The coat protein of prunus necrotic ringspot virus specifically binds to and regulates the conformation of its genomic RNA

Aparicio, Frederic; Vilar, Marçal; Pérez‐Payá, Enrique; Pallás, Vicente

doi:10.1016/s0042-6822(03)00284-8

Cited by 58 publications

(59 citation statements)

References 45 publications

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“…Addition of Hfq hexamer to a 1:2 RprA:Hfq stoichiometric ratio, showed only a small further decrease in ellipticity (0.46 Δε to 0.37 Δε) (Fig. 4A), which may be more indicative of a slight chromophore rearrangement upon Hfq binding, rather than a significant structural change (Aparicio et al 2003;Vincent et al 2012b;Henderson et al 2013). For OxyS, the addition of Hfq hexamer to a 1:1 stoichiometric ratio reduced the ellipticity at 265 nm by 35% (1.00 Δε to 0.65 Δε) (Fig.…”

Section: Hfq Changes the Structure Of Oxys And Rpramentioning

confidence: 95%

“…1A,B). Furthermore, like RprA, the addition of Hfq hexamer to a 1:2 OxyS:Hfq stoichiometric ratio showed only a small further decrease in ellipticity at 265 nm (0.65 Δε to 0.60 Δε), suggestive more of a binding rearrangement rather than further structural change (Aparicio et al 2003;Vincent et al 2012b;Henderson et al 2013).…”

Section: Hfq Changes the Structure Of Oxys And Rpramentioning

confidence: 97%

“…The protein contribution within the wavelength range of 240-350 nm of the CD spectrum was subtracted, but due to the small number of aromatic residues within Hfq, the contribution was negligible. This means the peaks at 240-350 nm are dominated by the contribution from the RNA (Daly et al 1990;Tan and Frankel 1992;Aparicio et al 2003;Vincent et al 2012b;Henderson et al 2013).…”

Section: Hfq Changes the Structure Of Oxys And Rpramentioning

confidence: 99%

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Hfq binding changes the structure ofEscherichia colismall noncoding RNAs OxyS and RprA, which are involved in the riboregulation ofrpoS

Henderson¹,

Vincent²,

Casamento³

et al. 2013

RNA

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OxyS and RprA are two small noncoding RNAs (sRNAs) that modulate the expression of rpoS, encoding an alternative sigma factor that activates transcription of multiple Escherichia coli stress-response genes. While RprA activates rpoS for translation, OxyS down-regulates the transcript. Crucially, the RNA binding protein Hfq is required for both sRNAs to function, although the specific role played by Hfq remains unclear. We have investigated RprA and OxyS interactions with Hfq using biochemical and biophysical approaches. In particular, we have obtained the molecular envelopes of the Hfq-sRNA complexes using smallangle scattering methods, which reveal key molecular details. These data indicate that Hfq does not substantially change shape upon complex formation, whereas the sRNAs do. We link the impact of Hfq binding, and the sRNA structural changes induced, to transcript stability with respect to RNase E degradation. In light of these findings, we discuss the role of Hfq in the opposing regulatory functions played by RprA and OxyS in rpoS regulation.

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Section: Hfq Changes the Structure Of Oxys And Rpramentioning

confidence: 95%

Section: Hfq Changes the Structure Of Oxys And Rpramentioning

confidence: 97%

Section: Hfq Changes the Structure Of Oxys And Rpramentioning

confidence: 99%

See 1 more Smart Citation

Hfq binding changes the structure ofEscherichia colismall noncoding RNAs OxyS and RprA, which are involved in the riboregulation ofrpoS

Henderson¹,

Vincent²,

Casamento³

et al. 2013

RNA

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“…Figure 9 highlights that CP dimerization region (DR) was less conserved than RNA-binding domain (RBD). The PNRSV CP has the capacity to bind to the 3'UTR of its RNA3 and 4 [58,59] through an RNA-binding domain (RBD) rich in R residues located at the N-terminal region between amino acid residues 25 to 50 of the protein [59,60]. RBD is necessary for different viral processes, e.g.…”

Section: Discussionmentioning

confidence: 99%

Evidence for Recombination in the Emerged Phylogroup SW6 of Prunus Necrotic Ringspot Virus and Estimate of Selection Pressure Acting on Capsid Protein of Affiliated Members

