A Pov-Ray model of a filovirus such as ebola virus
A Pov-Ray model of ebolavirus, cutaway to show internal structures
Ebolavirus
The ebola virus is an example of a filovirus - a group of filamentous viruses which attack animal
hosts. The ebolavirus is a group of related viruses, of which the Zaire form is considered to be
ebolavirus (EBOV) proper. Each viral particle (virion) is about 80 nm in diameter and of variable
length, but up to 1400 nm long. The virion is
pleomorphic, that is having variable form. It is flexible
and often adopts a U or 6 shape (it is not clear to what extent the form is fixed and to what extent it
changes due to thermal fluctuations). Filaments are also often branched and sometimes two
filaments may be connected by a bridge. The virion is
enveloped, being surrounded by a host-cell
derived phospholipid bilayer membrane, shown in yellow.

Ebola causes
haemorrhagic fever in humans and other primates, which has 60 to 90% fatality.
This is characterised by destruction of the internal membranes of the body resulting in massive
internal bleeding. The conjunctiva (membrane or epithelium over the front of the eyeball) are also
affected and bleeding from the eyes is characteristic of the disease.
Above: a model of an ebolavirus cutaway to show the
internal structures, and, left, in cross-section. The model is
not exact due to a lack of data.

The genome is about 19 kb (kilobases) and consists of a
single molecule of linear single-stranded negative-sense
RNA (ss(-)RNA) shown in red in the core of the filament.
This genome encodes 7 structural proteins and at least
one largely non-structural protein. The seven structural
proteins are: NP (
nucleoprotein) shown in blue entwining
the RNA which it stabilises, VP40 (
matrix protein, shown
in orange), VP24, GP (
glycoprotein) which forms spikes
on the surface of the virion, shown in cyan, RNA
polymerase (L) shown in green, polymerase cofactor
(VP35) and transcription activator (VP30).
Prerequisites

Protein synthesis

Gaining access to host cells

Viruses have been likened to 'pirates of the cell'. They will bind to and invade selected target cells
and take control of the cell's machinery to make more copies of themselves. They are totally
dependent on the host cell's chemical energy and protein-making ribosomes. Ebolavirus must first
bind to a suitable target cell. Some viruses are very specific in the type of cell they will attack.
Ebolavirus infects humans and other primates, but will target a wide range of cell types within the
host, from epithelial cells, including the conjunctiva and the linings of internal viscera, to immune
cells, such as macrophages, monocytes and dendritic cells.

The viral
GP spikes which project from the virus envelope are important in recognising and binding
to target cells. Each GP spike is a trimer (group of three) of GP1 and GP2 hetrodimers (groups of
two different proteins). There is only one GP gene, but the messenger RNA molecule produced by
transcription of this gene may undergo site-specific editing. Viruses have to be small and compact
so as to maximise the number of progeny virions that can be manufactured before the host cell is
exhausted, and hence increase the likelihood that one of the progeny will happen by chance upon
another suitable target cell. viruses are highly evolved genetically - their genome has evolved
remarkable ways of encoding proteins whilst using the minimum amount of DNA or RNA.

The unedited transcript codes for the main non-structural protein, soluble GP (sGP) which is
secreted by the infected cell, rather than for the GP spikes. The protein sGP probably has multiple
functions, but chief among them is the suppression of the immune response in endothelial cells (the
cells lining blood vessels) which reduces signalling to immune cells to reduce the number of
immune cells recruited to sites of infection. This clearly helps protect the virus from the immune
system of its host. The sGP exists as a homodimer (two molecules of sGP) aligned antiparallel
(pointing in opposite direction) and connected by a disulphide bridge (to give: sGP-S-S-sGP).

Insertion of an adenine (A) into the GP RNA transcript alters the reading frame by +1 which results
in a longing
open reading-frame (ORF) as an earlier STOP codon in the unedited message is
now absent. This gives rise to two peptides, GP1 and GP2, which together form the normal GP
spikes

Reading frame: RNA is read in groups of three bases, the bases acting like letters, and each
group of three bases acts like a word and is called a codon. Codons are non-overalpping and
contiguous (there are no bases inbetween adjacent codons) and so starting from a given base
determnines the message, e.g. UGC-GGC-UUA- ... . Inserting an extra base changes all the
groupings of three codons so that the rest of the message changes and a different protein is coded
for, e.g. UG
G-CGG-CUU- ... . The reading frame is said to be shifted by +1 base. An open-reading
frame (ORF) is the part of the mRNA that the ribosome reads when making the protein, and begins
at a START codon and finishes at a STOP codon.

