Limits...
Polyhedra structures and the evolution of the insect viruses.

Ji X, Axford D, Owen R, Evans G, Ginn HM, Sutton G, Stuart DI - J. Struct. Biol. (2015)

Bottom Line: Approximately 80% of residues are structurally equivalent between all polyhedrins (pairwise rmsd ⩽ 1.5 Å), whilst pairwise sequence identities, based on structural alignment, are as little as 12%.By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes.Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree showing relationship between the polyhedrin proteins. Superpositions were performed using SHP (Stuart et al., 1979) and the phylogenetic tree calculated with PHYLIP (Felsenstein, 1989). The length of the branch to baculovirus polyhedrin (BV) has been reduced to 20% of its actual length. Structures of the proteins are shown coloured from N-terminus to C-terminus, blue to red. NTPs are represented in thickened stick style with a black outline to aid visualization. Cysteines involved in disulphide bridges are shown as black spheres, and the calcium ion in CPV5 as a pink sphere.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4597613&req=5

f0030: Phylogenetic tree showing relationship between the polyhedrin proteins. Superpositions were performed using SHP (Stuart et al., 1979) and the phylogenetic tree calculated with PHYLIP (Felsenstein, 1989). The length of the branch to baculovirus polyhedrin (BV) has been reduced to 20% of its actual length. Structures of the proteins are shown coloured from N-terminus to C-terminus, blue to red. NTPs are represented in thickened stick style with a black outline to aid visualization. Cysteines involved in disulphide bridges are shown as black spheres, and the calcium ion in CPV5 as a pink sphere.

Mentions: Structures for a number of previously uncharacterised types of cypovirus polyhedrins have revealed a strongly conserved structural core. A phylogenetic tree constructed based on the structures (Fig. 6) shows, as expected, that CPV1 and CPV18 are closely related structurally, but otherwise the tree is rather star-like, with CPV17 being perhaps rather an outlier and closest to the markedly different baculovirus polyhedrin. It is conceivable that CPV17 retains some features of an ancestral insect virus polyhedrin. Given the evolutionary explosion of insects some 400 million years ago the considerable divergence of the polyhedra suggests that much of the substantial evolution of the CPVs took place alongside these events, perhaps explaining why the build-up of variation appears almost saturated, with only two amino acids fully conserved across all nine types. Away from the core of the polyhedrin we identify five regions of structural variability and show that NTPs are used in the assembly of some but not all proteins, so that they impose little constraint on the polyhedrin structure. We also find that the whole base domain is dispensable for polyhedra formation, although the biochemical features are altered dramatically when it is removed. The base domains include the most variable region of the protein and nestle around a point of 23 symmetry. The bases likely attach to the virus to be encapsidated and are therefore either packed together inside the crystal or exposed on the outside, furthermore, since they do not drive assembly they will tend to remain accessible on the surface of the growing crystal, ready to engage a protein-only icosahedral shaped CPV particle. The outer faces of the base domains are positively charged across nearly all the types, at present there is no little structural information for charge status of the virion component that is likely to attach to the polyhedrin. It seems that in the final stage of assembly the base domains pull the lattice into a closer knit form, presumably allowing useful flexibility in the lattice in the vicinity of the viral inclusions (note that the presumed ancestral CPV17 does not fully lock down the lattice, retaining a larger unit cell). The variety of NTPs seem to act as small molecule ‘fillers’ in the absence of virus particles, allowing lattice completion and the avoidance of crystal voids whilst permitting appropriate specificity in the virus recognition motifs between CPV types. Overall this domain is likely a late addition to the fold (it is dispensable for protein folding) and probably was a feature acquired to aid viral recognition (it is distal to the point of attack by ions which initiate the dissolution process by modifying a point critical for assembly). There may be potential for exploiting the variation in the base domain for nanotechnology applications.


Polyhedra structures and the evolution of the insect viruses.

Ji X, Axford D, Owen R, Evans G, Ginn HM, Sutton G, Stuart DI - J. Struct. Biol. (2015)

Phylogenetic tree showing relationship between the polyhedrin proteins. Superpositions were performed using SHP (Stuart et al., 1979) and the phylogenetic tree calculated with PHYLIP (Felsenstein, 1989). The length of the branch to baculovirus polyhedrin (BV) has been reduced to 20% of its actual length. Structures of the proteins are shown coloured from N-terminus to C-terminus, blue to red. NTPs are represented in thickened stick style with a black outline to aid visualization. Cysteines involved in disulphide bridges are shown as black spheres, and the calcium ion in CPV5 as a pink sphere.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4597613&req=5

f0030: Phylogenetic tree showing relationship between the polyhedrin proteins. Superpositions were performed using SHP (Stuart et al., 1979) and the phylogenetic tree calculated with PHYLIP (Felsenstein, 1989). The length of the branch to baculovirus polyhedrin (BV) has been reduced to 20% of its actual length. Structures of the proteins are shown coloured from N-terminus to C-terminus, blue to red. NTPs are represented in thickened stick style with a black outline to aid visualization. Cysteines involved in disulphide bridges are shown as black spheres, and the calcium ion in CPV5 as a pink sphere.
Mentions: Structures for a number of previously uncharacterised types of cypovirus polyhedrins have revealed a strongly conserved structural core. A phylogenetic tree constructed based on the structures (Fig. 6) shows, as expected, that CPV1 and CPV18 are closely related structurally, but otherwise the tree is rather star-like, with CPV17 being perhaps rather an outlier and closest to the markedly different baculovirus polyhedrin. It is conceivable that CPV17 retains some features of an ancestral insect virus polyhedrin. Given the evolutionary explosion of insects some 400 million years ago the considerable divergence of the polyhedra suggests that much of the substantial evolution of the CPVs took place alongside these events, perhaps explaining why the build-up of variation appears almost saturated, with only two amino acids fully conserved across all nine types. Away from the core of the polyhedrin we identify five regions of structural variability and show that NTPs are used in the assembly of some but not all proteins, so that they impose little constraint on the polyhedrin structure. We also find that the whole base domain is dispensable for polyhedra formation, although the biochemical features are altered dramatically when it is removed. The base domains include the most variable region of the protein and nestle around a point of 23 symmetry. The bases likely attach to the virus to be encapsidated and are therefore either packed together inside the crystal or exposed on the outside, furthermore, since they do not drive assembly they will tend to remain accessible on the surface of the growing crystal, ready to engage a protein-only icosahedral shaped CPV particle. The outer faces of the base domains are positively charged across nearly all the types, at present there is no little structural information for charge status of the virion component that is likely to attach to the polyhedrin. It seems that in the final stage of assembly the base domains pull the lattice into a closer knit form, presumably allowing useful flexibility in the lattice in the vicinity of the viral inclusions (note that the presumed ancestral CPV17 does not fully lock down the lattice, retaining a larger unit cell). The variety of NTPs seem to act as small molecule ‘fillers’ in the absence of virus particles, allowing lattice completion and the avoidance of crystal voids whilst permitting appropriate specificity in the virus recognition motifs between CPV types. Overall this domain is likely a late addition to the fold (it is dispensable for protein folding) and probably was a feature acquired to aid viral recognition (it is distal to the point of attack by ions which initiate the dissolution process by modifying a point critical for assembly). There may be potential for exploiting the variation in the base domain for nanotechnology applications.

Bottom Line: Approximately 80% of residues are structurally equivalent between all polyhedrins (pairwise rmsd ⩽ 1.5 Å), whilst pairwise sequence identities, based on structural alignment, are as little as 12%.By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes.Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.

No MeSH data available.


Related in: MedlinePlus