1
|
Liu Q, Li M, Dong X, Zuo C, Nie Z, Zhang Z, Han CG, Wang Y. Development of full-length infectious cDNA clones and host range identification of an echinacea strain of tobacco streak virus. Virology 2024; 593:110013. [PMID: 38373359 DOI: 10.1016/j.virol.2024.110013] [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: 11/25/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
Tobacco streak virus induces severe diseases on a wide range of plants and becomes an emerging threat to crop yields. However, the infectious clones of TSV remain to be developed for reverse genetics studies. Here, we obtained the full genome sequence of a TSV-CNB isolate and analyzed the phylogenetic characteristics. Subsequently, we developed the full-length infectious cDNA clones of TSV-CNB driven by 35 S promoter using yeast homologous recombination. Furthermore, the host range of TSV-CNB isolate was determined by Agrobacterium infiltration and mechanical inoculation. The results reveal that TSV-CNB can infect 10 plant species in 5 families including Glycine max, Vigna radiate, Lactuca sativa var. Ramosa, Dahlia pinnate, E. purpurea, Calendula officinalis, Helianthus annuus, Nicotiana. Benthamiana, Nicotiana tabacum and Chenopodium quinoa. Taken together, the TSV infectious clones will be a useful tool for future studies on viral pathogenesis and host-virus interactions.
Collapse
Affiliation(s)
- Qi Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Menglin Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xuanyu Dong
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Chengxiao Zuo
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Zhangyao Nie
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Zongying Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Cheng-Gui Han
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ying Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
2
|
AL-Saleh MA, Amer MA. Biological and Molecular Variability of Alfalfa mosaic virus Affecting Alfalfa Crop in Riyadh Region. THE PLANT PATHOLOGY JOURNAL 2013; 29:410-7. [PMID: 25288969 PMCID: PMC4174816 DOI: 10.5423/ppj.oa.05.2013.0050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 07/10/2013] [Accepted: 07/13/2013] [Indexed: 06/03/2023]
Abstract
In 2011-2012, sixty nine samples were collected from alfalfa plants showing viral infection symptoms in Riyadh region. Mechanical inoculation with sap prepared from two collected samples out of twenty five possitive for Alfalfa mosaic virus (AMV) by ELISA were produced systemic mosaic on Vigna unguiculata and Nicotiana tabacum, local lesion on Chenopodium amaranticolor and C. quinoa. Vicia faba indicator plants that induce mosaic and mottle with AMV-Sagir isolate and no infection with AMV-Wadi aldawasser isolate. Approximately 700-bp was formed by RT-PCR using AMV coat protein specific primer. Samples from infected alfalfa gave positive results, while healthy plant gave negative result using dot blot hybridization assay. The nucleotide sequences of the Saudi isolates were compared with corresponding viral nucleotide sequences reported in GenBank. The obtained results showed that the AMV from Australia, Brazil, Puglia and China had the highest similarity with AMV-Sajer isolate. While, the AMV from Spain and New Zealaland had the lowest similarity with AMV-Sajer and Wadi aldawasser isolates. The data obtained in this study has been deposited in the GenBank under the accession numbers KC434083 and KC434084 for AMV-Sajer and AMV- Wadialdawasser respectively. This is the first report regarding the gnetic make up of AMV in Saudi Arabia.
Collapse
Affiliation(s)
- Mohammed A. AL-Saleh
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Kingdom of Saudi Arabia. Box 2460, Riyadh 11451
| | - Mahmoud A. Amer
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Kingdom of Saudi Arabia. Box 2460, Riyadh 11451
- Viruses and Phytoplasma Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| |
Collapse
|
3
|
Randić M, Zupan J, Balaban AT, Vikić-Topić D, Plavšić D. Graphical Representation of Proteins. Chem Rev 2010; 111:790-862. [PMID: 20939561 DOI: 10.1021/cr800198j] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Milan Randić
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
| | - Jure Zupan
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
| | - Alexandru T. Balaban
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
| | - Dražen Vikić-Topić
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
| | - Dejan Plavšić
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
| |
Collapse
|
4
|
Zhang Y, Qiu J, Su L. Comparing RNA secondary structures based on 2D graphical representation. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.04.067] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
5
|
Abstract
In this article, we propose a relatively similar measure to compare RNA secondary structures. We first transform an RNA secondary structure into a special sequence representation. Then, on the basis of symbolic sequence complexity, we obtain the relative distance of RNA secondary structures. The examination of similarities/dissimilarities of a set of RNA secondary structures at the 3'-terminus of different viruses illustrates the utility of the approach.
Collapse
Affiliation(s)
- Chun Li
- Department of Mathematics, Bohai University, Jinzhou 121000, People's Republic of China.
| | | | | |
Collapse
|
6
|
Liao B, Wang T, Ding K. On a seven-dimensional representation of RNA secondary structures. MOLECULAR SIMULATION 2005. [DOI: 10.1080/08927020500371332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
7
|
|
8
|
Yao YH, Liao B, Wang TM. A 2D graphical representation of RNA secondary structures and the analysis of similarity/dissimilarity based on it. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
9
|
Guogas LM, Laforest SM, Gehrke L. Coat protein activation of alfalfa mosaic virus replication is concentration dependent. J Virol 2005; 79:5752-61. [PMID: 15827190 PMCID: PMC1082755 DOI: 10.1128/jvi.79.9.5752-5761.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Alfalfa mosaic virus (AMV) and ilarvirus RNAs are infectious only in the presence of the viral coat protein; therefore, an understanding of coat protein's function is important for defining viral replication mechanisms. Based on in vitro replication experiments, the conformational switch model states that AMV coat protein blocks minus-strand RNA synthesis (R. C. Olsthoorn, S. Mertens, F. T. Brederode, and J. F. Bol, EMBO J. 18:4856-4864, 1999), while another report states that coat protein present in an inoculum is required to permit minus-strand synthesis (L. Neeleman and J. F. Bol, Virology 254:324-333, 1999). Here, we report on experiments that address these contrasting results with a goal of defining coat protein's function in the earliest stages of AMV replication. To detect coat-protein-activated AMV RNA replication, we designed and characterized a subgenomic luciferase reporter construct. We demonstrate that activation of viral RNA replication by coat protein is concentration dependent; that is, replication was strongly stimulated at low coat protein concentrations but decreased progressively at higher concentrations. Genomic RNA3 mutations preventing coat protein mRNA translation or disrupting coat protein's RNA binding domain diminished replication. The data indicate that RNA binding and an ongoing supply of coat protein are required to initiate replication on progeny genomic RNA transcripts. The data do not support the conformational switch model's claim that coat protein inhibits the initial stages of viral RNA replication. Replication activation may correlate with low local coat protein concentrations and low coat protein occupancy on the multiple binding sites present in the 3' untranslated regions of the viral RNAs.
