Thursday, September 3, 2020

Exocytosis, Stage Left: Coronavirus strategies for spreading infection

On a cellular biology level, learning about SARS-CoV-2 opens up a micro-world of epic struggles: stealth and trickery, strategem and counter, adaptation and (usually) survival. This is an early stab at the fifth panel for the redo of Bat Soup: the Graphic Novel in which we attempt to teach really tough biology concepts in a fun way. In this panel, we show the strange ways the virus spreads itself once it successfully enters the cell, takes over its machinery, and  forces the ribosome to start transcribing its proteins to make copies. When I have it where I want it, I will do the final copy on an 11"x14" Bristol Board where I will able to get finer detail with a less cluttered layout.

Endocytosis: In previous panels, we show the dastardly virus using a disguise to evade the immune system to successfully approach the cell. Its spike protein is initially rotated downward and harder for the immune system to recognize. The virus makes use of a host pro-protein such as furin to properly align the spike protein at the S1/S2 boundary so it can activate the ACE2 receptor to make entry into the cell (endocytosis).
The SARS-CoV-2 virus needs a human proprotein, furin, to correctly position its spike protein at the S1/S2 boundary before it can invade a cell.
Snippet from Panel 1

Infiltration and Replication: Once inside, the coronavirus then makes further use of existing human proteins such as cathepsin to unpack its payload and start transcription of its own proteins encoded in its RNA genome. At about 30,000 basepairs, these SARS coronavirus are among the largest and most complex RNA genomes known. So, now that the virus has taken over the cell's fabrication facility, a fleet of new virus particles is being constructed!

So what happens next? Most (lay) descriptions of viral replication just say that the virus causes the cell membrane to rupture so it can surge forth and infect more cells. With most viruses, there is more to it than that and, anyway, with the SARS viruses, particularly SARS-CoV-2 it takes a very different path-- mediated by the "non-structural proteins" in its complex genome which is only partly understood. Programmed cell death, "Apoptosis", does likely happen, but the virus has already spread by then and it is done for a much more cunning reason (which we'll get to in Panel 6).
In the meantime, though, in Panel 5: the viral horde is unleashed.

Viral proteins are synthesized and folded in the Endoplasmic Reticulum and then packaged in smooth-walled vesicles; these vesicles can then merge with the cell membrane to release mature virus into the intercellular space; leaked S-proteins can also cause nearby cell-membranes to merge, allowing virus to directly invade neighboring cells
Bat Soup, the Graphic Novel, Panel 5 concept sketch
The Endoplasmic Reticulum: A long time ago in a galaxy far away when I tutored Cell Biology to make a little side money for college, the Endoplasmic Reticulum and the viral transcription process was something most people seemed to have trouble with. It's extraordinarily complicated, and we are still learning. But I always found it helped to picture it like an WWII-era industrial complex, tiers of concrete and banks of windows (some of them are broken out) rising, the ribosomes stuck to the sides. This is the Rough ER, where the magic of protein synthesis and folding happens. I then picture the Smooth ER, where lipid synthesis happens (the stuff that makes cell membranes, among other things), as rising stacks because they are round and smooth like chimneys or pipes. The nucleus is a walled-complex just beyond the factory.

This is the structure the virus has taken over. The ribosomes start decoding RNA sequences: cytosine, guanine, adenine, and uracil, and stringing together chains of amino acids, the building blocks of proteins. But finished proteins aren't just strings of amino acids (AAs), they are complex 3D structures. The Endoplasmic Reticulum is where those chains of AAs are folded into completed structures like enzymes or hormones... or the shell of a new virus particle.

Exocytosis: Once the viral structure is fabricated, the replicated RNA strand is placed inside and the whole assembled inside smooth-walled vesicles small bubbles inside the cell which are made out of pieces stolen from the Endoplasmic Reticulum. The result is little packets of virus-laden food service condiment packets (extra spicey!) being arrayed inside the cell. But the virus does not have to burst the cell open to escape. At the command of virus-provided S-proteins, pores form in the surface of the cell and merge with the smooth-walled vesicles, pouring virus into the intercellular space (the spike protein once more disguised) where they can find more cells to infect. This is "exocytosis".

Synctium: But, this virus has another trick for avoiding the immune system, particularly deep in the lungs: it doesn't have to leave the cell to spread. The hostage cell starts leaking S-proteins into the intercellular fluid. The S-proteins cause the cell membranes of nearby cells to merge together. Long multinucleated cells called "synctium" start to form which share the same cytoplasm-- and the same viral infection! As we will see in future panels, the cell, including these multi-nucleates mega-cells, can end up dying several different ways.

This cycle of formation of mega-cells, their destruction, and the body's attempt to heal and regrow tissue is a big reason the virus can cause such massive tissue damage and scarring inside lung tissue. The immune response often makes the situation even worse. Understanding how it works and why some people get away with minimal damage may be a key to effective treatment of severe cases.