Boulila¹

2017

JAMB

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Abstract. Recombination plays a key role in virus evolution. Except a limited number of works carried out so far on recombination in Prunus necrotic ringspot virus (PNRSV) genome, knowledge is still poor. Numerous phylogenetic studies particularly those based on capsid (CP) and movement protein (MP) of PNRSV showed that all accessions described so far split into three major phylogroups, i.e., PV96, PV32, and PE5. With the recent characterization of Chilean and Indian isolates which were phylogenetically closely related to the oldest member, i.e., SW6 (AF013287) from USA, a new phylogroup baptized SW6, emerged since it was outside of the evolutionary behavior of the classical PV96, PV32, and PE5 clusters. In order to understand how it evolved, six computerized methods were used to detect potential recombination in the CP sequences of nine components forming SW6 phylogroup. It was clearly demonstrated that various members underwent recombination. Additionally, networked relationships among them proved that numerous incompatibilities occurred in these sequences illustrated by the presence of boxes in the network implying therefore the possibility of recombination. According to inferred network, several sequences contained conflicting signals as illustrated by various splits and edges with special reference to Chilean (EF565255, EF565256), polish (AF332614) and Indian (AM494934) isolates. It is worth noting that the phylogenetic network provided a different clustering compared to the bifurcating tree. In fact, three distinct groups were delineated with SplitsTree4 software instead of a globally homogenous ensemble generated by MEGA7 algorithm. Furthermore, this study pointed out that members of SW6 phylogroup were the only recombinants among 205 tested accessions confirming that SW6 should be considered as the fourth phylogenetic group of PNRSV. On the other hand, CP was predominantly under purifying selection. However, positive selection was evidenced particularly in the C-terminal region of CP comprising part of dimerization region (DR). Such adaptive selection was exerted on a CP segment of AM494934 accession exchanged by recombination.

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“…Putative zinc-finger domains have also been found in case of ApMV and PNRSV [1,14,15,28]. In case of PNRSV CP 26 amino acid region located in between amino acids 25-50 from the N-terminal end represented as RNA binding domain and thus involved in genome activation [5]. Since it has been already proved that N-terminus of PNRSV CP is required for RNA binding, Present finding also showed that N-terminus might also be involved in protein-protein interaction during capsid formation whereas C-terminus is the most important for dimer formation.…”

Section: Discussionmentioning

confidence: 99%

Molecular characterization and intermolecular interaction of coat protein of Prunus necrotic ringspot virus: implications for virus assembly

Kulshrestha¹,

Hallan²,

Sharma

et al. 2013

Indian J. Virol.

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Coat protein (CP) and RNA3 from Prunus necrotic ringspot virus (PNRSV-rose), the most prevalent virus infecting rose in India, were characterized and regions in the coat protein important for self-interaction, during dimer formation were identified. The sequence analysis of CP and partial RNA 3 revealed that the rose isolate of PNRSV in India belongs to PV-32 group of PNRSV isolates. Apart from the already established group specific features of PV-32 group member's additional group-specific and host specific features were also identified. Presence of methionine at position 90 in the amino acid sequence alignment of PNRSV CP gene (belonging to PV-32 group) was identified as the specific conserved feature for the rose isolates of PNRSV. As protein-protein interaction plays a vital role in the infection process, an attempt was made to identify the portions of PNRSV CP responsible for self-interaction using yeast two-hybrid system. It was found (after analysis of the deletion clones) that the C-terminal region of PNRSV CP (amino acids 153-226) plays a vital role in this interaction during dimer formation. N-terminal of PNRSV CP is previously known to be involved in CP-RNA interactions, but our results also suggested that N-terminal of PNRSV CP represented by amino acids 1-77 also interacts with C-terminal (amino acids 153-226) in yeast two-hybrid system, suggesting its probable involvement in the CP-CP interaction.

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The coat protein of prunus necrotic ringspot virus specifically binds to and regulates the conformation of its genomic RNA

Cited by 58 publications

References 45 publications

Hfq binding changes the structure ofEscherichia colismall noncoding RNAs OxyS and RprA, which are involved in the riboregulation ofrpoS

Hfq binding changes the structure ofEscherichia colismall noncoding RNAs OxyS and RprA, which are involved in the riboregulation ofrpoS

Evidence for Recombination in the Emerged Phylogroup SW6 of Prunus Necrotic Ringspot Virus and Estimate of Selection Pressure Acting on Capsid Protein of Affiliated Members

Molecular characterization and intermolecular interaction of coat protein of Prunus necrotic ringspot virus: implications for virus assembly

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