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Dexheimer S, Shrestha N, Chapagain BS, Bujarski JJ, Yin Y. Characterization of Variant RNAs Encapsidated during Bromovirus Infection by High-Throughput Sequencing. Pathogens 2024; 13:96. [PMID: 38276169 PMCID: PMC10819421 DOI: 10.3390/pathogens13010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Previously, we described the RNA recombinants accumulating in tissues infected with the bromoviruses BMV (Brome mosaic virus) and CCMV (Cowpea chlorotic mottle virus). In this work, we characterize the recombinants encapsidated inside the purified virion particles of BMV and CCMV. By using a tool called the Viral Recombination Mapper (ViReMa) that detects recombination junctions, we analyzed a high number of high-throughput sequencing (HTS) short RNA sequence reads. Over 28% of BMV or CCMV RNA reads did not perfectly map to the viral genomes. ViReMa identified 1.40% and 1.83% of these unmapped reads as the RNA recombinants, respectively, in BMV and CCMV. Intra-segmental crosses were more frequent than the inter-segmental ones. Most intra-segmental junctions carried short insertions/deletions (indels) and caused frameshift mutations. The mutation hotspots clustered mainly within the open reading frames. Substitutions of various lengths were also identified, whereas a small fraction of crosses occurred between viral and their host RNAs. Our data reveal that the virions can package detectable amounts of multivariate recombinant RNAs, contributing to the flexible nature of the viral genomes.
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Affiliation(s)
- Sarah Dexheimer
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Nipin Shrestha
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Bandana Sharma Chapagain
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Jozef J. Bujarski
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Yanbin Yin
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska—Lincoln, Lincoln, NE 68588, USA
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Wang SH, Hu SY, Li M, Liu M, Sun H, Zhao JR, Chen WT, Yuan ML. Comparative Mitogenomic Analyses of Darkling Beetles (Coleoptera: Tenebrionidae) Provide Evolutionary Insights into tRNA-like Sequences. Genes (Basel) 2023; 14:1738. [PMID: 37761878 PMCID: PMC10530909 DOI: 10.3390/genes14091738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the evolutionary characteristics of the family. The tenebrionid mitogenomes were highly conserved with respect to genome size, gene arrangement, base composition, and codon usage. All protein-coding genes evolved under purifying selection. The largest non-coding region (i.e., control region) showed several unusual features, including several conserved repetitive fragments (e.g., A+T-rich regions, G+C-rich regions, Poly-T tracts, TATA repeat units, and longer repetitive fragments) and tRNA-like structures. These tRNA-like structures can bind to the appropriate anticodon to form a cloverleaf structure, although base-pairing is not complete. We summarized the quantity, types, and conservation of tRNA-like sequences and performed functional and evolutionary analyses of tRNA-like sequences with various anticodons. Phylogenetic analyses based on three mitogenomic datasets and two tree inference methods largely supported the monophyly of each of the three subfamilies (Stenochiinae, Pimeliinae, and Lagriinae), whereas both Tenebrioninae and Diaperinae were consistently recovered as polyphyletic. We obtained a tenebrionid mitogenomic phylogeny: (Lagriinae, (Pimeliinae, ((Tenebrioninae + Diaperinae), Stenochiinae))). Our results provide insights into the evolution and function of tRNA-like sequences in tenebrionid mitogenomes and contribute to our general understanding of the evolution of Tenebrionidae.
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Affiliation(s)
- Su-Hao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Min Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Hao Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Jia-Rui Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wen-Ting Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
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Chakravarty A, Rao ALN. Modulation of Capsid Dynamics in Bromoviruses by the Host and Heterologous Viral Replicase. J Virol 2023; 97:e0128422. [PMID: 36786601 PMCID: PMC10062129 DOI: 10.1128/jvi.01284-22] [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: 08/15/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023] Open
Abstract
The three genomic and a single subgenomic RNA of Cowpea chlorotic mottle virus (CCMV), which is pathogenic to plants, is packaged into three morphologically indistinguishable icosahedral virions with T=3 symmetry. The two virion types, C1V and C2V, package genomic RNAs 1 (C1) and 2 (C2), respectively. The third virion type, C3+4V, copackages genomic RNA3 and its subgenomic RNA (RNA4). In this study, we sought to evaluate how the alteration of native capsid dynamics by the host and viral replicase modulate the general biology of the virus. The application of a series of biochemical, molecular, and biological assays revealed the following. (i) Proteolytic analysis of the three virion types of CCMV assembled individually in planta revealed that, while retaining the structural integrity, C1V and C2V virions released peptide regions encompassing the N-terminal arginine-rich RNA binding motif. In contrast, a minor population of the C3+4V virion type was sensitive to trypsin-releasing peptides encompassing the entire capsid protein region. (ii) The wild-type CCMV virions purified from cowpea are highly susceptible to trypsin digestion, while those from Nicotiana benthamiana remained resistant, and (iii) finally, the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis evaluated the relative dynamics of C3+4V and B3+4V virions assembled under the control of the homologous versus heterologous replicase. The role of viral replicase in modulating the capsid dynamics was evident by the differential sensitivity to protease exhibited by B3+4V and C3+4V virions assembled under the homologous versus heterologous replicase. Our results collectively conclude that constant modulation of capsid dynamics by the host and viral replicase is obligatory for successful infection. IMPORTANCE Infectious virus particles or virions are considered static structures and undergo various conformational transitions to replicate and infect many eukaryotic cells. In viruses, conformational changes are essential for establishing infection and evolution. Although viral capsid fluctuations, referred to as dynamics or breathing, have been well studied in RNA viruses pathogenic to animals, such information is limited among plant viruses. The primary focus of this study is to address how capsid dynamics of plant-pathogenic RNA viruses, namely, Cowpea chlorotic mottle (CCMV) and Brome mosaic virus (BMV), are modulated by the host and viral replicase. The results presented have improved and transformed our understanding of the functional relationship between capsid dynamics and the general biology of the virus. They are likely to provide stimulus to extend similar studies to viruses pathogenic to eukaryotic organisms.
