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Kulshrestha S, Hallan V, Sharma A, Seth CA, Chauhan A, Zaidi AA. Molecular characterization and intermolecular interaction of coat protein of Prunus necrotic ringspot virus: implications for virus assembly. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2013; 24:235-41. [PMID: 24426281 DOI: 10.1007/s13337-013-0140-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/04/2013] [Indexed: 11/24/2022]
Abstract
Coat protein (CP) and RNA3 from Prunus necrotic ringspot virus (PNRSV-rose), the most prevalent virus infecting rose in India, were characterized and regions in the coat protein important for self-interaction, during dimer formation were identified. The sequence analysis of CP and partial RNA 3 revealed that the rose isolate of PNRSV in India belongs to PV-32 group of PNRSV isolates. Apart from the already established group specific features of PV-32 group member's additional group-specific and host specific features were also identified. Presence of methionine at position 90 in the amino acid sequence alignment of PNRSV CP gene (belonging to PV-32 group) was identified as the specific conserved feature for the rose isolates of PNRSV. As protein-protein interaction plays a vital role in the infection process, an attempt was made to identify the portions of PNRSV CP responsible for self-interaction using yeast two-hybrid system. It was found (after analysis of the deletion clones) that the C-terminal region of PNRSV CP (amino acids 153-226) plays a vital role in this interaction during dimer formation. N-terminal of PNRSV CP is previously known to be involved in CP-RNA interactions, but our results also suggested that N-terminal of PNRSV CP represented by amino acids 1-77 also interacts with C-terminal (amino acids 153-226) in yeast two-hybrid system, suggesting its probable involvement in the CP-CP interaction.
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Affiliation(s)
- Saurabh Kulshrestha
- Plant Virus Lab, Floriculture Division, IHBT (CSIR), Palampur, 176061 HP India ; Faculty of Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173212 HP India
| | - Vipin Hallan
- Plant Virus Lab, Floriculture Division, IHBT (CSIR), Palampur, 176061 HP India
| | - Anshul Sharma
- Faculty of Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173212 HP India
| | - Chandrika Attri Seth
- Faculty of Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173212 HP India
| | - Anjali Chauhan
- Department of Basic Sciences, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, India
| | - Aijaz Asghar Zaidi
- Plant Virus Lab, Floriculture Division, IHBT (CSIR), Palampur, 176061 HP India
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Abstract
In the family Bromoviridae, a mixture of the three genomic RNAs of bromo-, cucumo-, and oleaviruses is infectious as such, whereas the RNAs of alfamo- and ilarviruses require binding of a few molecules of coat protein (CP) to the 3' end to initiate infection. Most studies on the early function of CP have been done on the alfamovirus Alfalfa mosaic virus (AMV). The 3' 112 nucleotides of AMV RNAs can adopt two different conformations. One conformer consists of a tRNA-like structure that, together with an upstream hairpin, is required for minus-strand promoter activity. The other conformer consists of four hairpins interspersed by AUGC-sequences and represents a strong binding site for CP. Binding of CP to this conformer enhances the translational efficiency of viral RNAs in vivo 40-fold and blocks viral minus-strand RNA synthesis in vitro. AMV CP is proposed to initiate infection by mimicking the function of the poly(A)-binding protein.
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Affiliation(s)
- John F Bol
- Institute of Biology, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
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Neeleman L, Linthorst HJM, Bol JF. Efficient translation of alfamovirus RNAs requires the binding of coat protein dimers to the 3' termini of the viral RNAs. J Gen Virol 2004; 85:231-240. [PMID: 14718638 DOI: 10.1099/vir.0.19581-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The coat protein (CP) of Alfalfa mosaic virus (AMV) is required to initiate infection by the viral tripartite RNA genome whereas infection by the tripartite Brome mosaic virus (BMV) genome is independent of CP. AMV CP stimulates translation of AMV RNA in vivo 50- to 100-fold. The 3' untranslated region (UTR) of the AMV subgenomic CP messenger RNA 4 contains at least two CP binding sites. A CP binding site in the 3'-terminal 112 nucleotides of RNA 4 was found to be required for efficient translation of the RNA whereas an upstream binding site was not. Binding of CP to the AMV 3' UTR induces a conformational change of the RNA but this change alone was not sufficient to stimulate translation. CP mutant R17A is unable to bind to the 3' UTR and translation in vivo of RNA 4 encoding this mutant occurs at undetectable levels. Replacement of the 3' UTR of this mutant RNA 4 by the 3' UTR of BMV RNA 4 restored translation of R17A-CP to wild-type levels. Apparently, the BMV 3' UTR stimulates translation independently of CP. AMV CP mutant N199 is defective in the formation of CP dimers and did not stimulate translation of RNA 4 in vivo although the mutant CP did bind to the 3' UTR. The finding that N199-CP does not promote AMV infection corroborates the notion that the requirement of CP in the inoculum reflects its role in translation of the viral RNAs.
