Monday, May 07, 2007

Tree of Life: Why are we STILL ignoring viruses?

You all know the classic Tree of Life-- Archaea, Bacteria, Eukaryotes. Larry Moran has a nice series of posts up on the Tree of Life and how we've decided to arrange it. Hes right. Everything isnt as cut-and-dry as three nice big branches. The classic Tree is missing one big puzzle piece. Well... lots of teeny tiny puzzle pieces that add up to a huge piece :) You know what Im thinking folks: Viruses.

How the hell are we still getting away with ignoring a HUGE component of 'life' on this planet??

One of the first papers I read that tried to combine viruses with the classic Tree of Life is available online for free:

Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain.

One of the main problems with the Tree is that even though we 'get' there is a net of Archaea/Bacteria/Eukaryotes, we still dont have an understanding of how these groups originated or how their 'nets' are connected. Forterre discusses several potential models of how everything is arranged, and why each model is wrong, despite the proponents hopes they would be vindicated by genomic sequencing. He then quips:
"Proponents of each model have stuck to their favorite one and have found in genome data arguments to support their case. This suggests that something critical may be missing from the complete picture."
HMMMM!!! What could be missing??? hehehehehe!

Forterre begins his Tree of Life (Now with Viruses!) hypothesis by turning our attention to the origin of the three domain groupings: ribosomal RNA. Turns out that each group has a characteristic ribosomal RNA sequence. Well neato, right? You can just take everyones ribosomal RNA sequence, line them up, see what tree pops out at the end... right?

Ugh. Its never that easy.

A cog in this machine is DNA replication machinery. It appears to have no logic at all, when crossing over the three domains. Its not nice and homologous like with ribosomal RNA (one domain, one characteristic sequence). Bacteria have one version of DnaG primase, but there are two kinds for archaea/eukaryotes. Bacteria and archaea share a Type II DNA topoisomerase, but eukaryotes have their own. There are multiple DNA polymerases in eukaryotes, but bacteria and one in archaea... WHERE IS THE LOGIC???

You see why the genomic era led to a Net of Life rather than a Tree?

Forterre thinks he has an idea as to why it appears to be such a mess-- Were ignoring viruses. The classical Tree of Life belongs in the garbage can right next to the classical view of viruses (that viruses are simply 'de-evolved' cells or genomes gone wild). In an RNA virus world, a DNA virus would have an obvious advantage: it is safe from anti-RNA defense mechanisms and more stable. Enter in horizontal gene transfer (picking up more genes from invading pirates like plasmids), and Forterre says hes got an explination for why DNA replication machinery makes a nice little Web of Life.

Returning to the ribosomal RNA-- hes got an answer for that too. Viruses. He thinks that >3 'domains' originally arose from three RNA viruses, but the three we are left with today were the most fit. Or maybe it just happened three times, but far enough away from each other that each had its own niche figured out before they interacted. Or maybe they pushed and shoved each other into the niches we see today (bacteria pushed archaea into being extremophiles).

Forterre has some cool ideas (eh maybe some a little too far out there) in this paper--and its pretty short too! If you want to get through it on your own, bring your questions here and well see if the blag-hive-mind can get you some answers :)


Hume's Ghost said...

I find this depiction of the "tree" of life to be more illuminating

Zimmer explained

I guess it will be a while before they sort out how to incorporate viruses into the mix. I find this future area of gene swapping with relation to biogenesis and what not to be fascinating.

P.S. I dropped you a private message at Long time no see.

Dr. Duke said...

The species wikipedia also does not yet know what to do about viruses: