PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System

Phinet Name: Ebola Virus
Phinet Information
Pathogen Name: Ebola Virus
Pathogen NIAID Category: NIAID Category A
Bio-objects
Bio-object 1: Attached virus
Type: Microorganism or its component Location: Cell membrane Description: Replication begins with the attachment of the virion to a cell-surface receptor, which may be the alpha-folate receptor. After binding, the virus enters the cell through receptor-mediated endocytosis (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Bio-object 2: Budding virus
Type: Microorganism or its component Location: Cell membrane Description: Nascent virions become enveloped by the GP-bearing lipid bilayer and exit the cell through budding (Bray and Paragas, 2002). New data demonstrate the compartmentalization of Ebola and Marburg viral proteins in lipid rafts during viral assembly and budding (Bavari et al., 2002).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5299">Bavari et al., 2002</a>)
Bio-object 3: Cell membrane receptor
Type: Protein or gene Location: Cell membrane Function: Ligand binding or carrier Description: There is evidence that Marburg virus uses the asialoglycoprotein receptor to infect hepatocytes. For Ebola virus, it was suggested that integrins, especially the Beta1 group, might interact with the glycoprotein and perhaps be involved in entry into the cells. More recent studies indicate that the folate receptor-alpha serves as a cofactor for cellular entry by Marburg and Ebola viruses (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 4: Delta peptide
Type: Protein or gene Location: Extracellular Description: Delta peptide is secreted from cells but this process seems not to be as efficient as the secretion of sGP (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 5: Delta peptide
Type: Protein or gene Location: Organelle -- Golgi Description: The small cleavage product of pre-sGP, delta peptide, varies in length between 40 and 48 amino acids for the different Ebola viruses. Its molecular mass of about 10-14 kDa is significantly larger than the one predicted from the amino acid sequence (about 4.7 kDa). This difference in size is due to the attachment of several O-glycans that carry terminal sialic acids. In this respect, it differs from sGP, which seems mainly to carry N-linked carbohydrates (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 6: Furin
Type: Protein or gene Location: Organelle -- Golgi Description: >Furin belongs to the proprotein convertases, a family of subtilisin-like eukaryotic endoproteases. These enzymes are differentially expressed in cells and tissues, and they display similar by not identical specificity for basic motifs, such as RXK/RR, at the cleavage site of their substrates. Furin is expressed inmost cells and is localized predominantly in the trans Golgi network. Furin appears to be the key enzyme in virus activation. It is also noteworthy that furin, although ubiquitous, is particularly rich in hepatocytes and endothelial cells which are both prime targets of Ebola virus. These observations stress the importance of furin as a processing enzyme of GP (Volchkov, 1999). After oligomerization, pre-sGP is transported into the Golgi compartments where glycosylation is completed and post-translational cleavage into sGP and a small peptide, designated delta peptide, occurs. Cleavage is mediated by furin, which is also responsible for the cleavage of pre-GP (Feldmann et al., 2001).(<a href="#reference5301">Volchkov3</a>)(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 7: Fused virus
Type: Microorganism or its component Location: Cytoplasm Description: Fusion of the viral envelope with the cellular endosomal membrane releases the RNP into the cytoplasm (Bray and Paragas, 2002). Fusion activity has never been demonstrated experimentally. Early post-infection filovirus particles are associated with coated pits along the plasma membrane, indicating endocytosis as a possible mechanism for entry. This observation, together with mutational analysis of the putative fusion domain, offers compelling support for a role for the conserved hydrophobic region in the Ebola virus transmembrane glycoprotein GP as a fusion peptide (Feldmann et al., 2001).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 8: GP
Type: Protein or gene Location: Extracellular Function: Ligand binding or carrier Description: Cell entry is presumably mediated by GP (Feldmann and Kiley, 1999). Each molecule in the trimeric GP is composed of an external segment, GP1, which is linked by a disulfide bond to a transmembrane unit, GP2 (Bray and Paragas, 2002). Several groups have demonstrated independently that the transmembrane glycoprotein of filoviruses mediates receptor binding and subsequent fusion with susceptible cells (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5302">Feldmann2</a>)
