1
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Andronov L, Han M, Zhu Y, Balaji A, Roy AR, Barentine AES, Patel P, Garhyan J, Qi LS, Moerner WE. Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. Nat Commun 2024; 15:4644. [PMID: 38821943 PMCID: PMC11143195 DOI: 10.1038/s41467-024-48991-x] [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: 11/21/2023] [Accepted: 05/13/2024] [Indexed: 06/02/2024] Open
Abstract
The SARS-CoV-2 viral infection transforms host cells and produces special organelles in many ways, and we focus on the replication organelles, the sites of replication of viral genomic RNA (vgRNA). To date, the precise cellular localization of key RNA molecules and replication intermediates has been elusive in electron microscopy studies. We use super-resolution fluorescence microscopy and specific labeling to reveal the nanoscopic organization of replication organelles that contain numerous vgRNA molecules along with the replication enzymes and clusters of viral double-stranded RNA (dsRNA). We show that the replication organelles are organized differently at early and late stages of infection. Surprisingly, vgRNA accumulates into distinct globular clusters in the cytoplasmic perinuclear region, which grow and accommodate more vgRNA molecules as infection time increases. The localization of endoplasmic reticulum (ER) markers and nsp3 (a component of the double-membrane vesicle, DMV) at the periphery of the vgRNA clusters suggests that replication organelles are encapsulated into DMVs, which have membranes derived from the host ER. These organelles merge into larger vesicle packets as infection advances. Precise co-imaging of the nanoscale cellular organization of vgRNA, dsRNA, and viral proteins in replication organelles of SARS-CoV-2 may inform therapeutic approaches that target viral replication and associated processes.
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Affiliation(s)
- Leonid Andronov
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Mengting Han
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Yanyu Zhu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Ashwin Balaji
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Biophysics PhD Program; Stanford University, Stanford, CA, 94305, USA
| | - Anish R Roy
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | | | - Puja Patel
- In Vitro Biosafety Level 3 (BSL-3) Service Center, School of Medicine; Stanford University, Stanford, CA, 94305, USA
| | - Jaishree Garhyan
- In Vitro Biosafety Level 3 (BSL-3) Service Center, School of Medicine; Stanford University, Stanford, CA, 94305, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- Sarafan ChEM-H; Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, 94158, USA.
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
- Sarafan ChEM-H; Stanford University, Stanford, CA, 94305, USA.
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2
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Paul S, Arias MA, Wen L, Liao SE, Zhang J, Wang X, Regev O, Fei J. RNA molecules display distinctive organization at nuclear speckles. iScience 2024; 27:109603. [PMID: 38638569 PMCID: PMC11024929 DOI: 10.1016/j.isci.2024.109603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/05/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
RNA molecules often play critical roles in assisting the formation of membraneless organelles in eukaryotic cells. Yet, little is known about the organization of RNAs within membraneless organelles. Here, using super-resolution imaging and nuclear speckles as a model system, we demonstrate that different sequence domains of RNA transcripts exhibit differential spatial distributions within speckles. Specifically, we image transcripts containing a region enriched in binding motifs of serine/arginine-rich (SR) proteins and another region enriched in binding motifs of heterogeneous nuclear ribonucleoproteins (hnRNPs). We show that these transcripts localize to the outer shell of speckles, with the SR motif-rich region localizing closer to the speckle center relative to the hnRNP motif-rich region. Further, we identify that this intra-speckle RNA organization is driven by the strength of RNA-protein interactions inside and outside speckles. Our results hint at novel functional roles of nuclear speckles and likely other membraneless organelles in organizing RNA substrates for biochemical reactions.
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Affiliation(s)
- Sneha Paul
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Mauricio A. Arias
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
- Institute for System Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Li Wen
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA
| | - Susan E. Liao
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Jiacheng Zhang
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaoshu Wang
- The College, The University of Chicago, Chicago, IL 60637, USA
| | - Oded Regev
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
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3
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Andronov L, Han M, Zhu Y, Balaji A, Roy AR, Barentine AES, Patel P, Garhyan J, Qi LS, Moerner W. Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.07.566110. [PMID: 37986994 PMCID: PMC10659379 DOI: 10.1101/2023.11.07.566110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The SARS-CoV-2 viral infection transforms host cells and produces special organelles in many ways, and we focus on the replication organelle where the replication of viral genomic RNA (vgRNA) occurs. To date, the precise cellular localization of key RNA molecules and replication intermediates has been elusive in electron microscopy studies. We use super-resolution fluorescence microscopy and specific labeling to reveal the nanoscopic organization of replication organelles that contain vgRNA clusters along with viral double-stranded RNA (dsRNA) clusters and the replication enzyme, encapsulated by membranes derived from the host endoplasmic reticulum (ER). We show that the replication organelles are organized differently at early and late stages of infection. Surprisingly, vgRNA accumulates into distinct globular clusters in the cytoplasmic perinuclear region, which grow and accommodate more vgRNA molecules as infection time increases. The localization of ER labels and nsp3 (a component of the double-membrane vesicle, DMV) at the periphery of the vgRNA clusters suggests that replication organelles are enclosed by DMVs at early infection stages which then merge into vesicle packets as infection progresses. Precise co-imaging of the nanoscale cellular organization of vgRNA, dsRNA, and viral proteins in replication organelles of SARS-CoV-2 may inform therapeutic approaches that target viral replication and associated processes.
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Affiliation(s)
- Leonid Andronov
- Department of Chemistry; Stanford University, Stanford, CA 94305 U.S.A
| | - Mengting Han
- Department of Bioengineering; Stanford University, Stanford, CA 94305 U.S.A
| | - Yanyu Zhu
- Department of Bioengineering; Stanford University, Stanford, CA 94305 U.S.A
| | - Ashwin Balaji
- Department of Chemistry; Stanford University, Stanford, CA 94305 U.S.A
- Biophysics PhD Program; Stanford University, Stanford, CA 94305 U.S.A
| | - Anish R. Roy
- Department of Chemistry; Stanford University, Stanford, CA 94305 U.S.A
| | | | - Puja Patel
- In Vitro Biosafety Level 3 (BSL-3) Service Center, School of Medicine; Stanford University, Stanford, CA 94305 U.S.A
| | - Jaishree Garhyan
- In Vitro Biosafety Level 3 (BSL-3) Service Center, School of Medicine; Stanford University, Stanford, CA 94305 U.S.A
| | - Lei S. Qi
- Department of Bioengineering; Stanford University, Stanford, CA 94305 U.S.A
- Sarafan ChEM-H; Stanford University, Stanford, CA 94305 U.S.A
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA 94158 U.S.A
| | - W.E. Moerner
- Department of Chemistry; Stanford University, Stanford, CA 94305 U.S.A
- Sarafan ChEM-H; Stanford University, Stanford, CA 94305 U.S.A
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4
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Hlushko R, Pozharski E, Prabhu VM, Andrianov AK. Directly visualizing individual polyorganophosphazenes and their single-chain complexes with proteins. COMMUNICATIONS MATERIALS 2024; 5:36. [PMID: 38817739 PMCID: PMC11139433 DOI: 10.1038/s43246-024-00476-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/07/2024] [Indexed: 06/01/2024]
Abstract
Polyorganophosphazenes are water-soluble macromolecules with immunoadjuvant activity that self-assemble with proteins to enable biological functionality. Direct imaging by cryogenic electron microscopy uncovers the coil structure of those highly charged macromolecules. The successful visualization of individual polymer chains within the vitrified state is achieved in the absence of additives for contrast enhancement and is attributed to the high mass contrast of the inorganic backbone. Upon assembly with proteins, multiple protein copies bind at the single polymer chain level resulting in structures reminiscent of compact spherical complexes or stiffened coils. The outcome depends on protein characteristics and cannot be deduced by commonly used characterization techniques, such as light scattering, thus revealing direct morphological insights crucial for understanding biological activity. Atomic force microscopy supports the morphology outcomes while advanced analytical techniques confirm protein-polymer binding. The chain visualization methodology provides tools for gaining insights into the processes of supramolecular assembly and mechanistic aspects of polymer enabled vaccine delivery.
