1
|
de Alwis R, Gan ES, Chen S, Leong YS, Tan HC, Zhang SL, Yau C, Low JGH, Kalimuddin S, Matsuda D, Allen EC, Hartman P, Park KJJ, Alayyoubi M, Bhaskaran H, Dukanovic A, Bao Y, Clemente B, Vega J, Roberts S, Gonzalez JA, Sablad M, Yelin R, Taylor W, Tachikawa K, Parker S, Karmali P, Davis J, Sullivan BM, Sullivan SM, Hughes SG, Chivukula P, Ooi EE. A single dose of self-transcribing and replicating RNA-based SARS-CoV-2 vaccine produces protective adaptive immunity in mice. Mol Ther 2021; 29:1970-1983. [PMID: 33823303 PMCID: PMC8019652 DOI: 10.1016/j.ymthe.2021.04.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Abstract
A self-transcribing and replicating RNA (STARR)-based vaccine (LUNAR-COV19) has been developed to prevent SARS-CoV-2 infection. The vaccine encodes an alphavirus-based replicon and the SARS-CoV-2 full-length spike glycoprotein. Translation of the replicon produces a replicase complex that amplifies and prolongs SARS-CoV-2 spike glycoprotein expression. A single prime vaccination in mice led to robust antibody responses, with neutralizing antibody titers increasing up to day 60. Activation of cell-mediated immunity produced a strong viral antigen-specific CD8+ T lymphocyte response. Assaying for intracellular cytokine staining for interferon (IFN)γ and interleukin-4 (IL-4)-positive CD4+ T helper (Th) lymphocytes as well as anti-spike glycoprotein immunoglobulin G (IgG)2a/IgG1 ratios supported a strong Th1-dominant immune response. Finally, single LUNAR-COV19 vaccination at both 2 μg and 10 μg doses completely protected human ACE2 transgenic mice from both mortality and even measurable infection following wild-type SARS-CoV-2 challenge. Our findings collectively suggest the potential of LUNAR-COV19 as a single-dose vaccine.
Collapse
MESH Headings
- Alphavirus/genetics
- Alphavirus/immunology
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Viral/biosynthesis
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/virology
- COVID-19/immunology
- COVID-19/pathology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/biosynthesis
- COVID-19 Vaccines/genetics
- COVID-19 Vaccines/immunology
- Female
- Gene Expression
- Humans
- Immunity, Cellular/drug effects
- Immunity, Humoral/drug effects
- Interferon-gamma/genetics
- Interferon-gamma/immunology
- Interleukin-4/genetics
- Interleukin-4/immunology
- Mice
- Mice, Transgenic
- Replicon/immunology
- SARS-CoV-2/drug effects
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Th1 Cells/drug effects
- Th1 Cells/immunology
- Th1 Cells/virology
- Transgenes
- Treatment Outcome
- Vaccination/methods
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/biosynthesis
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- mRNA Vaccines
Collapse
Affiliation(s)
- Ruklanthi de Alwis
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Esther S Gan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Shiwei Chen
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Yan Shan Leong
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore
| | - Hwee Cheng Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Summer L Zhang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Clement Yau
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jenny G H Low
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; Department of Infectious Disease, Singapore General Hospital, Singapore, Singapore
| | - Shirin Kalimuddin
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; Department of Infectious Disease, Singapore General Hospital, Singapore, Singapore
| | - Daiki Matsuda
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Elizabeth C Allen
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Paula Hartman
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | | | - Maher Alayyoubi
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Hari Bhaskaran
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Adrian Dukanovic
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Yanjie Bao
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Brenda Clemente
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Jerel Vega
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Scott Roberts
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Jose A Gonzalez
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Marciano Sablad
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Rodrigo Yelin
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Wendy Taylor
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Kiyoshi Tachikawa
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Suezanne Parker
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Priya Karmali
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Jared Davis
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Brian M Sullivan
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Sean M Sullivan
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA.