Collapse
Affiliation(s)
- Laura M Guogas
- HST Division, MIT E25-545, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | | |
Collapse
|
10
|
|
11
|
Guogas LM, Filman DJ, Hogle JM, Gehrke L. Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication. Science 2005; 306:2108-11. [PMID: 15604410 PMCID: PMC1500904 DOI: 10.1126/science.1103399] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. Alternating AUGC residues have opposite orientation, and they base pair in different adjacent duplexes. Localized RNA backbone reversals stabilized by arginine-guanine interactions place the adenosines and guanines in reverse order in the duplex. The results suggest that a uniform, organized 3' conformation, similar to that found on viral RNAs with transfer RNA-like ends, may be essential for replication.
Collapse
Affiliation(s)
- Laura M Guogas
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | |
Collapse
|
12
|
Yao YH, Nan XY, Wang TM. A class of 2D graphical representations of RNA secondary structures and the analysis of similarity based on them. J Comput Chem 2005; 26:1339-46. [PMID: 16021599 DOI: 10.1002/jcc.20271] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Based on the concepts of cell and system of graphical representation, a class of 2D graphical representations of RNA secondary structures are given in terms of classifications of bases of nucleic acids. The representations can completely avoid loss of information associated with crossing and overlapping of the corresponding curve. As an application, we make quantitative comparisons for a set of RNA secondary structures at the 3'-terminus of different viruses based on the graphical representations. The examination of similarities/dissimilarities illustrates the utility of the approach.
Collapse
Affiliation(s)
- Yu-Hua Yao
- Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, People's Republic of China
| | | | | |
Collapse
|
13
|
Abstract
In this paper, we proposed a 3-D graphical representation of RNA secondary structures. Based on this representation, we outline an approach by constructing a 3-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with RNA secondary structure. The examination of similarities/dissimilarities among the secondary structure at the 3'-terminus of different viruses illustrates the utility of the approach.
Collapse
Affiliation(s)
- B Liao
- Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, China.
| | | |
Collapse
|
14
|
Laforest SM, Gehrke L. Spatial determinants of the alfalfa mosaic virus coat protein binding site. RNA (NEW YORK, N.Y.) 2004; 10:48-58. [PMID: 14681584 PMCID: PMC1370517 DOI: 10.1261/rna.5154104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2003] [Accepted: 09/26/2003] [Indexed: 05/19/2023]
Abstract
The biological functions of RNA-protein complexes are, for the most part, poorly defined. Here, we describe experiments that are aimed at understanding the functional significance of alfalfa mosaic virus RNA-coat protein binding, an interaction that parallels the initiation of viral RNA replication. Peptides representing the RNA-binding domain of the viral coat protein are biologically active in initiating replication and bind to a 39-nt 3'-terminal RNA with a stoichiometry of two peptides: 1 RNA. To begin to understand how RNA-peptide interactions induce RNA conformational changes and initiate replication, the AMV RNA fragment was experimentally manipulated by increasing the interhelical spacing, by interrupting the apparent nucleotide symmetry, and by extending the binding site. In general, both asymmetric and symmetric insertions between two proposed hairpins diminished binding, whereas 5' and 3' extensions had minimal effects. Exchanging the positions of the binding site hairpins resulted in only a moderate decrease in peptide binding affinity without changing the hydroxyl radical footprint protection pattern. To assess biological relevance in viral RNA replication, the nucleotide changes were transferred into infectious genomic RNA clones. RNA mutations that disrupted coat protein binding also prevented viral RNA replication without diminishing coat protein mRNA (RNA 4) translation. These results, coupled with the highly conserved nature of the AUGC865-868 sequence, suggest that the distance separating the two proposed hairpins is a critical binding determinant. The data may indicate that the 5' and 3' hairpins interact with one of the bound peptides to nucleate the observed RNA conformational changes.
Collapse
Affiliation(s)
- Siana M Laforest
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | | |
Collapse
|
15
|
Bol JF. Alfalfa mosaic virus: coat protein-dependent initiation of infection. MOLECULAR PLANT PATHOLOGY 2003; 4:1-8. [PMID: 20569357 DOI: 10.1046/j.1364-3703.2003.00146.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
UNLABELLED SUMMARY Taxonomy: Alfalfa mosaic virus (AMV) is the type species of the genus Alfamovirus and belongs to the family Bromoviridae. In this family, the tripartite RNA genomes of bromo-, cucumo- and probably oleaviruses are infectious as such, whereas infection with the three genomic RNAs of alfamo- and ilarviruses requires addition to the inoculum of a few molecules of coat protein (CP) per RNA molecule. RNAs 1 and 2 encode the replicase proteins P1 and P2, RNA 3 encodes the movement protein and CP. CP is translated from the subgenomic RNA 4. Physical properties: RNAs 1 (3.65 kb), 2 (2.6 kb) and 3 (2.2 kb) are separately encapsidated into bacilliform particles which are 19 nm wide and 35-56 nm long. In addition, the virus preparations contain spheroidal particles each containing two copies of RNA 4 (0.88 kb). Virus particles contain 16-17% RNA and are mainly stabilized by protein-RNA interactions. The 3'-termini of the viral RNAs contain a homologous sequence of 145 nucleotides that can adopt two alternative conformations: one represents a high-affinity binding site for CP, the other resembles a tRNA-like structure and is required for minus-strand promoter activity. Hosts: AMV mostly infects herbaceous plants, but several woody species are included in the natural host range. The experimental and natural host ranges include over 600 species in 70 families. At least 15 aphid species are known to transmit the virus in the stylet-borne or non-persistent manner. Economic importance: AMV is a significant pathogen in alfalfa and sweet clover and can spread from these forages to neighbouring crops like pepper, tobacco or soybean. The recent introduction of the soybean aphid (Aphis glycines) in the mid-west states of the USA has increased the incidence of AMV in soybean. AMV occurs world-wide in potato and is referred to as 'calico mosaic' because of its characteristic symptoms on the foliage. However, the economic importance of AMV in potato is limited. USEFUL WEBSITES <http://www.socgenmicrobiol.org.uk/JGV/080/1089/0801089A.PDF> review paper; <http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/10010001.htm> host range and physical properties; <http://mmtsb.scripps.edu/viper/1amv.html> structural information.