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Affiliation(s)
- Antara Chakravarty
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
| | - A. L. N. Rao
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
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4
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Shrestha N, Duvall MR, Bujarski JJ. Variability among the Isolates of Broad Bean Mottle Virus and Encapsidation of Host RNAs. Pathogens 2022; 11:pathogens11070817. [PMID: 35890061 PMCID: PMC9321246 DOI: 10.3390/pathogens11070817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/03/2022] [Accepted: 07/18/2022] [Indexed: 02/05/2023] Open
Abstract
Broad bean mottle bromovirus infects legume plants and is transmissible by insects. Several broad bean mottle virus (BBMV) isolates have been identified, including one in England (isolate Ba) and five in the Mediterranean countries: Libya (LyV), Morocco (MV), Syria (SV), Sudan (TU) and Tunisia (TV). Previously, we analyzed the nucleotide sequence of the Ba RNA and here we report on and compare it with another five Mediterranean variants. The RNA segments in the latter ones were extensively homologous, with some SNPs, single nucleotide deletions and insertions, while the number of mutations was higher in isolate Ba. Both the 5′ and 3′ untranslated terminal regions (UTRs) among the corresponding RNAs are highly conserved, reflecting their functionality in virus replication. The AUG initiation codons are within suboptimal contexts, possibly to adjust/regulate translation. The proteins 1a, 2a, 3a and coat protein (CP) are almost identical among the five isolates, but in Ba they have more amino acid (aa) substitutions. Phylogenetic analysis revealed the isolates from Morocco and Syria clustering with the isolate from England, while the variants from Libya, Tunisia and Sudan created a different clade. The BBMV isolates encapsidate a high content of host (ribosomal and messenger) RNAs. Our studies present BBMV as a useful model for bromoviruses infecting legumes.
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Affiliation(s)
- Nipin Shrestha
- Correspondence: (N.S.); (J.J.B.); Tel.: +1-305-684-2589 (N.S.); +1-815-753-0601 (J.J.B.); Fax: +1-815-753-7855 (J.J.B.)
| | | | - Jozef J. Bujarski
- Correspondence: (N.S.); (J.J.B.); Tel.: +1-305-684-2589 (N.S.); +1-815-753-0601 (J.J.B.); Fax: +1-815-753-7855 (J.J.B.)
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5
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Adlhart M, Poetsch F, Hlevnjak M, Hoogmoed M, Polyansky A, Zagrovic B. Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses. Nucleic Acids Res 2022; 50:4054-4067. [PMID: 35357492 PMCID: PMC9023274 DOI: 10.1093/nar/gkac202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 02/02/2023] Open
Abstract
During packaging in positive-sense single-stranded RNA (+ssRNA) viruses, coat proteins (CPs) interact directly with multiple regions in genomic RNA (gRNA), but the underlying physicochemical principles remain unclear. Here we analyze the high-resolution cryo-EM structure of bacteriophage MS2 and show that the gRNA/CP binding sites, including the known packaging signal, overlap significantly with regions where gRNA nucleobase-density profiles match the corresponding CP nucleobase-affinity profiles. Moreover, we show that the MS2 packaging signal corresponds to the global minimum in gRNA/CP interaction energy in the unstructured state as derived using a linearly additive model and knowledge-based nucleobase/amino-acid affinities. Motivated by this, we predict gRNA/CP interaction sites for a comprehensive set of 1082 +ssRNA viruses. We validate our predictions by comparing them with site-resolved information on gRNA/CP interactions derived in SELEX and CLIP experiments for 10 different viruses. Finally, we show that in experimentally studied systems CPs frequently interact with autologous coding regions in gRNA, in agreement with both predicted interaction energies and a recent proposal that proteins in general tend to interact with own mRNAs, if unstructured. Our results define a self-consistent framework for understanding packaging in +ssRNA viruses and implicate interactions between unstructured gRNA and CPs in the process.
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Affiliation(s)
- Marlene Adlhart
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
| | - Florian Poetsch
- Institute for Physiology and Pathophysiology, Center for Medical Research, Johannes Kepler University of Linz, Huemerstraße 3-5, 4020 Linz, Austria
| | - Mario Hlevnjak
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Megan Hoogmoed
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
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6
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Wu S, Li X, Wang G. tRNA-like structures and their functions. FEBS J 2021; 289:5089-5099. [PMID: 34117728 DOI: 10.1111/febs.16070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 06/10/2021] [Indexed: 11/27/2022]
Abstract
tRNA-like structures (TLSs) were first identified in the RNA genomes of turnip yellow mosaic virus. Since then, TLSs have been found in many other species including mammals, and the RNAs harboring these structures range from viral genomic RNAs to mRNAs and noncoding RNAs. Some progress has also been made on understanding their functions that include regulation of RNA replication, translation enhancement, RNA-protein interaction, and more. In this review, we summarize the current knowledge about the regulations and functions of these TLSs. Possible future directions of the field are also briefly discussed.
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Affiliation(s)
- Sipeng Wu
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Xiang Li
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Geng Wang
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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7
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Chakravarty A, Rao AL. The interplay between capsid dynamics and pathogenesis in tripartite bromoviruses. Curr Opin Virol 2021; 47:45-51. [PMID: 33517133 DOI: 10.1016/j.coviro.2020.12.005] [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: 11/05/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 11/18/2022]
Abstract
Infectious virus capsids or virions are considered static structures and undergo various conformational transitions to replicate and infect a wide range of eukaryotic cells. Therefore, virus capsids must be stable enough to overcome the physicochemical environment and flexible enough to reorganize their biologically relevant surface peptides for optimal interaction with the host machinery. Although viral capsid fluctuations, referred to as dynamics or breathing, have been well studied in RNA viruses pathogenic to animals, such information is limited among plant viruses. However, more recent attempts have been made in characterizing the capsid dynamics in the plant virus genus bromovirus characterized by having a tripartite, positive-sense RNA genome. Using the available research data on the genus bromovirus members, this review is focused on updating the readers on the interrelationships between the viral capsid dynamics and host-pathogen interactions.