Bio-object 9: GP mRNA
Type: Protein or gene Location: Cytoplasm Description: Glycoprotein (GP), encoded by gene 4 of the genome, is the only glycosylated structural protein of virions (Feldmann and Kiley, 1999). The GP is the sole structural protein that makes up the virion surface spikes that mediate virus entry into susceptible host cells through receptor binding (Peters et al., 1996).(<a href="#reference5302">Feldmann2</a>)(<a href="#reference5305">Peters</a>)
Bio-object 10: GP1 protein
Type: Protein or gene Location: Organelle -- Golgi Description: In the trans-Golgi apparatus, GP0 is cleaved by the convertase furin to generate GP1, whose role appears to involve receptor binding, and transmembrane GP2. These two subunits are linked by disulfide bonding (Jeffers et al., 2002). GP1 is highly glycosylated with N-linked and O-linked glycans. Glycosylation contributes approximately half of the mass of GP1, and O-linked glycans confer a mucin-like property to its C terminus (Jeffers et al., 2002).(<a href="#reference5294">Jeffers et al., 2002</a>)
Bio-object 11: GP1 protein
Type: Protein or gene Location: Extracellular Description: During maturation, GP1 is partly shed in monomeric form after the release of its disulphide linkage to the transmembrane subunit GP2 (Feldmann et al., 2001). This free GP1 is shed in a nonvirion-bound form and has been hypothesized to be pathogenic (Chan et al., 2000).(<a href="#reference5282">Feldmann et al., 2001</a>)(<a href="#reference5300">Chan et al., 2000</a>)
Bio-object 12: GP1/2 protein
Type: Protein or gene Location: Organelle -- Golgi membrane Description: A special arrangement of cysteine residues in the GP1/2 molecules allows the formation of an intramolecular disulphide bridge between the two cleavage products. This suggests a stem region consisting of GP1 and GP2 and a crown-like domain on the top formed by GP1 that carries the mass of the carbohydrate side chains. The mature transmembrane glycoprotein is a trimer comprising disulphide-bonded GP1/2 molecules. The mature transmembrane glycoprotein forms spikes without the need for other viral proteins (Feldmann et al., 2001).GP1/2 is the virion form of GP and it is also present in cells, presumably in the trans Golgi network and on the cell surface (Volchkov, 1999).(<a href="#reference5282">Feldmann et al., 2001</a>)(<a href="#reference5301">Volchkov3</a>)
Bio-object 13: GP1/2 protein
Type: Protein or gene Location: Cell membrane Description: The mature envelope glycoprotein GP1/2 is anchored in the membrane by a carboxy-terminal hydrophobic domain of GP2. The middle region of GP1/2 is variable, extremely hydrophilic and carries the bulk of N- and O-glycans, which account for more than one-third of the molecular mass of the mature protein. Oligosaccharide side chains differ in their terminal sialylation patterns. Two carboxy-terminal cysteine residues are acylated. GP2 contains a sequence of several uncharged, hydrophobic amino acids at a distance of 22 (EBOV) or 91 (MBGV) amino acids from the cleavage site and which bears some structural similarity to the fusion peptides of retroviruses. The special arrangement of the cysteine residues in the GP1/2 molecules allows the formation of an intramolecular disulphide bridge between the two cleavage products. This suggests a stem region consisting of GP1 and GP2 and a crown-like domain on the top formed by GP1 that carries the mass of the carbohydrate side chains. It can be assumed that cysteine residue 53 is also critical for maintaining the structure of GP1/2. The mature transmembrane glycoprotein is a trimer comprising disulphide-bonded GP1/2 molecules (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 14: GP2 protein
Type: Protein or gene Location: Organelle -- Golgi Description: In the trans-Golgi apparatus, GP0 is cleaved by the convertase furin to generate GP1, whose role appears to involve receptor binding, and transmembrane GP2. These two subunits are linked by disulfide bonding (Jeffers et al., 2002). GP2 contains a sequence of several, uncharged hydrophobic amino acids at a distance of 22 (Ebola virus) or 91 (Marburg virus) amino acids from the cleavage site and which bears some structural similarity to the fusion peptides of retroviruses (Feldmann et al., 2001). GP2 also contains N-linked glycans with two predicted N-linked sites but does not appear to contain O-linked glycans (Jeffers et al., 2002).(<a href="#reference5294">Jeffers et al., 2002</a>)(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 15: L mRNA
Type: Protein or gene Location: Cytoplasm Description: The large (L) protein is encoded at the 5' end of the linear genome (Feldmann and Kiley, 1999).(<a href="#reference5302">Feldmann2</a>)