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Affiliation(s)
- Raman Hlushko
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States of America
| | - Edwin Pozharski
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States of America
| | - Vivek M. Prabhu
- Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology‡, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States of America
| | - Alexander K. Andrianov
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States of America
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5
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Andrianov A, Hlushko R, Pozharski E, Prabhu V. Cryo-EM and AFM visualize linear polyorganophosphazene: individual chains and single-chain assemblies with proteins. RESEARCH SQUARE 2023:rs.3.rs-3411603. [PMID: 37961436 PMCID: PMC10635375 DOI: 10.21203/rs.3.rs-3411603/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Polyorganophosphazenes are biodegradable macromolecules with potent immunoadjuvant activity that self-assemble with protein antigens to provide biological activity. Direct imaging by cryogenic electron microscopy reveals the coil structure of the highly-charged high molecular mass synthetic polyorganophosphazenes within the vitrified state without any additives for contrast enhancement for the first time. Upon mixing with protein antigens under a controlled stoichiometric ratio, multiple proteins bind at the single chain level revealing a structural change reminiscent of compact spherical complexes or stiffened coils depending on the bound protein antigen. The structural outcome depends on the protein charge density that cannot be deduced by methods, such as dynamic light scattering, thus revealing direct morphological insight necessary to understand in vivo biological activity. Complementary atomic force microscopy supports the binding morphology outcomes as well as additional analytical techniques that indicate binding. These observations open opportunities to understand supramolecular assembly of proteins and other biomacromolecules at the single chain level with highly charged polyelectrolytes for vaccines as well as important to developing fields such as polyelectrolyte complex coacervation.
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6
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Henderson AN, McDonnell RT, Elcock AH. Modeling the 3D structure and conformational dynamics of very large RNAs using coarse-grained molecular simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543892. [PMID: 37333149 PMCID: PMC10274748 DOI: 10.1101/2023.06.06.543892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
We describe a computational approach to building and simulating realistic 3D models of very large RNA molecules (>1000 nucleotides) at a resolution of one "bead" per nucleotide. The method starts with a predicted secondary structure and uses several stages of energy minimization and Brownian dynamics (BD) simulation to build 3D models. A key step in the protocol is the temporary addition of a 4 th spatial dimension that allows all predicted helical elements to become disentangled from each other in an effectively automated way. We then use the resulting 3D models as input to Brownian dynamics simulations that include hydrodynamic interactions (HIs) that allow the diffusive properties of the RNA to be modelled as well as enabling its conformational dynamics to be simulated. To validate the dynamics part of the method, we first show that when applied to small RNAs with known 3D structures the BD-HI simulation models accurately reproduce their experimental hydrodynamic radii (Rh). We then apply the modelling and simulation protocol to a variety of RNAs for which experimental Rh values have been reported ranging in size from 85 to 3569 nucleotides. We show that the 3D models, when used in BD-HI simulations, produce hydrodynamic radii that are usually in good agreement with experimental estimates for RNAs that do not contain tertiary contacts that persist even under very low salt conditions. Finally, we show that sampling of the conformational dynamics of large RNAs on timescales of 100 µs is computationally feasible with BD-HI simulations.
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7
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Chatterjee S, Shioi R, Kool ET. Sulfonylation of RNA 2'-OH groups. ACS CENTRAL SCIENCE 2023; 9:531-539. [PMID: 36968531 PMCID: PMC10037496 DOI: 10.1021/acscentsci.2c01237] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Indexed: 06/18/2023]
Abstract
The nucleophilic reactivity of RNA 2'-OH groups in water has proven broadly useful in probing, labeling, and conjugating RNA. To date, reactions selective to ribose 2'-OH have been limited to bond formation with short-lived carbonyl electrophiles. Here we report that many activated small-molecule sulfonyl species can exhibit extended lifetimes in water and retain 2'-OH reactivity. The data establish favorable aqueous solubility for selected reagents and successful RNA-selective reactions at stoichiometric and superstoichiometric yields, particularly for aryl sulfonyltriazole species. We report that the latter are considerably more stable than most prior carbon electrophiles in aqueous environments and tolerate silica chromatography. Furthermore, an azide-substituted sulfonyltriazole reagent is developed to introduce labels into RNA via click chemistry. In addition to high-yield reactions, we find that RNA sulfonylation can also be performed under conditions that give trace yields necessary for structure mapping. Like acylation, the reaction occurs with selectivity for unpaired nucleotides over those in the duplex structure, and a sulfonate adduct causes reverse transcriptase stops, suggesting potential use in RNA structure analysis. Probing of rRNA is demonstrated in human cells, indicating possible cell permeability. The sulfonyl reagent class enables a new level of control, selectivity, versatility, and ease of preparation for RNA applications.
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Affiliation(s)
- Sayantan Chatterjee
- Department of Chemistry, Stanford
University, Stanford, California 94305, United States
| | - Ryuta Shioi
- Department of Chemistry, Stanford
University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford
University, Stanford, California 94305, United States
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8
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Angert I, Karuka SR, Mansky LM, Mueller JD. Partitioning of ribonucleoprotein complexes from the cellular actin cortex. SCIENCE ADVANCES 2022; 8:eabj3236. [PMID: 35984883 PMCID: PMC9390997 DOI: 10.1126/sciadv.abj3236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The cell cortex plays a crucial role in cell mechanics, signaling, and development. However, little is known about the influence of the cortical meshwork on the spatial distribution of cytoplasmic biomolecules. Here, we describe a fluorescence microscopy method with the capacity to infer the intracellular distribution of labeled biomolecules with subresolution accuracy. Unexpectedly, we find that RNA binding proteins are partially excluded from the cytoplasmic volume adjacent to the plasma membrane that corresponds to the actin cortex. Complementary diffusion measurements of RNA-protein complexes suggest that a rudimentary model based on excluded volume interactions can explain this partitioning effect. Our results suggest the actin cortex meshwork may play a role in regulating the biomolecular content of the volume immediately adjacent to the plasma membrane.
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Affiliation(s)
- Isaac Angert
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Siddarth Reddy Karuka
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Louis M. Mansky
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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9
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Xiao L, Fang L, Kool ET. Acylation probing of "generic" RNA libraries reveals critical influence of loop constraints on reactivity. Cell Chem Biol 2022; 29:1341-1352.e8. [PMID: 35662395 PMCID: PMC9391288 DOI: 10.1016/j.chembiol.2022.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/16/2022] [Accepted: 05/12/2022] [Indexed: 01/08/2023]
Abstract
The reactivity of RNA 2'-OH acylation is broadly useful both in probing structure and in preparing conjugates. To date, this reactivity has been analyzed in limited sets of biological RNA sequences, leaving open questions of how reactivity varies inherently without regard to sequence in structured contexts. We constructed and probed "generic" structured RNA libraries using homogeneous loop sequences, employing deep sequencing to carry out a systematic survey of reactivity. We find a wide range of RNA reactivities among single-stranded sequences, with nearest neighbors playing substantial roles. Remarkably, certain small loops are found to be far more reactive on average (up to 4,000-fold) than single-stranded RNAs, due to conformational constraints that enhance reactivity. Among loops, we observe large variations in reactivity based on size, type, and position. The results lend insights into RNA designs for achieving high-efficiency local conjugation and provide new opportunities to refine structure analysis.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Linglan Fang
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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10
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Henning-Knechtel A, Thirumalai D, Kirmizialtin S. Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts. SCIENCE ADVANCES 2022; 8:eabo1190. [PMID: 35857829 PMCID: PMC9299541 DOI: 10.1126/sciadv.abo1190] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The stability of RNA increases as the charge density of the alkali metal cations increases. The molecular mechanism for this phenomenon remains elusive. To fill this gap, we performed all-atom molecular dynamics pulling simulations of HIV-1 trans-activation response RNA. We first established that the free energy landscape obtained in the simulations is in excellent agreement with the single-molecule optical tweezer experiments. The origin of the stronger stability in sodium compared to potassium is found to be due to the differences in the charge density-related binding modes. The smaller hydrated sodium ion preferentially binds to the highly charged phosphates that have high surface area. In contrast, the larger potassium ions interact with the major grooves. As a result, more cations condense around phosphate groups in the case of sodium ions, leading to the reduction of electrostatic repulsion. Because the proposed mechanism is generic, we predict that the same conclusions are valid for divalent alkaline earth metal cations.
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Affiliation(s)
| | - D. Thirumalai
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
- Corresponding author. (D.T.); (S.K.)
| | - Serdal Kirmizialtin
- Chemistry Program, Math and Sciences, New York University Abu Dhabi, Abu Dhabi, UAE
- Corresponding author. (D.T.); (S.K.)
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11
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Kloczewiak M, Banks JM, Jin L, Brader ML. A Biopharmaceutical Perspective on Higher-Order Structure and Thermal Stability of mRNA Vaccines. Mol Pharm 2022; 19:2022-2031. [PMID: 35715255 PMCID: PMC9257798 DOI: 10.1021/acs.molpharmaceut.2c00092] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/27/2022]
Abstract
Preservation of the integrity of macromolecular higher-order structure is a tenet central to achieving biologic drug and vaccine product stability toward manufacturing, distribution, storage, handling, and administration. Given that mRNA lipid nanoparticles (mRNA-LNPs) are held together by an intricate ensemble of weak forces, there are some intriguing parallels to biologic drugs, at least at first glance. However, mRNA vaccines are not without unique formulation and stabilization challenges derived from the instability of unmodified mRNA and its limited history as a drug or vaccine. Since certain learning gained from biologic drug development may be applicable for the improvement of mRNA vaccines, we present a perspective on parallels and contrasts between the emerging role of higher-order structure pertaining to mRNA-LNPs compared to pharmaceutical proteins. In a recent publication, the location of mRNA encapsulated within lipid nanoparticles was identified, revealing new insights into the LNP structure, nanoheterogeneity, and microenvironment of the encapsulated mRNA molecules [Brader et al. Biophys. J. 2021, 120, 2766]. We extend those findings by considering the effect of encapsulation on mRNA thermal unfolding with the observation that encapsulation in LNPs increases mRNA unfolding temperatures.