| | - Steve G Hughes
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Pad Chivukula
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Eng Eong Ooi
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| |
Collapse
|
2
|
Feldmann J, Youngblood N, Karpov M, Gehring H, Li X, Stappers M, Le Gallo M, Fu X, Lukashchuk A, Raja AS, Liu J, Wright CD, Sebastian A, Kippenberg TJ, Pernice WHP, Bhaskaran H. Publisher Correction: Parallel convolutional processing using an integrated photonic tensor core. Nature 2021; 591:E13. [PMID: 33623119 DOI: 10.1038/s41586-021-03216-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- J Feldmann
- Institute of Physics, University of Münster, Münster, Germany
| | - N Youngblood
- Department of Materials, University of Oxford, Oxford, UK.,Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Karpov
- Laboratory of Photonics and Quantum Measurements, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - H Gehring
- Institute of Physics, University of Münster, Münster, Germany
| | - X Li
- Department of Materials, University of Oxford, Oxford, UK
| | - M Stappers
- Institute of Physics, University of Münster, Münster, Germany
| | - M Le Gallo
- IBM Research Europe, Rüschlikon, Switzerland
| | - X Fu
- Laboratory of Photonics and Quantum Measurements, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - A Lukashchuk
- Laboratory of Photonics and Quantum Measurements, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - A S Raja
- Laboratory of Photonics and Quantum Measurements, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - J Liu
- Laboratory of Photonics and Quantum Measurements, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - C D Wright
- Department of Engineering, University of Exeter, Exeter, UK
| | - A Sebastian
- IBM Research Europe, Rüschlikon, Switzerland.
| | - T J Kippenberg
- Laboratory of Photonics and Quantum Measurements, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| | - W H P Pernice
- Institute of Physics, University of Münster, Münster, Germany. .,Center for Soft Nanoscience, University of Münster, Münster, Germany.
| | - H Bhaskaran
- Department of Materials, University of Oxford, Oxford, UK.
| |
Collapse
|
3
|
Feldmann J, Youngblood N, Wright CD, Bhaskaran H, Pernice WHP. All-optical spiking neurosynaptic networks with self-learning capabilities. Nature 2019; 569:208-214. [PMID: 31068721 PMCID: PMC6522354 DOI: 10.1038/s41586-019-1157-8] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 03/21/2019] [Indexed: 11/08/2022]
Abstract
Software implementations of brain-inspired computing underlie many important computational tasks, from image processing to speech recognition, artificial intelligence and deep learning applications. Yet, unlike real neural tissue, traditional computing architectures physically separate the core computing functions of memory and processing, making fast, efficient and low-energy computing difficult to achieve. To overcome such limitations, an attractive alternative is to design hardware that mimics neurons and synapses. Such hardware, when connected in networks or neuromorphic systems, processes information in a way more analogous to brains. Here we present an all-optical version of such a neurosynaptic system, capable of supervised and unsupervised learning. We exploit wavelength division multiplexing techniques to implement a scalable circuit architecture for photonic neural networks, successfully demonstrating pattern recognition directly in the optical domain. Such photonic neurosynaptic networks promise access to the high speed and high bandwidth inherent to optical systems, thus enabling the direct processing of optical telecommunication and visual data.
Collapse
Affiliation(s)
- J Feldmann
- Institute of Physics, University of Münster, Münster, Germany
| | - N Youngblood
- Department of Materials, University of Oxford, Oxford, UK
| | - C D Wright
- Department of Engineering, University of Exeter, Exeter, UK
| | - H Bhaskaran
- Department of Materials, University of Oxford, Oxford, UK
| | - W H P Pernice
- Institute of Physics, University of Münster, Münster, Germany.