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Affiliation(s)
- Antara Chakravarty
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521-0122, United States
| | - Ayala Ln Rao
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521-0122, United States.
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Beren C, Cui Y, Chakravarty A, Yang X, Rao ALN, Knobler CM, Zhou ZH, Gelbart WM. Genome organization and interaction with capsid protein in a multipartite RNA virus. Proc Natl Acad Sci U S A 2020; 117:10673-10680. [PMID: 32358197 PMCID: PMC7245085 DOI: 10.1073/pnas.1915078117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content-specifically, RNAs 3 and 4-assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific "packaging signals" throughout the viral RNA to package their monopartite genomes.
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Affiliation(s)
- Christian Beren
- Department of Chemistry & Biochemistry, University of California, Los Angeles, CA 90095
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
| | - Antara Chakravarty
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Xue Yang
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095
| | - A L N Rao
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521;
| | - Charles M Knobler
- Department of Chemistry & Biochemistry, University of California, Los Angeles, CA 90095
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, CA 90095;
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095
| | - William M Gelbart
- Department of Chemistry & Biochemistry, University of California, Los Angeles, CA 90095;
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
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9
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Unravelling the Stability and Capsid Dynamics of the Three Virions of Brome Mosaic Virus Assembled Autonomously In Vivo. J Virol 2020; 94:JVI.01794-19. [PMID: 31996436 DOI: 10.1128/jvi.01794-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022] Open
Abstract
Viral capsids are dynamic assemblies that undergo controlled conformational transitions to perform various biological functions. The replication-derived four-molecule RNA progeny of Brome mosaic virus (BMV) is packaged by a single capsid protein (CP) into three types of morphologically indistinguishable icosahedral virions with T=3 quasisymmetry. Type 1 (B1V) and type 2 (B2V) virions package genomic RNA1 and RNA2, respectively, while type 3 (B3+4V) virions copackage genomic RNA3 (B3) and its subgenomic RNA4 (sgB4). In this study, the application of a robust Agrobacterium-mediated transient expression system allowed us to assemble each virion type separately in planta Experimental approaches analyzing the morphology, size, and electrophoretic mobility failed to distinguish between the virion types. Thermal denaturation analysis and protease-based peptide mass mapping experiments were used to analyze stability and the conformational dynamics of the individual virions, respectively. The crystallographic structure of the BMV capsid shows four trypsin cleavage sites (K65, R103, K111, and K165 on the CP subunits) exposed on the exterior of the capsid. Irrespective of the digestion time, while retaining their capsid structural integrity, B1V and B2V released a single peptide encompassing amino acids 2 to 8 of the N-proximal arginine-rich RNA binding motif. In contrast, B3+4V capsids were unstable with trypsin, releasing several peptides in addition to the peptides encompassing four predicted sites exposed on the capsid exterior. These results, demonstrating qualitatively different dynamics for the three types of BMV virions, suggest that the different RNA genes they contain may have different translational timing and efficiency and may even impart different structures to their capsids.IMPORTANCE The majority of viruses contain RNA genomes protected by a shell of capsid proteins. Although crystallographic studies show that viral capsids are static structures, accumulating evidence suggests that, in solution, virions are highly dynamic assemblies. The three genomic RNAs (RNA1, -2, and -3) and a single subgenomic RNA (RNA4) of Brome mosaic virus (BMV), an RNA virus pathogenic to plants, are distributed among three physically homogeneous virions. This study examines the thermal stability by differential scanning fluorimetry (DSF) and capsid dynamics by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analyses following trypsin digestion of the three virions assembled separately in vivo using the Agrobacterium-mediated transient expression approach. The results provide compelling evidence that virions packaging genomic RNA1 and -2 are distinct from those copackaging RNA3 and -4 in their stability and dynamics, suggesting that RNA-dependent capsid dynamics play an important biological role in the viral life cycle.
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10
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Bond KM, Lyktey NA, Tsvetkova IB, Dragnea B, Jarrold MF. Disassembly Intermediates of the Brome Mosaic Virus Identified by Charge Detection Mass Spectrometry. J Phys Chem B 2020; 124:2124-2131. [PMID: 32141748 DOI: 10.1021/acs.jpcb.0c00008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Capsid disassembly and genome release are critical steps in the lifecycle of a virus. However, their mechanisms are poorly understood, both in vivo and in vitro. Here, we have identified two in vitro disassembly pathways of the brome mosaic virus (BMV) by charge detection mass spectrometry and transmission electron microscopy. When subjected to a pH jump to a basic environment at low ionic strength, protein-RNA interactions are disrupted. Under these conditions, BMV appears to disassemble mainly through a global cleavage event into two main fragments: a near complete capsid that has released the RNA and the released RNA complexed to a small number of the capsid proteins. Upon slow buffer exchange to remove divalent cations at neutral pH, capsid protein interactions are disrupted. The BMV virions swell but there is no measurable loss of the RNA. Some of the virions break into small fragments, leading to an increase in the abundance of species with masses less than 1 MDa. The peak attributed to the BMV virion shifts to a higher mass with time. The mass increase is attributed to additional capsid proteins associating with the disrupted capsid protein-RNA complex, where the RNA is presumably partially exposed. It is likely that this pathway is more closely related to how the capsid disassembles in vivo, as it offers the advantage of protecting the RNA with the capsid protein until translation begins.
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Affiliation(s)
- Kevin M Bond
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Nicholas A Lyktey
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Irina B Tsvetkova
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Bogdan Dragnea
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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11
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Richert-Pöggeler KR, Franzke K, Hipp K, Kleespies RG. Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses. Front Microbiol 2019; 9:3255. [PMID: 30666247 PMCID: PMC6330349 DOI: 10.3389/fmicb.2018.03255] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/14/2018] [Indexed: 01/29/2023] Open
Abstract
The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).
