Saturday, September 18, 2010

Duel to a minature death

Bacterial viruses are fascinating, if only we squint really hard!

I ran across a lengthy review of the bacterial virus (or phage) called T4, and was inspired by the elegance and intricacy of this organism. Bacteria can hardly be seen through a light microscope. Their viruses can't be seen at all unless you have an electron microscope (90 nm across. For comparison, a water molecule is 0.2 nm across). These are the ultimate mite on the flea on the hair of the dog. But such viruses are everywhere, thought to outweigh humanity in overall biomass (with ~10E32 individuals). They pervade the oceans and anywhere else bacteria exist, and have been used in medicine as antibiotics.

The T4 virus, about 90 nm across, 200 nm long
The T4 virus uses a lunar-lander structure to detect and attach to its host, and then inserts a microscopic needle to inject DNA from its head capsule into the hapless victim. No consciousness is involved- this is a fateful dance of molecular entities, one battling the other for the prize of the bacterium's accumulated cytosol- chemicals and energy.

The bacterium has several weapons at its disposal. First, T4 docks on some simple sugars on the bacterial surface. But not all bacteria display them, so not all bacteria are equally susceptible. After the virus has injected its DNA, many bacteria are able to cut it apart with DNA-cleaving enzymes- which cut DNA at particular sequences, (which are specially shielded in the host cell), leading them to be called "restriction" enzymes for their ability to restrict which viruses infect that host.

But often enough, the virus wins and commandeers the host completely, using the bacterium's various materials to make copies of itself. T4 has about 300 genes (in 169,000 base pairs), devoted to such things as turning off the host's RNA, DNA, and protein synthesis, digesting these  host molecules, altering some of the host enzymes for its own uses, carrying out its own DNA replication, generating its own complex viral shell, and popping open the host cell to finally release the newly manufactured T4 particles. It even carries functions that block super-infection by other T4-like viruses. Greedy bastards!

The virus performs three distinct waves of gene transcription, called early, middle, and late. Each sets the table for the next stage, first using unmodified host RNA polymerase to express some of the genes important for shutting down central host processes like transcription, translation, and DNA synthesis. Some T4 genes cease expression within 1 minute of injection, though the full infection cycle lasts about 30 minutes at top speed.

Indeed, there are so many genes from T4 that shut down host functions that researchers have had a terrible time cloning many T4 genes (that is, replicating portions of its genome in what would otherwise be its host- E. coli bacteria). Workers trying to sequence the complete genome finally had to resort to non-biological means, using PCR to chemically replicate enough DNA.

Then, Borg-like, the virus modifies the host's RNA polymerase so that it transcribes only on its own genes. T4 genes expressed at this middle phase include components of the virus's own DNA replication machinery, which needs to assemble and begin making DNA before the late phase of T4 gene expression can begin. Finally, the proteins of the virus's shell are made- the head, tail, and tail fiber proteins, along with several scaffold and chaperone proteins that are needed for virion assembly, but then cast off.

There is a fest of DNA replication late in the infection (i.e at around 15 minutes) where stray strands of new DNA invade each other (called recombination) to prime further DNA synthesis, creating a messy catenated, branched network of T4 genomes. This allows replication to amplify exponentially at maximum speed. The mess is later resolved by DNA-cutting and repair enzymes that cut randomly in the genome, and lay one end into an empty viral head.

An ATP-dependent pump at the entrance of such this head then pumps in a headful of DNA, while DNA repair enzymes make sure any nicks or branches are resolved, since those can't get through the pump. A headful of DNA is on average 103% of the T4 genome, ensuring that a full genome's worth of T4 gets in, no matter where the DNA ends happen to be. This also places rather strict limits on how long the genome can be. If a new gene is accidentally captured from a host or fellow phage, some resident gene will likely have to go if the virus is to be successful.

Speaking of which, T4 even carries its own parasites, in the form of self-splicing introns. These are short genetic elements whose RNA form self-excises from longer RNA transcripts, and which encode a small protein that cuts other DNA molecules and promotes recombination that allows the intron to replicate into the new location, given the ambient DNA repair and synthesis activities. A virus with the intron will transfer it to a co-infecting virus without one. Truly, the rigors of natural selection go all the way down.

At this point, a set of whiskers attach to the base of the head, which later restrain the virus's landing gear from premature triggering. Then a tail assembly (tube, baseplate, and tail fibers) attaches to the head, and the virus is complete.

Electron micrographs or T4 particles. Note in the second image one injector needle has fired.
The tail of the virus is a double tube. The outer sheath is a remarkable collapsing tube of proteins that starts out 98 nm long, and when triggered by the tail fibers and virion base attaching to an appropriate bacterial host, shortens to 36 nm, a shortening to almost a third of its original length (see figure). The inner tube does not shorten, of course, and constitutes the needle that is driven into the bacterium by the collapse of the outer sheath, and from which flows the DNA, driven by the electrochemical gradient across the live bacterium's membrane, and possibly a special pore constructed by the virus.

The last stage of host cell lysis calls on yet more molecular wizardry. Late in the infection, viral proteins called holins quietly accumulate in the bacterial cell membrane. Then, upon a trigger that is not understood, these proteins very rapidly form huge holes in the membrane, finally executing the cell and allowing viral degradative enzymes out to chew up the cell wall, after which the expired cell pops open, releasing a new generation of viruses.

The cycle is now complete. The corpse of the bacterial cell is left behind, along with the infecting machinery and a wide variety of intermediate RNAs, scaffolding proteins, DNA polymerases, chaperones and other debris from the viral infection. Perhaps 100 to 300 viral particles go on to try their luck elsewhere.
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"In the past, the dilemma of capitalism was that the firms had to keep real wages growing in line with productivity to ensure that the consumption goods produced were sold. But in the recent period, capital has found a new way to accomplish this which allowed them to suppress real wage growth and pocket increasing shares of the national income produced as profits. Along the way, this munificence also manifested as the ridiculous executive pay deals that we have read about constantly over the last decade or so.
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