Phylogeny of capsid proteins of small icosahedral RNA plant viruses

Dolja, Valerian V.; Koonin, Eugene V.

doi:10.1099/0022-1317-72-7-1481

Cited by 59 publications

(40 citation statements)

References 42 publications

(32 reference statements)

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“…From the amino acid similarities it is clear the coat protein of OCSV has similar structurally defined domains to those of the other viruses. In agreement with observations made previously Riviere et al, 1989;Dolja & Koonin, 1991), OCSV also shows most sequence identity with the others within the S domain, and least within the P domain. OCSV also shows amino acid conservation at four of the six Ca 2+ binding sites within the S domain, identified as being important in the stabilization of the tombusvirus capsid (Hogle et al, 1983;Hillman et al, 1989); only two of these six are conserved in the members of the carmovirus group that were compared.…”

Section: Sequence Comparisonssupporting

confidence: 79%

“…Further comparisons show that the different structural domains share different degrees of amino acid sequence similarity among the viruses. The S domains are the most similar, whilst the P domain is the least similar, and the R and arm regions show intermediate similarity Riviere et al, 1989;Dolja & Koonin, 1991). A multiple sequence alignment was made using progressive, pairwise alignments between the amino acid sequences of the coat proteins of a number of tombusviruses, carmoviruses, necroviruses, SBMV, MCMV and RCNMV (see Fig.…”

Section: Sequence Comparisonsmentioning

confidence: 99%

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The nucleotide sequence and proposed genome organization of oat chlorotic stunt virus, a new soil-borne virus of cereals

Boonham

1995

Journal of General Virology

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The complete genomic sequence of a new virus, first found infecting oats in Wales, UK, has been determined. The genome is a positive-sense ssRNA molecule, 4114 nucleotides in length, examination of which indicates the presence of four ORFs. The first ORF initiating at the 5' terminus (ORF1) encodes a protein with a predicted M r of 23 476 (p23). ORF2 extends through the amber termination codon of ORF1 to give a protein with a predicted M r of 84 355 (p84). The readthrough domain of p84 contains amino acid sequence similarities with a number of putative RNA-dependent RNA polymerases. ORF3 is in a different reading frame from ORF1/2 and encodes a protein with an M r of 48 231 (p48), identified as the coat protein by direct peptide sequencing. ORF4 nests within ORF3 but is in a different frame from it and codes for a protein with a predicted M r of 8220 (p8). Comparisons of peptide sequence, particularly within the putative polymerase region and within the S domain of the coat protein, highlight similarities with members of both the tombusvirus and carmovirus groups. The coat protein region shows most similarity with members of the tombusvirus group, whilst the size and predicted strategy of the genome seem to be intermediate between that of the carmovirus and tombusvirus groups. These features highlight possible evolutionary links with each group whilst being distinct from both. We propose the name of oat chlorotic stunt for this new virus.

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Section: Sequence Comparisonssupporting

confidence: 79%

Section: Sequence Comparisonsmentioning

confidence: 99%

The nucleotide sequence and proposed genome organization of oat chlorotic stunt virus, a new soil-borne virus of cereals

Boonham

1995

Journal of General Virology

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“…Based on known structures and structural protein sequences of distantly related icosahedral RNA viruses, the CP can be divided into an N-terminal arginine-rich domain and the shell domain (7). The charged arginine-rich domain is likely found to be internal and interacting with the viral RNA.…”

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confidence: 99%

A Surface Loop of the Potato Leafroll Virus Coat Protein Is Involved in Virion Assembly, Systemic Movement, and Aphid Transmission

Lee

Kaplan²,

Ripoll

et al. 2005

J Virol

101

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Two acidic domains of the Potato leafroll virus (PLRV) coat protein, separated by 55 amino acids and predicted to be adjacent surface features on the virion, were the focus of a mutational analysis. Eleven site-directed mutants were generated from a cloned infectious cDNA of PLRV and delivered to plants by Agrobacterium-mediated mechanical inoculation. Alanine substitutions of any of the three amino acids of the sequence EWH (amino acids 170 to 172) or of D177 disrupted the ability of the coat protein to assemble stable particles and the ability of the viral RNA to move systemically in four host plant species. Alanine substitution of E109, D173, or E176 reduced the accumulation of virus in agrobacterium-infiltrated tissues, the efficiency of systemic infection, and the efficiency of aphid transmission relative to wild-type virus, but the mutations did not affect virion stability. A structural model of the PLRV capsid predicted that the amino acids critical for virion assembly were located within a depression at the center of a coat protein trimer. The other amino acids that affected plant infection and/or aphid transmission were predicted to be located around the perimeter of the depression. PLRV virions play key roles in phloem-limited virus movement in plant hosts as well as in transport and persistence in the aphid vectors. These results identified amino acid residues in a surfaceoriented loop of the coat protein that are critical for virus assembly and stability, systemic infection of plants, and movement of virus through aphid vectors.Members of the family Luteoviridae are icosahedral viruses with small (Ϸ6-kb) RNA genomes that infect phloem-associated tissues of their plant hosts (29). They are transmitted between plants by aphids in a circulative, persistent manner. Although the virus can survive for extended periods in often hostile environments in the aphid, the virus does not replicate in the insect (11). Features of the virion regulate local and systemic movement of the virus in plant hosts and regulate the recognition, transport, and persistence of virus in aphid tissues, yet little is known about the specific properties and biologically active domains of the luteovirus particle.The icosahedral virions of members of the Luteoviridae are composed of two structural proteins, the major 22-to 24-kDa capsid protein (CP) encoded by open reading frame (ORF) 3, and a minor species referred to as the readthrough protein (RT) (17). The RT, encoded by ORF 3 and the downstream adjacent ORF 5, is translated by occasional suppression of the CP termination codon (16). The virion structure has not been resolved for any member of the Luteoviridae, but the capsids are thought to be assembled from 180 subunits according to T ϭ 3 quasi-symmetry. A variable but minor number of the 180 capsids are RT subunits incorporated into the virion via their CP moiety (16), although sequences in the RT domain regulate the incorporation (24). The Ϸ50-kDa RT domain encoded by ORF 5 is believed to protrude from the surface of the virio...

