1
|
Functional expression, monodispersity and conformational changes in the SBMV virus viral VPg on binding TFE. Int J Biol Macromol 2015; 83:178-84. [PMID: 26592780 DOI: 10.1016/j.ijbiomac.2015.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/08/2015] [Accepted: 11/10/2015] [Indexed: 11/21/2022]
Abstract
Southern bean mosaic virus (SBMV) RNA purified from infected plants was used for cloning the viral genome-linked protein (VPg) and was subsequently expressed in Escherichia coli. Circular dichroism (CD), dynamic light scattering (DLS) and saturation transfer difference (STD) by nuclear magnetic resonance (NMR) measurements were employed to determine the degree of monodispersity and to investigate the conformational changes in the absence and presence of trifluoroethanol (TFE) which indicated increased helical content with increasing concentration of TFE. 8-Anilino-1-naphthalenesulfonic acid (ANS) was used as a probe to compare the unfolding regions of the protein before and after addition of TFE. The results indicated that although the TFE concentration influences VPg folding, it does not play a role in nucleotide binding and that the local solvent hydrophobicity causes significant conformational changes.
Collapse
|
2
|
Sobemovirus RNA linked to VPg over a threonine residue. FEBS Lett 2011; 585:2979-85. [DOI: 10.1016/j.febslet.2011.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 12/28/2022]
|
3
|
Olspert A, Peil L, Hebrard E, Fargette D, Truve E. Protein-RNA linkage and post-translational modifications of two sobemovirus VPgs. J Gen Virol 2010; 92:445-52. [DOI: 10.1099/vir.0.026476-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
4
|
Okade H, Fujita Y, Miyamoto S, Tomoo K, Muto S, Miyoshi H, Natsuaki T, Rhoads RE, Ishida T. Turnip mosaic virus genome-linked protein VPg binds C-terminal region of cap-bound initiation factor 4E orthologue without exhibiting host cellular specificity. J Biochem 2009; 145:299-307. [PMID: 19122207 DOI: 10.1093/jb/mvn180] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To investigate the binding specificity of turnip mosaic virus (TuMV) viral protein-genome linked (VPg) with translation initiation factor 4E, we evaluated here the kinetic parameters for the interactions of human eIF4E, Caenorhabditis elegans IFE-3 and IFE-5 and Arabidopsis eIFiso4E, by surface plasmon resonance (SPR). The results indicated that TuMV VPg does not show a binding preference for Arabidopsis eIFiso4E, even though it is from a host species whereas the other eIF4E orthologues are not. Surprisingly, the effect of m(7)GTP on both the rate constants and equilibrium binding constants for the interactions of VPg differed for the four eIF4E orthologues. In the case of eIFiso4E and IFE-3, m(7)GTP increased k(on), but for eIF4E and IFE-5, it decreased k(on). To provide insight into the structural basis for these differences in VPg binding, tertiary structures of the eIF4E orthologues were predicted on the basis of the previously determined crystal structure of m(7)GpppA-bound human eIF4E. The results suggested that in cap-bound eIF4E orthologues, the VPg binds to the C-terminal region, which constitutes one side of the entrance to the cap-binding pocket, whereas in the cap-free state, VPg binds to the widely opened cap-binding pocket and its surrounding region. The binding of VPg to the C-terminal region was confirmed by the SPR analyses of N- or C-terminal residues-deleted eIF4E orthologues.