Collapse
Affiliation(s)
- John F Bol
- Institute of Molecular Plant Sciences, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, the Netherlands
| |
Collapse
|
16
|
Hemenway CL, Lommel SA. Manipulating plant viral RNA transcription signals. GENETIC ENGINEERING 2001; 22:171-95. [PMID: 11501376 DOI: 10.1007/978-1-4615-4199-8_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- C L Hemenway
- Departments of Biochemistry Box 7622 & Plant Pathology Box 7616, North Carolina State University, Raleigh, NC 27695, USA
| | | |
Collapse
|
17
|
Dreher TW. FUNCTIONS OF THE 3'-UNTRANSLATED REGIONS OF POSITIVE STRAND RNA VIRAL GENOMES. ANNUAL REVIEW OF PHYTOPATHOLOGY 1999; 37:151-174. [PMID: 11701820 DOI: 10.1146/annurev.phyto.37.1.151] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Positive strand RNA viral genomes are unique in the viral world in serving a dual role as mRNA and replicon. Since the origin of the minus-strand RNA replication intermediate is at the 3'-end of the genome, the 3'-untranslated region (UTR) clearly plays a role in viral RNA replication. The messenger role of this same RNA likely places functional demands on the 3'-UTR to serve roles typical of cellular mRNAs, including the regulation of RNA stability and translation. Current understanding indicates varied roles for positive strand RNA viral 3'-UTRs, with the dominant roles differing between viruses. Three case studies are discussed: turnip yellow mosaic virus RNA, whose 3' tRNA mimicry is thought to negatively regulate minus strand synthesis; brome mosaic virus, whose 3'-UTR contains a unique promoter element directing minus strand synthesis; and tobacco mosaic virus, whose 3'-UTR contains an enhancer of translational expression.
Collapse
Affiliation(s)
- Theo W. Dreher
- Department of Microbiology and Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331-3804; e-mail:
| |
Collapse
|
18
|
Ansel-McKinney P, Gehrke L. RNA determinants of a specific RNA-coat protein peptide interaction in alfalfa mosaic virus: conservation of homologous features in ilarvirus RNAs. J Mol Biol 1998; 278:767-85. [PMID: 9614941 DOI: 10.1006/jmbi.1998.1656] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Alfalfa mosaic virus (AMV) coat protein and tobacco streak virus (TSV) coat protein bind specifically to the 3' untranslated regions of the viral RNAs and are required with the genomic RNAs to initiate virus replication. A combination of nucleotide substitutions, hydroxyl radical footprinting, and ethylation and chemical modification interference analysis has been used to define the RNA determinants important for the specific binding of the 3'-terminal 39 nucleotides of AMV RNA 3/4 (AMV843-881) to an amino-terminal coat protein peptide (CP26). The results demonstrate that potential phosphate and base-specific contacts as well as ribose moieties protected upon peptide binding cluster in lower hairpin stems and flanking AUGC sequences of the viral RNA, without direct involvement of loop nucleotides. Nucleotides identified in the modification-interference analyses as important for RNA-protein interactions are highly conserved among AMV and the ilarvirus RNAs. This RNA sequence homology, coupled with the recent identification of an RNA binding consensus sequence for AMV and ilarvirus coat proteins, provides a framework for understanding the functional equivalence of AMV and TSV coat proteins in binding RNA and activating virus replication and may explain why heterologous AMV and ilarvirus coat protein-RNA mixtures are infectious.
Collapse
Affiliation(s)
- P Ansel-McKinney
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | |
Collapse
|
19
|
Swanson MM, Ansel-McKinney P, Houser-Scott F, Yusibov V, Loesch-Fries LS, Gehrke L. Viral coat protein peptides with limited sequence homology bind similar domains of alfalfa mosaic virus and tobacco streak virus RNAs. J Virol 1998; 72:3227-34. [PMID: 9525649 PMCID: PMC109790 DOI: 10.1128/jvi.72.4.3227-3234.1998] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/1997] [Accepted: 12/12/1997] [Indexed: 02/06/2023] Open
Abstract
An unusual and distinguishing feature of alfalfa mosaic virus (AMV) and ilarviruses such as tobacco streak virus (TSV) is that the viral coat protein is required to activate the early stages of viral RNA replication, a phenomenon known as genome activation. AMV-TSV coat protein homology is limited; however, they are functionally interchangeable in activating virus replication. For example, TSV coat protein will activate AMV RNA replication and vice versa. Although AMV and TSV coat proteins have little obvious amino acid homology, we recently reported that they share an N-terminal RNA binding consensus sequence (Ansel-McKinney et al., EMBO J. 15:5077-5084, 1996). Here, we biochemically compare the binding of chemically synthesized peptides that include the consensus RNA binding sequence and lysine-rich (AMV) or arginine-rich (TSV) environment to 3'-terminal TSV and AMV RNA fragments. The arginine-rich TSV coat protein peptide binds viral RNA with lower affinity than the lysine-rich AMV coat protein peptides; however, the ribose moieties protected from hydroxyl radical attack by the two different peptides are localized in the same area of the predicted RNA structures. When included in an infectious inoculum, both AMV and TSV 3'-terminal RNA fragments inhibited AMV RNA replication, while variant RNAs unable to bind coat protein did not affect replication significantly. The data suggest that RNA binding and genome activation functions may reside in the consensus RNA binding sequence that is apparently unique to AMV and ilarvirus coat proteins.
