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A unique spumavirus Gag N-terminal domain with functional properties of orthoretroviral matrix and capsid.

Goldstone DC, Flower TG, Ball NJ, Sanz-Ramos M, Yap MW, Ogrodowicz RW, Stanke N, Reh J, Lindemann D, Stoye JP, Taylor IA - PLoS Pathog. (2013)

Bottom Line: Although FV infection is apparently benign, trans-species zoonosis is commonplace and has resulted in the isolation of the Prototypic Foamy Virus (PFV) from human sources and the potential for germ-line transmission.Furthermore, we present structural, biochemical and virological data that reveal the molecular details of the essential Gag-Env interaction and in addition we also examine the specificity of Trim5α restriction of PFV.These data provide the first information with regards to FV structural proteins and suggest a model for convergent evolution of gag genes where structurally unrelated molecules have become functionally equivalent.

View Article: PubMed Central - PubMed

Affiliation: Division of Molecular Structure, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom.

ABSTRACT
The Spumaretrovirinae, or foamyviruses (FVs) are complex retroviruses that infect many species of monkey and ape. Although FV infection is apparently benign, trans-species zoonosis is commonplace and has resulted in the isolation of the Prototypic Foamy Virus (PFV) from human sources and the potential for germ-line transmission. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. In addition, PFV Gag interacts with the FV Envelope (Env) protein to facilitate budding of infectious particles. Presently, there is a paucity of structural information with regards FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. Therefore, in order to probe the functional overlap of FV and orthoretroviral Gag and learn more about FV egress and replication we have undertaken a structural, biophysical and virological study of PFV-Gag. We present the crystal structure of a dimeric amino terminal domain from PFV, Gag-NtD, both free and in complex with the leader peptide of PFV Env. The structure comprises a head domain together with a coiled coil that forms the dimer interface and despite the shared function it is entirely unrelated to either the capsid or matrix of Gag from other retroviruses. Furthermore, we present structural, biochemical and virological data that reveal the molecular details of the essential Gag-Env interaction and in addition we also examine the specificity of Trim5α restriction of PFV. These data provide the first information with regards to FV structural proteins and suggest a model for convergent evolution of gag genes where structurally unrelated molecules have become functionally equivalent.

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Related in: MedlinePlus

Structure of the PFV Gag-Env complex.(A) Cartoon representation of the Gag-Env complex. The Gag-NtD homodimer is shown in the same orientation and colour scheme as in Figure 1. The helical Env peptides bound at the periphery of each head domain are coloured magenta and gold with N- and C-termini indicated. (B) A structural alignment shown in stick representation of free (orange) and bound (green) Gag-NtD is shown in the left-hand panel. The view is looking into the Env binding site at 90-degree rotation from that in A. Residue P30 is highlighted to show the backbone movement that occurs in the α1-β1 loop upon Env binding. The central and right-hand panels show the distribution of surface hydrophobicity on the Gag-NtD in the free and bound structures respectively. Hydrophobicity is represented by green shading with darker regions representing the most hydrophobic areas. The backbone movement of the α1-β1 loop in the bound structure (right panel) opens up a hydrophobic pocket in order to accommodate the Env peptide. (C) A cartoon representation of the bound PFV Env1–20 peptide is shown in the left hand panel. Intramolecular hydrogen bonding between residues in the N-terminal extended region and those in the helical section are displayed as dashed lines. Residues with apolar and aromatic side chains that line one face of the helix are also labelled. Details of the Gag-Env interface are shown in the right hand panel. Gag and Env molecules are coloured as in A. Residues with apolar side chains that contribute to the hydrophobic interface are shown in stick representation.
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ppat-1003376-g004: Structure of the PFV Gag-Env complex.(A) Cartoon representation of the Gag-Env complex. The Gag-NtD homodimer is shown in the same orientation and colour scheme as in Figure 1. The helical Env peptides bound at the periphery of each head domain are coloured magenta and gold with N- and C-termini indicated. (B) A structural alignment shown in stick representation of free (orange) and bound (green) Gag-NtD is shown in the left-hand panel. The view is looking into the Env binding site at 90-degree rotation from that in A. Residue P30 is highlighted to show the backbone movement that occurs in the α1-β1 loop upon Env binding. The central and right-hand panels show the distribution of surface hydrophobicity on the Gag-NtD in the free and bound structures respectively. Hydrophobicity is represented by green shading with darker regions representing the most hydrophobic areas. The backbone movement of the α1-β1 loop in the bound structure (right panel) opens up a hydrophobic pocket in order to accommodate the Env peptide. (C) A cartoon representation of the bound PFV Env1–20 peptide is shown in the left hand panel. Intramolecular hydrogen bonding between residues in the N-terminal extended region and those in the helical section are displayed as dashed lines. Residues with apolar and aromatic side chains that line one face of the helix are also labelled. Details of the Gag-Env interface are shown in the right hand panel. Gag and Env molecules are coloured as in A. Residues with apolar side chains that contribute to the hydrophobic interface are shown in stick representation.