Collapse
Affiliation(s)
- Hayato Okade
- Department of Physical Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Belliot G, Sosnovtsev SV, Chang KO, McPhie P, Green KY. Nucleotidylylation of the VPg protein of a human norovirus by its proteinase-polymerase precursor protein. Virology 2008; 374:33-49. [PMID: 18234264 DOI: 10.1016/j.virol.2007.12.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2007] [Revised: 08/05/2007] [Accepted: 12/18/2007] [Indexed: 11/30/2022]
Abstract
Caliciviruses have a positive strand RNA genome covalently-linked at the 5'-end to a small protein, VPg. This study examined the biochemical modification of VPg by the ProPol form of the polymerase of human norovirus strain MD145 (GII.4). Recombinant norovirus VPg was shown to be nucleotidylylated in the presence of Mn2+ by MD145 ProPol. Phosphodiesterase I treatment of the nucleotidylylated VPg released the incorporated UMP, which was consistent with linkage of RNA to VPg via a phosphodiester bond. Mutagenesis analysis of VPg identified Tyrosine 27 as the target amino acid for this linkage, and suggested that VPg conformation was important for the reaction. Nucleotidylylation was inefficient in the presence of Mg2+; however the addition of full- and subgenomic-length MD145 RNA transcripts led to a marked enhancement of the nucleotidylylation efficiency in the presence of this divalent cation. Furthermore, evidence was found for the presence of an RNA element near the 3'-end of the polyadenylated genome that enhanced the efficiency of nucleotidylylation in the presence of Mg2+.
Collapse
Affiliation(s)
- Gaël Belliot
- National Institutes of Health/DHHS, NIAID/LID, Building 50, Room 6316, 9000 Rockville Pike, Bethesda, MD 20892-8007, USA.
| | | | | | | | | |
Collapse
|
6
|
Ivanova OA, Venyaminova AG, Repkova MN, Drygin YF. Polyclonal Antibodies against a Structure Mimicking the Covalent Linkage Unit between Picornavirus RNA and VPg: An Immunochemical Study. BIOCHEMISTRY (MOSCOW) 2005; 70:1038-45. [PMID: 16266277 DOI: 10.1007/s10541-005-0222-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We propose that therapy of patients with anticancer drugs that poison DNA topoisomerases induces formation of covalent complexes of cellular RNAs and DNA topoisomerases. The appearance of these complexes can be detected with antibodies against a synthetic hapten mimicking the covalent linkage unit Tyr-pU(p) of picornavirus RNA and VPg. We synthesized hapten [N(Ac),CO(NH2)]Tyr-(5 P --> O)Up-O-(CH2)6NH2, conjugated it with BSA, and immunized rabbits with the antigen obtained. The raised polyclonal antibodies were purified by successive affinity chromatography on BSA-Sepharose and hapten-Sepharose columns. Target antibodies recognized hapten and encephalomyocarditis virus RNA-VPg complex specifically as found using the dot-immunogold method. We believe that these antibodies might be useful to study mechanism of picorna and similar virus RNA synthesis. The discovery and qualitative determination of the cellular RNA-DNA topoisomerases covalent complexes with these antibodies might be useful to monitor therapy efficacy by drugs "freezing" dead-end complexes of DNA topoisomerases and nucleic acids and to understand the mechanism of DNA topoisomerase poisoning in situ.
Collapse
Affiliation(s)
- O A Ivanova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | | | | | | |
Collapse
|
7
|
Mitra T, Sosnovtsev SV, Green KY. Mutagenesis of tyrosine 24 in the VPg protein is lethal for feline calicivirus. J Virol 2004; 78:4931-5. [PMID: 15078978 PMCID: PMC387666 DOI: 10.1128/jvi.78.9.4931-4935.2004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of feline calicivirus (FCV) is an approximately 7.7-kb single-stranded positive-sense RNA molecule that is polyadenylated at its 3' end and covalently linked to a VPg protein (calculated mass, 12.6 kDa) at its 5' end. We performed a mutational analysis of the VPg protein in order to identify amino acids potentially involved in linkage to the genome and replication. The tyrosine residues at positions 12, 24, 76, and 104 were changed to alanines by mutagenesis of an infectious FCV cDNA clone. Viruses were recovered when Tyr-12, Tyr-76, or Tyr-104 of the VPg protein was changed to alanine, but virus was not recovered when Tyr-24 was changed to alanine. Growth properties of the recovered viruses were similar to those of the parental virus. We examined whether the amino acids serine, threonine, and phenylalanine could substitute for the tyrosine at position 24, but these mutations were lethal as well. A tyrosine at this relative position is conserved among all calicivirus VPg proteins examined thus far, suggesting that the VPg protein of caliciviruses, like those of picornaviruses and potyviruses, utilizes tyrosine in the formation of a covalent bond with RNA.
