scholarly journals The structure of a plant-specific partitivirus capsid reveals a unique coat protein domain architecture with an intrinsically disordered protrusion

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Matthew Byrne ◽  
Aseem Kashyap ◽  
Lygie Esquirol ◽  
Neil Ranson ◽  
Frank Sainsbury
Keyword(s):  
Coat Protein ◽  
Domain Architecture ◽  
Plant Viruses ◽  
Protein Domain ◽  
Wild Plants ◽  
Structural Basis ◽  
Coat Proteins ◽  
Intrinsically Disordered ◽  
Binding Interface ◽  
Protein Dimers

AbstractPersistent plant viruses may be the most common viruses in wild plants. A growing body of evidence for mutualism between such viruses and their hosts, suggests that they play an important role in ecology and agriculture. Here we present the capsid structure of a plant-specific partitivirus, Pepper cryptic virus 1, at 2.9 Å resolution by Cryo-EM. Structural features, including the T = 1 arrangement of 60 coat protein dimers, are shared with fungal partitiviruses and the picobirnavirus lineage of dsRNA viruses. However, the topology of the capsid is markedly different with protrusions emanating from, and partly comprising, the binding interface of coat protein dimers. We show that a disordered region at the apex of the protrusion is not required for capsid assembly and represents a hypervariable site unique to, and characteristic of, the plant-specific partitiviruses. These results suggest a structural basis for the acquisition of additional functions by partitivirus coat proteins that enables mutualistic relationships with diverse plant hosts.

scholarly journals Structure of a Plant-Specific Partitivirus Capsid Reveals a Novel Coat Protein Architecture with a Hypervariable Protrusion

2021 ◽  
Author(s):  
Matthew Byrne ◽  
Aseem Kashyap ◽  
Lygie Esquirol ◽  
Neil Ranson ◽  
Frank Sainsbury
Keyword(s):  
Coat Protein ◽  
Structural Features ◽  
Plant Viruses ◽  
Wild Plants ◽  
Structural Basis ◽  
Coat Proteins ◽  
Protein Architecture ◽  
Binding Interface ◽  
Protein Dimers ◽  
Site Characteristic

SUMMARYPersistent plant viruses may be the most common viruses in wild plants. A growing body of evidence for mutualism between such viruses and their hosts, suggests that they play an important role in ecology and agriculture. Here we present the structure of a plant-specific partitivirus capsid at 2.9 Å resolution by Cryo-EM. Structural features, including the T=1 arrangement of 60 coat protein dimers, are shared with fungal partitiviruses and the picobirnavirus lineage of dsRNA viruses. However, the topology of the capsid is markedly different with protrusions emanating from, and partly comprising, the binding interface of coat protein dimers. We show that a disordered region at the apex of the protrusion is not required for capsid assembly and represents a hypervariable site characteristic of the plant-specific partitiviruses. These results suggest a structural basis for the acquisition of additional functions by partitivirus coat proteins that enables mutualistic relationships with diverse plant hosts.

Association of the IVR Gene with Virus Localization and Resistance

1995 ◽  
Author(s):  
Gad Loebenstein ◽  
William Dawson ◽  
Abed Gera
Keyword(s):  
Amino Acids ◽  
Coat Protein ◽  
Plant Viruses ◽  
Full Length ◽  
N Gene ◽  
Complete Suppression ◽  
Coat Proteins ◽  
Nicotiana Glutinosa ◽  
Nicotiana Debneyi ◽  
Full Length Gene