Mentions: The structure of the PFV-Gag-NtD bound to the Env1–20 leader peptide was determined by molecular replacement and refined at a resolution of 2.9 Å with a final Rwork/Rfree of 22.6% and 27.1% respectively, Table 1. The asymmetric unit comprises two dimers of the complex with residues 9–179 of the Gag-NtD clearly visible in the electron density map for two of the four monomers and residues 9–170 in the two remaining protomers. Four helical Env peptides are also present, bound at the periphery of each head domain close to α1 and the associated α1-β1 loop of the Gag-NtD monomers, Figure 4A. Largely, the conformation of the Gag-NtD head and stalk domains are the same as in the free structure (RMSD of 0.4 Å between all equivalent Cα atoms) excepting some small differences in the conformation of the β3–β4 loop, Supplementary Figure S1. However, in the bound structure the α1-β1 loop around the highly conserved residue Pro30 undergoes a concerted 2.5 Å shift, Figure 4B and Supplementary Figure S1. Comparison of surface hydrophobicity profiles of the free and bound structures Figure 4B, reveals that this movement opens the Env binding site exposing a deep apolar pocket to accommodate the hydrophobic side chains from the Env peptide. In the complex residues Met1Env to Thr6Env of Env constitute an extended N-terminal region and Leu7Env to Met16Env form the hydrophobic α-helix bound to Gag. Hydrogen bonding between the sidechains of Thr6Env in the N-terminal region and Gln9Env on the amino-terminal turn of the Env helix provides stabilising interactions that maintain the helical conformation of the Env, Figure 4C. Inspection of Gag-Env interface reveals a network of hydrophobic interactions with the apolar and aromatic sidechains of Leu7Env, Trp10Env and Trp13Env on one face of the Env helix packing against the Val14, Leu17, Val18 and Leu21 sidechains on α1 of Gag, Figure 4C. In particular, the side chain of Leu7Env is seated in the apolar pocket in the Gag-NtD were it makes hydrophobic interactions with the aliphatic side chains of both Leu17 and Leu21. Val14 packs against the ring of Trp10Env that also makes a hydrogen bonding interaction between the indole Nε proton and the carbonyl of Leu66 in the β2–β3 loop. This hydrophobic interface is accompanied by a number of polar contacts between the backbone of residues Ala2Env, Pro3Env and Met5Env in the Env N-terminal extended region with the sidechains of Asn63 and Gln59 in the β2–β3 loop and the mainchain of His32 and Pro30 in the α1-β1 loop. The bound conformation is further stabilised by an accompanying helix capping interaction between the Asn29 sidechain and the N-terminal turn of the Env helix.


A unique spumavirus Gag N-terminal domain with functional properties of orthoretroviral matrix and capsid.

Goldstone DC, Flower TG, Ball NJ, Sanz-Ramos M, Yap MW, Ogrodowicz RW, Stanke N, Reh J, Lindemann D, Stoye JP, Taylor IA - PLoS Pathog. (2013)

Structure of the PFV Gag-Env complex.(A) Cartoon representation of the Gag-Env complex. The Gag-NtD homodimer is shown in the same orientation and colour scheme as in Figure 1. The helical Env peptides bound at the periphery of each head domain are coloured magenta and gold with N- and C-termini indicated. (B) A structural alignment shown in stick representation of free (orange) and bound (green) Gag-NtD is shown in the left-hand panel. The view is looking into the Env binding site at 90-degree rotation from that in A. Residue P30 is highlighted to show the backbone movement that occurs in the α1-β1 loop upon Env binding. The central and right-hand panels show the distribution of surface hydrophobicity on the Gag-NtD in the free and bound structures respectively. Hydrophobicity is represented by green shading with darker regions representing the most hydrophobic areas. The backbone movement of the α1-β1 loop in the bound structure (right panel) opens up a hydrophobic pocket in order to accommodate the Env peptide. (C) A cartoon representation of the bound PFV Env1–20 peptide is shown in the left hand panel. Intramolecular hydrogen bonding between residues in the N-terminal extended region and those in the helical section are displayed as dashed lines. Residues with apolar and aromatic side chains that line one face of the helix are also labelled. Details of the Gag-Env interface are shown in the right hand panel. Gag and Env molecules are coloured as in A. Residues with apolar side chains that contribute to the hydrophobic interface are shown in stick representation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3649970&req=5