Collapse
Affiliation(s)
- Tanaji Mitra
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
| | | | | |
Collapse
|
8
|
Affiliation(s)
- E Sadowy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | |
Collapse
|
9
|
Carette JE, Kujawa A, Gühl K, Verver J, Wellink J, Van Kammen A. Mutational analysis of the genome-linked protein of cowpea mosaic virus. Virology 2001; 290:21-9. [PMID: 11883002 DOI: 10.1006/viro.2001.1137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study we have performed a mutational analysis of the cowpea mosaic comovirus (CPMV) genome-linked protein VPg to discern the structural requirements necessary for proper functioning of VPg. Either changing the serine residue linking VPg to RNA at a tyrosine or a threonine or changing the position of the serine from the N-terminal end to position 2 or 3 abolished virus infectivity. Some of the mutations affected the cleavage between the VPg and the 58K ATP-binding protein in vitro, which might have contributed to the lethal phenotype. RNA replication of some of the mutants designed to replace VPg with the related cowpea severe mosaic comovirus was completely abolished, whereas replication of others was not affected or only mildly affected, showing that amino acids that are not conserved between the comoviruses can be critical for the function of VPg. The replicative proteins of one of the mutants failed to accumulate in typical cytopathic structures and this might reflect the involvement of VPg in protein-protein interactions with the other replicative proteins.
Collapse
Affiliation(s)
- J E Carette
- Laboratory of Molecular Biology, Wageningen University, 6703 HA Wageningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
10
|
Abstract
It is clear from the experimental data that there are some similarities in RNA replication for all eukaryotic positive-stranded RNA viruses—that is, the mechanism of polymerization of the nucleotides is probably similar for all. It is noteworthy that all mechanisms appear to utilize host membranes as a site of replication. Membranes appear to function not only as a way of compartmentalizing virus RNA replication but also appear to have a central role in the organization and functioning of the replication complex, and further studies in this area are needed. Within virus supergroups, similarities are evident between animal and plant viruses—for example, in the nature and arrangements of replication genes and in sequence similarities of functional domains. However, it is also clear that there has been considerable divergence, even within supergroups. For example, the animal alpha-viruses have evolved to encode proteinases which play a central controlling function in the replication cycle, whereas this is not common in the plant alpha-like viruses and even when it occurs, as in the tymoviruses, the strategies that have evolved appear to be significantly different. Some of the divergence could be host-dependent and the increasing interest in the role of host proteins in replication should be fruitful in revealing how different systems have evolved. Finally, there are virus supergroups that appear to have no close relatives between animals and plants, such as the animal coronavirus-like supergroup and the plant carmo-like supergroup.
Collapse
Affiliation(s)
- K W Buck
- Department of Biology, Imperial College of Science, Technology and Medicine, London, England
| |
Collapse
|
11
|
Pinck M, Reinbolt J, Loudes AM, Le Ret M, Pinck L. Primary structure and location of the genome-linked protein (VPg) of grapevine fanleaf nepovirus. FEBS Lett 1991; 284:117-9. [PMID: 2060618 DOI: 10.1016/0014-5793(91)80775-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The genome linked protein VPg covalently linked to the RNAs of grapevine fanleaf nepovirus has been sequenced. The VPg (Mr = 2931) composed of 24 residues is linked by its N-terminal Ser beta-OH group to the viral RNAs. The VPg mapped from residues 1218 to 1241 of the 253K polyprotein encoded by GFLV RNA1.