Bio-object 16: L protein
Type: Protein or gene Location: Cytoplasm Function: Enzyme Description: Two other proteins present in lower copy number within the virion, VP35 and the RNA-dependent RNA polymerase, or L protein, associate with VP30 and NP to make up the Ebola replication complex (Bray and Paragas, 2002). The RNA-dependent RNA polymerase or L protein is the largest and least abundant viral protein in both the virion and in infected cells (Peters et al., 1996).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5305">Peters</a>)
Bio-object 17: L protein
Type: Protein or gene Location: Cytoplasm Function: Enzyme Description: The L protein is regarded as an RNA-dependent RNA polymerase (Feldmann and Kiley, 1999). As with other negative-strand RNA viruses, the RNA-dependent RNA polymerase of L protein of filoviruses is the largest and least abundant viral protein in both the virion and in infected cells (Peters et al., 1996).(<a href="#reference5302">Feldmann2</a>)(<a href="#reference5305">Peters</a>)
Bio-object 18: Negative sense genome
Type: Protein or gene complex Location: Cytoplasm Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Bio-object 19: Negative sense genome
Type: Protein or gene complex Location: Cytoplasm Description: Genomes of filoviruses consist of a single negative-stranded linear RNA molecule. The RNA is noninfectious, does not contain a poly(A) tail, and upon entry into the cytoplasm of host cells is transcribed to generated polyadenylated subgenomic mRNA species (Feldmann and Kiley, 1999). Filovirus transcription and replication take place in the cytoplasm of infected cells (Feldmann and Kiley, 1999).(<a href="#reference5302">Feldmann2</a>)
Bio-object 20: NP mRNA
Type: Protein or gene Location: Cytoplasm Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002). The nucleoprotein (NP) is encoded by gene 1 at the extreme 3' end of the linear unsegmented RNA genome (Feldmann and Kiley, 1999).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5302">Feldmann2</a>)
Bio-object 21: NP protein
Type: Protein or gene Location: Cytoplasm Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002).NP is the primary structural protein associates with filovirus nucleocapsids (Peters et al., 1996). Recent studies have demonstrated that cotransfection of 293T cells with NP, VP35, and VP24 supported capsid formation, and omission of any one of these three genes abolished the effect, demonstrating that they are necessary and sufficient for viral particle formation (Huang et al., 2002).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5305">Peters</a>)(<a href="#reference5285">Huang et al., 2002</a>)
Bio-object 22: Positive sense genome
Type: Protein or gene complex Location: Cytoplasm Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Bio-object 23: pre-GP protein
Type: Protein or gene Location: Cytoplasm Description: Glycoprotein (GP) is the only glycosylated structural protein of virions (Feldmann and Kiley, 1999). The GP is the sole structural protein that makes up the virion surface spikes that mediate virus entry into susceptible host cells through receptor binding (Peters et al., 1996).(<a href="#reference5302">Feldmann2</a>)(<a href="#reference5305">Peters</a>)
Bio-object 24: pre-GP protein
Type: Protein or gene Location: Organelle -- Golgi Description: pre-GP is processed to a fully glycosylated uncleaved form, GP0, in the Golgi apparatus. Trafficking to the Golgi apparatus also leads to the addition of O-linked glycans (Jeffers et al., 2002).(<a href="#reference5294">Jeffers et al., 2002</a>)
Bio-object 25: pre-GP protein
Type: Protein or gene Location: Organelle -- Endoplasmic reticulum Description: An N-glycosylated precursor form of GP (pre-GP), is found in the endoplasmic reticulum (Jeffers et al., 2002).(<a href="#reference5294">Jeffers et al., 2002</a>)
Bio-object 26: pre-sGP protein
Type: Protein or gene Location: Organelle -- Endoplasmic reticulum Description: The primary gene product of the Ebola virus GP gene is a secreted GP, cleaved to generate secreted GP (sGP) and delta peptide (Jeffers et al., 2002). pre-sGP undergoes several co- and post-translational processing events, such as signal peptide cleavage, glycosylation, oligomerization, and proteolytic cleavage. The limiting step during maturation and transport seems to be oligomerization in the endoplasmic reticulum (Feldmann et al., 2001).(<a href="#reference5294">Jeffers et al., 2002</a>)(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 27: pre-sGP protein