Collapse
Affiliation(s)
- M M Swanson
- Scottish Crop Research Institute, Invergowrie, Dundee, United Kingdom
| | | | | | | | | | | |
Collapse
|
20
|
Van Rossum CM, Neeleman L, Bol JF. Comparison of the role of 5' terminal sequences of alfalfa mosaic virus RNAs 1, 2, and 3 in viral RNA replication. Virology 1997; 235:333-41. [PMID: 9281513 DOI: 10.1006/viro.1997.8707] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The 5' untranslated regions (UTRs) of the genomic RNAs 1, 2, and 3 of alfalfa mosaic virus (AMV) are 100, 54, and 345 nucleotides (nt) long, respectively, and lack extensive sequence similarity to each other. RNA 3 encodes the movement protein P3 and the coat protein and can be replicated in transgenic tobacco plants expressing the replicase proteins P1 and P2 (P12 plants). 5' Cis-acting sequences involved in RNA 3 replication have been shown to be confined to the 5' UTR. When the 5' UTR of RNA 3 was replaced by the 5' UTRs of RNAs 1 or 2, the recombinant RNA was not infectious to P12 plants. Also, when the P3 gene in RNA 3 was put under the control of a subgenomic promoter and the 5' UTR of this RNA was replaced by 5' terminal RNA 1 sequences of 103 to 860 nt long or RNA 2 sequences of 57 to 612 nt long, no accumulation of the hybrid RNAs was observed. Deletion of the 5' 22 nucleotides of RNA 3 resulted in the accumulation of a major progeny that lacked the 5' 79 nt. However, when the 5' 22 nucleotides of RNA 3 were replaced by the complete 5' UTR of RNA 1 or 5' sequences of RNAs 1, 2, or 3 with a length of 5 to 15 nt, accumulation of the full-length mutant RNAs was observed. The effect of mutations in the 5' viral sequences of 5 to 15 nt was analyzed. It is concluded that although elements within nucleotides 80-345 of the 5' UTR of RNA 3 are sufficient for replication, a specific sequence of 3 to 5 nt is required to target the replicase to an initiation site corresponding to the 5' end of the RNA.
Collapse
Affiliation(s)
- C M Van Rossum
- Gorlaeus Laboratories, Leiden University, Leiden, 2300 RA, The Netherlands
| | | | | |
Collapse
|
21
|
van Rossum CM, Brederode FT, Neeleman L, Bol JF. Functional equivalence of common and unique sequences in the 3' untranslated regions of alfalfa mosaic virus RNAs 1, 2, and 3. J Virol 1997; 71:3811-6. [PMID: 9094656 PMCID: PMC191531 DOI: 10.1128/jvi.71.5.3811-3816.1997] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The 3' untranslated regions (UTRs) of alfalfa mosaic virus (AMV) RNAs 1, 2, and 3 consist of a common 3'-terminal sequence of 145 nucleotides (nt) and upstream sequences of 18 to 34 nt that are unique for each RNA. The common sequence can be folded into five stem-loop structures, A to E, despite the occurrence of 22 nt differences between the three RNAs in this region. Exchange of the common sequences or full-length UTRs between the three genomic RNAs did not affect the replication of these RNAs in vivo, indicating that the UTRs are functionally equivalent. Mutations that disturbed base pairing in the stem of hairpin E reduced or abolished RNA replication, whereas compensating mutations restored RNA replication. In vitro, the 3' UTRs of the three RNAs were recognized with similar efficiencies by the AMV RNA-dependent RNA polymerase (RdRp). A deletion analysis of template RNAs indicated that a 3'-terminal sequence of 127 nt in each of the three AMV RNAs was not sufficient for recognition by the RdRp. Previously, it has been shown that this 127-nt sequence is sufficient for coat protein binding. Apparently, sequences required for recognition of AMV RNAs by the RdRp are longer than sequences required for CP binding.
Collapse
Affiliation(s)
- C M van Rossum
- Institute of Molecular Plant Sciences, Leiden University, The Netherlands
| | | | | | | |
Collapse
|
22
|
Houser-Scott F, Ansel-McKinney P, Cai JM, Gehrke L. In vitro genetic selection analysis of alfalfa mosaic virus coat protein binding to 3'-terminal AUGC repeats in the viral RNAs. J Virol 1997; 71:2310-9. [PMID: 9032367 PMCID: PMC191340 DOI: 10.1128/jvi.71.3.2310-2319.1997] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The coat proteins of alfalfa mosaic virus (AMV) and the related ilarviruses bind specifically to the 3' untranslated regions of the viral RNAs, which contain conserved repeats of the tetranucleotide sequence AUGC. The purpose of this study was to develop a more detailed understanding of RNA sequence and/or structural determinants required for coat protein binding by characterizing the role of the AUGC repeats. Starting with a complex pool of 39-nucleotide RNA molecules containing random substitutions in the AUGC repeats, in vitro genetic selection was used to identify RNAs that bound coat protein. After six iterative rounds of selection, amplification, and reselection, 25% of the RNAs selected from the randomized pool were wild type; that is, they contained all four AUGC sequences. Among the 31 clones analyzed, AUGC was clearly the preferred selected sequence at the four repeats, but some nucleotide sequence variability was observed at AUGC(865-868) if the other three AUGC repeats were present. Variant RNAs that bound coat protein with affinities equal to or greater than that of the wild-type molecule were not selected. To extend the in vitro selection results, RNAs containing specific nucleotide substitutions were transcribed in vitro and tested in coat protein and peptide binding assays. The data strongly suggest that the AUGC repeats provide sequence-specific determinants and contribute to a structural platform for specific coat protein binding. Coat protein may function in maintaining the 3' ends of the genomic RNAs during replication by stabilizing an RNA structure that defines the 3' terminus as the initiation site for minus-strand synthesis.
