The Technical Stuff

A quick correction to my last post: there are typically only 72 ‘cloves’ stuck into the ‘orange’, and cloves are too small to make a good visualization. Golf tees stuck into a small orange might be closer. Go here to see numerous pictures of HIV-1 (scroll down to lentiviruses).

The cloves or tees are made up of a ‘stem’, glycoprotein (gp) 41 and a ‘knob’, gp120. The numbers are simply the molecular masses of the molecules, in kiloDaltons (a Dalton is the mass of a single hydrogen atom). The stem is inserted into a lipoprotein membrane (the skin of the ‘orange’, if you like; but stop thinking of an orange now, because the inside of the virus is nothing like that) which is derived from the host cell and surrounds a protein coat composed of the viral matrix protein. Taking up a good deal of the space inside this coat is the viral core, which is often appropriately described as ‘coffin-shaped’; the primary structural component of the core is the viral capsid protein. Inside the core are two copies of the viral genome, about 9000 bases of single stranded RNA, each complexed with (inter alia) one reverse transcriptase molecule. Other viral proteins, notably integrase and protease, are also present in the core, together with molecules ‘stolen’ from the host cell from which the virus particle emerged. One notable ‘stolen’ molecule illustrates just how intimately evolution has intertwined the biology of the virus with that of the human host: HIV-1 uses human tRNA as a primer for reverse transcription. Not only is a specific tRNA required, but mutations which allow the use of an alternative primer rapidly revert to the wild type. (Transfer (t) RNAs are the ‘connectors’ that recruit amino acids to the site of protein synthesis in normal cellular activity.)

To be susceptible to HIV-1 infection, a host cell must express a surface protein called CD4, which is only expressed on certain cells of the immune system (note: this makes clear the reason for the virus’ primary pathological effect, immune deficiency). When the virus particle encounters such a cell, interaction between CD4 and gp120 enables fusion of the viral with the cell membrane. (In so describing it I’ve simplified the fusion process considerably, in part because it is not fully understood.)

Now things get a bit fuzzy in terms of our understanding of the reproductive cycle (the term ‘life cycle’ is common, but I dislike it as the virus is not alive IMO). After fusion effectively inserts the protein coat into the host cell, stuff happens, at the end of which stuff happening the viral genome has been converted into double stranded DNA and inserted into the host cell genome. My studies over the last four years were concerned mainly with the nature of the stuff that happens, which I think is best understood as a series of events which overlap in space and time:

  • the outer and inner (matrix and capsid) protein coats essentially fall apart
  • the RNA genome is converted into DNA
  • the RNA genome together with its attendant proteins and the growing DNA copy moves from the cell membrane to the nucleus and then enter the nucleus
  • the completed DNA copy is inserted into the host cell genome (this is almost random, although I think that certain sites are favoured, probably on the basis of activity rather than sequence)

We don’t know the fine structure of these events, nor precisely how they overlap. I doubt, for instance, that “fall apart” is accurate: the removal of the protein coat(s) is, IMO, much more likely to be a regulated process that occurs in concert with other events such as the initiation of reverse transcription. In fact, I suspect that membrane fusion is part of the same concerted series of events. To indulge in a brief anthropomorphism, this is not a virus that leaves things to chance. It packs a dozen genes into about 9000 base pairs, using multiple reading frames; compare that with the human genome, which carries about 30000 genes on roughly 3 thousand million base pairs! (The average, ~100kbp/gene, is misleading because only about 10% of the human genome encodes protein, but that too is a useful comparison. The HIV-1 genome contains no “junk” and relatively little regulatory DNA.) With such a compact genome, streamlined by the need to evolve so as to stay out of the way of the host’s defenses, HIV is a designer particle specifically engineered to infect H. sapiens. I would be surprised to find any part of its reproduction that was not tightly regulated. That much of the regulation is achieved by subverting cellular mechanisms only increases my astonishment at the ingenuity of the damn’ thing!

From integration onwards, we know a lot more about what the virus does inside the cell — but my work did not involve post-integration steps in any detail, and this is already a long entry. Very briefly, the integrated viral genome (called a provirus) is expressed in much the same way as cellular genes, except that it is regulated by a viral protein called Tat. (Another example of the compact nature of the virus: Tat is also essential for efficient reverse transcription, a fact which underlies most of the research I was doing.) Viral proteins and RNA assemble at the cell membrane and form immature particles, and another series of concerted events results in budding of these particles from the cell (during which process they acquire their outer lipoprotein membrane). The viral protease, which will be familiar to many as the target of newer antiretroviral drugs, cleaves the proteins in the immature particle and the smaller proteins thereby formed rearrange into a mature virion capable of infecting a susceptible cell. Again, I’ve left an enormous amount of detail out of that thumbnail sketch, which I’ve only included for completeness, to round out the cycle. I haven’t touched on the dynamics of infection and treatment, the epidemiology of the virus, or any of a dozen other fascinating topics; but this was more or less just a brain dump, and I hope that perhaps some of Kitty’s readers and Link & Think browsers have found it interesting.

1 Responses to The Technical Stuff

  1. Linkmeister says:

    Yes. Very enlightening; thank you.