Type: Protein or gene Location: Cytoplasm Description: In the case of Ebola, but not Marburg virus, the primary product encoded by the GP gene is a truncated protein lacking a C-terminal hydrophobic membrane anchor. This `soluble GP' (sGP) is released from infected cells (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Bio-object 28: pre-sGP protein
Type: Protein or gene Location: Organelle -- Golgi Description: After oligomerization, pre-sGP is transported into the Golgi compartments where glycosylation is completed and post-translational cleavage into sGP and a small peptide, designated delta peptide, occurs. Cleavage is mediated by furin (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 29: Replication complex
Type: Protein or gene complex Location: Cytoplasm Description: The ribonucleoprotein (RNP) complex in the virion core, made up of the RNA genome and its encapsidating proteins, VP30 and NP, is linked by matrix proteins to the glycoprotein (GP)-bearing lipid envelope derived from the host cell membrane (Bray and Paragas, 2002). Two other proteins present in lower copy number within the virion, VP35 and the RNA-dependent RNA polymerase, or L protein, associate with VP30 and NP to make up the Ebola replication complex (Bray and Paragas, 2002). Genomes of filoviruses consist of a single negative-stranded linear RNA molecule. The RNA is noninfectious, does not contain a poly(A) tail, and upon entry into the cytoplasm of host cells is transcribed to generated polyadenylated subgenomic mRNA species (Feldmann and Kiley, 1999). Filovirus transcription and replication take place in the cytoplasm of infected cells (Feldmann and Kiley, 1999).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5302">Feldmann2</a>)
Bio-object 30: sGP mRNA
Type: Protein or gene Location: Cytoplasm Description: Filoviral glycoproteins are encoded by gene 4 (GP gene) of the non-segmented, negative-stranded RNA genome (Feldmann and Kiley, 1999). In the case of Ebola, but not Marburg virus, the primary product encoded by the GP gene is a truncated protein lacking a C-terminal hydrophobic membrane anchor. This `soluble GP' (sGP) is released from infected cells (Bray and Paragas, 2002).(<a href="#reference5302">Feldmann2</a>)(<a href="#reference5296">Bray et al., 2002</a>)
Bio-object 31: sGP protein
Type: Protein or gene Location: Organelle -- Golgi Description: After oligomerization, pre-sGP is transported into the Golgi compartments where glycosylation is completed and post-translational cleavage into sGP and a small peptide, designated delta peptide, occurs. Cleavage is mediated by furin, which is also responsible for the cleavage of pre-GP (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 32: sGP protein
Type: Protein or gene Location: Extracellular Description: Due to a lack of a transmembrane anchor, sGP is secreted efficiently from infected cells (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Bio-object 33: Uncoated virus
Type: Microorganism or its component Location: Cell membrane Description: Virus entry is probably receptor-mediated followed by fusion and uncoating, two steps which have not yet been examined (Feldmann and Kiley, 1999).(<a href="#reference5302">Feldmann2</a>)
Bio-object 34: Viral capsid
Type: Protein or gene Location: Cytoplasm Description: The assembly of new viral particles occurs on the inner surface of the plasma membrane, where VP24 and VP40 apparently associate both with new RNPs and with the cytoplasmic tail of GP2 (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Bio-object 35: Virion
Type: Microorganism or its component Location: Extracellular Description: The complete replication cycle takes approximately 12 hours. As for many other viruses, filovirus replication triggers a cascade of reactions in infected cells, including the de novo production of type I interferon (IFN-/), which collectively constitute the innate antiviral response. At the same time, certain viral proteins apparently suppress some of these antiviral mechanisms, giving the virus an advantage over its host. The ability of filoviruses to overcome initial defensive barriers and rapidly disseminate may be an essential factor in their virulence (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Bio-object 36: VP24 mRNA
Type: Protein or gene Location: Cytoplasm Description: Virion structural protein 24 (VP24) is encoded by gene 6 of filoviruses (Feldmann and Kiley, 1999). Recent studies have demonstrated that cotransfection of 293T cells with NP, VP35, and VP24 supported capsid formation, and omission of any one of these three genes abolished the effect, demonstrating that they are necessary and sufficient for viral particle formation (Huang et al., 2002).(<a href="#reference5302">Feldmann2</a>)(<a href="#reference5285">Huang et al., 2002</a>)
Bio-object 37: VP24 protein