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Affiliation(s)
- Marek Kloczewiak
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Jessica M. Banks
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Lin Jin
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Mark L. Brader
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
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12
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Yang TH. An Aggregation Method to Identify the RNA Meta-Stable Secondary Structure and its Functionally Interpretable Structure Ensemble. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:75-86. [PMID: 34014829 DOI: 10.1109/tcbb.2021.3082396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
RNA can provide vital cellular functions through its secondary or tertiary structure. Due to the low-throughput nature of experimental approaches, studies on RNA structures mainly resort to computational methods. However, current existing tools fail to consider RNA structure ensembles and do not provide ways to decipher functional hypotheses for the new predictions. In this research, a novel method was proposed to identify the functionally interpretable structure ensemble of a given RNA sequence and provide the meta-stable structure, or the most frequently observed functional RNA cellular conformation, based on the ensemble. In the prediction of meta-stable structures, the proposed method outperformed existing tools on a yeast test set. The inferred functional aspects were then manually checked and demonstrated a micro-averaging F1 value of 0.92. Further, a biological example of the yeast ASH1-E1 element was discussed to articulate that these functional aspects can also suggest testable hypotheses. Then the proposed method was verified to be well applicable to other species through a human test set. Finally, the proposed method was demonstrated to show resistance to sequence length-dependent performance deterioration.
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13
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Forman-Kay JD, Ditlev JA, Nosella ML, Lee HO. What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates? RNA (NEW YORK, N.Y.) 2022; 28:36-47. [PMID: 34772786 PMCID: PMC8675286 DOI: 10.1261/rna.079026.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Exciting recent work has highlighted that numerous cellular compartments lack encapsulating lipid bilayers (often called "membraneless organelles"), and that their structure and function are central to the regulation of key biological processes, including transcription, RNA splicing, translation, and more. These structures have been described as "biomolecular condensates" to underscore that biomolecules can be significantly concentrated in them. Many condensates, including RNA granules and processing bodies, are enriched in proteins and nucleic acids. Biomolecular condensates exhibit a range of material states from liquid- to gel-like, with the physical process of liquid-liquid phase separation implicated in driving or contributing to their formation. To date, in vitro studies of phase separation have provided mechanistic insights into the formation and function of condensates. However, the link between the often micron-sized in vitro condensates with nanometer-sized cellular correlates has not been well established. Consequently, questions have arisen as to whether cellular structures below the optical resolution limit can be considered biomolecular condensates. Similarly, the distinction between condensates and discrete dynamic hub complexes is debated. Here we discuss the key features that define biomolecular condensates to help understand behaviors of structures containing and generating RNA.
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Affiliation(s)
- Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jonathon A Ditlev
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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14
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Knobler CM, Gelbart WM. How and why RNA genomes are (partially) ordered in viral capsids. Curr Opin Virol 2021; 52:203-210. [PMID: 34959081 DOI: 10.1016/j.coviro.2021.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/25/2021] [Indexed: 11/26/2022]
Abstract
There is a long and productive progression of X-ray crystallographic and electron microscopy studies establishing the structures of the spherical/icosahedral and cylindrical/helical capsids of a wide range of virus particles. This is because of the high degree of order - down to the Angstrom scale - in the secondary/tertiary/quaternary structure of the proteins making up the capsids. In stark contradistinction, very little is known about the structure of DNA or RNA genomes inside these capsids. This is because of the relatively large extent of disorder in the confined DNA or RNA, due to several fundamental reasons: topological defects in the DNA case, and secondary/tertiary structural disorder in the RNA case. In this article we discuss the range of partial order associated with the encapsidated genomes of single-stranded RNA viruses, focusing on the contrast between mono-partite and multi-partite viruses and on the effects of sequence-specific and non-specific interactions between RNA and capsid proteins.
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Affiliation(s)
- Charles M Knobler
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, United States
| | - William M Gelbart
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, United States; Molecular Biology Institute, UCLA, United States; California NanoSystems Institute, UCLA, United States.
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15
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Dagenais P, Desjardins G, Legault P. An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme. Nucleic Acids Res 2021; 49:11959-11973. [PMID: 34718697 PMCID: PMC8599749 DOI: 10.1093/nar/gkab963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.
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Affiliation(s)
- Pierre Dagenais
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Geneviève Desjardins
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Pascale Legault
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
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16
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Mosbach ML, Pfafenrot C, von Strandmann EP, Bindereif A, Preußer C. Molecular Determinants for RNA Release into Extracellular Vesicles. Cells 2021; 10:2674. [PMID: 34685656 PMCID: PMC8534350 DOI: 10.3390/cells10102674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 01/05/2023] Open
Abstract
Extracellular vesicles (EVs) are important for intercellular communication and act as vehicles for biological material, such as various classes of coding and non-coding RNAs, a few of which were shown to selectively target into vesicles. However, protein factors, mechanisms, and sequence elements contributing to this specificity remain largely elusive. Here, we use a reporter system that results in different types of modified transcripts to decipher the specificity determinants of RNAs released into EVs. First, we found that small RNAs are more efficiently packaged into EVs than large ones, and second, we determined absolute quantities for several endogenous RNA transcripts in EVs (U6 snRNA, U1 snRNA, Y1 RNA, and GAPDH mRNA). We show that RNA polymerase III (pol III) transcripts are more efficiently secreted into EVs compared to pol II-derived transcripts. Surprisingly, our quantitative analysis revealed no RNA accumulation in the vesicles relative to the total cellular levels, based on both overexpressed reporter transcripts and endogenous RNAs. RNA appears to be EV-associated only at low copy numbers, ranging between 0.02 and 1 molecule per EV. This RNA association may reflect internal EV encapsulation or a less tightly bound state at the vesicle surface.
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Affiliation(s)
- Marie-Luise Mosbach
- Institute of Biochemistry, Justus Liebig University of Gießen, 35392 Gießen, Germany; (M.-L.M.); (C.P.)
| | - Christina Pfafenrot
- Institute of Biochemistry, Justus Liebig University of Gießen, 35392 Gießen, Germany; (M.-L.M.); (C.P.)
| | - Elke Pogge von Strandmann
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, 35043 Marburg, Germany;
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus Liebig University of Gießen, 35392 Gießen, Germany; (M.-L.M.); (C.P.)
| | - Christian Preußer
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, 35043 Marburg, Germany;
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17
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Marichal L, Gargowitsch L, Rubim RL, Sizun C, Kra K, Bressanelli S, Dong Y, Panahandeh S, Zandi R, Tresset G. Relationships between RNA topology and nucleocapsid structure in a model icosahedral virus. Biophys J 2021; 120:3925-3936. [PMID: 34418368 PMCID: PMC8511167 DOI: 10.1016/j.bpj.2021.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/21/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022] Open
Abstract
The process of genome packaging in most of viruses is poorly understood, notably the role of the genome itself in the nucleocapsid structure. For simple icosahedral single-stranded RNA viruses, the branched topology due to the RNA secondary structure is thought to lower the free energy required to complete a virion. We investigate the structure of nucleocapsids packaging RNA segments with various degrees of compactness by small-angle x-ray scattering and cryotransmission electron microscopy. The structural differences are mild even though compact RNA segments lead on average to better-ordered and more uniform particles across the sample. Numerical calculations confirm that the free energy is lowered for the RNA segments displaying the larger number of branch points. The effect is, however, opposite with synthetic polyelectrolytes, in which a star topology gives rise to more disorder in the capsids than a linear topology. If RNA compactness and size account in part for the proper assembly of the nucleocapsid and the genome selectivity, other factors most likely related to the host cell environment during viral assembly must come into play as well.
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Affiliation(s)
- Laurent Marichal
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Laetitia Gargowitsch
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Rafael Leite Rubim
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Christina Sizun
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Kalouna Kra
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Yinan Dong
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Sanaz Panahandeh
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France.