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Affiliation(s)
- Katja R. Richert-Pöggeler
- Federal Research Center for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Braunschweig, Germany
| | - Kati Franzke
- Institute of Infectiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Regina G. Kleespies
- Federal Research Centre for Cultivated Plants, Institute for Biological Control, Julius Kühn Institute, Darmstadt, Germany
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12
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Molecular and biological factors regulating the genome packaging in single-strand positive-sense tripartite RNA plant viruses. Curr Opin Virol 2018; 33:113-119. [DOI: 10.1016/j.coviro.2018.07.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/20/2018] [Accepted: 07/31/2018] [Indexed: 12/11/2022]
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13
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Shrestha N, Weber PH, Burke SV, Wysocki WP, Duvall MR, Bujarski JJ. Next generation sequencing reveals packaging of host RNAs by brome mosaic virus. Virus Res 2018; 252:82-90. [PMID: 29753892 DOI: 10.1016/j.virusres.2018.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/05/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022]
Abstract
Although RNA viruses evolved the mechanisms of specific encapsidation, miss-packaging of cellular RNAs has been reported in such RNA virus systems as flock house virus or cucumber necrosis virus. To find out if brome mosaic virus (BMV), a tripartite RNA virus, can package cellular RNAs, BMV was propagated in barley and in Nicotiana benthamiana hosts, purified by cesium chloride (CsCl) gradient ultracentrifugation followed by nuclease treatment to remove any contaminating cellular (host) RNAs. The extracted virion RNA was then sequenced by using next-generation sequencing (NGS RNA-Seq) with the Illumina protocol. Bioinformatic analysis revealed the content of host RNAs ranging from 0.07% for BMV extracted from barley to 0.10% for the virus extracted from N. benthamiana. The viruses from two sources appeared to co-encapsidate different patterns of host-RNAs, including ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) but also mitochondrial and plastid RNAs and, interestingly, transposable elements, both transposons and retrotransposons. Our data reveal that BMV virions can carry host RNAs, having a potential to mediate horizontal gene transfer (HGT) in plants.
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Affiliation(s)
- N Shrestha
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA
| | - P H Weber
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA.
| | - S V Burke
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA
| | - W P Wysocki
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA.
| | - M R Duvall
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA
| | - J J Bujarski
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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14
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Jacobs A, Hoover H, Smith E, Clemmer DE, Kim CH, Kao CC. The intrinsically disordered N-terminal arm of the brome mosaic virus coat protein specifically recognizes the RNA motif that directs the initiation of viral RNA replication. Nucleic Acids Res 2018; 46:324-335. [PMID: 29140480 PMCID: PMC5758871 DOI: 10.1093/nar/gkx1087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/28/2017] [Accepted: 10/20/2017] [Indexed: 12/18/2022] Open
Abstract
In the brome mosaic virus (BMV) virion, the coat protein (CP) selectively contacts the RNA motifs that regulate translation and RNA replication (Hoover et al., 2016. J. Virol. 90, 7748). We hypothesize that the unstructured N-terminal arm (NTA) of the BMV CP can specifically recognize RNA motifs. Using ion mobility spectrometry-mass spectrometry, we demonstrate that peptides containing the NTA of the CP were found to preferentially bind to an RNA hairpin motif that directs the initiation of BMV RNA synthesis. RNA binding causes the peptide to change from heterogeneous structures to a single family of structures. Fluorescence anisotropy, fluorescence quenching and size exclusion chromatography experiments all confirm that the NTA can specific recognize the RNA motif. The peptide introduced into plants along with BMV virion increased accumulation of the BMV CP and accelerated the rate of minus-strand RNA synthesis. The intrinsically disordered BMV NTA could thus specifically recognize BMV RNAs to affect viral infection.
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Affiliation(s)
- Alexander Jacobs
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Haley Hoover
- Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Edward Smith
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Chul-Hyun Kim
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - C Cheng Kao
- Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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15
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Strugała A, Bierwagen P, Rybka J, Giersig M, Figlerowicz M, Urbanowicz A. BMV Propagation, Extraction and Purification Using Chromatographic Methods. Bio Protoc 2018; 8:e2935. [DOI: 10.21769/bioprotoc.2935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/06/2018] [Accepted: 07/26/2018] [Indexed: 11/02/2022] Open
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16
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Richert-Pöggeler KR, Franzke K, Hipp K, Kleespies RG. Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses. Front Microbiol 2018. [PMID: 30666247 DOI: 10.3389/fmicb.2018.03255.ecollection] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).
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Affiliation(s)
- Katja R Richert-Pöggeler
- Federal Research Center for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Braunschweig, Germany
| | - Kati Franzke
- Institute of Infectiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Regina G Kleespies
- Federal Research Centre for Cultivated Plants, Institute for Biological Control, Julius Kühn Institute, Darmstadt, Germany
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17
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Alam SB, Reade R, Theilmann J, Rochon D. Evidence for the role of basic amino acids in the coat protein arm region of Cucumber necrosis virus in particle assembly and selective encapsidation of viral RNA. Virology 2017; 512:83-94. [PMID: 28946005 DOI: 10.1016/j.virol.2017.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/31/2017] [Accepted: 09/02/2017] [Indexed: 01/21/2023]
Abstract
Cucumber necrosis virus (CNV) is a T = 3 icosahedral virus with a (+)ssRNA genome. The N-terminal CNV coat protein arm contains a conserved, highly basic sequence ("KGRKPR"), which we postulate is involved in RNA encapsidation during virion assembly. Seven mutants were constructed by altering the CNV "KGRKPR" sequence; the four basic residues were mutated to alanine individually, in pairs, or in total. Virion accumulation and vRNA encapsidation were significantly reduced in mutants containing two or four substitutions and virion morphology was also affected, where both T = 1 and intermediate-sized particles were produced. Mutants with two or four substitutions encapsidated significantly greater levels of truncated RNA than that of WT, suggesting that basic residues in the "KGRKPR" sequence are important for encapsidation of full-length CNV RNA. Interestingly, "KGRKPR" mutants also encapsidated relatively higher levels of host RNA, suggesting that the "KGRKPR" sequence also contributes to selective encapsidation of CNV RNA.