Type: Protein or gene Location: Cytoplasm Description: The VP24 protein of Ebola virus is believed to be a secondary matrix protein and minor component of virions. In contrast, the VP40 protein of Ebola virus is the primary matrix protein and the most abundant virion component. VP24 possesses structural features commonly associated with viral matrix proteins and that VP24 may have a role in virus assembly and budding (Han et al., 2003).(<a href="#reference5298">Han et al., 2003</a>)
Bio-object 38: VP30 mRNA
Type: Protein or gene Location: Cytoplasm Description: Virion structural protein 30 (VP30) is encoded by gene 5 of filoviruses and is intimately associated with the RNP complex (Feldmann and Kiley, 1999).(<a href="#reference5302">Feldmann2</a>)
Bio-object 39: VP30 protein
Type: Protein or gene Location: Cytoplasm Description: Ebola virus VP30 is an essential activator of viral transcription. In viral particles, VP30 is closely associated with the nucleocapsid complex. A conspicuous structural feature of VP30 is an unconventional zinc-binding Cys(3)-His motif comprising amino acids 68 to 95 (Modrof et al., 2003).(<a href="#reference5297">Modrof et al., 2003</a>)
Bio-object 40: VP35 mRNA
Type: Protein or gene Location: Cytoplasm Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002). Virion structural protein 35 (VP35) is encoded by gene 2 (Feldmann and Kiley, 1999).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5302">Feldmann2</a>)
Bio-object 41: VP35 protein
Type: Protein or gene Location: Cytoplasm Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002).Recent studies have demonstrated that cotransfection of 293T cells with NP, VP35, and VP24 supported capsid formation, and omission of any one of these three genes abolished the effect, demonstrating that they are necessary and sufficient for viral particle formation (Huang et al., 2002).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5285">Huang et al., 2002</a>)
Bio-object 42: VP40 mRNA
Type: Protein or gene Location: Cytoplasm Description: Virion structural protein 40 (VP40) of filoviruses is encoded by gene 3 (Feldmann and Kiley, 1999).(<a href="#reference5302">Feldmann2</a>)
Bio-object 43: VP40 protein
Type: Protein or gene Location: Cytoplasm Description: VP40 facilitates the formation of hollow tubular membranes that may facilitate the formation of the surrounding envelope, but does not contribute to the generation of the filamentous viral capsid (Huang et al., 2002). The VP40 protein of Ebola virus is the primary matrix protein and the most abundant virion component (Han et al., 2003).(<a href="#reference5285">Huang et al., 2002</a>)(<a href="#reference5298">Han et al., 2003</a>)
Interactions
Interaction 1: I1
Input Objects: GP, Cell membrane receptor Output Objects: Attached virus GO Evidence Code: Traceable Author Statement Description: Replication begins with the attachment of the virion to a cell-surface receptor, which may be the alpha-folate receptor. After binding, the virus enters the cell through receptor-mediated endocytosis (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Interaction 2: I2
Input Objects: Attached virus Output Objects: Fused virus GO Evidence Code: Traceable Author Statement Description: Fusion of the viral envelope with the cellular endosomal membrane releases the RNP into the cytoplasm (Bray and Paragas, 2002). Fusion activity has never been demonstrated experimentally. Early post-infection filovirus particles are associated with coated pits along the plasma membrane, indicating endocytosis as a possible mechanism for entry. This observation, together with mutational analysis of the putative fusion domain, offers compelling support for a role for the conserved hydrophobic region in the Ebola virus transmembrane glycoprotein GP as a fusion peptide (Feldmann et al., 2001).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5282">Feldmann et al., 2001</a>)
Interaction 3: I3
Input Objects: Fused virus Output Objects: Uncoated virus GO Evidence Code: Traceable Author Statement Description: Virus entry is probably receptor-mediated followed by fusion and uncoating, two steps which have not yet been examined (Feldmann and Kiley, 1999).(<a href="#reference5302">Feldmann2</a>)
Interaction 4: I4
Input Objects: Uncoated virus Output Objects: Replication complex GO Evidence Code: Traceable Author Statement Description: The ribonucleoprotein (RNP) complex in the virion core, made up of the RNA genome and its encapsidating proteins, VP30 and NP, is linked by matrix proteins to the glycoprotein (GP)-bearing lipid envelope derived from the host cell membrane (Bray and Paragas, 2002). Two other proteins present in lower copy number within the virion, VP35 and the RNA-dependent RNA polymerase, or L protein, associate with VP30 and NP to make up the Ebola replication complex (Bray and Paragas, 2002). Genomes of filoviruses consist of a single negative-stranded linear RNA molecule. The RNA is noninfectious, does not contain a poly(A) tail, and upon entry into the cytoplasm of host cells is transcribed to generated polyadenylated subgenomic mRNA species (Feldmann and Kiley, 1999). Filovirus transcription and replication take place in the cytoplasm of infected cells (Feldmann and Kiley, 1999).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5302">Feldmann2</a>)
