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Heffron J, Mayer BK. Improved Virus Isoelectric Point Estimation by Exclusion of Known and Predicted Genome-Binding Regions. Appl Environ Microbiol 2020; 86:e01674-20. [PMID: 32978129 PMCID: PMC7657617 DOI: 10.1128/aem.01674-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/18/2020] [Indexed: 01/16/2023] Open
Abstract
Knowledge of the isoelectric points (pIs) of viruses is beneficial for predicting virus behavior in environmental transport and physical/chemical treatment applications. However, the empirically measured pIs of many viruses have thus far defied simple explanation, let alone prediction, based on the ionizable amino acid composition of the virus capsid. Here, we suggest an approach for predicting the pI of nonenveloped viruses by excluding capsid regions that stabilize the virus polynucleotide via electrostatic interactions. This method was applied first to viruses with known polynucleotide-binding regions (PBRs) and/or three-dimensional (3D) structures. Then, PBRs were predicted in a group of 32 unique viral capsid proteome sequences via conserved structures and sequence motifs. Removing predicted PBRs resulted in a significantly better fit to empirical pI values. After modification, mean differences between theoretical and empirical pI values were reduced from 2.1 ± 2.4 to 0.1 ± 1.7 pH units.IMPORTANCE This model fits predicted pIs to empirical values for a diverse set of viruses. The results suggest that many previously reported discrepancies between theoretical and empirical virus pIs can be explained by coulombic neutralization of PBRs of the inner capsid. Given the diversity of virus capsid structures, this nonarbitrary, heuristic approach to predicting virus pI offers an effective alternative to a simplistic, one-size-fits-all charge model of the virion. The accurate, structure-based prediction of PBRs of the virus capsid employed here may also be of general interest to structural virologists.
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Affiliation(s)
- Joe Heffron
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
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Virudachalam R, Sitaraman K, Heuss KL, Markley JL, Argos P. Evidence for pH-induced release of RNA from belladonna mottle virus and the stabilizing effect of polyamines and cations. Virology 2008; 130:351-9. [PMID: 18639151 DOI: 10.1016/0042-6822(83)90089-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/1983] [Accepted: 07/18/1983] [Indexed: 11/29/2022]
Abstract
The RNA of belladonna mottle virus (BDMV) is released from virions by increasing the pH to neutrality or above, leaving behind intact protein shells. In contrast, much harsher conditions are required to release the RNA from the closely related turnip yellow mosaic virus (TYMV). The heat-induced or pH-dependent escape of RNA from BDMV has been investigated by 31P NMR spectroscopy and ultracentrifugation. The methods show a transition pH near 6.8 at which the RNA undergoes a structural alteration probably caused by disruption of protein-RNA linkages. Addition of cations or polyamines to BDMV prevents the RNA loss at alkaline pH; the virions become stable to pH values up to 11.5 as observed for TYMV. We suggest that repulsion of the negatively charged phosphate groups of the nucleic acid provides the driving force for RNA release at pH values above the threshold point where protein-RNA interactions are broken. The polyamines effectively counter the phosphate charge in BDMV and thereby prevent RNA loss. Since TYMV is packaged with polyamines and BDMV is not (R. Virudachalam, K. Sitaraman, K. L. Heuss, P. Argos, and J. L. Markley, Virology 130, 360-371, 1983), the different conditions required for RNA escape from the two viruses are explained. Heating of BDMV virions at pH 7.0 to 40 degrees resulted in their partial disruption; the product some intact particles, empty capsids, and RNA fragments with a sedimentation coefficient of 5S.