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18
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Virion structure and in vitro genome release mechanism of dicistrovirus Kashmir bee virus. J Virol 2021; 95:JVI.01950-20. [PMID: 33658338 PMCID: PMC8139710 DOI: 10.1128/jvi.01950-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Infections of Kashmir bee virus (KBV) are lethal for honeybees and have been associated with colony collapse disorder. KBV and closely related viruses contribute to the ongoing decline in the number of honeybee colonies in North America, Europe, Australia, and other parts of the world. Despite the economic and ecological impact of KBV, its structure and infection process remain unknown. Here we present the structure of the virion of KBV determined to a resolution of 2.8 Å. We show that the exposure of KBV to acidic pH induces a reduction in inter-pentamer contacts within capsids and the reorganization of its RNA genome from a uniform distribution to regions of high and low density. Capsids of KBV crack into pieces at acidic pH, resulting in the formation of open particles lacking pentamers of capsid proteins. The large openings of capsids enable the rapid release of genomes and thus limit the probability of their degradation by RNases. The opening of capsids may be a shared mechanism for the genome release of viruses from the family Dicistroviridae ImportanceThe western honeybee (Apis mellifera) is indispensable for maintaining agricultural productivity as well as the abundance and diversity of wild flowering plants. However, bees suffer from environmental pollution, parasites, and pathogens, including viruses. Outbreaks of virus infections cause the deaths of individual honeybees as well as collapses of whole colonies. Kashmir bee virus has been associated with colony collapse disorder in the US, and no cure of the disease is currently available. Here we report the structure of an infectious particle of Kashmir bee virus and show how its protein capsid opens to release the genome. Our structural characterization of the infection process determined that therapeutic compounds stabilizing contacts between pentamers of capsid proteins could prevent the genome release of the virus.
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19
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Brader ML, Williams SJ, Banks JM, Hui WH, Zhou ZH, Jin L. Encapsulation state of messenger RNA inside lipid nanoparticles. Biophys J 2021; 120:2766-2770. [PMID: 33773963 PMCID: PMC8390897 DOI: 10.1016/j.bpj.2021.03.012] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 12/31/2022] Open
Abstract
Understanding the structure of messenger RNA (mRNA) lipid nanoparticles, and specifically the microenvironment of the mRNA molecules within these entities, is fundamental to advancing their biomedical potential. Here, we show that a permeating cationic dye, thionine, can serve as a cryogenic electron microscopy contrasting agent by binding selectively to encapsulated mRNA without disturbing lipid nanoparticle morphology. Cryo-electron microscopy images identify the mRNA location, revealing that mRNA may exist within solvent-filled cavities or may be substantially lipid associated.
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Affiliation(s)
| | | | | | - Wong H Hui
- Department of Microbiology, Immunology, and Molecular Genetics, Los Angeles, Los Angeles, California; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, Los Angeles, Los Angeles, California; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California
| | - Lin Jin
- Moderna, Inc., Cambridge, Massachusetts
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20
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Levy M, Falkovich R, Vonshak O, Bracha D, Tayar AM, Shimizu Y, Daube SS, Bar-Ziv RH. Boundary-Free Ribosome Compartmentalization by Gene Expression on a Surface. ACS Synth Biol 2021; 10:609-619. [PMID: 33595282 PMCID: PMC8023806 DOI: 10.1021/acssynbio.0c00613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 11/30/2022]
Abstract
The design of artificial cell models based on minimal surface-bound transcription-translation reactions aims to mimic the compartmentalization facilitated by organelles and inner interfaces in living cells. Dense DNA brushes as localized sources of RNA and proteins serve as synthetic operons that have recently proven useful for the autonomous synthesis and assembly of cellular machines. Here, we studied ribosome compartmentalization in a minimal gene-expression reaction on a surface in contact with a macroscopic reservoir. We first observed the accumulation and colocalization of RNA polymerases, ribosomes, nascent RNAs and proteins, in dense DNA brushes using evanescent field fluorescence, showing transcription-translation coupling in the brush. Fluorescence recovery after photobleaching showed that ribosomes engaged in translation in the brush had a 4-fold slower diffusion constant. In addition, ribosomes in the brush had over a 10-fold higher local concentration relative to free ribosomes, creating a boundary-free functional ribosome-rich compartment. To decouple translation from transcription, we immobilized dense phases of ribosomes next to DNA brushes. We demonstrated that immobilized ribosomes were capable of protein synthesis, forming 2D subcompartments of active ribosome patterns induced and regulated by DNA brush layout of coding and inhibitory genes. Localizing additional molecular components on the surface will further compartmentalize gene-expression reactions.
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Affiliation(s)
- Michael Levy
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Reuven Falkovich
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Ohad Vonshak
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Dan Bracha
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra M. Tayar
- Department
of Physics, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Yoshihiro Shimizu
- Laboratory
for Cell-Free Protein Synthesis, RIKEN Center
for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Shirley S. Daube
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Roy H. Bar-Ziv
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
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21
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Chang JY, Cui Z, Yang K, Huang J, Minary P, Zhang J. Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities. RNA (NEW YORK, N.Y.) 2020; 26:1755-1766. [PMID: 32826323 PMCID: PMC7668250 DOI: 10.1261/rna.071100.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/15/2020] [Indexed: 06/11/2023]
Abstract
Ribonucleic acids (RNAs) play essential roles in living cells. Many of them fold into defined three-dimensional (3D) structures to perform functions. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have enabled structure determinations of RNA to atomic resolutions. However, most RNA molecules are structurally flexible, limiting the resolution of their structures solved by cryo-EM. In modeling these molecules, several computational methods are limited by the requirement of massive computational resources and/or the low efficiency in exploring large-scale structural variations. Here we use hierarchical natural move Monte Carlo (HNMMC), which takes advantage of collective motions for groups of nucleic acid residues, to refine RNA structures into their cryo-EM maps, preserving atomic details in the models. After validating the method on a simulated density map of tRNA, we applied it to objectively obtain the model of the folding intermediate for the specificity domain of ribonuclease P from Bacillus subtilis and refine a flexible ribosomal RNA (rRNA) expansion segment from the Mycobacterium tuberculosis (Mtb) ribosome in different conformational states. Finally, we used HNMMC to model atomic details and flexibility for two distinct conformations of the complete genomic RNA (gRNA) inside MS2, a single-stranded RNA virus, revealing multiple pathways for its capsid assembly.
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Affiliation(s)
- Jeng-Yih Chang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, College Station, Texas 77843, USA
| | - Zhicheng Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, College Station, Texas 77843, USA
| | - Kailu Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, College Station, Texas 77843, USA
| | - Jianhua Huang
- Department of Statistics, Texas A&M University, College Station, Texas 77843, USA
| | - Peter Minary
- Department of Computer Science, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, College Station, Texas 77843, USA
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22
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Klein S, Cortese M, Winter SL, Wachsmuth-Melm M, Neufeldt CJ, Cerikan B, Stanifer ML, Boulant S, Bartenschlager R, Chlanda P. SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat Commun 2020; 11:5885. [PMID: 33208793 PMCID: PMC7676268 DOI: 10.1038/s41467-020-19619-7] [Citation(s) in RCA: 446] [Impact Index Per Article: 111.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/23/2020] [Indexed: 01/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID19 pandemic, is a highly pathogenic β-coronavirus. As other coronaviruses, SARS-CoV-2 is enveloped, replicates in the cytoplasm and assembles at intracellular membranes. Here, we structurally characterize the viral replication compartment and report critical insights into the budding mechanism of the virus, and the structure of extracellular virions close to their native state by in situ cryo-electron tomography and subtomogram averaging. We directly visualize RNA filaments inside the double membrane vesicles, compartments associated with viral replication. The RNA filaments show a diameter consistent with double-stranded RNA and frequent branching likely representing RNA secondary structures. We report that assembled S trimers in lumenal cisternae do not alone induce membrane bending but laterally reorganize on the envelope during virion assembly. The viral ribonucleoprotein complexes (vRNPs) are accumulated at the curved membrane characteristic for budding sites suggesting that vRNP recruitment is enhanced by membrane curvature. Subtomogram averaging shows that vRNPs are distinct cylindrical assemblies. We propose that the genome is packaged around multiple separate vRNP complexes, thereby allowing incorporation of the unusually large coronavirus genome into the virion while maintaining high steric flexibility between the vRNPs.
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Affiliation(s)
- Steffen Klein
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Sophie L Winter
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany
| | - Christopher J Neufeldt
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Berati Cerikan
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Megan L Stanifer
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Steeve Boulant
- Research Group "Host/Pathogen Interactions at Intestinal Epithelial Surfaces," Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany. .,Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany. .,German Center for Infection Research (DZIF), (Heidelberg Partner Site), Heidelberg, Germany.
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany. .,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.