| |
Collapse
|
4
|
Ghalei H, Trepreau J, Collins JC, Bhaskaran H, Strunk BS, Karbstein K. The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation. Mol Cell 2017; 68:1155. [PMID: 29272706 DOI: 10.1016/j.molcel.2017.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
5
|
Ghalei H, Trepreau J, Collins JC, Bhaskaran H, Strunk BS, Karbstein K. The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation. Mol Cell 2017; 67:990-1000.e3. [PMID: 28890337 PMCID: PMC6192259 DOI: 10.1016/j.molcel.2017.08.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 07/08/2017] [Accepted: 08/11/2017] [Indexed: 01/18/2023]
Abstract
Late in their maturation, nascent small (40S) ribosomal subunits bind 60S subunits to produce 80S-like ribosomes. Because of the analogy of this translation-like cycle to actual translation, and because 80S-like ribosomes do not produce any protein, it has been suggested that this represents a quality control mechanism for subunit functionality. Here we use genetic and biochemical experiments to show that the essential ATPase Fap7 promotes formation of the rotated state, a key intermediate in translocation, thereby releasing the essential assembly factor Dim1 from pre-40S subunits. Bypassing this quality control step produces defects in reading frame maintenance. These results show how progress in the maturation cascade is linked to a test for a key functionality of 40S ribosomes: their ability to translocate the mRNA⋅tRNA pair. Furthermore, our data demonstrate for the first time that the translation-like cycle is a quality control mechanism that ensures the fidelity of the cellular ribosome pool.
Collapse
Affiliation(s)
- Homa Ghalei
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Juliette Trepreau
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jason C Collins
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hari Bhaskaran
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Bethany S Strunk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA.
| |
Collapse
|
6
|
Abstract
![]()
Folding
dynamics are ubiquitously involved in controlling the multivariate
functions of RNAs. While the high thermodynamic stabilities of some
RNAs favor purely native states at equilibrium, it is unclear whether
weakly stable RNAs exist in random, partially folded states or sample
well-defined, globally folded conformations. Using a folding assay
that precisely tracks the formation of native aminoacylable tRNA,
we show that the folding of a weakly stable human mitochondrial (hmt)
leucine tRNA is hierarchical with a distinct kinetic folding intermediate.
The stabilities of the native and intermediate conformers are separated
by only about 1.2 kcal/mol, and the species are readily interconvertible.
Comparison of folding dynamics between unmodified and fully modified
tRNAs reveals that post-transcriptional modifications produce a more
constrained native structure that does not sample intermediate conformations.
These structural dynamics may thus be crucial for recognition by some
modifying enzymes in vivo, especially those targeting
the globular core region, by allowing access to pretransition state
conformers. Reduced conformational sampling of the native, modified
tRNAs could then permit improved performance in downstream processes
of translation. More generally, weak stabilities of small RNAs that
fold in the absence of chaperone proteins may facilitate conformational
switching that is central to biological function.
Collapse
Affiliation(s)
- Hari Bhaskaran
- Department of Chemistry, Portland State University , 1825 SW Broadway, Portland Oregon 97209, United States
| | | | | | | | | |
Collapse
|
7
|
Bhaskaran H, Rodriguez-Hernandez A, Perona JJ. Kinetics of tRNA Folding Monitored by Aminoacylation. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.945.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
8
|
Abstract
We describe a strategy for tracking Mg²⁺-initiated folding of ³²P-labeled tRNA molecules to their native structures based on the capacity for aminoacylation by the cognate aminoacyl-tRNA synthetase enzyme. The approach directly links folding to function, paralleling a common strategy used to study the folding of catalytic RNAs. Incubation of unfolded tRNA with magnesium ions, followed by the addition of aminoacyl-tRNA synthetase and further incubation, yields a rapid burst of aminoacyl-tRNA formation corresponding to the prefolded tRNA fraction. A subsequent slower increase in product formation monitors continued folding in the presence of the enzyme. Further analysis reveals the presence of a parallel fraction of tRNA that folds more rapidly than the majority of the population. The application of the approach to study the influence of post-transcriptional modifications in folding of Escherichia coli tRNA₁(Gln) reveals that the modified bases increase the folding rate but do not affect either the equilibrium between properly folded and misfolded states or the folding pathway. This assay allows the use of ³²P-labeled tRNA in integrated studies combining folding, post-transcriptional processing, and aminoacylation reactions.