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Affiliation(s)
- R Virudachalam
- Purdue University Biochemical Magnetic Resonance Laboratory, Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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Carbon-13 and proton nuclear magnetic resonance spectroscopy of plant viruses: evidence for protein-nucleic acid interactions in belladonna mottle virus and detection of polyamines in turnip yellow mosaic virus. Virology 2008; 130:360-71. [PMID: 18639152 DOI: 10.1016/0042-6822(83)90090-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/1983] [Accepted: 07/19/1983] [Indexed: 11/20/2022]
Abstract
Belladonna mottle virus (BDMV) enriched in carbon-13 was isolated from infected tobacco plants grown in a 2% 13C02, 8% 12CO2 atmosphere. The enrichment led to a fivefold improvement in the signal to noise ratio of the (13)C NMR spectrum of BDMV. 1H and 13C NMR peaks of the intact virion are broad. However, upon removal of the RNA, many sharp peaks appear in spectra of the empty capsid which are attributed to aliphatic amino acid side chains at the inner surface of the protein shell that have gained segmental mobility. These include resonances assigned to the side chain of glutamate. Internal motions are necessary to account for the experimental 13C NMR linewidths. Aliphatic 13CHn (n = 1-3) groups must have correlation times on the order of 10 nsec and quaternary carbons must have correlation times between 50 and 300 nsec to explain the narrow line widths. No sharp peaks were observed in the aromatic regions of 1H or 13C NMR spectra; thus all the aromatic side chains seem to be tightly packed in the capsid as well as the virion. 1H and 13C NMR have been used for the first time to detect polyamines in virus particles. 1H NMR studies confirmed the presence of polyamines, apparently packaged during assembly, in turnip yellow mosaic virus (TYMV) and demonstrated their absence in BDMV. Sedimentation analysis has shown that the RNA is released upon increasing the pH above neutrality for BDMV but only above pH 11.5 for TYMV (R. Virudachalam, K. Sitaraman, K. L. Heuss, J. L. Markley, and P. Argos, Virology 130, 351-359, 1983). 1H NMR studies demonstrated that the BDMV capsid is permeable to polyamines and that the pH stability of BDMV with added spermidine is comparable to that of TYMV.
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van Roon AMM, Bink HHJ, Plaisier JR, Pleij CWA, Abrahams JP, Pannu NS. Crystal Structure of an Empty Capsid of Turnip Yellow Mosaic Virus. J Mol Biol 2004; 341:1205-14. [PMID: 15321716 DOI: 10.1016/j.jmb.2004.06.085] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 06/24/2004] [Accepted: 06/30/2004] [Indexed: 11/26/2022]
Abstract
Empty capsids (artificial top component) of turnip yellow mosaic virus were co-crystallized with an encapsidation initiator RNA hairpin. No clear density was observed for the RNA, but there were clear differences in the conformation of a loop of the coat protein at the opening of the pentameric capsomer (formed by five A-subunits) protruding from the capsid, compared to the corresponding loop in the intact virus. Further differences were found at the N terminus of the A-subunit. These differences have implications for the mechanism of decapsidation of the virus, required for infection.
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Affiliation(s)
- Anne-Marie M van Roon
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Bink HHJ, Roepan SK, Pleij CWA. Two histidines of the coat protein of turnip yellow mosaic virus at the capsid interior are crucial for viability. Proteins 2004; 55:236-44. [PMID: 15048817 DOI: 10.1002/prot.10600] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
RNA-coat protein interactions in turnip yellow mosaic virus (TYMV) have been shown to involve low pK proton-donating groups. Two different types of interaction have been proposed. In the so-called type I interaction, protonated C-residues interact with acidic amino acids at low pH, thereby providing a rationale for the high C-content (38%) of the genomic RNA. The type II interaction involves charged histidines interacting with phosphates of the RNA backbone. Site-directed mutagenesis of the TYMV coat protein and subsequent in vivo analysis were performed to distinguish between these two types of RNA-protein interaction. The results reveal a prominent role for the histidines H68 and H180, since mutation to an alanine residue inhibits symptom development on secondary leaves, indicating that spreading of the virus in the plant is blocked. Viral RNA and coat protein synthesis are not altered, showing that these two histidines may play a role in the process of RNA encapsidation. Overexpression of the TYMV coat protein in Escherichia coli leads to the formation of bona fide capsids, showing that the two histidines are not critical in capsid assembly. Mutagenesis of the acidic amino acids D11, E135, and D143 to alanine apparently did not interfere with virus viability. The functional role of the histidines during the infection cycle is discussed in terms of the structure of the coat protein, both at the level of amino acid sequence conservation among the members of the Tymoviridae family and as the three-dimensional structure of the coat protein.