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23
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Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:809-818. [PMID: 33067686 DOI: 10.1007/s00249-020-01470-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/26/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022]
Abstract
Analytical ultracentrifugation (AUC) has emerged as a robust and reliable technique for biomolecular characterization with extraordinary sensitivity. AUC is widely used to study purity, conformational changes, biomolecular interactions, and stoichiometry. Furthermore, AUC is used to determine the molecular weight of biomolecules such as proteins, carbohydrates, and DNA and RNA. Due to the multifaceted role(s) of non-coding RNAs from viruses, prokaryotes, and eukaryotes, research aimed at understanding the structure-function relationships of non-coding RNAs is rapidly increasing. However, due to their large size, flexibility, complicated secondary structures, and conformations, structural studies of non-coding RNAs are challenging. In this review, we are summarizing the application of AUC to evaluate the homogeneity, interactions, and conformational changes of non-coding RNAs from adenovirus as well as from Murray Valley, Powassan, and West Nile viruses. We also discuss the application of AUC to characterize eukaryotic long non-coding RNAs, Xist, and HOTAIR. These examples highlight the significant role AUC can play in facilitating the structural determination of non-coding RNAs and their complexes.
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24
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Kwapiszewska K, Szczepański K, Kalwarczyk T, Michalska B, Patalas-Krawczyk P, Szymański J, Andryszewski T, Iwan M, Duszyński J, Hołyst R. Nanoscale Viscosity of Cytoplasm Is Conserved in Human Cell Lines. J Phys Chem Lett 2020; 11:6914-6920. [PMID: 32787203 PMCID: PMC7450658 DOI: 10.1021/acs.jpclett.0c01748] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Metabolic reactions in living cells are limited by diffusion of reagents in the cytoplasm. Any attempt to quantify the kinetics of biochemical reactions in the cytosol should be preceded by careful measurements of the physical properties of the cellular interior. The cytoplasm is a complex, crowded fluid characterized by effective viscosity dependent on its structure at a nanoscopic length scale. In this work, we present and validate the model describing the cytoplasmic nanoviscosity, based on measurements in seven human cell lines, for nanoprobes ranging in diameters from 1 to 150 nm. Irrespective of cell line origin (epithelial-mesenchymal, cancerous-noncancerous, male-female, young-adult), we obtained a similar dependence of the viscosity on the size of the nanoprobes, with characteristic length-scales of 20 ± 11 nm (hydrodynamic radii of major crowders in the cytoplasm) and 4.6 ± 0.7 nm (radii of intercrowder gaps). Moreover, we revealed that the cytoplasm behaves as a liquid for length scales smaller than 100 nm and as a physical gel for larger length scales.
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Affiliation(s)
- Karina Kwapiszewska
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Krzysztof Szczepański
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Tomasz Kalwarczyk
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Bernadeta Michalska
- Nencki
Institute of Experimental Biology, Pasteura 3, Warsaw, 02-093, Poland
| | | | - Jędrzej Szymański
- Nencki
Institute of Experimental Biology, Pasteura 3, Warsaw, 02-093, Poland
| | - Tomasz Andryszewski
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Michalina Iwan
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Jerzy Duszyński
- Nencki
Institute of Experimental Biology, Pasteura 3, Warsaw, 02-093, Poland
| | - Robert Hołyst
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
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25
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Tomezsko P, Swaminathan H, Rouskin S. Viral RNA structure analysis using DMS-MaPseq. Methods 2020; 183:68-75. [PMID: 32251733 DOI: 10.1016/j.ymeth.2020.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
RNA structure is critically important to RNA viruses in every part of the replication cycle. RNA structure is also utilized by DNA viruses in order to regulate gene expression and interact with host factors. Advances in next-generation sequencing have greatly enhanced the utility of chemical probing in order to analyze RNA structure. This review will cover some recent viral RNA structural studies using chemical probing and next-generation sequencing as well as the advantages of dimethyl sulfate (DMS)-mutational profiling and sequencing (MaPseq). DMS-MaPseq is a robust assay that can easily modify RNA in vitro, in cell and in virion. A detailed protocol for whole-genome DMS-MaPseq from cells transfected with HIV-1 and the structure of TAR as determined by DMS-MaPseq is presented. DMS-MaPseq has the ability to answer a variety of integral questions about viral RNA, including how they change in different environments and when interacting with different host factors.
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Affiliation(s)
- Phillip Tomezsko
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Program in Virology, Harvard Medical School, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | | | - Silvi Rouskin
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
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26
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Zhang H, Rombouts K, Raes L, Xiong R, De Smedt SC, Braeckmans K, Remaut K. Fluorescence-Based Quantification of Messenger RNA and Plasmid DNA Decay Kinetics in Extracellular Biological Fluids and Cell Extracts. ACTA ACUST UNITED AC 2020; 4:e2000057. [PMID: 32402121 DOI: 10.1002/adbi.202000057] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 12/22/2022]
Abstract
Extracellular and intracellular degradation of nucleic acids remains an issue in non-viral gene therapy. Understanding biodegradation is critical for the rational design of gene therapeutics in order to maintain stability and functionality at the target site. However, there are only limited methods available that allow determining the stability of genetic materials in biological environments. In this context, the decay kinetics of fluorescently labeled plasmid DNA (pDNA) and messenger RNA (mRNA) in undiluted biological samples (i.e., human serum, human ascites, bovine vitreous) and cell extracts is studied using fluorescence correlation spectroscopy (FCS) and single particle tracking (SPT). It is demonstrated that FCS is suitable to follow mRNA degradation, while SPT is better suited to investigate pDNA integrity. The half-life of mRNA and pDNA is ≈1-2 min and 1-4 h in biological samples, respectively. The resistance against biodegradation drastically improves by complexation with lipid-based carriers. Taken together, FCS and SPT are able to quantify the integrity of mRNA and pDNA, respectively, as a function of time, both in the extracellular biological fluids and cell extracts. This in turn allows to focus on the important but less understood issue of nucleic acids degradation in more detail and to rationally optimize gene delivery system as therapeutics.
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Affiliation(s)
- Heyang Zhang
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Koen Rombouts
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Laurens Raes
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Ranhua Xiong
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Katrien Remaut
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
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27
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Abstract
The proper regulation of mRNA processing, localization, translation, and degradation occurs on mRNPs. However, the global principles of mRNP organization are poorly understood. We utilize the limited, but existing, information available to present a speculative synthesis of mRNP organization with the following key points. First, mRNPs form a compacted structure due to the inherent folding of RNA. Second, the ribosome is the principal mechanism by which mRNA regions are partially decompacted. Third, mRNPs are 50%-80% protein by weight, consistent with proteins modulating mRNP organization, but also suggesting the majority of mRNA sequences are not directly interacting with RNA-binding proteins. Finally, the ratio of mRNA-binding proteins to mRNAs is higher in the nucleus to allow effective RNA processing and limit the potential for nuclear RNA based aggregation. This synthesis of mRNP understanding provides a model for mRNP biogenesis, structure, and regulation with multiple implications.
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Affiliation(s)
- Anthony Khong
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Roy Parker
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
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28
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Buzón P, Maity S, Roos WH. Physical virology: From virus self-assembly to particle mechanics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1613. [PMID: 31960585 PMCID: PMC7317356 DOI: 10.1002/wnan.1613] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/01/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022]
Abstract
Viruses are highly ordered supramolecular complexes that have evolved to propagate by hijacking the host cell's machinery. Although viruses are very diverse, spreading through cells of all kingdoms of life, they share common functions and properties. Next to the general interest in virology, fundamental viral mechanisms are of growing importance in other disciplines such as biomedicine and (bio)nanotechnology. However, in order to optimally make use of viruses and virus-like particles, for instance as vehicle for targeted drug delivery or as building blocks in electronics, it is essential to understand their basic chemical and physical properties and characteristics. In this context, the number of studies addressing the mechanisms governing viral properties and processes has recently grown drastically. This review summarizes a specific part of these scientific achievements, particularly addressing physical virology approaches aimed to understand the self-assembly of viruses and the mechanical properties of viral particles. Using a physicochemical perspective, we have focused on fundamental studies providing an overview of the molecular basis governing these key aspects of viral systems. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
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29
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Integrative Structural Biology of Protein-RNA Complexes. Structure 2020; 28:6-28. [DOI: 10.1016/j.str.2019.11.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022]
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30
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Brandão HB, Paul P, van den Berg AA, Rudner DZ, Wang X, Mirny LA. RNA polymerases as moving barriers to condensin loop extrusion. Proc Natl Acad Sci U S A 2019; 116:20489-20499. [PMID: 31548377 PMCID: PMC6789630 DOI: 10.1073/pnas.1907009116] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with ongoing transcription. How transcription interferes with the condensin loop-extrusion process is largely unexplored, but recent experiments have shown that sites of high transcription may directionally affect condensin loop extrusion. We quantitatively investigate different mechanisms of interaction between condensin and elongating RNA polymerases (RNAPs) and find that RNAPs are likely steric barriers that can push and interact with condensins. Supported by chromosome conformation capture and chromatin immunoprecipitation for cells after transcription inhibition and RNAP degradation, we argue that translocating condensins must bypass transcribing RNAPs within ∼1 to 2 s of an encounter at rRNA genes and within ∼10 s at protein-coding genes. Thus, while individual RNAPs have little effect on the progress of loop extrusion, long, highly transcribed operons can significantly impede the extrusion process. Our data and quantitative models further suggest that bacterial condensin loop extrusion occurs by 2 independent, uncoupled motor activities; the motors translocate on DNA in opposing directions and function together to enlarge chromosomal loops, each independently bypassing steric barriers in their path. Our study provides a quantitative link between transcription and 3D genome organization and proposes a mechanism of interactions between SMC complexes and elongating transcription machinery relevant from bacteria to higher eukaryotes.