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Affiliation(s)
- Lyda Neeleman
- Institute of Biology, Leiden University, Gorlaeus Laboratories, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Huub J M Linthorst
- Institute of Biology, Leiden University, Gorlaeus Laboratories, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - John F Bol
- Institute of Biology, Leiden University, Gorlaeus Laboratories, PO Box 9502, 2300 RA Leiden, The Netherlands
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Aparicio F, Vilar M, Perez-Payá E, Pallás V. The coat protein of prunus necrotic ringspot virus specifically binds to and regulates the conformation of its genomic RNA. Virology 2003; 313:213-23. [PMID: 12951034 DOI: 10.1016/s0042-6822(03)00284-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binding of coat protein (CP) to the 3' nontranslated region (3'-NTR) of viral RNAs is a crucial requirement to establish the infection of Alfamo- and Ilarviruses. In vitro binding properties of the Prunus necrotic ringspot ilarvirus (PNRSV) CP to the 3'-NTR of its genomic RNA using purified E. coli- expressed CP and different synthetic peptides corresponding to a 26-residue sequence near the N-terminus were investigated by electrophoretic mobility shift assays. PNRSV CP bound to, at least, three different sites existing on the 3'-NTR. Moreover, the N-terminal region between amino acid residues 25 to 50 of the protein could function as an independent RNA-binding domain. Single exchange of some arginine residues by alanine eliminated the RNA-interaction capacity of the synthetic peptides, consistent with a crucial role for Arg residues common to many RNA-binding proteins possessing Arg-rich domains. Circular dichroism spectroscopy revealed that the RNA conformation is altered when amino-terminal CP peptides bind to the viral RNA. Finally, mutational analysis of the 3'-NTR suggested the presence of a pseudoknotted structure at this region on the PNRSV RNA that, when stabilized by the presence of Mg(2+), lost its capability to bind the coat protein. The existence of two mutually exclusive conformations for the 3'-NTR of PNRSV strongly suggests a similar regulatory mechanism at the 3'-NTR level in Alfamo- and Ilarvirus genera.
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Affiliation(s)
- Frederic Aparicio
- Instituto de Biologia Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Avenida de los Naranjos s/n, E-46022 Valencia, Spain
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Vlot AC, Neeleman L, Linthorst HJ, Bol JF. Role of the 3'-untranslated regions of alfalfa mosaic virus RNAs in the formation of a transiently expressed replicase in plants and in the assembly of virions. J Virol 2001; 75:6440-9. [PMID: 11413311 PMCID: PMC114367 DOI: 10.1128/jvi.75.14.6440-6449.2001] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alfalfa mosaic virus (AMV) RNAs 1 and 2 encode the replicase proteins P1 and P2, respectively, whereas RNA 3 encodes the movement protein and the coat protein (CP). When RNAs 1 and 2 were transiently expressed from a T-DNA vector (R12 construct) by agroinfiltration of Nicotiana benthamiana, the infiltrated leaves accumulated minus-strand RNAs 1 and 2 and relatively small amounts of plus-strand RNAs. In addition, RNA-dependent RNA polymerase (RdRp) activity could be detected in extracts of the infiltrated leaves. After transient expression of RNAs 1 and 2 with the 3'-untranslated regions (UTRs) of both RNAs deleted (R1Delta/2Delta construct), no replication of RNAs 1 and 2 was observed, while the infiltrated leaves supported replication of RNA 3 after inoculation of the leaves with RNA 3 or expression of RNA 3 from a T-DNA vector (R3 construct). No RdRp activity could be isolated from leaves infiltrated with the R1Delta/2Delta construct, although P1 and P2 sedimented in a region of a glycerol gradient where active RdRp was found in plants infiltrated with R12. RdRp activity could be isolated from leaves infiltrated with constructs R1Delta/2 (3'-UTR of RNA 1 deleted), R1/2Delta (3'-UTR of RNA 2 deleted), or R1Delta/2Delta plus R3. This demonstrates that the 3'-UTR of AMV RNAs is required for the formation of a complex with in vitro enzyme activity. RNAs 1 and 2 with the 3'-UTRs deleted were encapsidated into virions by CP expressed from RNA 3. This shows that the high-affinity binding site for CP at the 3'-termini of AMV RNAs is not required for assembly of virus particles.
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Affiliation(s)
- A C Vlot
- Institute of Molecular Plant Sciences, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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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.
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Affiliation(s)
- P Ansel-McKinney
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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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.
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Affiliation(s)
- M M Swanson
- Scottish Crop Research Institute, Invergowrie, Dundee, United Kingdom
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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
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Savithri HS, Suryanarayana S, Murthy MR. Structure-function relationships of icosahedral plant viruses. Arch Virol 1989; 109:153-72. [PMID: 2692536 DOI: 10.1007/bf01311078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary organization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.