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Affiliation(s)
- Hugo H J Bink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands
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Bink HHJ, Hellendoorn K, van der Meulen J, Pleij CWA. Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA. Proc Natl Acad Sci U S A 2002; 99:13465-70. [PMID: 12361978 PMCID: PMC129696 DOI: 10.1073/pnas.202287499] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 5' UTR of turnip yellow mosaic virus RNA contains two conserved hairpins with internal loops consisting of C.C and C.A mismatches. In this article, evidence is presented indicating that the 5' proximal hairpin functions as an encapsidation initiation signal. Extensive mutagenesis studies on this hairpin and sequencing of virus progeny showed a clear preference for C.C and C.A mismatches within the internal loop. The importance of these mismatches lies in their pH-dependent protonation and stable base pair formation. Encapsidation efficiency was found to be severely affected for several mutants lacking the protonatable mismatches in the internal loop of the 5' proximal hairpin. Furthermore, gel mobility-shift assays were performed with various RNA hairpins and empty capsids with a hole. Protonatable hairpins containing C.C and/or C.A pairs were found to bind specifically to the interior of the protein shell under acidic conditions (pH 4.5) in the presence of spermidine. Based on these results we propose that this binding of protonated cytosines to the coat protein of turnip yellow mosaic virus may represent a new motif in RNA-protein interactions.
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Affiliation(s)
- Hugo H J Bink
- Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2300 RA Leiden, The Netherlands
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Vriend G, Verduin B, Hemminga M, Schaafsma T. Mobility involved in protein-RNA interaction in spherical plant viruses, studied by nuclear magnetic resonance spectroscopy. FEBS Lett 2001. [DOI: 10.1016/0014-5793(82)81204-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Canady MA, Larson SB, Day J, McPherson A. Crystal structure of turnip yellow mosaic virus. NATURE STRUCTURAL BIOLOGY 1996; 3:771-81. [PMID: 8784351 DOI: 10.1038/nsb0996-771] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The structure of turnip yellow mosaic virus (TYMV) has been solved to 3.2 A resolution and an R-value of 18.7%. The structure is consistent with models based on low resolution X-ray and electron microscopy studies, with pentameric and hexameric protein aggregates protruding from the surface and forming deep valleys at the quasi three-fold axes. The N-terminal 26 residues of the A-subunit are disordered, while those of the B- and C-subunits are seen to interact around the interior of the quasi six-fold cluster where they form an annulus. The three histidine residues of each protein subunit are located in the interior and accessible for interaction with the RNA genome. The appearance of the interior surface of the virus capsid, along with buried surface area calculations, suggest that a pentameric unit is lost during decapsidation.
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Affiliation(s)
- M A Canady
- Department of Biochemistry, University of California, Riverside 92521, USA
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Böttcher B, Crowther RA. Difference imaging reveals ordered regions of RNA in turnip yellow mosaic virus. Structure 1996; 4:387-94. [PMID: 8740361 DOI: 10.1016/s0969-2126(96)00044-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Turnip yellow mosaic virus (TYMV) is a small icosahedral plant virus with a capsid containing 180 subunits arranged with hexamer-pentamer clustering. Cross-linking studies have indicated extensive contacts between RNA and coat protein, suggesting that substantial parts of the RNA might be icosahedrally ordered. RESULTS Comparison of maps computed to a Fourier cut-off of 1.5 nm from electron micrographs of ice-embedded specimens of TYMV and of empty capsids produced by freeze-thawing reveals strong inner features around the threefold axes in the virus but not in the empty capsid. Internal features of subunit packing indicate that interhexamer contacts are closer than those between pentamers and hexamers and that pentamer density in the empty capsid is reduced relative to that in the virus. CONCLUSIONS The differences between virus and empty capsid indicate that substantial parts of the RNA are icosahedrally ordered and that the exit of RNA on freeze-thawing is accompanied by the loss of at least one pentamer unit.