We have reported that localization of TMV in tobacco cultivars with the N gene, is associated with a 23 K protein (IVR) that inhibited replication of several plant viruses. This protein was also found in induced resistant tissue of Nicotiana glutinosa x Nicotiana debneyi. During the present grant we found that TMV production is enhanced in protoplasts and plants of local lesion responding tobacco cultivars exposed to 35oC, parallel to an almost complete suppression of the production of IVR. We also found that IVR is associated with resistance mechanisms in pepper cultivars. We succeeded to clone the IVR gene. In the first attempt we isolated a clone - "101" which had a specific insert of 372 bp (the full length gene for the IVR protein of 23 kD should be around 700 bp). However, attempts to isolate the full length gene did not give clear cut results, and we decided not to continue with this clone. The amino acid sequence of the N-terminus of IVR was determined and an antiserum was prepared against a synthetic peptide representing amino acids residues 1-20 of IVR. Using this antiserum as well as our polyclonal antiserum to IVR a new clone NC-330 was isolated using lamba-ZAP library. This NC-330 clone has an insert of about 1 kB with an open reading frame of 596 bp. This clone had 86.6% homology with the first 15 amino acids of the N-terminal part of IVR and 61.6% homology with the first 23 amino acids of IVR. In the QIA expression system and western blotting of the expressed protein, a clear band of about 21 kD was obtained with IVR antiserum. This clone was used for transformation of Samsun tobacco plants and we have presently plantlets which were rooted on medium containing kanamycin. Hybridization with this clone was also obtained with RNA from induced resistant tissue of Samsun NN but not with RNA from healthy control tissue of Samsun NN, or infected or healthy tissue of Samsun. This further strengthens the previous data that the NC 330 clone codes for IVR. In the U.S. it was shown that IVR is induced in plants containing the N' gene when infected with mutants of TMV that elicit the HR. This is a defined system in which the elicitor is known to be due to permutations of the coat protein which can vary in elicitor strength. The objective was to understand how IVR synthesis is induced after recognition of elicitor coat protein in the signal transduction pathway that leads to HR. We developed systems to manipulate induction of IVR by modifying the elicitor and are using these elicitor molecules to isolate the corresponding plant receptor molecules. A "far-western" procedure was developed that found a protein from N' plants that specifically bind to elicitor coat proteins. This protein is being purified and sequenced. This objective has not been completed and is still in progress. We have reported that localization of TMV in tobacco cultivars with the N gene, is associated with a 23 K protein (IVR) that inhibited replication of several plant viruses. This protein was also found in induced resistant tissue of Nicotiana glutinosa x Nicotiana debneyi.

Structures of plant viruses from vibrational circular dichroism

2005 ◽  
Vol 86 (8) ◽  
pp. 2371-2377 ◽  
Author(s):  
Ganesh Shanmugam ◽  
Prasad L. Polavarapu ◽  
Amy Kendall ◽  
Gerald Stubbs
Keyword(s):  
Circular Dichroism ◽  
Coat Protein ◽  
Mosaic Virus ◽  
Structural Information ◽  
Protein Structures ◽  
Plant Viruses ◽  
Vibrational Circular Dichroism ◽  
Coat Proteins ◽  
Helical Structures ◽  
Circular Dichroïsm

Vibrational circular dichroism (VCD) spectra in the amide I and II regions have been measured for viruses for the first time. VCD spectra were recorded for films prepared from aqueous buffer solutions and also for solutions using D2O buffers at pH 8. Investigations of four filamentous plant viruses, Tobacco mosaic virus (TMV), Papaya mosaic virus, Narcissus mosaic virus (NMV) and Potato virus X (PVX), as well as a deletion mutant of PVX, are described in this paper. The film VCD spectra of the viruses clearly revealed helical structures in the virus coat proteins; the nucleic acid bases present in the single-stranded RNA could also be characterized. In contrast, the solution VCD spectra showed the characteristic VCD bands for α-helical structures in the coat proteins but not for RNA. Both sets of results clearly indicated that the coat protein conformations are dominated by helical structures, in agreement with earlier reports. VCD results also indicated that the coat protein structures in PVX and NMV are similar to each other and somewhat different from that of TMV. The present study demonstrates the feasibility of measuring VCD spectra for viruses and extracting structural information from these spectra.

scholarly journals Structures of Qβ virions, virus-like particles, and the Qβ–MurA complex reveal internal coat proteins and the mechanism of host lysis

2017 ◽  
Vol 114 (44) ◽  
pp. 11697-11702 ◽  
Author(s):  
Zhicheng Cui ◽  
Karl V. Gorzelnik ◽  
Jeng-Yih Chang ◽  
Carrie Langlais ◽  
Joanita Jakana ◽  
...  
Keyword(s):  
Coat Protein ◽  
Conformational Changes ◽  
Early Stage ◽  
Protein A ◽  
Single Copy ◽  
Coat Proteins ◽  
Virus Like Particles ◽  
Binding Interface ◽  
Protein Dimer ◽  
Maturation Protein