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Affiliation(s)
- Syed Benazir Alam
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, B.C., Canada
| | - Ron Reade
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, B.C., Canada
| | - Jane Theilmann
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, B.C., Canada
| | - D'Ann Rochon
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, B.C., Canada; Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, B.C., Canada.
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18
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Biophysical analysis of BMV virions purified using a novel method. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1068-1069:157-163. [PMID: 29069631 DOI: 10.1016/j.jchromb.2017.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/03/2017] [Accepted: 10/09/2017] [Indexed: 01/12/2023]
Abstract
Brome mosaic virus (BMV) has been successfully loaded with different types of nanoparticles. However, studies concerning its application as a nanoparticle carrier demand high-purity virions in large amounts. Existing BMV purification protocols rely on multiple differential ultracentrifugation runs of the initially purified viral preparation. Herein, we describe an alternative method for BMV purification based on ion-exchange chromatography and size-exclusion chromatography (SEC) yielding 0.2mg of virus from 1g of plant tissue. Our method is of similar efficiency to previously described protocols and can easily be scaled up. The method results in high-quality BMV preparations as confirmed by biophysical analyses, including cryogenic transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS), static light scattering (SLS), and circular dichroism (CD) measurements and attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) spectroscopy. Our results revealed that purified BMV capsids are stable and monodisperse and can be used for further downstream applications. In this work, we also characterize secondary structure and size fluctuations of the BMV virion at different pH values.
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19
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Zeng C, Hernando-Pérez M, Dragnea B, Ma X, van der Schoot P, Zandi R. Contact Mechanics of a Small Icosahedral Virus. PHYSICAL REVIEW LETTERS 2017; 119:038102. [PMID: 28777631 DOI: 10.1103/physrevlett.119.038102] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Indexed: 06/07/2023]
Abstract
A virus binding to a surface causes stress of the virus cage near the contact area. Here, we investigate the potential role of substrate-induced structural perturbation in the mechanical response of virus particles to adsorption. This is particularly relevant to the broad category of viruses stabilized by weak noncovalent interactions. We utilize atomic force microscopy to measure height distributions of the brome mosaic virus upon adsorption from solution on atomically flat substrates and present a continuum model that captures our observations and provides estimates of elastic properties and of the interfacial energy of the virus, without recourse to indentation.
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Affiliation(s)
- Cheng Zeng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | | | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Xiang Ma
- Department of Chemistry, Idaho State University, Pocatello, Idaho 83209, USA
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California at Riverside, 900 University Avenue, Riverside, California 92521, USA
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20
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Wu B, Zwart MP, Sánchez-Navarro JA, Elena SF. Within-host Evolution of Segments Ratio for the Tripartite Genome of Alfalfa Mosaic Virus. Sci Rep 2017; 7:5004. [PMID: 28694514 PMCID: PMC5504059 DOI: 10.1038/s41598-017-05335-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/25/2017] [Indexed: 12/19/2022] Open
Abstract
The existence of multipartite viruses is an intriguing mystery in evolutionary virology. Several hypotheses suggest benefits that should outweigh the costs of a reduced transmission efficiency and of segregation of coadapted genes associated with encapsidating each segment into a different particle. Advantages range from increasing genome size despite high mutation rates, faster replication, more efficient selection resulting from reassortment during mixed infections, better regulation of gene expression, or enhanced virion stability and cell-to-cell movement. However, support for these hypotheses is scarce. Here we report experiments testing whether an evolutionary stable equilibrium exists for the three genomic RNAs of Alfalfa mosaic virus (AMV). Starting infections with different segment combinations, we found that the relative abundance of each segment evolves towards a constant ratio. Population genetic analyses show that the segment ratio at this equilibrium is determined by frequency-dependent selection. Replication of RNAs 1 and 2 was coupled and collaborative, whereas the replication of RNA 3 interfered with the replication of the other two. We found that the equilibrium solution is slightly different for the total amounts of RNA produced and encapsidated, suggesting that competition exists between all RNAs during encapsidation. Finally, we found that the observed equilibrium appears to be host-species dependent.
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Affiliation(s)
- Beilei Wu
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
- Institute of Theoretical Physics, University of Cologne, Cologne, Germany
| | - Jesús A Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain.
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Valencia, Spain.
- The Santa Fe Institute, New Mexico, USA.
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21
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Kao CC, Chuang E, Ford J, Huang J, Podicheti R, Rusch D. Mapping RNA Sequences that Contact Viral Capsid Proteins in Virions. Bio Protoc 2017; 7:e2398. [DOI: 10.21769/bioprotoc.2398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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22
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Abstract
Multipartite viruses have one of the most puzzling genetic organizations found in living organisms. These viruses have several genome segments, each containing only a part of the genetic information, and each individually encapsidated into a separate virus particle. While countless studies on molecular and cellular mechanisms of the infection cycle of multipartite viruses are available, just as for other virus types, very seldom is their lifestyle questioned at the viral system level. Moreover, the rare available “system” studies are purely theoretical, and their predictions on the putative benefit/cost balance of this peculiar genetic organization have not received experimental support. In light of ongoing progresses in general virology, we here challenge the current hypotheses explaining the evolutionary success of multipartite viruses and emphasize their shortcomings. We also discuss alternative ideas and research avenues to be explored in the future in order to solve the long-standing mystery of how viral systems composed of interdependent but physically separated information units can actually be functional.