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Affiliation(s)
- B Böttcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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Bransom KL, Weiland JJ, Tsai CH, Dreher TW. Coding density of the turnip yellow mosaic virus genome: roles of the overlapping coat protein and p206-readthrough coding regions. Virology 1995; 206:403-12. [PMID: 7831796 DOI: 10.1016/s0042-6822(95)80056-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
More than one-third of the turnip yellow mosaic virus (TYMV) genome simultaneously encodes two ORFs. We have investigated the functions of the overlapping coat protein ORF and readthrough domain of ORF-206 in the 3' region of the genome. TYMC-206 RNA, in which a second stop codon has been positioned to prevent ORF-206 readthrough, induced infections in protoplasts and plants that were indistinguishable from wild type. ORF-206 readthrough is thus nonessential. Nevertheless, TYMV-221 RNA, in which the ORF-206 stop codon was replaced with a tyrosine codon to force readthrough, was infectious to protoplasts, suggesting that a role for ORF-206 readthrough under certain conditions is possible. TYMV RNA variants that produce truncated or no coat protein were used to show that the coat protein is dispensable for local movement but necessary for systemic spread of virus in plants. Studies in protoplasts showed that (-) RNA levels are normal in the absence of coat protein, but (+) strand levels are decreased about 10-fold relative to wild-type infections. A mutant with a short C-terminal coat protein extension that formed virions less stable than normal demonstrated the protective role of capsids toward genomic RNA. The evolutionary implications of the dense information content of the TYMV genome are discussed.
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Affiliation(s)
- K L Bransom
- Department of Agricultural Chemistry, Oregon State University, Corvallis 97331
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Canady MA, Day J, McPherson A. Preliminary X-ray diffraction analysis of crystals of turnip yellow mosaic virus (TYMV). Proteins 1995; 21:78-81. [PMID: 7716173 DOI: 10.1002/prot.340210111] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Turnip yellow mosaic virus (TYMV) was purified from Chinese cabbage and crystallized in a form that permits high resolution structural analysis using X-ray diffraction. The crystals have a hexagonal bipyramidal morphology and often achieve dimensions of 1.0 x 1.0 x 0.5 mm. The crystals appear to be of hexagonal space group P6(2)22 with a=b=525 A, c=315 A, but we cannot strictly rule out the possibility that the space group is P622. They appear different than any crystals of TYMV previously reported. There are three T = 3 virus particles in the unit cell, which implies that one quarter of the particle, or 45 protein subunits, comprises the asymmetric unit of the crystal. Native data have been collected using synchrotron radiation to a resolution of 3.2 A.
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Affiliation(s)
- M A Canady
- Department of Biochemistry, University of California, Riverside 92521, USA
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12
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Shetlar MD, Carbone J, Steady E, Hom K. Photochemical addition of amino acids and peptides to polyuridylic acid. Photochem Photobiol 1984; 39:141-4. [PMID: 6709720 DOI: 10.1111/j.1751-1097.1984.tb03419.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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13
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Immunochemical studies of turnip yellow mosaic virus III. Localization of two viral epitopes in residues 57–64 and 183–189 of the coat protein. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/0167-4838(83)90218-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Quesniaux V, Briand JP, Van Regenmortel MH. Immunochemical studies of turnip yellow mosaic virus--II. Localization of a viral epitope in the N-terminal residues of the coat protein. Mol Immunol 1983; 20:179-85. [PMID: 6188950 DOI: 10.1016/0161-5890(83)90129-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Cuillel M, Jacrot B, Zulauf M. A T = 1 capsid formed by protein of brome mosaic virus in the presence of trypsin. Virology 1981; 110:63-72. [DOI: 10.1016/0042-6822(81)90008-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/1980] [Indexed: 10/26/2022]
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Abstract
Contact-site cross-linking agents comprise a heterogeneous grouping of cross-linkers which share the common property of being able to cross-link only very closely juxtaposed residues in macromolecular complexes. We have defined contact-site cross-linking arbitrarily as the covalent joining of residues such that they are constrained to a distance which is equivalent to or less than their closest possible steric approach prior to becoming linked (1). We recognize two classes of contact-site cross-linkers, bridge type and zero-length type. The former, such as formaldehyde, become incorporated during cross-linking as one-atom bridges. The latter, such as the carbodiimides, operate as condensing agents with the result that the cross-linked residues become interjoined directly. Contact-site cross-linkers have been used in several ways as specific probes of both the static and dynamic aspects of macromolecular structure. They can yield precise structural information about macromolecular contacts when actual sites of cross-linking are determined by peptide or nucleotide mapping techniques. In this way exact contacts between histones in the nucleosome, between protein and RNA in the ribosome, and between RNA polymerase and DNA have been determined. Contact-site cross-linkers have also been used to probe the perturbation of contacts following macromolecular conformational changes. Certain histone-histone 'cross-linkable' sites are rendered unreactive after induction of chromatin conformational changes thus serving to localize sites of perturbation.
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