PMID:30185597

Citation	Alejo, A, Matamoros, T, Guerra, M and Andrés, G (2018) A Proteomic Atlas of the African Swine Fever Virus Particle. J. Virol. 92
Abstract	African swine fever virus (ASFV) is a large and complex DNA virus that causes a highly lethal swine disease for which there is no vaccine available. The ASFV particle, with an icosahedral multilayered structure, contains multiple polypeptides whose identity is largely unknown. Here, we analyzed by mass spectroscopy the protein composition of highly purified extracellular ASFV particles and performed immunoelectron microscopy to localize several of the detected proteins. The proteomic analysis identified 68 viral proteins, which account for 39% of the genome coding capacity. The ASFV proteome includes essentially all the previously described virion proteins and, interestingly, 44 newly identified virus-packaged polypeptides, half of which have an unknown function. A great proportion of the virion proteins are committed to the virus architecture, including two newly identified structural proteins, p5 and p8, which are derived from the core polyproteins pp220 and pp62, respectively. In addition, the virion contains a full complement of enzymes and factors involved in viral transcription, various enzymes implicated in DNA repair and protein modification, and some proteins concerned with virus entry and host defense evasion. Finally, 21 host proteins, many of them localized at the cell surface and related to the cortical actin cytoskeleton, were reproducibly detected in the ASFV particle. Immunoelectron microscopy strongly supports the suggestion that these host membrane-associated proteins are recruited during virus budding at actin-dependent membrane protrusions. Altogether, the results of this study provide a comprehensive model of the ASFV architecture that integrates both compositional and structural information. African swine fever virus causes a highly contagious and lethal disease of swine that currently affects many countries of sub-Saharan Africa, the Caucasus, the Russian Federation, and Eastern Europe and has very recently spread to China. Despite extensive research, effective vaccines or antiviral strategies are still lacking, and many basic questions on the molecular mechanisms underlying the infective cycle remain. One such gap regards the composition and structure of the infectious virus particle. In the study described in this report, we identified the set of viral and host proteins that compose the virion and determined or inferred the localization of many of them. This information significantly increases our understanding of the biological and structural features of an infectious African swine fever virus particle and will help direct future research efforts.
Links	PubMed Online version:10.1128/JVI.01293-18
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
ASFB7:P49		GO:0019030: icosahedral viral capsid	ECO:0005592: immunogold labelling electron microscopy assay evidence used in manual assertion		C		Figure 3 suggests localized putative capsid component structural protein p49 is a component of the viral proteome of the African Swine Fever Virus.	complete CACAO 13800
ASFB7:P10		GO:0039642: virion nucleoid	ECO:0000314: direct assay evidence used in manual assertion		C		based on synthesizing figure 1, table 1, and immunogold in figure 3	complete CACAO 13490
ASFB7:P17		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF D117L in the African Swine Fever Virus, strain Ba71V, was isolated by SDS-PAGE in figure 1B and noted as p17. It was then identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Major structural protein p17, Ba71V-107	complete
ASF:Q5IZK2		GO:0039660: structural constituent of virion	ECO:0000314:		F		Figure 1 uses a Western Blot to show P72/B646L CDS protein is a structural protein found in African Swine Fever Virus particles.	complete CACAO 13492
ASFB7:FLSO		GO:0019012: virion	ECO:0001582:		C		Table 1 shows that ORFB119L FAD-Linked Sulfhydryl Oxidase was found to be a component of African Swine Fever Virus strain Ba71V by liquid chromatography tandem mass spectroscopy.	complete CACAO 13689
ASFB7:PP62		GO:0019012: virion	ECO:0001582: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion		C		The protein characterized by ORF CP530R and p15 in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. This protein is a product of the cleavage of polyprotein 62 and therefore is labelled under it. Uniprot: Polyprotein pp62, Ba71V-94 p15/p35/p8 proteins from the polypeptide of CP530R (which is pp62)	complete CACAO 13710
ASFB7:VHLP		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF A104R in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry as shown in table 1. Uniprot: BA71V-033, Viral histone-like protein	complete CACAO 13687
ASFB7:P14		GO:0019012: virion	ECO:0001582:		C		Table 1 shows that ORFE120R Protein pE120R (uniprot: Structural protein p14.5) was found to be a component of African Swine Fever Virus strain Ba71V by liquid chromatography tandem mass spectroscopy.	complete
ASFB7:H962L		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF B962L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Putative RNA helicase B962L, Ba71V-072	complete
ASFB7:CD2H		GO:0019012: virion	ECO:0001582: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion		C		Table 1 shows that ORFEP402R (uniprot: CD2 homolog) was found to be a component of African Swine Fever Virus strain Ba71V by liquid chromatography tandem mass spectroscopy.	complete CACAO 13697
ASFB7:VF113		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF D1133L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Putative ATP-dependent RNA helicase D1133L, Ba71V-106	complete
ASFB7:RPB1		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF NP1450L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Probable DNA-directed RNA polymerase subunit 1 homolog, Ba71V-99	complete
ASFB7:VF249		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF M1249L in the African Swine Fever Virus, strain Ba71V was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Uncharacterized protein M1249L, Ba71V-060	complete
ASFB7:VF123		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF CP123L in the African Swine Fever Virus, strain Ba71V was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Uncharacterized protein CP123L, Ba71V-91	complete
ASFB7:RPB2		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF EP1242L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: DNA-directed RNA polymerase subunit 2, Ba71V-053	complete
ASFB7:VF129		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF C129R in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Uncharacterized Protein C129R, Ba71V-062	complete
ASFB7:VF717		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF C717R in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Uncharacterized Protein C717R, Ba71V-064	complete
ASFB7:VF177		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF I177L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Membrane protein I177L, BA71V-145	complete
ASFB7:VF145		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF K145R in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Uncharacterized protein K145R, Ba71V-051	complete
ASFB7:E248R		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF E248R in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Protein E248R, Ba71V-132	complete
ASFB7:VF706		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF Q706L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Putative ATP-dependent RNA helicase Q706L, Ba71V-122	complete
ASFB7:VF421		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF K421R in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Uncharacterized protein K421R, Ba71V-052	complete
ASFB7:VF146		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF E146L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Uncharacterized protein E146L, Ba71V-129	complete CACAO 13761
ASFB7:RPB3		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF H359L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Putative DNA-directed RNA polymerase subunit 3 homolog, Ba71V-113	complete
ASFB7:VF317		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF F317L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Uncharacterized protein F317L, Ba71V-043	complete
ASFB7:PK1		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF R298L in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Serine/threonine-protein kinase 1, Ba71V-121	complete
ASFB7:VF137		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF A137R in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Structural protein A137R, GeneBa71V-042	complete
ASFB7:VF240		GO:0019012: virion	ECO:0001582:		C		The protein characterized by ORF H240R in the African Swine Fever Virus, strain Ba71V, was identified as a component of the virion through liquid chromatography with tandem mass spectrometry, as shown in table 1. Uniprot: Uncharacterized protein H240R, Ba71V-120	complete

References

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