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23
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Delalande L, Tsvetkova IB, Zeng C, Bond K, Jarrold MF, Dragnea B. Catching a virus in a molecular net. NANOSCALE 2016; 8:16221-16228. [PMID: 27469039 DOI: 10.1039/c6nr04469g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A metal-organic molecular net composed of tannic acid (TA) and iron(iii) was constructed around the brome mosaic virus (BMV) particle to determine whether the added net could act as a transport barrier for water, and if the net could stabilize the virus in physically or chemically challenging environments. This new virus engineering strategy is expected to provide benefits both in the study and technological applications of viruses. For instance, a virus wrapped in a thin molecular layer could be extracted from solution either in air or vacuum, and its structure, composition and even internal dynamics could be interrogated by methods not compatible with a liquid environment. Atomic force microscopy (AFM) studies of Fe(iii)-TA coated BMV in liquid and in air supported a marked resistance to dehydration when compared to wtBMV. Native charge detection mass spectrometry (CDMS), was employed to estimate the number of molecules in the molecular net which wrapped the virus. The CDMS data suggested that less than one molecular monolayer wrapped the virus. Additionally, it was found, that this very thin molecular coat was sufficient to render the coated viruses resistant to storage conditions that typically lead to virus disassembly over time. A temporary coat imparting increased resistance to disassembly could be useful in adding time delay control or alleviate required storage conditions of engineered viruses for therapeutic purposes.
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Affiliation(s)
- L Delalande
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
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24
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Phosphorylation of the Brome Mosaic Virus Capsid Regulates the Timing of Viral Infection. J Virol 2016; 90:7748-60. [PMID: 27334588 DOI: 10.1128/jvi.00833-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The four brome mosaic virus (BMV) RNAs (RNA1 to RNA4) are encapsidated in three distinct virions that have different disassembly rates in infection. The mechanism for the differential release of BMV RNAs from virions is unknown, since 180 copies of the same coat protein (CP) encapsidate each of the BMV genomic RNAs. Using mass spectrometry, we found that the BMV CP contains a complex pattern of posttranslational modifications. Treatment with phosphatase was found to not significantly affect the stability of the virions containing RNA1 but significantly impacted the stability of the virions that encapsidated BMV RNA2 and RNA3/4. Cryo-electron microscopy reconstruction revealed dramatic structural changes in the capsid and the encapsidated RNA. A phosphomimetic mutation in the flexible N-terminal arm of the CP increased BMV RNA replication and virion production. The degree of phosphorylation modulated the interaction of CP with the encapsidated RNA and the release of three of the BMV RNAs. UV cross-linking and immunoprecipitation methods coupled to high-throughput sequencing experiments showed that phosphorylation of the BMV CP can impact binding to RNAs in the virions, including sequences that contain regulatory motifs for BMV RNA gene expression and replication. Phosphatase-treated virions affected the timing of CP expression and viral RNA replication in plants. The degree of phosphorylation decreased when the plant hosts were grown at an elevated temperature. These results show that phosphorylation of the capsid modulates BMV infection. IMPORTANCE How icosahedral viruses regulate the release of viral RNA into the host is not well understood. The selective release of viral RNA can regulate the timing of replication and gene expression. Brome mosaic virus (BMV) is an RNA virus, and its three genomic RNAs are encapsidated in separate virions. Through proteomic, structural, and biochemical analyses, this work shows that posttranslational modifications, specifically, phosphorylation, on the capsid protein regulate the capsid-RNA interaction and the stability of the virions and affect viral gene expression. Mutational analysis confirmed that changes in modification affected virion stability and the timing of viral infection. The mechanism for modification of the virion has striking parallels to the mechanism of regulation of chromatin packaging by nucleosomes.
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25
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Rolfsson Ó, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG. Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol 2016; 428:431-48. [PMID: 26608810 PMCID: PMC4751978 DOI: 10.1016/j.jmb.2015.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/06/2015] [Accepted: 11/08/2015] [Indexed: 01/20/2023]
Abstract
Using cross-linking coupled to matrix-assisted laser desorption/ionization mass spectrometry and CLIP-Seq sequencing, we determined the peptide and oligonucleotide sequences at the interfaces between the capsid proteins and the genomic RNA of bacteriophage MS2. The results suggest that the same coat protein (CP)-RNA and maturation protein (MP)-RNA interfaces are used in every viral particle. The portions of the viral RNA in contact with CP subunits span the genome, consistent with a large number of discrete and similar contacts within each particle. Many of these sites match previous predictions of the locations of multiple, dispersed and degenerate RNA sites with cognate CP affinity termed packaging signals (PSs). Chemical RNA footprinting was used to compare the secondary structures of protein-free genomic fragments and the RNA in the virion. Some PSs are partially present in protein-free RNA but others would need to refold from their dominant solution conformations to form the contacts identified in the virion. The RNA-binding peptides within the MP map to two sections of the N-terminal half of the protein. Comparison of MP sequences from related phages suggests a similar arrangement of RNA-binding sites, although these N-terminal regions have only limited sequence conservation. In contrast, the sequences of the C-termini are highly conserved, consistent with them encompassing pilin-binding domains required for initial contact with host cells. These results provide independent and unambiguous support for the assembly of MS2 virions via a PS-mediated mechanism involving a series of induced-fit viral protein interactions with RNA.
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Affiliation(s)
- Óttar Rolfsson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefani Middleton
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA; The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Baochang Fan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Robert Vaughan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Eric Dykeman
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - James Ford
- The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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26
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Fan B, Ni P, Kao CC. Mapping RNA interactions to proteins in virions using CLIP-Seq. Methods Mol Biol 2016; 1297:213-24. [PMID: 25896006 DOI: 10.1007/978-1-4939-2562-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
RNA nanotechnology often involves protein-RNA complexes that require significant understanding of how the proteins and RNAs contact each other. The CLIP-Seq (cross-linking immunoprecipitation, and DNA sequencing) protocol can be used to probe the RNA molecules that interact with proteins. We have optimized the procedures for RNA fragmentation, immunoprecipitation, and library construction in CLIP-Seq to map the interactions between the RNA and the capsid of a simple positive-strand RNA virus. The results show that distinct portions of the viral RNA contact the capsid. The protocol should be applicable to other RNA virions and also RNA-protein nanoparticles.
