Re: COMPOSITION AND ORIGIN OF VIRAL CAPSIDS

Dear Aleksandr,

Viral capsids are made of viral capsid proteins. I am not aware of any virus that uses a host-endcoded protein as a part of its capsid, although that would not be impossible to imagine. Viruses, including bacteriophages which infect bacteria as well as viruses which infect plants, invertebrate and vertebrate animals, fungi, plants and single-celled eukaryotes (protists) are as diverse or more diverse than their hosts. Thus the capsid protein of a particular human retrovirus such as HTLV-1 or HIV-2, has absolutely nothing in common other than its function of packaging the viral genome, with the capsid protein of another virus such as avian influenza virus or tobacco mosaic virus.

As far as protein function is concerned, if not protein amino acid sequence, the capsid proteins are probably most similar to other DNA or RNA binding proteins. The job of the capsid proteins is to specifically recognize the viral genome (some viruses use an RNA genome, others use a DNA genome, some viral genomes are single stranded, others are double stranded) and package the genome into the virus particle. Every host cell, even a bacterial cell, contains a lot more host DNA and RNA than viral genome. So if DNA or RNA was packaged at random, most of the viral particles would not contain the viral genome, they would contain random bits of host DNA or RNA and these would not be viable viruses.

The question of where viruses came from is very interesting, meaning that we do not yet have many answers. It seems clear that there have been at least dozens of different viral origins, bacteriophages most likely evolved in tandem with bacteria, and it is quite possible that a phage such as M13 has a completely seperate origin than another phage such as T4. Likewise, there is no reason to suspect that eukaryotic viruses such as Tobacco Mosaic Virus and Human T-cell Leukemia Virus Type I shared a common ancestor. It is more likely that they had completely independant origins.

It is possible that some eukarytic viruses evolved from bacteriophages while others evolved de novo from eukarytoic genes.

The rate of evolution (the amount of change that happens per unit of time) of a given type of oganism is dependent not only upon the basic mutation rate of that organism, but also on other factors such as population size, number of generations per unit of time (bacteria have a generation time of mintues or hours, mice have a generation time of weeks or months, humans have a generation time of decades), habitat size, and competition for resources. Bacteriophages and viruses not only have higher basic mutation rates than their hosts, but they also have shorter generation times and most often have larger population sizes. A single host cell might turn out hundreds or thousands of virus particles per day. The result is that the viruses have evolved more over the past billion years or so, than have the virus hosts. They have evolved so much, and left no fossil records, that we can no longer expect to recognize any similarity, even between members of a set of viruses that we might expect to have shared a single common origin.

Viral polymerases (many viruses and phages carry their own DNA or RNA polymerase to copy their genomes, rather than relying on the host cell DNA or RNA polymerases) and capsid proteins are more conserved, they evolve more slowly, than viral envelope proteins. Within a single rather closely related group of viruses, such as the beta group of vertebrate retroviruses which appear to share a single common ancestral pol gene, it is possible that there were multiple independent origins of envelope genes. Although it is fairly rare, retroviruses sometimes loose a bit of their viral genome and replace it with a bit of host genome. They can thus acquire a new envelope protein from a host. After a retrovirus picks up a new envelope protein from the host, the virus env gene (and protein) evolves at a much faster rate than the host, so within just a few millions years time the virus envelope may no longer be recognizably similar to the host gene that it came from.