Collapse
Affiliation(s)
| | | | - John J. Perona
- Department of Chemistry and Biochemistry
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
- Corresponding author.E-mail .
| |
Collapse
|
9
|
Bhaskaran H, Perona JJ. Erratum to “Two-Step Aminoacylation of tRNA without Channeling in Archaea” [J. Mol. Biol. 411/4 (2011) 854–869]. J Mol Biol 2011. [DOI: 10.1016/j.jmb.2011.08.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
10
|
Bhaskaran H, Perona JJ. Two-step aminoacylation of tRNA without channeling in Archaea. J Mol Biol 2011; 411:854-69. [PMID: 21726564 DOI: 10.1016/j.jmb.2011.06.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 06/21/2011] [Accepted: 06/22/2011] [Indexed: 10/18/2022]
Abstract
Catalysis of sequential reactions is often envisaged to occur by channeling of substrate between enzyme active sites without release into bulk solvent. However, while there are compelling physiological rationales for direct substrate transfer, proper experimental support for the hypothesis is often lacking, particularly for metabolic pathways involving RNA. Here, we apply transient kinetics approaches developed to study channeling in bienzyme complexes to an archaeal protein synthesis pathway featuring the misaminoacylated tRNA intermediate Glu-tRNA(Gln). Experimental and computational elucidation of a kinetic and thermodynamic framework for two-step cognate Gln-tRNA(Gln) synthesis demonstrates that the misacylating aminoacyl-tRNA synthetase (GluRS(ND)) and the tRNA-dependent amidotransferase (GatDE) function sequentially without channeling. Instead, rapid processing of the misacylated tRNA intermediate by GatDE and preferential elongation factor binding to the cognate Gln-tRNA(Gln) together permit accurate protein synthesis without formation of a binary protein-protein complex between GluRS(ND) and GatDE. These findings establish an alternate paradigm for protein quality control via two-step pathways for cognate aminoacyl-tRNA formation.
Collapse
Affiliation(s)
- Hari Bhaskaran
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | | |
Collapse
|
11
|
Rodríguez-Hernández A, Bhaskaran H, Hadd A, Perona JJ. Synthesis of Glu-tRNA(Gln) by engineered and natural aminoacyl-tRNA synthetases. Biochemistry 2010; 49:6727-36. [PMID: 20617848 DOI: 10.1021/bi100886z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A protein engineering approach to delineating which distinct elements of homologous tRNA synthetase architectures are responsible for divergent RNA-amino acid pairing specificities is described. Previously, we constructed a hybrid enzyme in which 23 amino acids from the catalytic domain of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) were replaced with the corresponding residues of human glutamyl-tRNA synthetase (GluRS). The engineered hybrid (GlnRS S1/L1/L2) synthesizes Glu-tRNA(Gln) more than 10(4)-fold more efficiently than GlnRS. Detailed comparison of kinetic parameters between GlnRS S1/L1/L2 and the naturally occurring Methanothermobacter thermautotrophicus GluRS(ND), which is also capable of Glu-tRNA(Gln) synthesis, now shows that both k(cat) and K(m) for glutamate are recapitulated in the engineered enzyme, but that K(m) for tRNA is 200-fold higher. Thus, the simultaneous optimization of paired amino acid and tRNA binding sites found in a naturally occurring enzyme is not recapitulated in a hybrid that is successfully engineered for amino acid complementarity. We infer that the GlnRS architecture has differentiated to match only cognate amino acid-RNA pairs, and that the substrate selection functions do not operate independently of each other. Design and characterization of four additional hybrids identify further residues involved in improving complementarity for glutamate and in communicating between amino acid and tRNA binding sites. The robust catalytic function demonstrated in this engineered system offers a novel platform for exploring the stereochemical origins of coding as a property of the ancient Rossmann fold.
