Ear­li­est Ar­chae­ol­ogy

by Merry

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.

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

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.