ppat-1003376-g004: Structure of the PFV Gag-Env complex.(A) Cartoon representation of the Gag-Env complex. The Gag-NtD homodimer is shown in the same orientation and colour scheme as in Figure 1. The helical Env peptides bound at the periphery of each head domain are coloured magenta and gold with N- and C-termini indicated. (B) A structural alignment shown in stick representation of free (orange) and bound (green) Gag-NtD is shown in the left-hand panel. The view is looking into the Env binding site at 90-degree rotation from that in A. Residue P30 is highlighted to show the backbone movement that occurs in the α1-β1 loop upon Env binding. The central and right-hand panels show the distribution of surface hydrophobicity on the Gag-NtD in the free and bound structures respectively. Hydrophobicity is represented by green shading with darker regions representing the most hydrophobic areas. The backbone movement of the α1-β1 loop in the bound structure (right panel) opens up a hydrophobic pocket in order to accommodate the Env peptide. (C) A cartoon representation of the bound PFV Env1–20 peptide is shown in the left hand panel. Intramolecular hydrogen bonding between residues in the N-terminal extended region and those in the helical section are displayed as dashed lines. Residues with apolar and aromatic side chains that line one face of the helix are also labelled. Details of the Gag-Env interface are shown in the right hand panel. Gag and Env molecules are coloured as in A. Residues with apolar side chains that contribute to the hydrophobic interface are shown in stick representation.
Mentions: The structure of the PFV-Gag-NtD bound to the Env1–20 leader peptide was determined by molecular replacement and refined at a resolution of 2.9 Å with a final Rwork/Rfree of 22.6% and 27.1% respectively, Table 1. The asymmetric unit comprises two dimers of the complex with residues 9–179 of the Gag-NtD clearly visible in the electron density map for two of the four monomers and residues 9–170 in the two remaining protomers. Four helical Env peptides are also present, bound at the periphery of each head domain close to α1 and the associated α1-β1 loop of the Gag-NtD monomers, Figure 4A. Largely, the conformation of the Gag-NtD head and stalk domains are the same as in the free structure (RMSD of 0.4 Å between all equivalent Cα atoms) excepting some small differences in the conformation of the β3–β4 loop, Supplementary Figure S1. However, in the bound structure the α1-β1 loop around the highly conserved residue Pro30 undergoes a concerted 2.5 Å shift, Figure 4B and Supplementary Figure S1. Comparison of surface hydrophobicity profiles of the free and bound structures Figure 4B, reveals that this movement opens the Env binding site exposing a deep apolar pocket to accommodate the hydrophobic side chains from the Env peptide. In the complex residues Met1Env to Thr6Env of Env constitute an extended N-terminal region and Leu7Env to Met16Env form the hydrophobic α-helix bound to Gag. Hydrogen bonding between the sidechains of Thr6Env in the N-terminal region and Gln9Env on the amino-terminal turn of the Env helix provides stabilising interactions that maintain the helical conformation of the Env, Figure 4C. Inspection of Gag-Env interface reveals a network of hydrophobic interactions with the apolar and aromatic sidechains of Leu7Env, Trp10Env and Trp13Env on one face of the Env helix packing against the Val14, Leu17, Val18 and Leu21 sidechains on α1 of Gag, Figure 4C. In particular, the side chain of Leu7Env is seated in the apolar pocket in the Gag-NtD were it makes hydrophobic interactions with the aliphatic side chains of both Leu17 and Leu21. Val14 packs against the ring of Trp10Env that also makes a hydrogen bonding interaction between the indole Nε proton and the carbonyl of Leu66 in the β2–β3 loop. This hydrophobic interface is accompanied by a number of polar contacts between the backbone of residues Ala2Env, Pro3Env and Met5Env in the Env N-terminal extended region with the sidechains of Asn63 and Gln59 in the β2–β3 loop and the mainchain of His32 and Pro30 in the α1-β1 loop. The bound conformation is further stabilised by an accompanying helix capping interaction between the Asn29 sidechain and the N-terminal turn of the Env helix.

Bottom Line: Although FV infection is apparently benign, trans-species zoonosis is commonplace and has resulted in the isolation of the Prototypic Foamy Virus (PFV) from human sources and the potential for germ-line transmission.Furthermore, we present structural, biochemical and virological data that reveal the molecular details of the essential Gag-Env interaction and in addition we also examine the specificity of Trim5α restriction of PFV.These data provide the first information with regards to FV structural proteins and suggest a model for convergent evolution of gag genes where structurally unrelated molecules have become functionally equivalent.

View Article: PubMed Central - PubMed

Affiliation: Division of Molecular Structure, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom.

ABSTRACT
The Spumaretrovirinae, or foamyviruses (FVs) are complex retroviruses that infect many species of monkey and ape. Although FV infection is apparently benign, trans-species zoonosis is commonplace and has resulted in the isolation of the Prototypic Foamy Virus (PFV) from human sources and the potential for germ-line transmission. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. In addition, PFV Gag interacts with the FV Envelope (Env) protein to facilitate budding of infectious particles. Presently, there is a paucity of structural information with regards FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. Therefore, in order to probe the functional overlap of FV and orthoretroviral Gag and learn more about FV egress and replication we have undertaken a structural, biophysical and virological study of PFV-Gag. We present the crystal structure of a dimeric amino terminal domain from PFV, Gag-NtD, both free and in complex with the leader peptide of PFV Env. The structure comprises a head domain together with a coiled coil that forms the dimer interface and despite the shared function it is entirely unrelated to either the capsid or matrix of Gag from other retroviruses. Furthermore, we present structural, biochemical and virological data that reveal the molecular details of the essential Gag-Env interaction and in addition we also examine the specificity of Trim5α restriction of PFV. These data provide the first information with regards to FV structural proteins and suggest a model for convergent evolution of gag genes where structurally unrelated molecules have become functionally equivalent.

Show MeSH
Related in: MedlinePlus