Collapse
Affiliation(s)
- Annia Rodríguez-Hernández
- Department of Chemistry and Biochemistry and Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
| | | | | | | |
Collapse
|
12
|
Chadee AB, Bhaskaran H, Russell R. Protein roles in group I intron RNA folding: the tyrosyl-tRNA synthetase CYT-18 stabilizes the native state relative to a long-lived misfolded structure without compromising folding kinetics. J Mol Biol 2009; 395:656-70. [PMID: 19913030 DOI: 10.1016/j.jmb.2009.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Revised: 11/04/2009] [Accepted: 11/04/2009] [Indexed: 10/20/2022]
Abstract
The Neurospora crassa CYT-18 protein is a mitochondrial tyrosyl-tRNA synthetase that also promotes self-splicing of group I intron RNAs by stabilizing the functional structure in the conserved core. CYT-18 binds the core along the same surface as a common peripheral element, P5abc, suggesting that CYT-18 can replace P5abc functionally. In addition to stabilizing structure generally, P5abc stabilizes the native conformation of the Tetrahymena group I intron relative to a globally similar misfolded conformation that has only local differences within the core and is populated significantly at equilibrium by a ribozyme variant lacking P5abc (E(DeltaP5abc)). Here, we show that CYT-18 specifically promotes formation of the native group I intron core from this misfolded conformation. Catalytic activity assays demonstrate that CYT-18 shifts the equilibrium of E(DeltaP5abc) toward the native state by at least 35-fold, and binding assays suggest an even larger effect. Thus, similar to P5abc, CYT-18 preferentially recognizes the native core, despite the global similarity of the misfolded core and despite forming crudely similar complexes, as revealed by dimethyl sulfate footprinting. Interestingly, the effects of CYT-18 and P5abc on folding kinetics differ. Whereas P5abc inhibits refolding of the misfolded conformation by forming peripheral contacts that must break during refolding, CYT-18 does not display analogous inhibition, most likely because it relies to a greater extent on direct interactions with the core. Although CYT-18 does not encounter this RNA in vivo, our results suggest that it stabilizes its cognate group I introns relative to analogous misfolded intermediates. By specifically recognizing native structural features, CYT-18 may also interact with earlier folding intermediates to avoid RNA misfolding or to trap native contacts as they form. More generally, our results highlight the ability of a protein cofactor to stabilize a functional RNA structure specifically without incurring associated costs in RNA folding kinetics.
Collapse
Affiliation(s)
- Amanda B Chadee
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX 78712, USA
| | | | | |
Collapse
|
13
|
Del Campo M, Tijerina P, Bhaskaran H, Mohr S, Yang Q, Jankowsky E, Russell R, Lambowitz AM. Do DEAD-box proteins promote group II intron splicing without unwinding RNA? Mol Cell 2008; 28:159-66. [PMID: 17936712 DOI: 10.1016/j.molcel.2007.07.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 07/12/2007] [Accepted: 07/26/2007] [Indexed: 11/16/2022]
Abstract
The DEAD-box protein Mss116p promotes group II intron splicing in vivo and in vitro. Here we explore two hypotheses for how Mss116p promotes group II intron splicing: by using its RNA unwinding activity to act as an RNA chaperone or by stabilizing RNA folding intermediates. We show that an Mss116p mutant in helicase motif III (SAT/AAA), which was reported to stimulate splicing without unwinding RNA, retains ATP-dependent unwinding activity and promotes unfolding of a structured RNA. Its unwinding activity increases sharply with decreasing duplex length and correlates with group II intron splicing activity in quantitative assays. Additionally, we show that Mss116p can promote ATP-independent RNA unwinding, presumably via single-strand capture, also potentially contributing to DEAD-box protein RNA chaperone activity. Our findings favor the hypothesis that DEAD-box proteins function in group II intron splicing as in other processes by using their unwinding activity to act as RNA chaperones.