In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Allolevivirus Qβ the maturation protein, A2, has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis. Here, we determined structures of Qβ virions, virus-like particles, and the Qβ–MurA complex using single-particle cryoelectron microscopy, at 4.7-Å, 3.3-Å, and 6.1-Å resolutions, respectively. We identified the outer surface of the β-region in A2 as the MurA-binding interface. Moreover, the pattern of MurA mutations that block Qβ lysis and the conformational changes of MurA that facilitate A2 binding were found to be due to the intimate fit between A2 and the region encompassing the closed catalytic cleft of substrate-liganded MurA. Additionally, by comparing the Qβ virion with Qβ virus-like particles that lack a maturation protein, we observed a structural rearrangement in the capsid coat proteins that is required to package the viral gRNA in its dominant conformation. Unexpectedly, we found a coat protein dimer sequestered in the interior of the virion. This coat protein dimer binds to the gRNA and interacts with the buried α-region of A2, suggesting that it is sequestered during the early stage of capsid formation to promote the gRNA condensation required for genome packaging. These internalized coat proteins are the most asymmetrically arranged major capsid proteins yet observed in virus structures.

scholarly journals Assembly of Sesbania mosaic virus: Role of the coat protein N-terminal R domain

2014 ◽  
Vol 70 (a1) ◽  
pp. C1820-C1820
Author(s):  
Ashutosh Gulati ◽  
H.S. Savithri ◽  
M.R.N Murthy
Keyword(s):  
Coat Protein ◽  
Mosaic Virus ◽  
Protein A ◽  
Dimensional Structure ◽  
Globular Domain ◽  
Coat Proteins ◽  
Divalent Metal Ions ◽  
Intrinsically Disordered ◽  
R Domain

Coat proteins of several isometric viruses consist of two domains, a disordered N-terminal R-domain consisting of several positively charged residues and a shell (S) domain characterized by a jelly roll β-barrel structure. The three-dimensional structure of Sesbania mosaic virus (SeMV), a T=3 plant virus, has been determined at 3 Å resolution. The full length coat protein, when expressed in E. coli, assembles into T=3 icosahedral shells (VLPs) resembling native virus particles. In the present investigations, the role of N-terminal R domain in the assembly of VLPs was explored by replacing the R domain with a presumably globular domain (SeMV-P10) and other intrinsically disordered (SeMV-P8, and SeMV-VPg) SeMV encoded domains. The R domain was also replaced with the non-viral globular B-domain of Staphyloccocus aureus protein A. These domains were of nearly the same size as that of the R-domain. Most of the chimeric coat proteins, when expressed in E.coli, formed VLPs, which could be purified by ultra-centrifugation. The purified VLPs were examined by transmission electron microscopy (TEM), which suggested that a fraction of the expressed proteins could assemble into T=3 VLPs, although often, the particles were heterogeneous. Interestingly, the SeMV NΔ65B CP could also be purified by Ni-NTA chromatography as a dimer which assembled into T=1 VLPs under crystallization conditions. The structure of NΔ65B-CP VLPs revealed that the assembled particles were devoid of divalent metal ions at the canonical site and there was no density corresponding to the B domain. However, the S domain could be superimposed on that of SeMV NΔ65VLPs determined earlier. The other VLPs- SeMVNΔ65P10 CP, SeMVNΔ65P8 CP and SeMVNΔ65VPg could not be crystallized because of their heterogeneity. These studies suggest a subtle interplay between the length, sequence and structure of the R-domain polypeptide and the assembly of particles.

Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

2020 ◽  
Vol 477 (7) ◽  
pp. 1219-1225 ◽  
Author(s):  
Nikolai N. Sluchanko
Keyword(s):  
Protein Function ◽  
Intrinsically Disordered Protein ◽  
Structural Basis ◽  
Major Protein ◽  
Post Translational Modifications ◽  
Protein Protein Interaction ◽  
Intrinsically Disordered ◽  
Biochemical Journal ◽  
Multiple Binding ◽  
And Control

Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that ‘read’ the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273–1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.

Self-Assembling Micelles Based on an Intrinsically Disordered Protein Domain

2018 ◽  
Author(s):  
Sarah Klass ◽  
Matthew J. Smith ◽  
Tahoe Fiala ◽  
Jessica Lee ◽  
Anthony Omole ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Fusion Proteins ◽  
Organic Molecules ◽  
Intrinsically Disordered Protein ◽  
Protein Domain ◽  
Enzymatic Cleavage ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Self Assembling ◽  
Protein Tag

Herein, we describe a new series of fusion proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing protein tag. The sequences of the proteins are based on a human intrinsically disordered protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CMC) values below 1 µM being observed in some cases. The reported micelles were found to solubilize hydrophobic metal complexes and organic molecules, suggesting their potential suitability for catalysis and drug delivery applications.

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