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Affiliation(s)
- Hugo B Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138
| | - Payel Paul
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Aafke A van den Berg
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47405;
| | - Leonid A Mirny
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138;
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
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31
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Thurm AR, Beren C, Duran-Meza AL, Knobler CM, Gelbart WM. RNA Homopolymers Form Higher-Curvature Virus-like Particles Than Do Normal-Composition RNAs. Biophys J 2019; 117:1331-1341. [PMID: 31514968 PMCID: PMC6818174 DOI: 10.1016/j.bpj.2019.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/17/2019] [Accepted: 08/07/2019] [Indexed: 11/15/2022] Open
Abstract
Unlike double-stranded DNA, single-stranded RNA can be spontaneously packaged into spherical capsids by viral capsid protein (CP) because it is a more compact and flexible polymer. Many systematic investigations of this self-assembly process have been carried out using CP from cowpea chlorotic mottle virus, with a wide range of sequences and lengths of single-stranded RNA. Among these studies are measurements of the relative packaging efficiencies of these RNAs into spherical capsids. In this work, we address a fundamental issue that has received very little attention, namely the question of the preferred curvature of the capsid formed around different RNA molecules. We show in particular that homopolymers of RNA-polyribouridylic acid and polyriboadenylic acid-form exclusively T = 2-sized (∼22-nm diameter) virus-like particles (VLPs) when mixed with cowpea chlorotic mottle virus CP, independent of their length, ranging from 500 to more than 4000 nucleotides. This is in contrast to "normal-composition" RNAs (i.e., molecules with comparable numbers of each of the four nucleotides and hence capable of developing a large amount of secondary structure because of intramolecular complementarity/basepairing); a curvature corresponding to T = 3-size (∼28 nm in diameter) is preferred for the VLPs formed with such RNAs. Our work is consistent with the preferred curvature of VLPs being a consequence of interaction of CP with RNA-in particular, the presence or absence of short RNA duplexes-and suggests that the equilibrium size of the capsid results from a trade-off between this optimum size and the cost of confinement.
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Affiliation(s)
- Abby R Thurm
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California
| | - Christian Beren
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California
| | - Ana Luisa Duran-Meza
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California; Molecular Biology Institute, University of California, Los Angeles, California; California NanoSystems Institute, University of California, Los Angeles, California.
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32
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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.
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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
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33
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Kelly J, Grosberg AY, Bruinsma R. Generalized Flory Theory for Rotational Symmetry Breaking of Complex Macromolecules. PHYSICAL REVIEW LETTERS 2019; 122:128003. [PMID: 30978098 DOI: 10.1103/physrevlett.122.128003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 06/09/2023]
Abstract
We report on spontaneous rotational symmetry breaking in a minimal model of complex macromolecules with branches and cycles. The transition takes place as the strength of the self-repulsion is increased. At the transition point, the density distribution transforms from isotropic to anisotropic. We analyze this transition using a variational mean-field theory that combines the Gibbs-Bogolyubov-Feynman inequality with the concept of the Laplacian matrix. The density distribution of the broken symmetry state is shown to be determined by the eigenvalues and eigenvectors of this Laplacian matrix. Physically, this reflects the increasing role of the underlying topological structure in determining the density of the macromolecule when repulsive interactions generate internal tension. Eventually, the variational free energy landscape develops a complex structure with multiple competing minima.
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Affiliation(s)
- Josh Kelly
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
| | - Alexander Y Grosberg
- Department of Physics and Center for Soft Matter Research, New York University, 726 Broadway, New York, New York 10003, USA
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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34
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Adivarahan S, Livingston N, Nicholson B, Rahman S, Wu B, Rissland OS, Zenklusen D. Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway. Mol Cell 2018; 72:727-738.e5. [PMID: 30415950 PMCID: PMC6592633 DOI: 10.1016/j.molcel.2018.10.010] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/24/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022]
Abstract
mRNAs form ribonucleoprotein complexes (mRNPs) by association with proteins that are crucial for mRNA metabolism. While the mRNP proteome has been well characterized, little is known about mRNP organization. Using a single-molecule approach, we show that mRNA conformation changes depending on its cellular localization and translational state. Compared to nuclear mRNPs and lncRNPs, association with ribosomes decompacts individual mRNAs, while pharmacologically dissociating ribosomes or sequestering them into stress granules leads to increased compaction. Moreover, translating mRNAs rarely show co-localized 5' and 3' ends, indicating either that mRNAs are not translated in a closed-loop configuration, or that mRNA circularization is transient, suggesting that a stable closed-loop conformation is not a universal state for all translating mRNAs.
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Affiliation(s)
- Srivathsan Adivarahan
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Nathan Livingston
- The Department of Biophysics and Biophysical Chemistry, the Solomon Snyder Department of Neuroscience, Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Beth Nicholson
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Samir Rahman
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Bin Wu
- The Department of Biophysics and Biophysical Chemistry, the Solomon Snyder Department of Neuroscience, Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Olivia S Rissland
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada.
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35
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Beren C, Liu KN, Dreesens LL, Knobler CM, Gelbart WM. Enzymatic Synthesis and Fractionation of Fluorescent PolyU RNAs. Bio Protoc 2018; 8:e2988. [PMID: 34395788 DOI: 10.21769/bioprotoc.2988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/07/2018] [Accepted: 08/17/2018] [Indexed: 11/02/2022] Open
Abstract
The physical properties of viral-length polyuridine (PolyU) RNAs, which cannot base-pair and form secondary structures, are compared with those of normal-composition RNAs, composed of comparable numbers of each of A, U, G and C nucleobases. In this protocol, we describe how to synthesize fluorescent polyU RNAs using the enzyme polynucleotide phosphorylase (PNPase) from Uridine diphosphate (UDP) monomers and how to fractionate the polydisperse synthesis mixture using gel electrophoresis, and, after electroelution, how to quantify the amount of polyU recovered with UV-Vis spectrophotometry. Dynamic light scattering was used to determine the hydrodynamic radii of normal-composition RNAs as compared to polyU. It showed that long polyU RNAs behave like linear polymers for which the radii scale with chain length as N1/2, as opposed to normal-composition RNAs that act as compact, branched RNAs for which the radii scale as N1/3.
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Affiliation(s)
- Christian Beren
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Katherine N Liu
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Lisa L Dreesens
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - William M Gelbart
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
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36
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 406] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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37
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Grosberg AY, Bruinsma R. Confining annealed branched polymers inside spherical capsids. J Biol Phys 2018; 44:133-145. [PMID: 29442192 PMCID: PMC5928018 DOI: 10.1007/s10867-018-9483-x] [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: 11/28/2017] [Accepted: 01/19/2018] [Indexed: 10/18/2022] Open
Abstract
The Lifshitz equation for the confinement of a linear polymer in a spherical cavity of radius R has the form of the Schrödinger equation for a quantum particle trapped in a potential well with flat bottom and infinite walls at radius R. We show that the Lifshitz equation of a confined annealed branched polymer has the form of the Schrödinger equation for a quantum harmonic oscillator. The resulting confinement energy has a 1/R4 dependence on the confinement radius R, in contrast to the case of confined linear polymers, which have a 1/R2 dependence. We discuss the application of this result to the problem of the confinement of single-stranded RNA molecules inside spherical capsids.
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Affiliation(s)
- Alexander Y Grosberg
- Department of Physics and Center for Soft Matter Research, New York University, 726 Broadway, New York, NY, 10003, USA.