Interaction 5: I5
Input Objects: Replication complex Output Objects: NP mRNA, VP35 mRNA, VP40 mRNA, GP mRNA, sGP mRNA, VP30 mRNA, VP24 mRNA, L mRNA, Positive sense genome GO Evidence Code: Traceable Author Statement Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002). The nucleoprotein (NP) is encoded by gene 1 at the extreme 3' end of the linear unsegmented RNA genome (Feldmann and Kiley, 1999).Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002). Virion structural protein 35 (VP35) is encoded by gene 2 (Feldmann and Kiley, 1999).Virion structural protein 40 (VP40) of filoviruses is encoded by gene 3 (Feldmann and Kiley, 1999).Glycoprotein (GP), encoded by gene 4 of the genome, is the only glycosylated structural protein of virions (Feldmann and Kiley, 1999). The GP is the sole structural protein that makes up the virion surface spikes that mediate virus entry into susceptible host cells through receptor binding (Peters et al., 1996).Filoviral glycoproteins are encoded by gene 4 (GP gene) of the non-segmented, negative-stranded RNA genome (Feldmann and Kiley, 1999). In the case of Ebola, but not Marburg virus, the primary product encoded by the GP gene is a truncated protein lacking a C-terminal hydrophobic membrane anchor. This `soluble GP' (sGP) is released from infected cells (Bray and Paragas, 2002).Virion structural protein 30 (VP30) is encoded by gene 5 of filoviruses and is intimately associated with the RNP complex (Feldmann and Kiley, 1999).Virion structural protein 24 (VP24) is encoded by gene 6 of filoviruses (Feldmann and Kiley, 1999). Recent studies have demonstrated that cotransfection of 293T cells with NP, VP35, and VP24 supported capsid formation, and omission of any one of these three genes abolished the effect, demonstrating that they are necessary and sufficient for viral particle formation (Huang et al., 2002).The large (L) protein is encoded at the 5' end of the linear genome (Feldmann and Kiley, 1999).Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5302">Feldmann2</a>)
Interaction 6: I14
Input Objects: Positive sense genome Output Objects: Negative sense genome GO Evidence Code: Traceable Author Statement Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Interaction 7: I15
Input Objects: NP mRNA Output Objects: NP protein GO Evidence Code: Traceable Author Statement Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002).NP is the primary structural protein associates with filovirus nucleocapsids (Peters et al., 1996). Recent studies have demonstrated that cotransfection of 293T cells with NP, VP35, and VP24 supported capsid formation, and omission of any one of these three genes abolished the effect, demonstrating that they are necessary and sufficient for viral particle formation (Huang et al., 2002).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5305">Peters</a>)(<a href="#reference5285">Huang et al., 2002</a>)
Interaction 8: I16
Input Objects: VP35 mRNA Output Objects: VP35 protein GO Evidence Code: Traceable Author Statement Description: Transcription by the viral RNA-dependent RNA polymerase initiates at the 3' end of the genome, resulting in synthesis of a leader RNA and seven polyadenylated mRNAs. Accumulation of the first two proteins encoded at the 3' end of the genome (NP and VP35) in some way triggers a switch to production of full-length, positive-sense `antigenomes', which serve, in turn, as templates for genome synthesis (Bray and Paragas, 2002).Recent studies have demonstrated that cotransfection of 293T cells with NP, VP35, and VP24 supported capsid formation, and omission of any one of these three genes abolished the effect, demonstrating that they are necessary and sufficient for viral particle formation (Huang et al., 2002).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5285">Huang et al., 2002</a>)
Interaction 9: I17
Input Objects: VP40 mRNA Output Objects: VP40 protein GO Evidence Code: Traceable Author Statement Description: VP40 facilitates the formation of hollow tubular membranes that may facilitate the formation of the surrounding envelope, but does not contribute to the generation of the filamentous viral capsid (Huang et al., 2002). The VP40 protein of Ebola virus is the primary matrix protein and the most abundant virion component (Han et al., 2003).(<a href="#reference5285">Huang et al., 2002</a>)(<a href="#reference5298">Han et al., 2003</a>)
