Adaptive Covariation between the Coat and Movement Proteins of Prunus Necrotic Ringspot Virus

Codoñer, Francisco M.; Fares, Mario A.; Elena, Santiago F.

doi:10.1128/jvi.00122-06

Cited by 24 publications

(31 citation statements)

References 54 publications

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“…In addition, most of the MIC values were above 0.2 suggesting strong coevolution. These values are in the range of MIC values obtained in previous studies examining the coevolution between amino acid sites involved in the interaction between proteins [29]. These results indicate together with the functional divergence analysis that in fact the three GroEL proteins have functionally diverged.…”

Section: Resultssupporting

confidence: 76%

In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae

McNally

Fares

2007

BMC Evol Biol

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Background: Heat-shock proteins are specialized molecules performing different and essential roles in the cell including protein degradation, folding and trafficking. GroEL is a 60 Kda heat-shock protein ubiquitous in bacteria and has been regarded as an important molecule implicated in chronic inflammatory processes caused by Chlamydiae infections. GroEL in Chlamydiae became duplicated at the origin of the Chlamydiae lineage presenting three distinct molecular chaperones, namely the original protein GroEL1 (Ct110), and its paralogous proteins GroEL2 (Ct604) and GroEL3 (Ct755). These chaperones present differential and independent expressions during the different stages of Chlamydiae infections and have been suggested to present differential physiological and regulatory roles.

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Section: Resultssupporting

confidence: 76%

In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae

McNally

Fares

2007

BMC Evol Biol

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“…9). Such intermolecular amino acid covariation has been described for numerous viruses and is indicative of functional/physical protein coadaptation (7,(76)(77)(78). For the DC RV proteins, we quantitated the levels of interdependence between all possible positions of concatenated amino acid sequence alignments using a mutual information-based approach (35).…”

Section: Discussionmentioning

confidence: 99%

Analysis of Human Rotaviruses from a Single Location Over an 18-Year Time Span Suggests that Protein Coadaption Influences Gene Constellations

Zhang

McDonald

Thompson

et al. 2014

J Virol

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Rotaviruses (RVs) are 11-segmented, double-stranded RNA viruses that cause severe gastroenteritis in children. In addition to an error-prone genome replication mechanism, RVs can increase their genetic diversity by reassorting genes during host coinfection. Such exchanges allow RVs to acquire advantageous genes and adapt in the face of selective pressures. However, reassortment may also impose fitness costs if it unlinks genes/proteins that have accumulated compensatory, coadaptive mutations and that operate best when kept together. To better understand human RV evolutionary dynamics, we analyzed the genome sequences of 135 strains (genotype G1/G3/G4-P[8]-I1-C1-R1-A1-N1-T1-E1-H1) that were collected at a single location in Washington, DC, during the years 1974 to 1991. Intragenotypic phylogenetic trees were constructed for each viral gene using the nucleotide sequences, thereby defining novel allele level gene constellations (GCs) and illuminating putative reassortment events. The results showed that RVs with distinct GCs cocirculated during the vast majority of the collection years and that some of these GCs persisted in the community unchanged by reassortment. To investigate the influence of protein coadaptation on GC maintenance, we performed a mutual information-based analysis of the concatenated amino acid sequences and identified an extensive covariance network. Unexpectedly, amino acid covariation was highest between VP4 and VP2, which are structural components of the RV virion that are not thought to directly interact. These results suggest that GCs may be influenced by the selective constraints placed on functionally coadapted, albeit noninteracting, viral proteins. This work raises important questions about mutation-reassortment interplay and its impact on human RV evolution. IMPORTANCERotaviruses are devastating human pathogens that cause severe diarrhea and kill >450,000 children each year. The virus can evolve by accumulating mutations and by acquiring new genes from other strains via a process called reassortment. However, little is known about the relationship between mutation accumulation and gene reassortment for rotaviruses and how it impacts viral evolution. In this study, we analyzed the genome sequences of human strains found in clinical fecal specimens that were collected at a single hospital over an 18-year time span. We found that many rotaviruses did not reassort their genes but instead maintained them as specific sets (i.e., constellations). By analyzing the encoded proteins, we discovered concurrent amino acid changes among them, which suggests that they are functionally coadapted to operate best when kept together. This study increases our understanding of how rotaviruses evolve over time in the human population.

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“…This protein is involved in viral RNA anchoring in the site of assembly and functioning of the replication complex. RNA2 encodes the viral RNA-dependent RNA polymerase (RdRp) responsible for viral RNA replication (Codoñer et al 2005(Codoñer et al , 2006. The PDV RNA3 encodes two proteins, i.e., movement protein (MP) and coat protein (CP).…”

Section: Introductionmentioning

confidence: 99%

Subcelullar localization of proteins associated with Prune dwarf virus replication

et al. 2017

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Prune dwarf virus (PDV) is one of the most dangerous pathogens of fruit trees worldwide. One of the most important proteins required for PDV infection is replicase. (P1 protein) which anchored viral RNA and builds replication complex along with RNA depended polymerase. Despite the importance of PDV as a pathogen, our knowledge regarding tissue/cellular localization and structure of PDV P1 protein is still incomplete. The aim of this work was to localize replicase distribution in leaf tissues and cells by immunofluorescent and immunogold labeling of Nicotiana tobaccum cv Samsun and development of a 3D model of PDV replicase. In this paper we demonstrate that PDV replication, is similar to that of Alfalfa mosaic virus and is strongly connected with tonoplasts. In addition, PDV replicase and coat protein (CP) were also found to be strongly associated with membranes of endoplasmic reticulum and, indicating the potential involvement of these membrane structures in the processes related to viral infection. Bioinformatic analyzes based on 3D modeling and structure prediction revealed that P1 protein has a potential transmembrane domain which enables protein anchoring to tonoplast during replication complex assembly.

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Adaptive Covariation between the Coat and Movement Proteins of Prunus Necrotic Ringspot Virus

Cited by 24 publications

References 54 publications

In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae

In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae

Analysis of Human Rotaviruses from a Single Location Over an 18-Year Time Span Suggests that Protein Coadaption Influences Gene Constellations

Subcelullar localization of proteins associated with Prune dwarf virus replication

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