Collapse
Affiliation(s)
- F Houser-Scott
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | | | | | | |
Collapse
|
23
|
Reusken CB, Bol JF. Structural elements of the 3'-terminal coat protein binding site in alfalfa mosaic virus RNAs. Nucleic Acids Res 1996; 24:2660-5. [PMID: 8758992 PMCID: PMC145989 DOI: 10.1093/nar/24.14.2660] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The 3'-terminal of the three genomic RNAs of alfalfa mosaic virus (AIMV) and ilarviruses contain a number of AUGC-motifs separated by hairpin structures. Binding of coat protein (CP) to such elements in the RNAs is required to initiate infection of these viruses. Determinants for CP binding in the 3'-terminal 39 nucleotides (nt) of AIMV RNA 3 were analyzed by band-shift assays. From the 5'- to 3'-end this 39 nt sequence contains AUGC-motif 3, stem-loop structure 2 (STLP2), AUGC-motif 2, stem-loop structure 1 (STLP1) and AUGC-motif 1. A mutational analysis showed that all three AUGC-motifs were involved in CP binding. Mutation of the A- and U-residues of motifs 1 or 3 had no effect on CP binding but similar mutations in motif 2 abolished CP binding. A mutational analysis of the stem of STLP1 and STLP2 confirmed the importance of these hairpins for CP binding. Randomization of the sequence of the stems and loops of STLP1 and STLP2 had no effect on CP binding as long as the secondary structure was maintained. This indicates that the two hairpins are not involved in sequence-specific interactions with CP. They may function in a secondary structure-specific interaction with CP and/or in the assembly of the AUGC-motifs in a configuration required for CP binding.
Collapse
Affiliation(s)
- C B Reusken
- Institute of Molecular Plant Sciences, Goriaeus Laboratories, Leiden University, The Netherlands
| | | |
Collapse
|
24
|
Abstract
BACKGROUND Parvoviruses are small icosahedral single-stranded (ss) DNA viruses which replicate in rapidly proliferating cells, causing a variety of serious and often lethal diseases in mammals, including humans. The structure of canine parvovirus (CPV) showed an 11-nucleotide oligomeric fragment of its genome bound to 60 equivalent binding sites on the inside surface of the capsid. This provides an opportunity to study the conformation of ssDNA, its interactions with protein, and its role in viral assembly. RESULTS The icosahedrally ordered part of CPV ssDNA has an unusual loop conformation with the bases pointing outwards and the phosphates surrounding metal ions on the inside. The protein interacts with the bases, making 15 putative hydrogen bonds. The DNA electron density indicates preferences for particular base types in parts of the binding site. Statistical analysis of the genome yields approximately 30 regions with sequences similar to that observed in the structure, demonstrating a low level of sequence specificity for binding to capsid protein. CONCLUSIONS ssDNA can adopt unusual conformations upon association with protein by using phosphoribose backbone rotamers that are found in tRNA, but not in DNA duplexes. The CPV DNA-protein interactions differ from the non-specific backbone interactions seen in some plant and insect viruses. The sequence specificity, albeit low level, of the protein for CPV DNA may contribute both to distinguishing the viral DNA from other nucleic acids and to the DNA packaging process during viral assembly.
Collapse
Affiliation(s)
- M S Chapman
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA
| | | |
Collapse
|
25
|
Gallie DR, Kobayashi M. The role of the 3'-untranslated region of non-polyadenylated plant viral mRNAs in regulating translational efficiency. Gene 1994; 142:159-65. [PMID: 8194747 DOI: 10.1016/0378-1119(94)90256-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Tobacco mosaic virus (TMV) is a positive-sense RNA virus in which the single genomic RNA functions as a messenger RNA. It is a member of a class of plant viral RNAs that are the only known non-polyadenylated mRNAs in plants. The 3'-untranslated region (UTR) of TMV genomic RNA is the functional equivalent of a poly(A) tail in that it increases mRNA stability and regulates translational efficiency. To determine whether the 3'-UTR of other non-polyadenylated plant viral mRNAs regulate translation, those from turnip yellow mosaic (TYMV), brome mosaic (BMV), and alfalfa mosaic (AlMV) viruses were investigated. Chimeric gene constructs were made in which the viral 3'-UTRs were introduced immediately downstream from the reporter genes encoding beta-glucuronidase (GUS) and luciferase (LUC), and were translated in plant protoplasts following delivery of the mRNA using electroporation. The 3'-UTR from BMV RNA3 regulated reporter gene expression in vivo to an extent comparable to that observed for the TMV 3'-UTR. The BMV 3'-UTR increased both message stability and translational efficiency. As regulators of translation, the BMV and TMV 3'-UTR were dependent on the presence of a cap at the 5' terminus for function. The 3' UTR of TYMV or AlMV RNA4 had little impact on translation or transcript stability. These data suggest that although the TMV 3'-UTR is not unique in regulating translation, the 3'-UTR of plant viral mRNAs do vary in their regulatory ability.
