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Animal: DNA Viruses |
Department of Microbiology, University of Otago, PO Box 56, Dunedin, New Zealand1
Dipartimento di Sanità Pubblica Veterinaria e Patologia Animale, Università degli Studi di Bologna, Bologna, Italy2
Moredun Research Institute, Edinburgh, UK3
Institute of Immunology, Federal Research Centre for Virus Diseases of Animals, Tübingen, Germany4
Author for correspondence: Andrew Mercer. Fax +64 3 4797744. e-mail andy.mercer{at}stonebow.otago.ac.nz
| Abstract |
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| Introduction |
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We and others have recently demonstrated that VEGF encoded by Orf virus is a cystine-knot homodimer that has some of the functional features of mammalian VEGF (Meyer et al., 1999
; Ogawa et al., 1998
; Wise et al., 1999
). The purified factor derived from Orf virus strain NZ2 was able to stimulate proliferation of vascular endothelial cells, promote vascular permeability and was shown to bind VEGFR-2 but not VEGFR-1 or VEGFR-3. As such the viral VEGF forms a new member of the VEGF family of molecules with a unique profile of receptor recognition. We have also shown that infection of sheep with a recombinant Orf virus in which the viral VEGF gene was partially deleted resulted in lesions that lacked the extensive dermal vascularization seen in wild-type infections (Savory et al., 2000
). No other virus has been reported to encode a form of VEGF.
The original report of a possible viral VEGF described two independent New Zealand isolates of Orf virus (Lyttle et al., 1994
). The isolates (NZ2 and NZ7) encode predicted peptides of similar size with similar levels of sequence relatedness to mammalian VEGFs and both peptides have been shown to have similar VEGF-like activities (Ogawa et al., 1998
; Wise et al., 1999
). However, the two viral genes are unexpectedly different from each other sharing only 41·1% predicted amino acid sequence identity. This raised the possibility that further variants of VEGF are encoded by other isolates of Orf virus. In order to investigate the sequence variation and distribution of VEGF genes of Orf virus we examined a selection of isolates from diverse sources.
| Methods |
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Viruses and cells.
DNA manipulations.
Virus was purified and DNA recovered as previously described (Mercer et al., 1987
). The primer pairs used in PCRs were derived from the first and last six codons of D1701 VEGF (Meyer et al., 1999
), NZ2 VEGF or NZ7 VEGF (Lyttle et al., 1994
). PCRs were performed using 30 cycles of 50 °C 20 s, 72 °C 20 s and 95 °C 20 s. The DNA sequences of the PCR products were either determined directly or the amplified products were cloned into plasmid vectors and the sequence determined from at least five different clones. Double-stranded DNA templates were prepared and sequenced by procedures recommended by Applied Biosystems Inc. (ABI). The products of sequencing reactions were analysed with an ABI model 373A sequencing system. Assembly and analysis of nucleotide sequence was conducted using programs of the DNASTAR package. Phylogenetic analysis of aligned sequences was conducted using programs of the PHYLIP package version 3·6 (Felsenstein, 1989
); genetic distances were calculated using PROTDIST (JonesTaylorThornton matrix) and phylogenetic trees constructed by the neighbour-joining method (NEIGHBOR).
Prediction of the tertiary structure of the VEGF-variants of Orf virus.
The structure of the VEGF-variants of Orf virus were modelled using SWISSMODEL and the SWISSPDBVIEWER protein modelling program (version 3.5; Guex & Peitsch, 1997
), which are both available from the ExPASy website (http://www.expasy.ch/spdbv). The sequences of the variants were aligned using SWISSMODEL against protein subunits A and B of human VEGF-A (Muller et al., 1997a
) (PDB identifier, 2VPF). The Iterative Magic Fit function was used for energy minimization and the alignments were manually optimized. Ramachandran plots for the viral VEGF models, VEGF-A and PlGF, were compared to determine if the viral models contained residues that did not conform to acceptable
and/or
angles.
| Results and Discussion |
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The majority of isolates tested (18) encoded VEGF-like genes with sequences related to that of NZ2 VEGF. An alignment of the predicted amino acid sequences of these NZ2-like VEGFs is shown in Fig. 1
along with the established sequences for NZ2, D1701 and NZ7. The nucleotide and amino acid relationships between the NZ2-like VEGFs are listed in Table 1
. In only one case (NZ9) was the VEGF nucleotide sequence identical to that of NZ2. The NZ2-like VEGF genes were on average 93·5% identical to NZ2 VEGF in nucleotide sequence. In all 190 combinations of the 20 NZ2-like VEGFs, there were only eight combinations that were identical at the amino acid level and the average amino acid identity between pairs of sequences was 86·1% with a standard deviation of 7·6.