Collapse
Affiliation(s)
- M Pinck
- Institut de Biologie Moléculaire des Plantes du C.N.R.S., Strasbourg, France
| | | | | | | | | |
Collapse
|
12
|
Eggen R, Verver J, Wellink J, Pleij K, van Kammen A, Goldbach R. Analysis of sequences involved in cowpea mosaic virus RNA replication using site-specific mutants. Virology 1989; 173:456-64. [PMID: 2596026 DOI: 10.1016/0042-6822(89)90558-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Using a full-length cDNA clone of cowpea mosaic virus (CPMV) B-RNA from which infectious transcripts can be generated, we examined the influence of a sequence of 11 nucleotides, UUUUAUUAAAA, comprising the nucleotides 5883 to 5893 in the 3' noncoding region of B-RNA, on viral RNA replication. This sequence is not only present in B-RNA but also in M-RNA and represents the 7 nucleotides preceding the poly(A) tail and the first four A residues of the poly(A) tail. Replication of B-RNA transcripts derived from a series of mutants in this region was tested in cowpea plants and protoplasts. Only mutant transcripts with minor modifications appeared able to replicate, which indicates that the region has a function in viral RNA replication. In addition, the results suggest the existence of a hairpin loop in this region. Those transcripts with deletions which disturb the putative hairpin structure have decreased specific infectivities. Mutant transcripts reversed stepwise to the wild-type sequence during replication in plants. This observation strengthens the idea that the sequence of 11 nucleotides has a function in viral RNA replication.
Collapse
Affiliation(s)
- R Eggen
- Department of Molecular Biology, Agricultural University, Wageningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
13
|
Drygin YuF, Shabanov AA, Bogdanov AA. An enzyme which specifically splits a covalent bond between picornaviral RNA and VPg. FEBS Lett 1988; 239:343-6. [PMID: 2846361 DOI: 10.1016/0014-5793(88)80948-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An enzyme which specifically splits a covalent bond between VPg and picornaviral RNAs (tentatively designated Y-pUpN PDE) has been partially purified from mouse ascites Krebs II cells. Using substrates labelled in vitro with 125I-Bolton-Hunter reagent and a new assay based on Kieselgel thin-layer chromatography, several biochemical characteristics of the enzyme have been determined, depending on the pH and on Mg2+, K+, spermidine and PEG concentrations, etc. We found that the enzyme does not 'unlink' VPg from comoviral RNA. We suggest that Y-pUpN PDE represents a new class of enzymes.
Collapse
Affiliation(s)
- Drygin YuF
- A.N. Belozersky Laboratory of Molecular Biology and Bioorganic Chemistry, Moscow State University, USSR
| | | | | |
Collapse
|
14
|
Garcia JA, Schrijvers L, Tan A, Vos P, Wellink J, Goldbach R. Proteolytic activity of the cowpea mosaic virus encoded 24K protein synthesized in Escherichia coli. Virology 1987; 159:67-75. [PMID: 3300014 DOI: 10.1016/0042-6822(87)90348-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The function of the 24-kilodalton (24K) protein encoded by cowpea mosaic virus (CPMV) has been studied by constructing a bacterial expression plasmid that contained a cloned chimeric segment consisting of partial DNA copies of CPMV M-RNA (including sequences coding for both capsid proteins) and B-RNA (including sequences coding for the 24K protein). Viral sequences were transcribed from the phage T7 promoter phi 10 of plasmid pT7-6 using T7-RNA polymerase expressed from plasmid pGP1-2 present in the same cells. Upon inducing the synthesis of T7-RNA polymerase several new polypeptides that contained CPMV-specific sequences were expressed, as demonstrated by immunoprecipitation and immunoblotting. Furthermore a proteolytic activity was detected in induced cells which cleaved the viral protein sequences specifically at two glutamine-glycine sites. One of the cleavage products represented capsid protein VP23. The proteolytic activity was absent when an 87-bp deletion was introduced in the coding region for the 24K protein, indicating that this protein represented the protease involved in the proteolytic processing at those specific sites.
Collapse
|