Collapse
Affiliation(s)
- D R Gallie
- Department of Biochemistry, University of California, Riverside 92521-0129
| | | |
Collapse
|
26
|
Houser-Scott F, Baer ML, Liem KF, Cai JM, Gehrke L. Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3' untranslated region of alfalfa mosaic virus RNA 4. J Virol 1994; 68:2194-205. [PMID: 8139004 PMCID: PMC236695 DOI: 10.1128/jvi.68.4.2194-2205.1994] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The specific binding of alfalfa mosaic virus coat protein to viral RNA requires determinants in the 3' untranslated region (UTR). Coat protein and peptide binding sites in the 3' UTR of alfalfa mosaic virus RNA 4 have been analyzed by hydroxyl radical footprinting, deletion mapping, and site-directed mutagenesis experiments. The 3' UTR has several stable hairpins that are flanked by single-stranded (A/U)UGC sequences. Hydroxyl radical footprinting data show that five sites in the 3' UTR of alfalfa mosaic virus RNA 4 are protected by coat protein, and four of the five protected regions contain AUGC or UUGC. Electrophoretic mobility band shift results suggest four coat protein binding sites in the 3' UTR. A 3'-terminal 39-nucleotide RNA fragment containing four AUGC repeats bound coat protein and coat protein peptides with high affinity; however, coat protein bound poorly to antisense 3' UTR transcripts and poly(AUGC)10. Site-directed mutagenesis of AUGC865-868 resulted in a loss of coat protein binding and peptide binding by the RNA fragment. Alignment of alfalfa mosaic RNA sequences with those from several closely related ilarviruses demonstrates that AUGC865-868 is perfectly conserved; moreover, the RNAs are predicted to form similar 3'-terminal secondary structures. The data strongly suggest that alfalfa mosaic virus coat protein and ilavirus coat proteins recognize invariant AUGC sequences in the context of conserved structural elements.
Collapse
Affiliation(s)
- F Houser-Scott
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge 02139
| | | | | | | | | |
Collapse
|
27
|
Baer ML, Houser F, Loesch-Fries LS, Gehrke L. Specific RNA binding by amino-terminal peptides of alfalfa mosaic virus coat protein. EMBO J 1994; 13:727-35. [PMID: 8313916 PMCID: PMC394864 DOI: 10.1002/j.1460-2075.1994.tb06312.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Specific RNA-protein interactions and ribonucleoprotein complexes are essential for many biological processes, but our understanding of how ribonucleoprotein particles form and accomplish their biological functions is rudimentary. This paper describes the interaction of alfalfa mosaic virus (A1MV) coat protein or peptides with viral RNA. A1MV coat protein is necessary both for virus particle formation and for the initiation of replication of the three genomic RNAs. We have examined protein determinants required for specific RNA binding and analyzed potential structural changes elicited by complex formation. The results indicate that the amino-terminus of the viral coat protein, which lacks primary sequence homology with recognized RNA binding motifs, is both necessary and sufficient for binding to RNA. Circular dichroism spectra and electrophoretic mobility shift experiments suggest that the RNA conformation is altered when amino-terminal coat protein peptides bind to the viral RNA. The peptide--RNA interaction is functionally significant because the peptides will substitute for A1MV coat protein in initiating RNA replication. The apparent conformational change that accompanies RNA--peptide complex formation may generate a structure which, unlike the viral RNA alone, can be recognized by the viral replicase.
Collapse
Affiliation(s)
- M L Baer
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge 02139
| | | | | | | |
Collapse
|
28
|
David C, Gargouri-Bouzid R, Haenni AL. RNA replication of plant viruses containing an RNA genome. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1992; 42:157-227. [PMID: 1574587 DOI: 10.1016/s0079-6603(08)60576-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- C David
- Institut Jacques Monod, Paris, France
| | | | | |
Collapse
|
29
|
van der Kuyl AC, Langereis K, Houwing CJ, Jaspars EM, Bol JF. cis-acting elements involved in replication of alfalfa mosaic virus RNAs in vitro. Virology 1990; 176:346-54. [PMID: 2345958 DOI: 10.1016/0042-6822(90)90004-b] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A DNA copy of alfalfa mosaic virus (AIMV) RNA3 was transcribed in vitro in two different orientations with T7 RNA polymerase and the transcripts were used as templates for a virus-specific RNA-dependent RNA polymerase (RdRp) purified from AIMV-infected bean plants. Minus-stranded templates were transcribed by the RdRp into subgenomic plus-stranded RNA4. A deletion analysis showed that a sequence in minus-strand RNA3, located between nucleotides -8 and -55 upstream of the initiation site for RNA4 synthesis, was sufficient for subgenomic promoter activity in vitro. Plus-stranded templates were transcribed by the RdRp into full-length minus-stranded copies. A deletion analysis indicated that a sequence located between nucleotides 133 and 163 from the 3'-end of AIMV RNA3 was sufficient to direct the synthesis of minus-stranded products by the RdRp. Thus, the 3'-terminal region of the AIMV RNAs, which contains the binding sites with a high affinity for coat protein, appears not to be involved in recognition of the RNAs by the RdRp in vitro.
Collapse
|
30
|
Viral Sequences. Viruses 1987. [DOI: 10.1016/b978-0-12-512516-1.50005-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
31
|
|
32
|
Zuidema D, Jaspars E. Comparative investigations on the coat protein binding sites of the genomic RNAs of alfalfa mosaic and tobacco streak viruses. Virology 1984; 135:43-52. [DOI: 10.1016/0042-6822(84)90115-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/1983] [Accepted: 02/11/1984] [Indexed: 10/26/2022]
|
33
|
Cornelissen BJ, Janssen H, Zuidema D, Bol JF. Complete nucleotide sequence of tobacco streak virus RNA 3. Nucleic Acids Res 1984; 12:2427-37. [PMID: 6546793 PMCID: PMC318673 DOI: 10.1093/nar/12.5.2427] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Double-stranded cDNA of in vitro polyadenylated tobacco streak virus (TSV) RNA 3 has been cloned and sequenced. The complete primary structure of 2,205 nucleotides reveals two open reading frames flanked by a leader sequence of 210 bases, an intercistronic region of 123 nucleotides and a 3'-extracistronic sequence of 288 nucleotides. The 5'-terminal open reading frame codes for a Mr 31,742 protein, which probably corresponds to the only in vitro translation product of TSV RNA 3. The 3'-terminal coding region predicts a Mr 26,346 protein, probably the viral coat protein, which is the translation product of the subgenomic messenger, RNA 4. Although the coat proteins of alfalfa mosaic virus (A1MV) and TSV are functionally equivalent in activating their own and each others genomes, no homology between the primary structures of those two proteins is detectable.