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Affiliation(s)
- H S Savithri
- Department of Biochemistry, Indian Institute of Science, Bangalore
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van Dun CM, Overduin B, van Vloten-Doting L, Bol JF. Transgenic tobacco expressing tobacco streak virus or mutated alfalfa mosaic virus coat protein does not cross-protect against alfalfa mosaic virus infection. Virology 1988; 164:383-9. [PMID: 3369086 DOI: 10.1016/0042-6822(88)90551-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Transgenic tobacco plants expressing the coat protein (CP) genes of tobacco streak virus (TSV) and alfalfa mosaic virus (AIMV) were used in studies on cross-protection and genome activation. Plants expressing the TSV CP gene were highly resistant to infection with TSV nucleoproteins but were susceptible to infection with AIMV nucleoproteins. Moreover, these plants could be infected with a mixture of AIMV RNAs 1, 2, and 3 in contrast to the nontransformed control plants. This demonstrates that the endogenously produced TSV CP is able to activate the AIMV genome but does not cross-protect against this virus. Conversely, it was shown that plants expressing the AIMV CP gene did not resist TSV infection. Transgenic tobacco plants transformed with an AIMV CP gene with a frame-shift mutation in the reading frame were found to accumulate viral transcripts to a level similar to that obtained in plants expressing a wild-type AIMV CP gene. However, these plants did not produce detectable amounts of viral protein and showed no resistance to infection with AIMV nucleoproteins in contrast to transgenic plants accumulating wild-type AIMV CP. This demonstrates that it is the CP that is responsible for cross-protection in transgenic plants and not the chimeric CP mRNA.
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Affiliation(s)
- C M van Dun
- Department of Biochemistry, State University of Leiden, The Netherlands
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Langereis K, Neeleman L, Bol JF. Biologically active transcripts of cloned DNA of the coat protein messenger of two plant viruses. PLANT MOLECULAR BIOLOGY 1986; 6:281-288. [PMID: 24307327 DOI: 10.1007/bf00015234] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/1985] [Revised: 12/03/1985] [Accepted: 01/14/1986] [Indexed: 06/02/2023]
Abstract
To initiate infection, a mixture of the three genomic RNAs of alfalfa mosaic virus (AIMV) has to be supplemented with a small amount of coat protein or RNA 4, the subgenomic messenger for coat protein. The possibility to replace RNA 4 in the inoculum by in vitro synthesized transcripts of a cloned DNA copy of the coat protein cistron was investigated using the SP6 transcription system. Transcripts with or without the cap structure m(7)G(5')ppp(5')G were both translated in vitro in viral coat protein, but only capped transcripts yielded an infectious mixture when added to the AIMV genomic RNAs. This indicates that the cap structure is essential to the in vivo translatin of RNA 4. Similar results were obtained with RNAs transcribed in vitro from a DNA copy of the putative coat protein cistron of tobacco streak virus (TSV). re]19850822 rv]19851203 ac]19860114.
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Affiliation(s)
- K Langereis
- Department of Biochemistry, State University of Leiden, Wassenaarseweg 64, 2333 AL, Leiden, The Netherlands
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Sarachu AN, Huisman MJ, Van Vloten-Doting L, Bol JF. Alfalfa mosaic virus temperature-sensitive mutants. Virology 1985; 141:14-22. [DOI: 10.1016/0042-6822(85)90178-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/1984] [Accepted: 10/06/1984] [Indexed: 11/16/2022]
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Zuidema D, Jaspars E. Specificity of RNA and coat protein interaction in alfalfa mosaic virus and related viruses. Virology 1985; 140:342-50. [DOI: 10.1016/0042-6822(85)90370-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/1983] [Accepted: 09/19/1984] [Indexed: 10/26/2022]
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Cornelissen BJ, Bol JF. Homology between the proteins encoded by tobacco mosaic virus and two tricornaviruses. PLANT MOLECULAR BIOLOGY 1984; 3:379-384. [PMID: 24310571 DOI: 10.1007/bf00033385] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/1984] [Revised: 05/22/1984] [Accepted: 05/30/1984] [Indexed: 06/02/2023]
Abstract
A comparison was made of the amino acid sequences of the proteins encoded by RNAs 1 and 2 of alfalfa mosaic virus (A1MV) and brome mosaic virus (BMV), and the 126K and 183K proteins encoded by tobacco mosaic virus (TMV). Three blocks of extensive homology of about 200 to 350 amino acids each were observed. Two of these blocks are located in the A1MV and BMV RNA 1 encoded proteins and the TMV encoded 126K protein; they are situated at the N-terminus and C-terminus, respectively. The third block is located in the A1MV and BMV RNA 2 encoded proteins and the C-terminal part of the TMV encoded 183K protein. These homologies are discussed with respect to the functional equivalence of these putative replicase proteins and a possible evolutionary connection between A1MV, BMV and TMV.
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Affiliation(s)
- B J Cornelissen
- Department of Biochemistry, State University of Leiden, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
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