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“…With few exceptions, CP monomers have a protruding and flexible N-terminal arm (NTA), a central core called the shell (S) domain, and, in most cases, a C-terminal projecting domain (P) (Dolja and Koonin 1991;Rossmann and Johnson 1989). The NTA are usually oriented toward the internal lumen of the capsid and they are frequently rich in positively charged residues (Guerra-Peraza et al 2005;Hsu et al 2006;Hu and Ghabrial 1995;Lee and Hacker 2001;Olspert et al 2010;Rao and Grantham 1995;Reade et al 2010;Sharma and Ikegami 2009;Yusibov and Loesch-Fries 1995).…”

Section: Discussionmentioning

confidence: 99%

The Importance of the KR-Rich Region of the Coat Protein of Ourmia melon virus for Host Specificity, Tissue Tropism, and Interference With Antiviral Defense

Rossi¹,

Vallino²,

Abbà³

et al. 2015

MPMI

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The N-terminal region of the Ourmia melon virus (OuMV) coat protein (CP) contains a short lysine/arginine-rich (KR) region. By alanine scanning mutagenesis, we showed that the KR region influences pathogenicity and virulence of OuMV without altering viral particle assembly. A mutant, called OuMV 6710 , with three basic residue substitutions in the KR region, was impaired in the ability to maintain the initial systemic infection in Nicotiana benthamiana and to infect both cucumber and melon plants systemically. The integrity of this protein region was also crucial for encapsidation of viral genomic RNA; in fact, certain mutations within the KR region partially compromised the RNA encapsidation efficiency of the CP. In Arabidopsis thaliana Col-0, OuMV 6710 was impaired in particle accumulation; however, this phenotype was abolished in dcl2/dcl4 and dcl2/dcl3/dcl4 Arabidopsis mutants defective for antiviral silencing. Moreover, in contrast to CP wt , in situ immunolocalization experiments indicated that CP 6710 accumulates efficiently in the spongy mesophyll tissue of infected N. benthamiana and A. thaliana leaves but only occasionally infects palisade tissues. These results provided strong evidence of a crucial role for OuMV CP during viral infection and highlighted the relevance of the KR region in determining tissue tropism, host range, pathogenicity, and RNA affinity, which may be all correlated with a possible CP silencing-suppression activity.Ourmia melon virus (OuMV) is the best-characterized species of the Ourmiaviridae family, which also consists of Epirus cherry virus (EpCV) and Cassava virus C (CaVC) species (King et al. 2012). Three plus-strand RNA molecules form the OuMV genome and each segment encodes a single protein: RNA1 directs synthesis of an RNA-dependent RNA polymerase (RdRp), RNA2 encodes a movement protein (MP), and RNA3 specifies the 22-kDa coat protein (CP) (Rastgou et al. 2009). Ourmiaviruses have affinities with other postive single stranded RNA multipartite viruses, such as the members of the family Bromoviridae, but their unique structural and molecular features have resulted in their classification in a novel viral family. In fact, phylogenetic analyses showed that the members of the family likely went through a very unusual evolutionary process based on a possible reassortment between a plant virus and a mycovirus. In particular, OuMV RdRp shares distant similarity only with RdRp of narnaviruses, a group of viruses which mainly infects fungi; however, the MP is distantly related to MP of plant tombusviruses. The CP has limited but significant similarity with CP of plant and mammalian viruses, although its phylogenetic origin remains uncertain (Rastgou et al. 2009). Another peculiarity of the OuMV CP is the unique morphology of the virions among plant viruses: bacilliform particles of three different lengths with pointed ends (Lisa et al. 1988). Ectopic expression of RNA3 in Nicotiana benthamiana does not result in virion formation because the active replication of OuMV is necessary fo...

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Phylogeny of capsid proteins of small icosahedral RNA plant viruses

Cited by 59 publications

References 42 publications

The nucleotide sequence and proposed genome organization of oat chlorotic stunt virus, a new soil-borne virus of cereals

The nucleotide sequence and proposed genome organization of oat chlorotic stunt virus, a new soil-borne virus of cereals

A Surface Loop of the Potato Leafroll Virus Coat Protein Is Involved in Virion Assembly, Systemic Movement, and Aphid Transmission

The Importance of the KR-Rich Region of the Coat Protein of Ourmia melon virus for Host Specificity, Tissue Tropism, and Interference With Antiviral Defense

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