Durham, NC 27713, USA(1)
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Department of Chemistry, Duke University, Durham, NC 27710, USA.
| |
Collapse
|
46
|
Zhang H, Keane SC. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1541. [PMID: 31025514 PMCID: PMC7169810 DOI: 10.1002/wrna.1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high-resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
47
|
Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM. QRNAS: software tool for refinement of nucleic acid structures. BMC STRUCTURAL BIOLOGY 2019; 19:5. [PMID: 30898165 PMCID: PMC6429776 DOI: 10.1186/s12900-019-0103-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/05/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Computational models of RNA 3D structure often present various inaccuracies caused by simplifications used in structure prediction methods, such as template-based modeling or coarse-grained simulations. To obtain a high-quality model, the preliminary RNA structural model needs to be refined, taking into account atomic interactions. The goal of the refinement is not only to improve the local quality of the model but to bring it globally closer to the true structure. RESULTS We present QRNAS, a software tool for fine-grained refinement of nucleic acid structures, which is an extension of the AMBER simulation method with additional restraints. QRNAS is capable of handling RNA, DNA, chimeras, and hybrids thereof, and enables modeling of nucleic acids containing modified residues. CONCLUSIONS We demonstrate the ability of QRNAS to improve the quality of models generated with different methods. QRNAS was able to improve MolProbity scores of NMR structures, as well as of computational models generated in the course of the RNA-Puzzles experiment. The overall geometry improvement may be associated with increased model accuracy, especially on the level of correctly modeled base-pairs, but the systematic improvement of root mean square deviation to the reference structure should not be expected. The method has been integrated into a computational modeling workflow, enabling improved RNA 3D structure prediction.
Collapse
Affiliation(s)
- Juliusz Stasiewicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| |
Collapse
|
48
|
Anzalone AV, Zairis S, Lin AJ, Rabadan R, Cornish VW. Interrogation of Eukaryotic Stop Codon Readthrough Signals by in Vitro RNA Selection. Biochemistry 2019; 58:1167-1178. [PMID: 30698415 DOI: 10.1021/acs.biochem.8b01280] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RNA signals located downstream of stop codons in eukaryotic mRNAs can stimulate high levels of translational readthrough by the ribosome, thereby giving rise to functionally distinct C-terminally extended protein products. Although many readthrough events have been previously discovered in Nature, a broader description of the stimulatory RNA signals would help to identify new reprogramming events in eukaryotic genes and provide insights into the molecular mechanisms of readthrough. Here, we explore the RNA reprogramming landscape by performing in vitro translation selections to enrich RNA readthrough signals de novo from a starting randomized library comprising >1013 unique sequence variants. Selection products were characterized using high-throughput sequencing, from which we identified primary sequence and secondary structure readthrough features. The activities of readthrough signals, including three novel sequence motifs, were confirmed in cellular reporter assays. Then, we used machine learning and our HTS data to predict readthrough activity from human 3'-untranslated region sequences. This led to the discovery of >1.5% readthrough in four human genes (CDKN2B, LEPROTL1, PVRL3, and SFTA2). Together, our results provide valuable insights into RNA-mediated translation reprogramming, offer tools for readthrough discovery in eukaryotic genes, and present new opportunities to explore the biological consequences of stop codon readthrough in humans.
Collapse
Affiliation(s)
- Andrew V Anzalone
- Department of Chemistry , Columbia University , New York , New York 10027 , United States
| | - Sakellarios Zairis
- Department of Systems Biology , Columbia University , New York , New York 10032 , United States
| | - Annie J Lin
- Department of Chemistry , Columbia University , New York , New York 10027 , United States.,Department of Systems Biology , Columbia University , New York , New York 10032 , United States
| | - Raul Rabadan
- Department of Systems Biology , Columbia University , New York , New York 10032 , United States
| | - Virginia W Cornish
- Department of Chemistry , Columbia University , New York , New York 10027 , United States.,Department of Systems Biology , Columbia University , New York , New York 10032 , United States
| |
Collapse
|
49
|
Keller H, Weickhmann AK, Bock T, Wöhnert J. Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches. RNA (NEW YORK, N.Y.) 2018; 24:1390-1402. [PMID: 30006500 PMCID: PMC6140456 DOI: 10.1261/rna.067470.118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/09/2018] [Indexed: 05/22/2023]
Abstract
In certain structural or functional contexts, RNA structures can contain protonated nucleotides. However, a direct role for stably protonated nucleotides in ligand binding and ligand recognition has not yet been demonstrated unambiguously. Previous X-ray structures of c-GAMP binding riboswitch aptamer domains in complex with their near-cognate ligand c-di-GMP suggest that an adenine of the riboswitch either forms two hydrogen bonds to a G nucleotide of the ligand in the unusual enol tautomeric form or that the adenine in its N1 protonated form binds the G nucleotide of the ligand in its canonical keto tautomeric state. By using NMR spectroscopy we demonstrate that the c-GAMP riboswitches bind c-di-GMP using a stably protonated adenine in the ligand binding pocket. Thereby, we provide novel insights into the putative biological functions of protonated nucleotides in RNA, which in this case influence the ligand selectivity in a riboswitch.
Collapse
Affiliation(s)
- Heiko Keller
- Institute for Molecular Biosciences and Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - A Katharina Weickhmann
- Institute for Molecular Biosciences and Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Thomas Bock
- Institute for Molecular Biosciences and Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences and Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| |
Collapse
|
50
|
Hellen CUT. Translation Termination and Ribosome Recycling in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a032656. [PMID: 29735640 DOI: 10.1101/cshperspect.a032656] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Termination of mRNA translation occurs when a stop codon enters the A site of the ribosome, and in eukaryotes is mediated by release factors eRF1 and eRF3, which form a ternary eRF1/eRF3-guanosine triphosphate (GTP) complex. eRF1 recognizes the stop codon, and after hydrolysis of GTP by eRF3, mediates release of the nascent peptide. The post-termination complex is then disassembled, enabling its constituents to participate in further rounds of translation. Ribosome recycling involves splitting of the 80S ribosome by the ATP-binding cassette protein ABCE1 to release the 60S subunit. Subsequent dissociation of deacylated transfer RNA (tRNA) and messenger RNA (mRNA) from the 40S subunit may be mediated by initiation factors (priming the 40S subunit for initiation), by ligatin (eIF2D) or by density-regulated protein (DENR) and multiple copies in T-cell lymphoma-1 (MCT1). These events may be subverted by suppression of termination (yielding carboxy-terminally extended read-through polypeptides) or by interruption of recycling, leading to reinitiation of translation near the stop codon.
Collapse
Affiliation(s)
- Christopher U T Hellen
- Department of Cell Biology, State University of New York, Downstate Medical Center, New York, New York 11203
| |
Collapse
|