Although non-structural, meaning that it is not an essential component of the virion itself, sGP can
be incorporated into the GP spikes in place of GP1 (forming sGP-S-S-GP2 heterodimers) and so is
an optional structural protein. A third product of GP RNA transcriptional editing has been identified:
a small, soluble GP, ssGP, which is a secrted monomer resulting from a +2 frame-shift, which
results in the introduction of an early STOP codon, so the ORF is short.

The GP spikes recognise and bind to a specific receptor found on certain host cells - the TIM-1
protein, which is found on certain immune cells as well as mucosal epithelial cells and the
conjunctiva and kidney tubule cells. This allows the virus to target cells which will then enable it to
gain deeper access to the body (it may breach the conjunctiva, or hitch a ride inside an immune
cells, and go on to infect visceral epithelial cells). The GP spikes have also been reported as
binding to lectins, proteins found on the surface of a wide variety of cells. Disrupting the epithelial
cell layers of the body results in the massive bleeding so characteristic of ebola disease.

GP1 is the component of the spikes which contains the actual receptor-binding domain (RBD)
which binds to TIM-1. Once the TIM-1 receptor is engaged, this triggers endocytosis (specifically
macropinocytosis) by the target cell. In this process the region of membrane with the TIM-1 and
bound virus is internalised inside a vesicle called an endosome which is taken into the cell's
cytoplasm. TIM-1 (TIM stands for t-cell immunoglobulin and mucin) is normally used by cells to
engulf fragments of other cells which have undergone apoptosis (programmed self-destruction).
This may be part of both a clean-up operation and an attempt by the immune system to process
the fragments of self-destructed cells to see what pathogens may have triggered the self-destruct
mechanism. TIM-1 does this by recognising and binding to the phospholipid component of cell
membranes phosphatidylserine, which will also be present in cell fragments. Phosphatidylserine in
the viral envelope have also been reported capable of binding to TIM-1 to initiate infection.

The cell now attempts to process the contents of its endosome. Vesicles fuse with the endosome,
releasing acid, noxious enzymes and reactive oxygen species into the endosome. Such a noxious
mixture will destroy most biological molecules. However, specific damage to the GP1 (attack by
endosomal proteins cathepsin L and B in acid pH) triggers a conformational change in the GP
spikes which brings the viral envelope in close proximity to the endosomal membrane. GP2 now
comes into play, initiating fusion of the viral and endosomal proteins which releases the viral core
into the host cell's cytosol. The virion has escaped destruction and is now truly inside the host cell!

The exact mechanics of membrane fusion are complicated. Membranes do not freely fuse and GP2
lowers the activation energy of membrane fusion, by inserting its fusion loop, and triggers a
conformation change in the GP spike, which forms a 6-helix bundle. A pore is formed in the
endosomal membrane through which the viral core (the genome plus associated proteins) enters
the cytosol.

Switching off host defences

We have already discussed how secreted sGP can reduce the host's inflammatory response,
essentially switching off the body's alarm systems which signal infection. In addition, every cell has
its own systems for recognising invading viruses and the immune system also has special anti-virus
defence mechanisms. Ebolavirus must reduce the effectiveness of these defences if it is to
replicate freely. This is the role of VP24, which is a minor matrix protein (forming part of the protein
matrix which underlies the viral envelope and which is ejected into the cytosol along with the viral
core).

VP24 inhibits the
interferon system. This is a cell signalling system which switches on genes for
dealing with viral infection. Immune cells can synthesise and secrete IFN-gamma which activates
macrophages to engulf and destroy virus and viral-infected cells and also activates the generals of
the immune system, the T-helper cells which can then activate antibody synthesis by B cells, and
also activates specialised cells which deal with viral-infected cells: the cytotoxic-T (Tc) cells and
natural killer (NK) cells which deal with any aberrant cell. A second interferon system, the IFN-
alpha/beta system operates in the infected cell. This second IFN system can result in the synthesis
of a sensor protein, PKR (protein kinase R), which detects viral RNA in the infected cell and
switches off mRNA translation (and hence protein synthesis) when viral RNA is detected; this
essentially shuts down the cell's factories so that viruses cannot be made. It will also alert other
cells nearby to raise their defences.

VP24 works by blocking the signal from IFN receptors to the command centre of the cell, the cell
nucleus. Cells can then no longer detect IFN signals and so IFN is rendered more-or-less useless.

