Monday, April 30, 2007

The Ancient Virus World and Evolution of Cells: Part Two,The egg CANT come before the chicken! Oh wait...

Oh as usual, unwanted drama got in the way of science posts-- but finally! Second edition of 'Ancient Viral World'! The paper Im reading is available online for free!

If you asked someone which came first, the virus or the cell, theyd most likely say 'The cell! Viruses need cells to replicate, so they couldnt come first.' hehehe This isnt a trick 'If a rooster lays an egg' question. The Average Joe understanding of viruses might be right in this case! 'Viruses second' is the traditional scientific explanation for viruses, and there are two obvious ways viruses could have arisen after cells:

  1. Unicellular organisms, maybe parasites, lost some of their genes and became obligate parasites.
  2. Renegade genomes - bits of genes/genomes and such escaped from the host genome, selfish bastards that are only looking out for Number One.
But there is a big problem with these hypotheses that surfaced when we started sequencing and comparing viruses: Viruses have lots of genes that arent found in their host cells.

These 'viral hallmark genes' can be found in lots of viruses, spanning the seemingly unconnectable gaps between say, ssRNA to dsDNA viruses. These genes are only distantly related to cellular genes, if a cellular counterpart can be found at all, so they probably arent degraded stolen host genes. Plus, they all have virus-specific uses. For instance, the most widely distributed viral hallmark genes are 'jelly-roll capsid protein' and 'superfamily 3 helicase' (mmm jelly-roll...). Superfamily 3 helicase is a protein involved in genome replication in DNA viruses (and plasmids), whether that DNA virus infects us or an Archaea. The capsid (protein coat) of icosahedral viruses is made of a complex of capsid proteins:Each of the capsid subunits has a 'jelly-roll' domain-- a motif conserved across the viral world.

Viral hallmark genes also include:
  • Archaeo-eukaryotic DNA primase (genome replication)
  • UL9-like Superfamily 2 helicase (genome replication)
  • Rolling-circle replication initiation endonuclease (genome replication)
  • Packaging ATPase of the FtsK family (DNA packaging into virion)
  • ATPase subunit of terminase (DNA packaging into virion)
Now, nobody is saying that because some viruses share genes, all viruses have a LUCA (oh Im sure *someone* is saying it). 'Viruses' as a whole are just too diverse for anyone to humor that idea, so we think that viral phylogenies are polyphyletic, rather than monophyletic. We can tease out a few roots of their tree:
  • Positive strand RNA viruses
  • Retroid viruses and elements
  • Small DNA viruses, plasmids, transposons with rolling circle replication
  • Tailed bactereophages
  • Nucleo-cytoplasmic large DNA viruses
But, if cells arent ancestral to viruses... How could viruses come first?

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