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The inclusion of MRI11 in the NZ2-like group is also supported by the phylogenetic analysis shown in Fig. 2
. This phylogenetic tree illustrates the relationships between the viral VEGFs and demonstrates the clear separation of NZ2-like and NZ7-like VEGFs. It also reveals some evidence of geographical clustering with peptides of identical (ITtor, ITC2 and IT90, NZ10, Acsl and NZh1) or very similar sequences (IT19 and IT20, and NZ2, NZ66 and NZ9) likely to have come from the same country. However, the differences between MRI1 and MRI3, between NZ2 and NZ12 and between IT90 and IT20 clearly indicate that more than one clone is present in each country. The amino acid sequence identity between the human derived clone (NZh1) and NZ10 suggests that there is not a specific clone infecting humans rather than sheep and is consistent with the evidence that human infection by Orf virus is sourced from sheep. Similarly, the sequence identity between IT90, ITtor and ITC2 suggests that the same clones of Orf virus infect both sheep and chamois.
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The sequence variation seen in VEGF genes of Orf virus is not a general feature of genes of this virus. For example, Orf virus also encodes a homologue of the cytokine interleukin-10 (IL-10) (Fleming et al., 2000
). The predicted amino acid sequences for the IL-10s encoded by Orf virus strains NZ2 and NZ7 differ by only 2·7%. Two further examples are provided by an interferon resistance element and an inhibitor of GM-CSF encoded by Orf virus. Inter-strain amino acid sequence variation for both these elements is less than 3% (Deane et al., 2000
; McInnes et al., 1998
).
Nor is the sequence variation seen in VEGF genes of Orf virus likely to reflect accelerated genetic drift of silent genes. In all isolates key functional motifs such as the cystine-knot motif are conserved. Furthermore, in addition to the characterized activity of the VEGFs encoded by strains NZ2, D1701 and NZ7 (Meyer et al., 1999
; Ogawa et al., 1998
; Wise et al., 1999
), we detected VEGF-like activity in conditioned medium of cells infected with each of strains D15, D23, D47 or MRI11 (not shown).
Receptor-binding motifs
Members of the VEGF family share a VEGF homology domain (VHD) containing eight cysteine residues that form the cystine-knot motif and link the subunits of the anti-parallel homodimer. Despite the sequence variation detailed above, all eight cysteines are conserved in all of the VEGF-variants of Orf virus (Fig. 1
). Also conserved in each of the VEGFs of Orf virus are a potential signal sequence and potential N- and O-linked glycosylation sites (Fig. 1
). A threonine/proline-rich motif seen in the C terminus of VEGFs encoded by both NZ2 and NZ7 but not seen in mammalian VEGFs is retained in all viral VEGFs (Fig. 1
).
The conservation of structure within the VEGF family of growth factors suggests that residues important in mediating the binding of different members to their receptors are likely to be conserved. We aligned representatives of the VEGF family with the viral VEGFs and looked for any correlation with the ability to bind VEGFR-1 or VEGFR-2 (Fig. 3
). We focused initially on residues that have been implicated in mediating binding to these receptors.
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Correlations with the ability to recognize specific VEGF receptors were detected in other residues. Ser-50 of VEGF-A is retained in all factors that recognize VEGFR-1 but is not present in any of the factors that do not recognize this receptor (Fig. 3
). The NZ2-like viral VEGFs along with VEGF-C and VEGF-D generally have a Pro at this position. Mutational analysis of this residue has not been reported.
A strong correlation is apparent between binding of VEGFR-2 and the presence of Asn at a position equivalent to Asn-62 of VEGF-A. This residue is conserved in 11 of 12 species of VEGF-A, four species of VEGF-C, three species of VEGF-D and all 24 viral isolates. In contrast this residue is not found in PlGF-1 (three species have Gly) or VEGF-B (4 species have Pro) which do not recognize VEGFR-2. Crystal structure determination of VEGF-A has shown that Asn-62 is an accessible residue on the receptor-binding face of the ligand (Muller et al., 1997a
). However substitution of this residue by Ala reduced the relative affinity of VEGF-A for VEGFR-2 only modestly (Muller et al., 1997b
).