Assembly of progeny virions

Ebolavirus encodes its genetic information as negative-sense RNA. The ribosomes of the host cell,
protein-making factories, can decode or translate RNA directly into proteins if the RNA is positive
sense. In the case of negative RNA, the message is complimentary to the message of the mRNA
recognised by the ribosomes and must first be decoded into positive-sense RNA. Since the host
cell does not normally deal with (-)RNA, the viral brings along its own RNA polymerase,
polymerase L. This enzyme will read the viral (-)RNA and transcribe it into (+)RNA. In fact, about 9
separate (+)RNA or mRNA molecules are transcribed from the (-)RNA. In addition, the virus must
manufacture more copies of its genome. this is accomplished by transcribing the (-)RNA into a (+)
RNA template which is then transcribed into many copies of (-)RNA (viral RNA, vRNA) for
incorporation into viral progeny. An additional function of VP24 appears to be to inhibit both RNA
transcription into mRNA and viral genome replication and so it may be involved in regulating these
processes - viruses generally conduct these operations in well-timed sequences as they first have
to subdue the host cell's defences.

Assembly of new virions occurs at the inner surface of the host cell membrane. GP spikes are
inserted into the cell-surface membrane, after being processed by the host cell's Golgi apparatus
(which attaches the sugar chains to convert the initial protein into the final glycoprotein). VP40 is
the major component of the viral capsid or 'shell' and matures at the cell-surface membrane where
clusters of VP40 assemble. VP40 is shuttled to the cell-surface membrane in the form of butterfly-
shaped dimers and is then converted into linear hexamers which are then assembled into the matrix
or shell of the virus (apparently with 3 subunits forming the inner layer, 3 forming the outer layer
and where they join forming the core layer). The capsid then self-assembles.

We have already discussed the need to economise on genetic material and VP40 is another
example of a highly evolved viral protein which is multifunctional. It can adopt a third configuration,
that of 8 units joined in a ring, in which state it can bind RNA and appears to play a role in
regulating viral RNA transcription.

Genomic material and core proteins (NP, VP24 and VP35) assemble into the nuclear complex,
enclosed by the assembling matrix. When mature, the virus particle, attached to the GP spikes and
surrounding phospholipids, buds from the host cell, taking some of the modified host membrane
with it which encloses around it to form the envelope. We have already seen how this envelope
helps the virus attach to the host cell and gain entry and it presumable also shields the underlying
viral proteins from detection and attack by the immune system.

Suggested Reading

Lee, J.E. and E.O. Saphire, 2009.  Ebolavirus glycoprotein structure and mechanism of entry.
Future Virol. 4(6): 621–635.

Bornholdt,Z.A., T. Noda, D.M. Abelson, P. Halfmann, M.R. Wood, Y. Kawaoka, and E.O. Saphire,
2013. Structural Rearrangement of Ebola Virus VP40 Begets Multiple Functions in the Virus Life
Cycle.
Cell 154: 763–774.

Dessen, A., V. Volchfov, O. Dolnik, H.-D. klenk and W. Weissenhorn, 2000. Crystal structure of the
matrix protein VP40 from Ebola virus.
The EMBO Journal 19: 4228-4236.

Watanabe, S., T. Noda, P. Halfmann, L. Jasenosky, and Y. Kawaoka, 2007. Ebola Virus (EBOV)
VP24 Inhibits Transcription and Replication of the EBOV Genome.
JID 196 (Suppl 2).

Iwasa, A., M. Shimojima, and Y. Kawaoka, 2011. sGP Serves as a Structural Protein in Ebola
Virus Infection.
JID 204 (Suppl 3).

Mehedi, M., D. Falzarano, J. Seebach, X. Hu, M.S. Carpenter, H.-J. Schnittler, and H. Feldmann,
2011. A New Ebola Virus Nonstructural Glycoprotein Expressed through RNA Editing.
J. Virology,
85: 5406–5414.

Weissenhorn, W., A. Carfı´, K.-H. Lee, J.J. Skehel, and D.C. Wiley, 1998. Crystal Structure of the
Ebola Virus Membrane Fusion Subunit, GP2, from the Envelope Glycoprotein Ectodomain.
Molecular Cell, 2: 605–616.

Volchkova, V.A., H. Feldmann, H.-D. Klenk, and V.E. Volchkov, 1998. The Nonstructural Small
Glycoprotein sGP of Ebola Virus Is Secreted as an Antiparallel-Orientated Homodimer.
Virology
250: 408-414.

Moller-Tank, S. A.S. Kondratowicz, R.A. Davey, P.D. Rennert, W. Maury, 2013. Role of the
Phosphatidylserine Receptor TIM-1 in Enveloped-Virus Entry. J. Virology 87: 8327–8341.
Pov-Ray ebola virus model, up close
A close-up view of part of the ebolavirus computer model.