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Affiliation(s)
- Baochang Fan
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne St., 201A Simon Hall, Bloomington, IN, 47405, USA
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27
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Stockley PG, White SJ, Dykeman E, Manfield I, Rolfsson O, Patel N, Bingham R, Barker A, Wroblewski E, Chandler-Bostock R, Weiß EU, Ranson NA, Tuma R, Twarock R. Bacteriophage MS2 genomic RNA encodes an assembly instruction manual for its capsid. BACTERIOPHAGE 2016; 6:e1157666. [PMID: 27144089 PMCID: PMC4836477 DOI: 10.1080/21597081.2016.1157666] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
Using RNA-coat protein crosslinking we have shown that the principal RNA recognition surface on the interior of infectious MS2 virions overlaps with the known peptides that bind the high affinity translational operator, TR, within the phage genome. The data also reveal the sequences of genomic fragments in contact with the coat protein shell. These show remarkable overlap with previous predictions based on the hypothesis that virion assembly is mediated by multiple sequences-specific contacts at RNA sites termed Packaging Signals (PSs). These PSs are variations on the TR stem-loop sequence and secondary structure. They act co-operatively to regulate the dominant assembly pathway and ensure cognate RNA encapsidation. In MS2, they also trigger conformational change in the dimeric capsomere creating the A/B quasi-conformer, 60 of which are needed to complete the T=3 capsid. This is the most compelling demonstration to date that this ssRNA virus, and by implications potentially very many of them, assemble via a PS-mediated assembly mechanism.
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Affiliation(s)
- Peter G. Stockley
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Simon J. White
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Eric Dykeman
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Iain Manfield
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, University of Iceland Biomedical Center, Reykjavik, Iceland
| | - Nikesh Patel
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Richard Bingham
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Amy Barker
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Emma Wroblewski
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | | | - Eva U. Weiß
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Neil A. Ranson
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Roman Tuma
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Reidun Twarock
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
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28
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Nikitin N, Trifonova E, Evtushenko E, Kirpichnikov M, Atabekov J, Karpova O. Comparative Study of Non-Enveloped Icosahedral Viruses Size. PLoS One 2015; 10:e0142415. [PMID: 26545232 PMCID: PMC4636260 DOI: 10.1371/journal.pone.0142415] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/20/2015] [Indexed: 11/18/2022] Open
Abstract
Now, as before, transmission electron microscopy (TEM) is a widely used technique for the determination of virions size. In some studies, dynamic light scattering (DLS) has also been applied for this purpose. Data obtained by different authors and using different methods could vary significantly. The process of TEM sample preparation involves drying on the substrate, which can cause virions to undergo morphology changes. Therefore, other techniques should be used for measurements of virions size in liquid, (i.e. under conditions closer to native). DLS and nanoparticle tracking analysis (NTA) provide supplementary data about the virions hydrodynamic diameter and aggregation state in liquid. In contrast to DLS, NTA data have a higher resolution and also are less sensitive to minor admixtures. In the present work, the size of non-enveloped icosahedral viruses of different nature was analyzed by TEM, DLS and NTA: the viruses used were the encephalomyocarditis virus (animal virus), and cauliflower mosaic virus, brome mosaic virus and bean mild mosaic virus (plant viruses). The same, freshly purified, samples of each virus were used for analysis using the different techniques. The results were compared with earlier published data and description databases. DLS data about the hydrodynamic diameter of bean mild mosaic virus, and NTA data for all examined viruses, were obtained for the first time. For all virus samples, the values of size obtained by TEM were less than virions sizes determined by DLS and NTA. The contribution of the electrical double layer (EDL) in virions hydrodynamic diameter was evaluated. DLS and NTA data adjusted for EDL thickness were in better agreement with TEM results.
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Affiliation(s)
| | | | | | | | | | - Olga Karpova
- Lomonosov Moscow State University, Moscow, Russia
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29
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Kalnciema I, Balke I, Skrastina D, Ose V, Zeltins A. Potato Virus M-Like Nanoparticles: Construction and Characterization. Mol Biotechnol 2015; 57:982-92. [DOI: 10.1007/s12033-015-9891-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Fan B, Sutandy FXR, Syu GD, Middleton S, Yi G, Lu KY, Chen CS, Kao CC. Heterogeneous Ribonucleoprotein K (hnRNP K) Binds miR-122, a Mature Liver-Specific MicroRNA Required for Hepatitis C Virus Replication. Mol Cell Proteomics 2015; 14:2878-86. [PMID: 26330540 DOI: 10.1074/mcp.m115.050344] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Indexed: 12/12/2022] Open
Abstract
Heterogeneous ribonucleoprotein K (hnRNP K) binds to the 5' untranslated region of the hepatitis C virus (HCV) and is required for HCV RNA replication. The hnRNP K binding site on HCV RNA overlaps with the sequence recognized by the liver-specific microRNA, miR-122. A proteome chip containing ∼17,000 unique human proteins probed with miR-122 identified hnRNP K as one of the strong binding proteins. In vitro kinetic study showed hnRNP K binds miR-122 with a nanomolar dissociation constant, in which the short pyrimidine-rich residues in the central and 3' portion of the miR-122 were required for hnRNP K binding. In liver hepatocytes, miR-122 formed a coprecipitable complex with hnRNP K. High throughput Illumina DNA sequencing of the RNAs precipitated with hnRNP K was enriched for mature miR-122. SiRNA knockdown of hnRNP K in human hepatocytes reduced the levels of miR-122. These results show that hnRNP K is a cellular protein that binds and affects the accumulation of miR-122. Its ability to also bind HCV RNA near the miR-122 binding site suggests a role for miR-122 recognition of HCV RNA.
