Molecular Characterization of a Subgroup Specificity Associated with the Rotavirus Inner Capsid Protein VP2

McDonald, Sarah; Patton, John T.

doi:10.1128/jvi.02492-07

Cited by 18 publications

(18 citation statements)

References 35 publications

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“…The single-letter abbreviation for each protein is indicated in parentheses (30). VP6 and VP2 SG specificities and NSP4 genotypes (A, B, and C) are classified according to previous studies (17,26,32). The NSP6 ORFs were found to be identical to that of the Wa strain (WT), truncated (Tr), or extended (Ex) (also see Fig.…”

Section: Resultsmentioning

confidence: 85%

Group A Human Rotavirus Genomics: Evidence that Gene Constellations Are Influenced by Viral Protein Interactions

Heiman

McDonald

Barro

et al. 2008

J Virol

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157

127

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Group A human rotaviruses (HRVs) are the major cause of severe viral gastroenteritis in infants and young children. To gain insight into the level of genetic variation among HRVs, we determined the genome sequences for 10 strains belonging to different VP7 serotypes (G types). The HRVs chosen for this study, D, DS-1, P, ST3, IAL28, Se584, 69M, WI61, A64, and L26, were isolated from infected persons and adapted to cell culture to use as serotype references. Our sequencing results revealed that most of the individual proteins from each HRV belong to one of three genotypes (1, 2, or 3) based on their similarities to proteins of genogroup strains (Wa, DS-1, or AU-1, respectively). Strains D, P, ST3, IAL28, and WI61 encode genotype 1 (Wa-like) proteins, whereas strains DS-1 and 69M encode genotype 2 (DS-1-like) proteins. Of the 10 HRVs sequenced, 3 of them (Se584, A64, and L26) encode proteins belonging to more than one genotype, indicating that they are intergenogroup reassortants. We used amino acid sequence alignments to identify residues that distinguish proteins belonging to HRV genotype 1, 2, or 3. These genotype-specific changes cluster in definitive regions within each viral protein, many of which are sites of known protein-protein interactions. For the intermediate viral capsid protein (VP6), the changes map onto the atomic structure at the VP2-VP6, VP4-VP6, and VP7-VP6 interfaces. The results of this study provide evidence that group A HRV gene constellations exist and may be influenced by interactions among viral proteins during replication.

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Section: Resultsmentioning

confidence: 85%

Group A Human Rotavirus Genomics: Evidence that Gene Constellations Are Influenced by Viral Protein Interactions

Heiman

McDonald

Barro

et al. 2008

J Virol

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157

127

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“…So far, each of the molecularly characterized rotavirus groups possesses unique terminal sequences, which are most evident at the 3Ј-terminal genome segment ends (62). These sequences are specifically bound by the group-specific replication proteins and contribute also to gene expression and packaging of the genome segments into the viral particles (37,44,45,46,57,73). It has been proposed that these conserved sequences influence the ability of genome segment exchanges between different rotavirus strains by reassortment (21,44,62).…”

Section: Discussionmentioning

confidence: 99%

“…These sequences are specifically bound by the group-specific replication proteins and contribute also to gene expression and packaging of the genome segments into the viral particles (37,44,45,46,57,73). It has been proposed that these conserved sequences influence the ability of genome segment exchanges between different rotavirus strains by reassortment (21,44,62). It may be therefore speculated that the finding of nearly identical terminal sequences in group A and group D rotaviruses may allow reassortment of genome segments between viruses of these groups.…”

Section: Discussionmentioning

confidence: 99%

The Genome Segments of a Group D Rotavirus Possess Group A-Like Conserved Termini but Encode Group-Specific Proteins

