Earliest Archaeology

by Merry
 

3D representation of a phenyalanine tRNA. Source: Department of Biosciences and Nutrition, Karolinska Institute, Stock­holm

It has been dazzling, the insights into the evolutionary history and relationships of organisms gained in recent years through phylogenetic approaches. As the mountain of sequence data continues to grow exponentially and increasingly clever methods of analysis are devised, we can't help but wonder how far back in evolutionary his­tory we might be able to see . We'd surely like to know who came first (Bacteria? Archaea?) and where viruses fit in and how an RNA world led to the DNA world and…and… A recent paper gives us a glimpse into long long ago.
 

tRNAs are good candidates for studies of the early evolu­tion of life. These central components of the protein translation machinery are known to be ancient. They are universal components found in all organisms – and even in some viruses (not only in the gargantuan Mimivirus, but also in some bacteriophage, a herpes virus, and others). They are complex structures, with multiple "arms" and two functional domains. Two portions of these molecules may have had different evolutionary histories. (For a paper detailing a study of the molecular evolution of tRNAs, click here.)
 

Our simplified diagram contrasting the tree proposed from tRNA structures with the currently accepted tree from small-subunit rRNA sequences.

The function of tRNA is closely tied to its structure, and that structure is more evolutionarily conserved than nucleotide sequence. The authors of a recent paper devised a way to build a universal phylogenetic tree of life using information embedded in both sequence and secondary structure of tRNAs. They made specific as­sumptions and used sophisticated strategies to uncover the significant relationships despite the confounding effects of “recruitment” (the process whereby structures such as tRNA molecules "gain or co-opt new identities and functions or takeover established ones".)
 

What arose from their analyses is a picture wherein the Archaea consistently emerged as the most ancestral group. That group subsequently split into two lineages, one archaeal and the other eukaryal-bacterial. Further­more, the first two domains were the Archaea and Eukarya. The Bacteria emerged later. The origin of viruses is linked to the Archaea, thus making them ancient, indeed. The authors obtained similar results in their recent analysis based on protein domains and structure (submitted for publication). We expect that this proposal may well cause a ruckus, or at least be seriously challenged. But maybe the Archaea weren't misnamed after all!
 

Thanks to Miguel Vicente’s blog, Esos Pequeños bichitos, for calling our attention to this article.
 

 
 

 
 

Comments

[Paul Orwin]

This is very interesting - it's the first time i've seen a molecular phylogenetic tree that disagrees at the base with the ssu-RNA tree. I'm a little concerned about horizontal gene tranfer (HGT) in interpreting this, though. If I'm not mistaken, tRNA genes are frequently sites of phage integration, leading me to think (perhaps naively) that specialized transduction in nature could lead to significant mixing of these genes among species. This seems to me like it could confound the data in a fundamental and intractable way. I haven't had a chance to look at the paper yet (even though it is open access! just lazy I guess), but I wonder if they addressed this notion?