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Affiliation(s)
- Baochang Fan
- From the ‡Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - F X Reymond Sutandy
- §Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
| | - Guan-Da Syu
- §Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
| | - Stefani Middleton
- From the ‡Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Guanghui Yi
- From the ‡Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Kuan-Yi Lu
- §Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
| | - Chien-Sheng Chen
- §Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
| | - C Cheng Kao
- From the ‡Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA;
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31
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Kitayama M, Hoover H, Middleton S, Kao CC. Brome mosaic virus Infection of Rice Results in Decreased Accumulation of RNA1. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:626-632. [PMID: 26024443 DOI: 10.1094/mpmi-12-14-0389-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Brome mosaic virus (BMV) (the Russian strain) infects monocot plants and has been studied extensively in barley and wheat. Here, we report BMV can systemically infect rice (Oryza sativa var. japonica), including cultivars in which the genomes have been determined. The BMV capsid protein can be found throughout the inoculated plants. However, infection in rice exhibits delayed symptom expression or no symptoms when compared with wheat (Triticum aestivum). The sequences of BMV RNAs isolated from rice did not reveal any nucleotide changes in RNA1 or RNA2, while RNA3 had only one synonymous nucleotide change from the inoculum sequence. Preparations of purified BMV virions contained RNA1 at a significantly reduced level relative to the other two RNAs. Analysis of BMV RNA replication in rice revealed that minus-strand RNA1 was replicated at a reduced rate when compared with RNA2. Thus, rice appears to either inhibit RNA1 replication or lacks a sufficient amount of a factor needed to support efficient RNA1 replication.
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32
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Geraets JA, Dykeman EC, Stockley PG, Ranson NA, Twarock R. Asymmetric genome organization in an RNA virus revealed via graph-theoretical analysis of tomographic data. PLoS Comput Biol 2015; 11:e1004146. [PMID: 25793998 PMCID: PMC4368512 DOI: 10.1371/journal.pcbi.1004146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Cryo-electron microscopy permits 3-D structures of viral pathogens to be determined in remarkable detail. In particular, the protein containers encapsulating viral genomes have been determined to high resolution using symmetry averaging techniques that exploit the icosahedral architecture seen in many viruses. By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection. Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization of viral genomes in proximity to the capsid in such viruses. The method uses geometric constraints on genome organization, formulated based on knowledge of icosahedrally-averaged reconstructions and the roles of the RNA-capsid protein contacts, to analyse cryo-electron tomographic data. We apply this method to the low-resolution tomographic data of a model virus and infer the unique asymmetric organization of its genome in contact with the protein shell of the capsid. This opens unprecedented opportunities to analyse viral genomes, revealing conserved structural features and mechanisms that can be targeted in antiviral drug design.
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Affiliation(s)
- James A Geraets
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Eric C Dykeman
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
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33
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Rao ALN, Cheng Kao C. The brome mosaic virus 3' untranslated sequence regulates RNA replication, recombination, and virion assembly. Virus Res 2015; 206:46-52. [PMID: 25687214 DOI: 10.1016/j.virusres.2015.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 11/18/2022]
Abstract
The 3' untranslated region in each of the three genomic RNAs of Brome mosaic virus (BMV) is highly homologous and contains a sequence that folds into a tRNA-like structure (TLS). Experiments performed over the past four decades revealed that the BMV 3' TLS regulates many important steps in BMV infection. This review summarizes in vitro and in vivo studies of the roles of the BMV 3' TLS functioning as a minus-strand promoter, in RNA recombination, and to nucleate virion assembly.
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Affiliation(s)
- A L N Rao
- Department of Plant Pathology, University of California, Riverside, CA 925210-0122, USA.
| | - C Cheng Kao
- Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
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34
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Rao ALN, Chaturvedi S, Garmann RF. Integration of replication and assembly of infectious virions in plant RNA viruses. Curr Opin Virol 2014; 9:61-6. [DOI: 10.1016/j.coviro.2014.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/04/2014] [Accepted: 09/18/2014] [Indexed: 02/08/2023]
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35
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The tripartite virions of the brome mosaic virus have distinct physical properties that affect the timing of the infection process. J Virol 2014; 88:6483-91. [PMID: 24672042 DOI: 10.1128/jvi.00377-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The three subsets of virions that comprise the Brome mosaic virus (BMV) were previously thought to be indistinguishable. This work tested the hypothesis that distinct capsid-RNA interactions in the BMV virions allow different rates of viral RNA release. Several results support distinct interactions between the capsid and the BMV genomic RNAs. First, the deletion of the first eight residues of the BMV coat protein (CP) resulted in the RNA1-containing particles having altered morphologies, while those containing RNA2 were unaffected. Second, subsets of the BMV particles separated by density gradients into a pool enriched for RNA1 (B1) and for RNA2 and RNA3/4 (B2.3/4) were found to have different physiochemical properties. Compared to the B2.3/4 particles, the B1 particles were more sensitive to protease digestion and had greater resistivity to nanoindentation by atomic force microscopy and increased susceptibility to nuclease digestion. Mapping studies showed that portions of the arginine-rich N-terminal tail of the CP could interact with RNA1. Mutational analysis in the putative RNA1-contacting residues severely reduced encapsidation of BMV RNA1 without affecting the encapsidation of RNA2. Finally, during infection of plants, the more easily released RNA1 accumulated to higher levels early in the infection. IMPORTANCE Viruses with genomes packaged in distinct virions could theoretically release the genomes at different times to regulate the timing of gene expression. Using an RNA virus composed of three particles, we demonstrated that the RNA in one of the virions is released more easily than the other two in vitro. The differential RNA release is due to distinct interactions between the viral capsid protein and the RNAs. The ease of RNA release is also correlated with the more rapid accumulation of that RNA in infected plants. Our study identified a novel role for capsid-RNA interactions in the regulation of a viral infection.
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