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
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38
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Hoople GD, Richards A, Wu Y, Pisano AP, Zhang K. Gel-seq: A Method for Simultaneous Sequencing Library Preparation of DNA and RNA Using Hydrogel Matrices. J Vis Exp 2018. [PMID: 29630040 DOI: 10.3791/57315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The ability to amplify and sequence either DNA or RNA from small starting samples has only been achieved in the last five years. Unfortunately, the standard protocols for generating genomic or transcriptomic libraries are incompatible and researchers must choose whether to sequence DNA or RNA for a particular sample. Gel-seq solves this problem by enabling researchers to simultaneously prepare libraries for both DNA and RNA starting with 100 - 1000 cells using a simple hydrogel device. This paper presents a detailed approach for the fabrication of the device as well as the biological protocol to generate paired libraries. We designed Gel-seq so that it could be easily implemented by other researchers; many genetics labs already have the necessary equipment to reproduce the Gel-seq device fabrication. Our protocol employs commonly-used kits for both whole-transcript amplification (WTA) and library preparation, which are also likely to be familiar to researchers already versed in generating genomic and transcriptomic libraries. Our approach allows researchers to bring to bear the power of both DNA and RNA sequencing on a single sample without splitting and with negligible added cost.
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Affiliation(s)
| | - Andrew Richards
- Department of Bioengineering, University of California, San Diego
| | - Yan Wu
- Department of Bioengineering, University of California, San Diego
| | - Albert P Pisano
- Department of Mechanical and Aerospace Engineering, University of California, San Diego
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego
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39
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Zhang K, Keane SC, Su Z, Irobalieva RN, Chen M, Van V, Sciandra CA, Marchant J, Heng X, Schmid MF, Case DA, Ludtke SJ, Summers MF, Chiu W. Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach. Structure 2018; 26:490-498.e3. [PMID: 29398526 PMCID: PMC5842133 DOI: 10.1016/j.str.2018.01.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/12/2017] [Accepted: 01/03/2018] [Indexed: 02/01/2023]
Abstract
Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS]2; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs.
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Affiliation(s)
- Kaiming Zhang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah C Keane
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Zhaoming Su
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rossitza N Irobalieva
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muyuan Chen
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Verna Van
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Carly A Sciandra
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Jan Marchant
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Case
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Michael F Summers
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA.
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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40
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Lošdorfer Božič A, Micheletti C, Podgornik R, Tubiana L. Compactness of viral genomes: effect of disperse and localized random mutations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:084006. [PMID: 29334364 PMCID: PMC7104904 DOI: 10.1088/1361-648x/aaa7b0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/29/2017] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
Genomes of single-stranded RNA viruses have evolved to optimize several concurrent properties. One of them is the architecture of their genomic folds, which must not only feature precise structural elements at specific positions, but also allow for overall spatial compactness. The latter was shown to be disrupted by random synonymous mutations, a disruption which can consequently negatively affect genome encapsidation. In this study, we use three mutation schemes with different degrees of locality to mutate the genomes of phage MS2 and Brome Mosaic virus in order to understand the observed sensitivity of the global compactness of their folds. We find that mutating local stretches of their genomes' sequence or structure is less disruptive to their compactness compared to inducing randomly-distributed mutations. Our findings are indicative of a mechanism for the conservation of compactness acting on a global scale of the genomes, and have several implications for understanding the interplay between local and global architecture of viral RNA genomes.
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Affiliation(s)
- Anže Lošdorfer Božič
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | | | - Rudolf Podgornik
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Luca Tubiana
- Faculty of Physics, University of Vienna, A-1090 Vienna, Austria
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41
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Haque L, Bhuiya S, Das S. Self-structure assembly in single stranded polyriboadenylic acid by benzophenanthridine alkaloid: Spectroscopic and calorimetric exploration. Int J Biol Macromol 2018; 106:1130-1138. [DOI: 10.1016/j.ijbiomac.2017.08.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
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42
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Erdemci-Tandogan G, Orland H, Zandi R. RNA Base Pairing Determines the Conformations of RNA Inside Spherical Viruses. PHYSICAL REVIEW LETTERS 2017; 119:188102. [PMID: 29219580 DOI: 10.1103/physrevlett.119.188102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Indexed: 05/21/2023]
Abstract
Many simple RNA viruses enclose their genetic material by a protein shell called the capsid. While the capsid structures are well characterized for most viruses, the structure of RNA inside the shells and the factors contributing to it remain poorly understood. We study the impact of base pairing on the conformations of RNA and find that it undergoes a swollen coil to globule continuous transition as a function of the strength of the pairing interaction. We also observe a first order transition and kink profile as a function of RNA length. All these transitions could explain the different RNA profiles observed inside viral shells.
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Affiliation(s)
- Gonca Erdemci-Tandogan
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - Henri Orland
- Institut de Physique Théorique, CEA-Saclay, CEA, F-91191 Gif-sur-Yvette, France
- Beijing Computational Science Research Center, No. 10 East Xibeiwang Road, Haidan District, Beijing 100193, China
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
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43
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Bayrak CS, Kim N, Schlick T. Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction. Nucleic Acids Res 2017; 45:5414-5422. [PMID: 28158755 PMCID: PMC5435971 DOI: 10.1093/nar/gkx045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/22/2017] [Indexed: 12/15/2022] Open
Abstract
Kink turns are widely occurring motifs in RNA, located in internal loops and associated with many biological functions including translation, regulation and splicing. The associated sequence pattern, a 3-nt bulge and G-A, A-G base-pairs, generates an angle of ∼50° along the helical axis due to A-minor interactions. The conserved sequence and distinct secondary structures of kink-turns (k-turn) suggest computational folding rules to predict k-turn-like topologies from sequence. Here, we annotate observed k-turn motifs within a non-redundant RNA dataset based on sequence signatures and geometrical features, analyze bending and torsion angles, and determine distinct knowledge-based potentials with and without k-turn motifs. We apply these scoring potentials to our RAGTOP (RNA-As-Graph-Topologies) graph sampling protocol to construct and sample coarse-grained graph representations of RNAs from a given secondary structure. We present graph-sampling results for 35 RNAs, including 12 k-turn and 23 non k-turn internal loops, and compare the results to solved structures and to RAGTOP results without special k-turn potentials. Significant improvements are observed with the updated scoring potentials compared to the k-turn-free potentials. Because k-turns represent a classic example of sequence/structure motif, our study suggests that other such motifs with sequence signatures and unique geometrical features can similarly be utilized for RNA structure prediction and design.
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Affiliation(s)
- Cigdem Sevim Bayrak
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
| | - Namhee Kim
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
| | - Tamar Schlick
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
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Abstract
Recently, dozens of virus structures have been solved to resolutions between 2.5 and 5.0 Å by means of electron cryomicroscopy. With these structures we are now firmly within the "atomic age" of electron cryomicroscopy, as these studies can reveal atomic details of protein and nucleic acid topology and interactions between specific residues. This improvement in resolution has been the result of direct electron detectors and image processing advances. Although enforcing symmetry facilitates reaching near-atomic resolution with fewer particle images, it unfortunately obscures some biologically interesting components of a virus. New approaches on relaxing symmetry and exploring structure dynamics and heterogeneity of viral assemblies have revealed important insights into genome packaging, virion assembly, cell entry, and other stages of the viral life cycle. In the future, novel methods will be required to reveal yet-unknown structural conformations of viruses, relevant to their biological activities. Ultimately, these results hold the promise of answering many unresolved questions linking structural diversity of viruses to their biological functions.
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Affiliation(s)
- Jason T Kaelber
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030.,National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Corey F Hryc
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030;
| | - Wah Chiu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030.,National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030;
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45
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Beren C, Dreesens LL, Liu KN, Knobler CM, Gelbart WM. The Effect of RNA Secondary Structure on the Self-Assembly of Viral Capsids. Biophys J 2017; 113:339-347. [PMID: 28711172 DOI: 10.1016/j.bpj.2017.06.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/31/2017] [Accepted: 06/20/2017] [Indexed: 12/31/2022] Open
Abstract
Previous work has shown that purified capsid protein (CP) of cowpea chlorotic mottle virus (CCMV) is capable of packaging both purified single-stranded RNA molecules of normal composition (comparable numbers of A, U, G, and C nucleobases) and of varying length and sequence, and anionic synthetic polymers such as polystyrene sulfonate. We find that CCMV CP is also capable of packaging polyU RNAs, which-unlike normal-composition RNAs-do not form secondary structures and which act as essentially structureless linear polymers. Following our canonical two-step assembly protocol, polyU RNAs ranging in length from 1000 to 9000 nucleotides (nt) are completely packaged. Surprisingly, negative-stain electron microscopy shows that all lengths of polyU are packaged into 22-nm-diameter particles despite the fact that CCMV CP prefers to form 28-nm-diameter (T = 3) particles when packaging normal-composition RNAs. PolyU RNAs >5000 nt in length are packaged into multiplet capsids, in which a single RNA molecule is shared between two or more 22-nm-diameter capsids, in analogy with the multiplets of 28-nm-diameter particles formed with normal-composition RNAs >5000 nt long. Experiments in which viral RNA competes for viral CP with polyUs of equal length show that polyU, despite its lack of secondary structure, is packaged more efficiently than viral RNA. These findings illustrate that the secondary structure of the RNA molecule-and its absence-plays an essential role in determining capsid structure during the self-assembly of CCMV-like particles.