Collapse
Affiliation(s)
- Mark Del Campo
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Bhaskaran H, Russell R. Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone. Nature 2007; 449:1014-8. [PMID: 17960235 DOI: 10.1038/nature06235] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 09/11/2007] [Indexed: 11/09/2022]
Abstract
DExD/H-box proteins are ubiquitously involved in RNA-mediated processes and use ATP to accelerate conformational changes in RNA. However, their mechanisms of action, and what determines which RNA species are targeted, are not well understood. Here we show that the DExD/H-box protein CYT-19, a general RNA chaperone, mediates ATP-dependent unfolding of both the native conformation and a long-lived misfolded conformation of a group I catalytic RNA with efficiencies that depend on the stabilities of the RNA species but not on specific structural features. CYT-19 then allows the RNA to refold, changing the distribution from equilibrium to kinetic control. Because misfolding is favoured kinetically, conditions that allow unfolding of the native RNA yield large increases in the population of misfolded species. Our results suggest that DExD/H-box proteins act with sufficient breadth and efficiency to allow structured RNAs to populate a wider range of conformations than would be present at equilibrium. Thus, RNAs may face selective pressure to stabilize their active conformations relative to inactive ones to avoid significant redistribution by DExD/H-box proteins. Conversely, RNAs whose functions depend on forming multiple conformations may rely on DExD/H-box proteins to increase the populations of less stable conformations, thereby increasing their overall efficiencies.
Collapse
Affiliation(s)
- Hari Bhaskaran
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | | |
Collapse
|
15
|
Russell R, Tijerina P, Chadee AB, Bhaskaran H. Deletion of the P5abc peripheral element accelerates early and late folding steps of the Tetrahymena group I ribozyme. Biochemistry 2007; 46:4951-61. [PMID: 17419589 PMCID: PMC2582984 DOI: 10.1021/bi0620149] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The P5abc peripheral element stabilizes the Tetrahymena group I ribozyme and enhances its catalytic activity. Despite its beneficial effects on the native structure, prior studies have shown that early formation of P5abc structure during folding can slow later folding steps. Here we use a P5abc deletion variant E(deltaP5abc) to systematically probe the role of P5abc throughout tertiary folding. Time-resolved hydroxyl radical footprinting shows that E(deltaP5abc) forms its earliest stable tertiary structure on the millisecond time scale, approximately 5-fold faster than the wild-type ribozyme, and stable structure spreads throughout E(deltaP5abc) in seconds. Nevertheless, activity measurements show that the earliest detectable formation of native E(deltaP5abc) ribozyme is much slower (approximately 0.6 min(-1)), in a manner similar to that of the wild type. Also similar, only a small fraction of E(deltaP5abc) attains the native state on this time scale under standard conditions at 25 degrees C, whereas the remainder misfolds; footprinting experiments show that the misfolded conformer shares structural features with the long-lived misfolded conformer of the wild-type ribozyme. Thus, P5abc does not have a large overall effect on the rate-limiting step(s) along this pathway. However, once misfolded, E(deltaP5abc) refolds to the native state 80-fold faster than the wild-type ribozyme and is less accelerated by urea, indicating that P5abc stabilizes the misfolded structure relative to the less-ordered transition state for refolding. Together, the results suggest that, under these conditions, even the earliest tertiary folding intermediates of the wild-type ribozyme represent misfolded species and that P5abc is principally a liability during the tertiary folding process.