Interaction 10: I18
Input Objects: GP mRNA Output Objects: pre-GP protein GO Evidence Code: Traceable Author Statement Description: Glycoprotein (GP) is the only glycosylated structural protein of virions (Feldmann and Kiley, 1999). The GP is the sole structural protein that makes up the virion surface spikes that mediate virus entry into susceptible host cells through receptor binding (Peters et al., 1996).(<a href="#reference5302">Feldmann2</a>)(<a href="#reference5305">Peters</a>)
Interaction 11: I19
Input Objects: sGP mRNA Output Objects: pre-sGP protein GO Evidence Code: Traceable Author Statement Description: In the case of Ebola, but not Marburg virus, the primary product encoded by the GP gene is a truncated protein lacking a C-terminal hydrophobic membrane anchor. This `soluble GP' (sGP) is released from infected cells (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Interaction 12: I20
Input Objects: VP30 mRNA Output Objects: VP30 protein GO Evidence Code: Traceable Author Statement Description: Ebola virus VP30 is an essential activator of viral transcription. In viral particles, VP30 is closely associated with the nucleocapsid complex. A conspicuous structural feature of VP30 is an unconventional zinc-binding Cys(3)-His motif comprising amino acids 68 to 95 (Modrof et al., 2003).(<a href="#reference5297">Modrof et al., 2003</a>)
Interaction 13: I21
Input Objects: VP24 mRNA Output Objects: VP24 protein GO Evidence Code: Traceable Author Statement Description: The VP24 protein of Ebola virus is believed to be a secondary matrix protein and minor component of virions. In contrast, the VP40 protein of Ebola virus is the primary matrix protein and the most abundant virion component. VP24 possesses structural features commonly associated with viral matrix proteins and that VP24 may have a role in virus assembly and budding (Han et al., 2003).(<a href="#reference5298">Han et al., 2003</a>)
Interaction 14: I22
Input Objects: L mRNA Output Objects: L protein GO Evidence Code: Traceable Author Statement Description: The L protein is regarded as an RNA-dependent RNA polymerase (Feldmann and Kiley, 1999). As with other negative-strand RNA viruses, the RNA-dependent RNA polymerase of L protein of filoviruses is the largest and least abundant viral protein in both the virion and in infected cells (Peters et al., 1996).(<a href="#reference5302">Feldmann2</a>)(<a href="#reference5305">Peters</a>)
Interaction 15: I23
Input Objects: pre-GP protein Output Objects: pre-GP protein GO Evidence Code: Traceable Author Statement Description: An N-glycosylated precursor form of GP (pre-GP), is found in the endoplasmic reticulum (Jeffers et al., 2002).(<a href="#reference5294">Jeffers et al., 2002</a>)
Interaction 16: I24
Input Objects: pre-sGP protein Output Objects: pre-sGP protein GO Evidence Code: Traceable Author Statement Description: The primary gene product of the Ebola virus GP gene is a secreted GP, cleaved to generate secreted GP (sGP) and delta peptide (Jeffers et al., 2002). pre-sGP undergoes several co- and post-translational processing events, such as signal peptide cleavage, glycosylation, oligomerization, and proteolytic cleavage. The limiting step during maturation and transport seems to be oligomerization in the endoplasmic reticulum (Feldmann et al., 2001)(<a href="#reference5294">Jeffers et al., 2002</a>)(<a href="#reference5282">Feldmann et al., 2001</a>)
Interaction 17: I25
Input Objects: pre-GP protein Output Objects: pre-GP protein GO Evidence Code: Traceable Author Statement Description: pre-GP is processed to a fully glycosylated uncleaved form, GP0, in the Golgi apparatus. Trafficking to the Golgi apparatus also leads to the addition of O-linked glycans (Jeffers et al., 2002).(<a href="#reference5294">Jeffers et al., 2002</a>)
Interaction 18: I26
Input Objects: pre-sGP protein Output Objects: pre-sGP protein GO Evidence Code: Traceable Author Statement Description: After oligomerization, pre-sGP is transported into the Golgi compartments where glycosylation is completed and post-translational cleavage into sGP and a small peptide, designated delta peptide, occurs. Cleavage is mediated by furin (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Interaction 19: I31