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Affiliation(s)
- Christian Beren
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Lisa L Dreesens
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Katherine N Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California.
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
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46
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Titlow JS, Yang L, Parton RM, Palanca A, Davis I. Super-Resolution Single Molecule FISH at the Drosophila Neuromuscular Junction. Methods Mol Biol 2017; 1649:163-175. [PMID: 29130196 PMCID: PMC6128253 DOI: 10.1007/978-1-4939-7213-5_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The lack of an effective, simple, and highly sensitive protocol for fluorescent in situ hybridization (FISH) at the Drosophila larval neuromuscular junction (NMJ) has hampered the study of mRNA biology. Here, we describe our modified single molecule FISH (smFISH) methods that work well in whole mount Drosophila NMJ preparations to quantify primary transcription and count individual cytoplasmic mRNA molecules in specimens while maintaining ultrastructural preservation. The smFISH method is suitable for high-throughput sample processing and 3D image acquisition using any conventional microscopy imaging modality and is compatible with the use of antibody colabeling and transgenic fluorescent protein tags in axons, glia, synapses, and muscle cells. These attributes make the method particularly amenable to super-resolution imaging. With 3D Structured Illumination Microscopy (3D-SIM), which increases spatial resolution by a factor of 2 in X, Y, and Z, we acquire super-resolution information about the distribution of single molecules of mRNA in relation to covisualized synaptic and cellular structures. Finally, we demonstrate the use of commercial and open source software for the quality control of single transcript expression analysis, 3D-SIM data acquisition and reconstruction as well as image archiving management and presentation. Our methods now allow the detailed mechanistic and functional analysis of sparse as well as abundant mRNAs at the NMJ in their appropriate cellular context.
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Affiliation(s)
- Joshua S. Titlow
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Lu Yang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Richard M. Parton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Ana Palanca
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
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47
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Li C, Kneller AR, Jacobson SC, Zlotnick A. Single Particle Observation of SV40 VP1 Polyanion-Induced Assembly Shows That Substrate Size and Structure Modulate Capsid Geometry. ACS Chem Biol 2017; 12:1327-1334. [PMID: 28323402 DOI: 10.1021/acschembio.6b01066] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Simian virus 40 capsid protein (VP1) is a unique system for studying substrate-dependent assembly of a nanoparticle. Here, we investigate a simplest case of this system where 12 VP1 pentamers and a single polyanion, e.g., RNA, form a T = 1 particle. To test the roles of polyanion substrate length and structure during assembly, we characterized the assembly products with size exclusion chromatography, transmission electron microscopy, and single-particle resistive-pulse sensing. We found that 500 and 600 nt RNAs had the optimal length and structure for assembly of uniform T = 1 particles. Longer 800 nt RNA, shorter 300 nt RNA, and a linear 600 unit poly(styrene sulfonate) (PSS) polyelectrolyte produced heterogeneous populations of products. This result was surprising as the 600mer PSS and 500-600 nt RNA have similar mass and charge. Like ssRNA, PSS also has a short 4 nm persistence length, but unlike RNA, PSS lacks a compact tertiary structure. These data indicate that even for flexible substrates, shape as well as size affect assembly and are consistent with the hypothesis that work, derived from protein-protein and protein-substrate interactions, is used to compact the substrate.
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Affiliation(s)
- Chenglei Li
- Department
of Molecular and Cellular Biochemistry and ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Andrew R. Kneller
- Department
of Molecular and Cellular Biochemistry and ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Stephen C. Jacobson
- Department
of Molecular and Cellular Biochemistry and ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry and ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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48
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Borodavka A, Singaram SW, Stockley PG, Gelbart WM, Ben-Shaul A, Tuma R. Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures. Biophys J 2016; 111:2077-2085. [PMID: 27851933 PMCID: PMC5113152 DOI: 10.1016/j.bpj.2016.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/25/2016] [Accepted: 10/11/2016] [Indexed: 12/26/2022] Open
Abstract
Long RNA molecules are at the core of gene regulation across all kingdoms of life, while also serving as genomes in RNA viruses. Few studies have addressed the basic physical properties of long single-stranded RNAs. Long RNAs with nonrepeating sequences usually adopt highly ramified secondary structures and are better described as branched polymers. To test whether a branched polymer model can estimate the overall sizes of large RNAs, we employed fluorescence correlation spectroscopy to examine the hydrodynamic radii of a broad spectrum of biologically important RNAs, ranging from viral genomes to long noncoding regulatory RNAs. The relative sizes of long RNAs measured at low ionic strength correspond well to those predicted by two theoretical approaches that treat the effective branching associated with secondary structure formation-one employing the Kramers theorem for calculating radii of gyration, and the other featuring the metric of maximum ladder distance. Upon addition of multivalent cations, most RNAs are found to be compacted as compared with their original, low ionic-strength sizes. These results suggest that sizes of long RNA molecules are determined by the branching pattern of their secondary structures. We also experimentally validate the proposed computational approaches for estimating hydrodynamic radii of single-stranded RNAs, which use generic RNA structure prediction tools and thus can be universally applied to a wide range of long RNAs.
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Affiliation(s)
- Alexander Borodavka
- Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Surendra W Singaram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; The Institute of Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Peter G Stockley
- Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Avinoam Ben-Shaul
- The Institute of Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roman Tuma
- Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.
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49
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Kelly J, Grosberg AY, Bruinsma R. Sequence Dependence of Viral RNA Encapsidation. J Phys Chem B 2016; 120:6038-50. [PMID: 27116641 DOI: 10.1021/acs.jpcb.6b01964] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We develop a Flory mean-field theory for viral RNA (vRNA) molecules that extends the current RNA folding algorithms to include interactions between different sections of the secondary structure. The theory is applied to sequence-selective vRNA encapsidation. The dependence on sequence enters through a single parameter: the largest eigenvalue of the Kramers matrix of the branched polymer obtained by coarse graining the secondary structure. Differences between the work of encapsidation of vRNA molecules and of randomized isomers are found to be in the range of 20 kBT, more than sufficient to provide a strong bias in favor of vRNA encapsidation. The method is applied to a packaging competition experiment where large vRNA molecules compete for encapsidation with two smaller RNA species that together have the same nucleotide sequence as the large molecule. We encounter a substantial, generic free energy bias, that also is of the order of 20 kBT, in favor of encapsidating the single large RNA molecule. The bias is mainly the consequence of the fact that dividing up a large vRNA molecule involves the release of stored elastic energy. This provides an important, nonspecific mechanism for preferential encapsidation of single larger vRNA molecules over multiple smaller mRNA molecules with the same total number of nucleotides. The result is also consistent with recent RNA packaging competition experiments by Comas-Garcia et al.1 Finally, the Flory method leads to the result that when two RNA molecules are copackaged, they are expected to remain segregated inside the capsid.
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Affiliation(s)
- Joshua Kelly
- Department of Physics and Astronomy, University of California , Los Angeles, California 90095, United States
| | - Alexander Y Grosberg
- Department of Physics and Center for Soft Matter Research, New York University , New York, New York 10003, United States
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California , Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
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50
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Tokuda JM, Pabit SA, Pollack L. Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS. Biophys Rev 2016; 8:139-149. [PMID: 27551324 PMCID: PMC4991782 DOI: 10.1007/s12551-016-0196-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/10/2016] [Indexed: 12/29/2022] Open
Abstract
Understanding how DNA carries out its biological roles requires knowledge of its interactions with biological partners. Since DNA is a polyanionic polymer, electrostatic interactions contribute significantly. These interactions are mediated by positively charged protein residues or charge compensating cations. Direct detection of these partners and/or their effect on DNA conformation poses challenges, especially for monitoring conformational dynamics in real time. Small-angle x-ray scattering (SAXS) is uniquely sensitive to both the conformation and local environment (i.e. protein partner and associated ions) of the DNA. The primary challenge of studying multi-component systems with SAXS lies in resolving how each component contributes to the measured scattering. Here, we review two contrast variation (CV) strategies that enable targeted studies of the structures of DNA or its associated partners. First, solution contrast variation enables measurement of DNA conformation within a protein-DNA complex by masking out the protein contribution to the scattering profile. We review a specific example, in which the real-time unwrapping of DNA from a nucleosome core particle is measured during salt-induced disassembly. The second method, heavy atom isomorphous replacement, reports the spatial distribution of the cation cloud around duplex DNA by exploiting changes in the scattering strength of cations with varying atomic numbers. We demonstrate the application of this approach to provide the spatial distribution of monovalent cations (Na+, K+, Rb+, Cs+) around a standard 25-base pair DNA. The CV strategies presented here are valuable tools for understanding DNA interactions with its biological partners.
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Affiliation(s)
- Joshua M. Tokuda
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Suzette A. Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
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