Collapse
Affiliation(s)
- Rick Russell
- Department of Chemistry and Biochemistry and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
| | | | | | | |
Collapse
|
16
|
Grohman JK, Campo MD, Bhaskaran H, Tijerina P, Lambowitz AM, Russell R. Probing the mechanisms of DEAD-box proteins as general RNA chaperones: the C-terminal domain of CYT-19 mediates general recognition of RNA. Biochemistry 2007; 46:3013-22. [PMID: 17311413 PMCID: PMC2271177 DOI: 10.1021/bi0619472] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The DEAD-box protein CYT-19 functions in the folding of several group I introns in vivo and a diverse set of group I and group II RNAs in vitro. Recent work using the Tetrahymena group I ribozyme demonstrated that CYT-19 possesses a second RNA-binding site, distinct from the unwinding active site, which enhances unwinding activity by binding nonspecifically to the adjacent RNA structure. Here, we probe the region of CYT-19 responsible for that binding by constructing a C-terminal truncation variant that lacks 49 amino acids and terminates at a domain boundary, as defined by limited proteolysis. This truncated protein unwinds a six-base-pair duplex, formed between the oligonucleotide substrate of the Tetrahymena ribozyme and an oligonucleotide corresponding to the internal guide sequence of the ribozyme, with near-wild-type efficiency. However, the truncated protein is activated much less than the wild-type protein when the duplex is covalently linked to the ribozyme or single-stranded or double-stranded extensions. Thus, the active site for RNA unwinding remains functional in the truncated CYT-19, but the site that binds the adjacent RNA structure has been compromised. Equilibrium binding experiments confirmed that the truncated protein binds RNA less tightly than the wild-type protein. RNA binding by the compromised site is important for chaperone activity, because the truncated protein is less active in facilitating the folding of a group I intron that requires CYT-19 in vivo. The deleted region contains arginine-rich sequences, as found in other RNA-binding proteins, and may function by tethering CYT-19 to structured RNAs, so that it can efficiently disrupt exposed, non-native structural elements, allowing them to refold. Many other DExD/H-box proteins also contain arginine-rich ancillary domains, and some of these domains may function similarly as nonspecific RNA-binding elements that enhance general RNA chaperone activity.
Collapse
Affiliation(s)
| | | | | | | | | | - Rick Russell
- *To whom correspondence should be addressed. Tel: 512-471-1514; Fax: 512-232-3432; E-mail:
| |
Collapse
|
17
|
Tijerina P, Bhaskaran H, Russell R. Nonspecific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone. Proc Natl Acad Sci U S A 2006; 103:16698-703. [PMID: 17075070 PMCID: PMC1636518 DOI: 10.1073/pnas.0603127103] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We explore the interactions of CYT-19, a DExD/H-box protein that functions in folding of group I RNAs, with a well characterized misfolded species of the Tetrahymena ribozyme. Consistent with its function, CYT-19 accelerates refolding of the misfolded RNA to its native state. Unexpectedly, CYT-19 performs another reaction much more efficiently; it unwinds the 6-bp P1 duplex formed between the ribozyme and its oligonucleotide substrate. Furthermore, CYT-19 performs this reaction 50-fold more efficiently than it unwinds the same duplex free in solution, suggesting that it forms additional interactions with the ribozyme, most likely using a distinct RNA binding site from the one responsible for unwinding. This site can apparently bind double-stranded RNA, as attachment of a simple duplex adjacent to P1 recapitulates much of the activation provided by the ribozyme. Unwinding the native P1 duplex does not accelerate refolding of the misfolded ribozyme, implying that CYT-19 can disrupt multiple contacts on the RNA, consistent with its function in folding of multiple RNAs. Further experiments showed that the P1 duplex unwinding activity is virtually the same whether the ribozyme is misfolded or native but is abrogated by formation of tertiary contacts between the P1 duplex and the body of the ribozyme. Together these results suggest a mechanism for CYT-19 and other general DExD/H-box RNA chaperones in which the proteins bind to structured RNAs and efficiently unwind loosely associated duplexes, which biases the proteins to disrupt nonnative base pairs and gives the liberated strands an opportunity to refold.
Collapse
Affiliation(s)
- Pilar Tijerina
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712
| | - Hari Bhaskaran
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712
| | - Rick Russell
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|