PCP Consensus Sequences of Flaviviruses: Correlating Variance with Vector Competence and Disease Phenotype

Danecek, Petr; Lu, Wenzhe; Schein, Catherine H.

doi:10.1016/j.jmb.2009.11.070

Cited by 26 publications

(29 citation statements)

References 70 publications

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“…On the contrary, the PXAP and YCYL motifs were quite conserved indicating their functional relevance. Moreover, substantial changes in the consensus sequences are also found to occur in only a few areas of the E protein and may have relevance to growth in insect cells versus vertebrates [69]. Although mutational analysis confirms the importance of these domains in WNV assembly and particle formation, the role of Tsg101 and Alix in this phenomenon remains inconclusive from this study.…”

Section: Discussionmentioning

confidence: 77%

Identification of conserved motifs in the Westnile virus envelope essential for particle secretion

et al. 2013

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BackgroundEnveloped viruses utilize cellular membranes to bud from infected cells. The process of virion assembly and budding is often facilitated by the presence of certain conserved motifs within viral proteins in conjunction with cellular factors. We hence examined the West Nile Virus (WNV) Envelope protein for the presence of any such motifs and their functional characterization.ResultsWe identified conserved 461PXAP464 and 349YCYL352 motifs in the WNV envelope glycoprotein bearing resemblance to retroviral late domains. Disruptive mutations of PXAP to LAAL and of the highly conserved Cys350 in the YCYL motif, led to a severe reduction in WNV particle production. Similar motifs in case of retroviruses are known to interact with components of host sorting machinery like PXAP with Tsg101 and YXXL with Alix. However, in the case of WNV, siRNA mediated depletion of Alix or Tsg101 did not have an effect on WNV release. Molecular modeling suggested that while the 461PXAP464 motif is surface accessible and could potentially interact with cellular proteins required for WNV assembly, the 349YCYL352 motif was found to be internal with Cys350 important for protein folding via disulphide bonding.ConclusionsThe conserved 461PXAP464 and 349YCYL352 motifs in the WNV envelope are indispensable for WNV particle production. Although these motifs bear sequence similarity to retroviral late domains and are essential for WNV assembly, they are functionally distinct suggesting that they are not the typical late domain like motifs of retroviruses and may play a role other than Alix/Tsg101 utilization/dependence.

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Section: Discussionmentioning

confidence: 77%

Identification of conserved motifs in the Westnile virus envelope essential for particle secretion

et al. 2013

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“…In the meantime, this structure could be a starting point for designing mutations of VPg or mimetics of VPgpU that could interfere either with the uridylylation or priming steps, perhaps using a consensus approach[15, 16] to account for variability in the sequences of related enteroviruses. At least one mutant of PV1-VPg mutant can inhibit uridylylation in vitro (our unpublished data), and others have shown that VPg mutations can slow or eliminate PV replication in trans[13].…”

Section: Discussionmentioning

confidence: 99%

NMR solution structure of poliovirus uridylyated peptide linked to the genome (VPgpU)

et al. 2010

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Picornaviruses have a 22-24 amino acid peptide, VPg, bound covalently at the 5' end of their RNA, that is essential for replication. VPgs are uridylylated at a conserved Tyrosine to form VPgpU, the primer of RNA synthesis by the viral polymerase. This first complete structure for any uridylylated VPg, of poliovirus type 1 (PV1)-VPgpU, shows that conserved amino acids in VPg stabilize the bound UMP, with the uridine atoms involved in base pairing and chain elongation projected outward. Comparing this structure to PV1-VPg and partial structures of VPg/VPgpU from other picornaviruses suggests that enteroviral polymerases require a more stable VPg structure than does the distantly related aphthovirus, foot and mouth disease virus (FMDV). The glutamine residue at the C-terminus of PV1-VPgpU lies in back of the uridine base and may stabilize its position during chain elongation and/or contribute to base specificity. Under in vivo-like conditions with the authentic cre(2C) hairpin RNA and Mg ++ , 5-methylUTP cannot compete with UTP for VPg uridylyation in an in vitro uridylyation assay, but both nucleotides are equally incorporated by PV1-polymerase with Mn ++ and a poly-A RNA template. This indicates the 5 position is recognized under in vivo conditions. The compact VPgpU structure docks within the active site cavity of the PV-polymerase, close to the position seen for the fragment of FMDV-VPgpU with its polymerase. This structure could aid in design of novel enterovirus inhibitors, and stabilization upon uridylylation may also be pertinent for post-translational uridylylation reactions that underlie other biological processes.

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“…It is designed to be useful for sets with many sequences (such as viral isolates) that have a high superficial redundancy (i.e., nearly identical sequences that differ at only a few positions). The rationale and details of the method are described in detail elsewhere (Bowen et al, 2012; Danecek et al, 2010; Danecek and Schein, 2010; Schein et al, 2012). Here, the PCP-con program was used to determine a consensus of 31 of the most diverse EV VPg sequences (Figure 1).…”

Section: Methodsmentioning

confidence: 99%

Sequence specificity for uridylylation of the viral peptide linked to the genome (VPg) of enteroviruses

Schein

Paul

et al. 2015

Virology

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Enteroviruses (EV) uridylylate a peptide, VPg, as the first step in their replication. VPgpUpU, found free in infected cells, serves as the primer for RNA elongation. The abilities of four polymerases (3Dpol), from EV-species A-C, to uridylylate VPgs that varied by up to 60% of their residues were compared. Each 3Dpol was able to uridylylate all five VPgs using polyA RNA as template, while showing specificity for its own genome encoded peptide. All 3Dpol uridylylated a consensus VPg representing the physical chemical properties of 31 different VPgs. Thus the residues required for uridylylation and the enzymatic mechanism must be similar in diverse EV. As VPg-binding sites differ in co-crystal structures, the reaction is probably done by a second 3Dpol molecule. The conservation of polymerase residues whose mutation reduces uridylylation but not RNA elongation is compared.

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PCP Consensus Sequences of Flaviviruses: Correlating Variance with Vector Competence and Disease Phenotype

Abstract: Background-Computational methods are needed to design multivalent vaccines against flaviviruses such as West Nile (WNV) or Dengue (DENV).

Cited by 26 publications

References 70 publications

Identification of conserved motifs in the Westnile virus envelope essential for particle secretion

Identification of conserved motifs in the Westnile virus envelope essential for particle secretion

NMR solution structure of poliovirus uridylyated peptide linked to the genome (VPgpU)

Sequence specificity for uridylylation of the viral peptide linked to the genome (VPg) of enteroviruses

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