Trojnar

Otto

Roth

et al. 2010

J Virol

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Rotaviruses are a leading cause of viral acute gastroenteritis in humans and animals. They are grouped according to gene composition and antigenicity of VP6. Whereas group A, B, and C rotaviruses are found in humans and animals, group D rotaviruses have been exclusively detected in birds. Despite their broad distribution among chickens, no nucleotide sequence data exist so far. Here, the first complete genome sequence of a group D rotavirus (strain 05V0049) is presented, which was amplified using sequence-independent amplification strategies and degenerate primers. Open reading frames encoding homologues of rotavirus proteins VP1 to VP4, VP6, VP7, and NSP1 to NSP5 were identified. Amino acid sequence identities between the group D rotavirus and the group A, B, and C rotaviruses varied between 12.3% and 51.7%, 11.0% and 23.1%, and 9.5% and 46.9%, respectively. Segment 10 of the group D rotavirus has an additional open reading frame. Generally, phylogenetic analysis indicated a common evolution of group A, C, and D rotaviruses, separate from that of group B. However, the NSP4 sequence of group C has only very low identities in comparison with cogent sequences of all other groups. The avian group A NSP1 sequences are more closely related to those of group D than those of mammalian group A rotaviruses. Most interestingly, the nucleotide sequences at the termini of the 11 genome segments are identical between group D and group A rotaviruses. Further investigations should clarify whether these conserved structures allow an exchange of genome segments between group A and group D rotaviruses.Rotaviruses are a major cause of acute gastroenteritis in young children (22,32,54,55). They are also etiological agents of diarrhea in several mammalian and avian species (7,9,10,39,52,65,75). Rotaviruses belong to the family Reoviridae and have a nonenveloped viral capsid containing a genome of 11 double-stranded RNA (dsRNA) segments (21, 62). The outer layer of the virus particle is formed by VP4 and VP7 proteins, which possess neutralization antigens. The intermediate layer consists of VP6, a conserved protein, which defines the rotavirus groups. The inner layer is formed by VP2 surrounding a complex of VP1 and VP3, which represent the RNA-dependent RNA polymerase and the guanylyl transferase, respectively (12, 60), and the viral genomic RNAs. In addition, at least five nonstructural proteins are encoded by the rotavirus genome and have diverse functions, e.g

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“…We also found that the VP2 proteins of typical modern human Wa-like strains, but not porcine strains, have an asparagine-lysine (N-K)-rich insertion at positions ~40–50 in the alignment. This insertion differs in length among human Wa-like strains and is not seen in human DS-1-like or AU-like strains with genotype 2 or 3 VP2 proteins, respectively (McDonald and Patton, 2008). Residues 140, 258, and 891 of VP2 reside in the central carapace subdomain of the core shell, whereas reside 417 is in the apical subdomain near the fivefold axis and near predicted VP1 contact sites (Fig.…”

Section: Resultsmentioning

confidence: 99%

Distinguishing the genotype 1 genes and proteins of human Wa-like rotaviruses vs. porcine rotaviruses

Silva

Gregori

McDonald

2016

Infection, Genetics and Evolution

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Group A rotaviruses (RVAs) are 11-segmented, double-stranded RNA viruses and important causes of gastroenteritis in the young of many animal species. Previous studies have suggested that human Wa-like RVAs share a close evolutionary relationship with porcine RVAs. Specifically, the VP1-VP3 and NSP2-5/6 genes of these viruses are usually classified as genotype 1 with >81% nucleotide sequence identity. Yet, it remains unknown whether the genotype 1 genes and proteins of human Wa-like strains are distinguishable from those of porcine strains. To investigate this, we performed comprehensive bioinformatic analyses using all known genotype 1 gene sequences. The RVAs analyzed represent wildtype strains isolated from humans or pigs at various geographical locations during the years of 2004–2013, including 11 newly-sequenced porcine RVAs from Brazil. We also analyzed archival strains that were isolated during the years of 1977–1992 as well as atypical strains involved in inter-species transmission between humans and pigs. We found that, in general, the genotype 1 genes of typical modern human Wa-like RVAs clustered together in phylogenetic trees and were separate from those of typical modern porcine RVAs. The only exception was for the NSP5/6 gene, which showed no host-specific phylogenetic clustering. Using amino acid sequence alignments, we identified 34 positions that differentiated the VP1-VP3, NSP2, and NSP3 genotype 1 proteins of typical modern human Wa-like RVAs versus typical modern porcine RVAs and documented how these positions vary in the archival/unusual isolates. No host-specific amino acid positions were identified for NSP4, NSP5, or NSP6. Altogether, the results of this study support the notion that human Wa-like RVAs and porcine RVAs are evolutionarily related, but indicate that some of their genotype 1 genes and proteins have diverged over time possibly as a reflection of sequestered replication and protein co-adaptation in their respective hosts.

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Molecular Characterization of a Subgroup Specificity Associated with the Rotavirus Inner Capsid Protein VP2

Cited by 18 publications

References 35 publications

Group A Human Rotavirus Genomics: Evidence that Gene Constellations Are Influenced by Viral Protein Interactions

Group A Human Rotavirus Genomics: Evidence that Gene Constellations Are Influenced by Viral Protein Interactions

The Genome Segments of a Group D Rotavirus Possess Group A-Like Conserved Termini but Encode Group-Specific Proteins

Distinguishing the genotype 1 genes and proteins of human Wa-like rotaviruses vs. porcine rotaviruses

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