Collapse
|
34
|
Rossmann MG, Abad-Zapatero C, Erickson JW, Savithri HS. RNA-protein interactions in some small plant viruses. J Biomol Struct Dyn 1983; 1:565-79. [PMID: 6401119 DOI: 10.1080/07391102.1983.10507462] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The structure of the three quasi-equivalent protein subunits A, B and C of the spherical, T = 3 southern bean mosaic virus (SBMV) have been carefully built in accordance with a refined electron density map of the complete virus. The lower electron density in the RNA portion of the map could not be explicitly interpreted in terms of a preferred RNA structure on which some icosahedral symmetry might have been imposed. However, the extremely basic nature of the interior surface of the coat protein must be associated with the binding and organization of the RNA. Comparison with the small spherical, T = 1 satellite tobacco necrosis virus (STNV; Liljas et al., J. Mol. Biol. 159, 93-108, 1982) and the T = 1 aggregate of alfalfa mosaic virus (AMV) protein (Fukuyama et al., J. Mol. Biol. 150, 33-41, 1981) showed similar results. The pattern of basic residues on the SBMV coat protein surface facing the RNA is able to dock a 9 base pair double-helical A-RNA structure with surprising accuracy. The basic residues are each associated with a different phosphate and the protein can make interactions with five bases in the minor groove. This may be one of a small number of ways in which the RNA interacts with SBMV coat protein. The self-assembly of SBMV has been studied in relation to the presence of the 63 basic amino-terminal coat protein sequence, pH, Ca2+ and Mg2+ ions and RNA. These results have led to a two-state model where the "relaxed" dimers initially self-assemble into 10-mer caps which nucleate the assembly of T = 1 or T = 3 capsids depending on the charge state of the carboxyl group clusters in the subunit contact region. The two-state condition of dimers in a viral coat protein extends the range of structures originally envisaged by Caspar and Klug (Cold Spring Harbor Symp. Quant. Biol. 27, 1-24, 1962).
Collapse
Affiliation(s)
- M G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | | | | | | |
Collapse
|
35
|
Fukuyama K, Abdel-Meguid SS, Johnson JE, Rossmann MG. Structure of a T = 1 aggregate of alfalfa mosaic virus coat protein seen at 4.5 A resolution. J Mol Biol 1983; 167:873-90. [PMID: 6876169 DOI: 10.1016/s0022-2836(83)80116-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A T = 1 empty aggregate of alfalfa mosaic virus coat protein had been crystallized in a hexagonal unit cell and its orientation was determined with the rotation function. A single heavy-atom derivative has now been prepared and the position of the two Hg atoms per protein subunit were determined using a systematic Patterson search procedure, given the particle orientation. Phases, initially determined by single isomorphous replacement, were refined by six cycles of electron density averaging and solvent leveling to produce a 4.5 A resolution electron density map. The protein coat is confined between 95 and 58 A radius. The subunit boundary could be delineated easily. It has a central cavity reminiscent of the beta-barrel in other spherical plant viruses, but its topology could not be determined unambiguously. The spherical particle has large holes at the 5-fold axes, consistent with previous observations. The subunits have substantial interactions at the 2 and 3-fold axes. The structure of the elongated particles is discussed in relation to these results.
Collapse
|
36
|
Barker RF, Jarvis NP, Thompson DV, Loesch-Fries LS, Hall TC. Complete nucleotide sequence of alfalfa mosaic virus RNA3. Nucleic Acids Res 1983; 11:2881-91. [PMID: 6856479 PMCID: PMC325930 DOI: 10.1093/nar/11.9.2881] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A full-length cDNA clone of alfalfa mosaic virus (AMV) RNA3 was prepared and sequenced. The 2,037 base sequence contains two open reading frames of 903 and 666 nucleotides that code for a 32,400 dalton protein (32.4K protein) and the 24,380 dalton coat protein, respectively. A 5'-noncoding sequence of 240 bases preceeding the 32.4K protein contains homologous regions that may have a function in its translation. The intercistronic junction is 49 bases long, the last 36 bases representing the 5'-end of the subgenomic RNA4. The remaining 179 bases comprise the 3'-terminal noncoding sequence.
Collapse
|
37
|
Rossmann MG, Chandrasekaran R, Abad-Zapatero C, Erickson JW, Arnott S. RNA-protein binding in southern bean mosaic virus. J Mol Biol 1983; 166:73-80. [PMID: 6854634 DOI: 10.1016/s0022-2836(83)80050-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
38
|
Zuidema D, Bierhuizen MF, Cornelissen BJ, Bol JF, Jaspars EM. Coat protein binding sites on RNA 1 of alfalfa mosaic virus. Virology 1983; 125:361-9. [PMID: 6404055 DOI: 10.1016/0042-6822(83)90208-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The largest genome segment, RNA 1, of alfalfa mosaic virus forms complexes with viral coat protein. These complexes were subjected to digestion with ribonucleases T1 or A and filtered onto Millipore filters. Specific fragments were collected from the filters by phenol extraction. After electrophoretic separation in denaturing polyacrylamide gels, these fragments were sequenced. Besides extracistronic fragments originating from the 3'-terminal region of RNA 1, fragments were found originating from an intracistronic region of the RNA. A striking phenomenon is that the intracistronic fragments were not found when ribonuclease A was used to degrade RNA/protein complexes. The findings are in agreement with the postulation of Houwing and Jaspars (1978), that a conformational change at the 3' ends of the genome RNAs induced by the coat protein is a prerequisite to start an infection cycle.