Structural modelling
Predicted structures of the VEGF-variants of Orf virus were determined by comparison to the solved crystal structure of subunits A and B of VEGF-A. Despite only moderate sequence identity, the structures predicted for the viral VEGF monomers are very similar both to each other and to the structure determined by X-ray crystallography for VEGF-A (Fig. 4
). They conserve the central anti-parallel, four-stranded
sheet and two
-helical segments. With the exception of the VEGFs encoded by Orf virus strains NZ7 (ORFVNZ7VEGF) and MRI11 (ORFVMRI11VEGF), the modelling program we used did not detect interruptions in the fourth and fifth
sheets so as to generate
4/
5 and
6/
7 as determined for published structures of VEGF (Muller et al., 1997a
). However, for greater clarity we have retained the published nomenclature of seven
sheets. The orientations of the cysteines forming the intra-chain disulphide bonds responsible for the cystine-knot motif are maintained in the viral VEGFs (Muller et al., 1997a
). Also maintained is the three-stranded anti-parallel
sheet (
2,
5 and
6) at the opposite end of the monomer to the cystine-knot and shown to be part of the receptor-binding face of VEGF-A (Muller et al., 1997a
, b
). The viral VEGF monomers also contain the three variable loop regions, connecting strands
1 to
3,
3 to
4 and
5 to
6. The third loop region is extended by three and five amino acids in ORFVMRI11VEGF and ORFVNZ7VEGF, respectively.
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VEGF-A dimerizes in an anti-parallel, side-by-side fashion, with the monomers being covalently linked by two symmetrical disulphide bonds between Cys-51 and Cys-60. These cysteine residues are also conserved in the viral VEGFs, some of which have been shown to act as dimers (Meyer et al., 1999
; Ogawa et al., 1998
; Wise et al., 1999
). The viral VEGFs were therefore predicted to dimerize in a similar fashion to VEGF-A and modelling revealed dimeric structures very similar to that of VEGF-A (Fig. 5
).
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2,
5 and
6 from one monomer and helix 1, the
3-
4 loop and the
7 strand from the other monomer (Muller et al., 1997a
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wide groove between the VEGF-A monomers and thereby positions domain 3 in contact with the bottom face of VEGF-A (Wiesmann et al., 1997
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Recombination during co-infection by Orf virus and another species of parapoxvirus might have resulted in the transfer of the NZ7-like VEGF into Orf virus. The minimal variation seen in NZ7-like sequences might suggest that such an event happened recently. Despite the surprising extent of sequence variation among the viral VEGFs, key motifs of structural and functional importance are conserved. These include the eight cysteines of the cystine-knot motif and potential glycosylation sites. A sequence motif rich in threonine and proline seen in the C terminus of the VEGFs encoded by both NZ2 and NZ7 is unique to the viral VEGFs (Lyttle et al., 1994
) and is retained in all isolates. Determining the functional significance of the sequence variations reported here will require further examination.
This collection of natural variants of VEGF provides opportunities to examine the importance of specific sequence motifs in the various activities of VEGF. The precise nature of the interaction between the viral VEGFs and VEGFR-2 is clearly of interest. It is intriguing that, despite the lack of retention of residues implicated as being critical in the binding of VEGF-A to VEGFR-2 and the lack of conservation of residues between NZ2- and NZ7-like viruses, both NZ2- and NZ7-like VEGFs have been shown to bind and activate VEGFR-2 (Meyer et al., 1999
; Ogawa et al., 1998
; Wise et al., 1999
). This indicates that the viral VEGFs binding site(s) may differ, or that considerable variability can be tolerated while still maintaining the ability to bind VEGFR-2. We hypothesize that the failure of viral VEGFs to bind VEGFR-1 may relate to the absence in these factors of a groove able to accept the VEGFR-1 domain 23 linker. Site-directed mutagenesis of the relevant residues will be required to test this hypothesis.
| Acknowledgments |
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Received 12 April 2002;
accepted 10 July 2002.
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