Input Objects: GP1 protein, GP2 protein Output Objects: GP1/2 protein GO Evidence Code: Traceable Author Statement Description: A special arrangement of cysteine residues in the GP1/2 molecules allows the formation of an intramolecular disulphide bridge between the two cleavage products. This suggests a stem region consisting of GP1 and GP2 and a crown-like domain on the top formed by GP1 that carries the mass of the carbohydrate side chains. The mature transmembrane glycoprotein is a trimer comprising disulphide-bonded GP1/2 molecules. The mature transmembrane glycoprotein forms spikes without the need for other viral proteins (Feldmann et al., 2001).GP1/2 is the virion form of GP and it is also present in cells, presumably in the trans Golgi network and on the cell surface (Volchkov, 1999).(<a href="#reference5282">Feldmann et al., 2001</a>)(<a href="#reference5301">Volchkov3</a>)
Interaction 20: I32
Input Objects: GP1/2 protein Output Objects: GP1/2 protein GO Evidence Code: Traceable Author Statement Description: The mature envelope glycoprotein GP1/2 is anchored in the membrane by a carboxy-terminal hydrophobic domain of GP2. The middle region of GP1/2 is variable, extremely hydrophilic and carries the bulk of N- and O-glycans, which account for more than one-third of the molecular mass of the mature protein. Oligosaccharide side chains differ in their terminal sialylation patterns. Two carboxy-terminal cysteine residues are acylated. GP2 contains a sequence of several uncharged, hydrophobic amino acids at a distance of 22 (EBOV) or 91 (MBGV) amino acids from the cleavage site and which bears some structural similarity to the fusion peptides of retroviruses. The special arrangement of the cysteine residues in the GP1/2 molecules allows the formation of an intramolecular disulphide bridge between the two cleavage products. This suggests a stem region consisting of GP1 and GP2 and a crown-like domain on the top formed by GP1 that carries the mass of the carbohydrate side chains. It can be assumed that cysteine residue 53 is also critical for maintaining the structure of GP1/2. The mature transmembrane glycoprotein is a trimer comprising disulphide-bonded GP1/2 molecules (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Interaction 21: I33
Input Objects: Delta peptide Output Objects: Delta peptide GO Evidence Code: Traceable Author Statement Description: Delta peptide is secreted from cells but this process seems not to be as efficient as the secretion of sGP (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Interaction 22: I34
Input Objects: sGP protein Output Objects: sGP protein GO Evidence Code: Traceable Author Statement Description: >Due to a lack of a transmembrane anchor, sGP is secreted efficiently from infected cells (Feldmann et al., 2001).(<a href="#reference5282">Feldmann et al., 2001</a>)
Interaction 23: I35
Input Objects: GP1/2 protein Output Objects: GP1 protein GO Evidence Code: Traceable Author Statement Description: During maturation, GP1 is partly shed in monomeric form after the release of its disulphide linkage to the transmembrane subunit GP2 (Feldmann et al., 2001). This free GP1 is shed in a nonvirion-bound form and has been hypothesized to be pathogenic (Chan et al., 2000).(<a href="#reference5282">Feldmann et al., 2001</a>)(<a href="#reference5300">Chan et al., 2000</a>)
Interaction 24: I36
Input Objects: Negative sense genome, NP protein, VP35 protein, VP40 protein, VP30 protein, VP24 protein, L protein Output Objects: Viral capsid GO Evidence Code: Traceable Author Statement Description: The assembly of new viral particles occurs on the inner surface of the plasma membrane, where VP24 and VP40 apparently associate both with new RNPs and with the cytoplasmic tail of GP2 (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Interaction 25: I37
Input Objects: GP1/2 protein, Viral capsid Output Objects: Budding virus GO Evidence Code: Traceable Author Statement Description: Nascent virions become enveloped by the GP-bearing lipid bilayer and exit the cell through budding (Bray and Paragas, 2002). New data demonstrate the compartmentalization of Ebola and Marburg viral proteins in lipid rafts during viral assembly and budding (Bavari et al., 2002).(<a href="#reference5296">Bray et al., 2002</a>)(<a href="#reference5299">Bavari et al., 2002</a>)
Interaction 26: I38
Input Objects: Budding virus Output Objects: Virion GO Evidence Code: Traceable Author Statement Description: The complete replication cycle takes approximately 12 hours. As for many other viruses, filovirus replication triggers a cascade of reactions in infected cells, including the de novo production of type I interferon (IFN-/), which collectively constitute the innate antiviral response. At the same time, certain viral proteins apparently suppress some of these antiviral mechanisms, giving the virus an advantage over its host. The ability of filoviruses to overcome initial defensive barriers and rapidly disseminate may be an essential factor in their virulence (Bray and Paragas, 2002).(<a href="#reference5296">Bray et al., 2002</a>)
Pathways

Phinet Name: Ebola Virus