Collapse
|
39
|
Nassuth A, Bol JF. Altered balance of the synthesis of plus- and minus-strand RNAs induced by RNAs 1 and 2 of alfalfa mosaic virus in the absence of RNA 3. Virology 1983; 124:75-85. [DOI: 10.1016/0042-6822(83)90291-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/1982] [Accepted: 08/09/1982] [Indexed: 11/29/2022]
|
40
|
Strauss EG, Strauss JH. Replication strategies of the single stranded RNA viruses of eukaryotes. Curr Top Microbiol Immunol 1983; 105:1-98. [PMID: 6354610 DOI: 10.1007/978-3-642-69159-1_1] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
41
|
|
42
|
Houwing CJ, Jaspars EM. Protein binding sites in nucleation complexes of alfalfa mosaic virus RNA 4. Biochemistry 1982; 21:3408-14. [PMID: 6810924 DOI: 10.1021/bi00257a025] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The subgenomic coat protein messenger RNA 4 of alfalfa mosaic virus forms complexes with one and three coat protein dimers, which are designated complexes I and III, respectively. These complexes were separated, subjected to digestion with ribonuclease T1, and filtered onto Millipore filters. Phenol extracts of the filters contained specific fragments of RNA 4, which were sequenced after electrophoretic separation on nondenaturing and denaturing polyacrylamide gels. Complex I yielded only a 68-nucleotide fragment including the 3' terminus [fragment 814-881 according to the numbering of Brederode, F. Th., Koper-Zwarthoff, E. C., & Bol, J. F. (1980) Nucleic Acids Res. 8, 2213-2223]. Complex III yielded in addition to the former fragment also other, mostly extracistronic, fragments from the 3'-terminal region, as well as fragments from an intracistronic region, comprising positions 425-474, in the middle of RNA 4. The 3'-terminal region was subdivided by small gaps into three coat protein binding sites: 799-881, 759-787, and 667-753, designated sites 1, 2, and 3, respectively, and possibly representing the sites occupied by the three coat protein dimers. A similarity may exist between the secondary structure of sites 1 and 3, which both may have three hairpins, two of which flanked at their 3' side by an AUGC sequence. Furthermore, a complementarity was noted between the loop of a large hairpin which can be drawn in the intracistronic site and the upper part of one of the three hairpins in the 3'-terminal site 1. These binding features have been combined in a model structure for the complex of RNA 4 with three coat protein dimers.
Collapse
|
43
|
Thiele DJ, Wang RW, Leibowitz MJ. Separation and sequence of the 3' termini of M double-stranded RNA from killer yeast. Nucleic Acids Res 1982; 10:1661-78. [PMID: 7041093 PMCID: PMC320557 DOI: 10.1093/nar/10.5.1661] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Four subspecies of M double-stranded RNA from a killer strain of Saccharomyces cerevisiae were isolated. Each subspecies were susceptible to heat cleavage, presumably at an internal 190 base pair A,U-rich region, generating two discrete fragments corresponding to each side of the A, U-rich region. Enzymatic and chemical RNA sequence analysis defined the 3'-terminal 175 bases for the larger fragment (M-1) and 231 bases for the smaller fragment (M-2). All four subspecies of M have identical size and 3'-terminal sequences. Potential translation initiation codons are present on the corresponding 5' termini of both fragments, and a possible 18S ribosomal RNA binding site is also present on the 5' terminus of M-1. Stem and loop structures for the 5' and 3' termini of M-1 may function as recognition sites for replication, transcription, and translation.
Collapse
|
44
|
Brennan VE, Bobek LA, Bruenn JA. Yeast deRNA viral transcriptase pause products: identification of the transcript strand. Nucleic Acids Res 1981; 9:5049-59. [PMID: 7031603 PMCID: PMC327498 DOI: 10.1093/nar/9.19.5049] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
ScV-L is a double-stranded RNA virus of the yeast Saccharomyces cerevisiae. The virus possesses a capsid-associated transcriptase activity the product of which is a single-stranded RNA complementary to only one strand of the double-stranded RNA template (L). We show that the U-rich 3' terminus of L is the initiation site of transcription and that a number of pause products are made. One prominent product has the sequence pppGAAAAAUUUUUAAAUUCAUAUAACUOH.
Collapse
|
45
|
Brennan VE, Field L, Cizdziel P, Bruenn JA. Sequences at the 3' ends of yeast viral dsRNAs: proposed transcriptase and replicase initiation sites. Nucleic Acids Res 1981; 9:4007-21. [PMID: 7029463 PMCID: PMC327411 DOI: 10.1093/nar/9.16.4007] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
ScV is a double-stranded RNA virus of yeast consisting of two separately encapsidated dsRNAs (L and M). ScV-1 and ScV-2 are two dsRNA viruses present in two different yeast killer strains, K1 and K2. Our 3' end sequence analysis shows that the two sets of viral dsRNAs from ScV-1 and ScV-2 are very similar. Consensus sequences for transcriptase and replicase initiation are proposed. A stem and loop structure with a 3' terminal AUGC sequence, like that of several plant virus plus strand RNAs, is present at the putative replicase initiation site of one of the yeast viral RNA plus strands.
Collapse
|
46
|
Fukuyama K, Abdel-Meguid SS, Rossmann MG. Crystallization of alfalfa mosaic virus coat protein as a T = 1 aggregate. J Mol Biol 1981; 150:33-41. [PMID: 7299819 DOI: 10.1016/0022-2836(81)90323-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
47
|
Koper-Zwarthoff EC, Brederode FT, Veeneman G, van Boom JH, Bol JF. Nucleotide sequences at the 5'-termini of the alfalfa mosaic virus RNAs and the intercistronic junction in RNA 3. Nucleic Acids Res 1980; 8:5635-47. [PMID: 6927843 PMCID: PMC324331 DOI: 10.1093/nar/8.23.5635] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Nucleotide sequences at the 5'-termini of the alfalfa mosaic virus genomic RNAs and the intercistronic junction in RNA 3 were deduced and compared to identify possible common recognition signals for replicating enzymes in the corresponding minus-stranded viral RNAs. Homology between the 5'-terminal sequences is less than 11 nucleotides and no complementarity with the homologous sequence occurring at the 3'-end of the viral RNAs was observed. Homology between the 5'-terminus and intercistronic region in RNA 3 is compatible with the synthesis of subgenomic RNA 4 by internal initiation of transcription on the RNA 3 minus strands. The sequence around the intercistronic junction can be folded into a very stable secondary structure.
Collapse
|