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Possible explanations for the unity of the genetic code entertained by Crick 1) Frozen-accident – once the complete code was formed this defined the universal common ancestor from which all life evolved. 2) Steric constraint - The current code is functionally constrained because because of a chemical fit between codon and amino acid. Possible explanations for the unity of the genetic code entertained by Crick 1) Frozen-accident – once the complete code evolved this defined the universal common ancestor from which to all life evolved. 2) Steric constraint - The current code is functionally constrained because because of a chemical fit between codon and amino acid. But there was a third possible explanation 3) Genetic code is unified because of natural selection for unity per se – i.e. horizontal gene transfer is essential to evolution itself. Ribosomal protein tree Yeast Sulfolobus Aeropyrum Pyrobac ae Plasmodium Neurospora C.elegans Human Catfish Rice Pyroco-ab Metthe th Metpyr ka Archae fu Aquifex Metcoc ja Thermo ac Thermot ma Metsar ma Haloba ma CAUCR Strep coe 0.1 Ecoli B.subtilus Synecococ Chloro te Chlamy tr Quartet partitions gram (+) archaea Tree 1 gram (-) eukaryote eukaryote archaea Tree 2 gram (-) gram (+) archaea gram (+) gram (-) eukaryote Tree 3 What was found was support for NONE of the three trees, instead: gram (+) archaea gram (-) eukaryote Star phylogeny 18 of the 26 homologue submitted to the quartet analysis displayed the star phylogeny. They include: argD argT argH trpA trpB mutS,H purA purB pur5 pur6 ornithine carbamoyl transferase arginine tRNA synthetase arginine biosynthesis tryptophan synthetase α tryptophan synthetase β mismatched DNA repair purine biosynthesis “ “ “ Ribosomal protein tree Yeast Sulfolobus Aeropyrum Pyrobac ae Plasmodium Neurospora C.elegans Human Catfish Rice Pyroco-ab Metthe th Metpyr ka Archae fu Aquifex Metcoc ja Thermo ac Thermot ma Metsar ma Haloba ma CAUCR Strep coe 0.1 Ecoli B.subtilus Synecococ Chloro te Chlamy tr Ornithine carbamoyl transferase Bifurcated tree Streptomyc pyrobac aquifex aeropyrumB.subtilis metthe th metpyr ka halobacter thermo ma chlorobium E.coli CAUCR pyrococ ab metsar ma synecoc rice Arabidopsi Neurospora themoc ac metcoc ja C.elegans Zebrafish Human 0.1 Drosophila sch pombe Yeast Ornithine carbamoyl transferase Colapse unsupported bifurcations pyrobac Streptomyc aquifex aeropyrumB.subtilis metthe th metpyr ka E.coli halobacter thermo ma chlorobium CAUCR pyrococ ab Arabidopsi metsar ma synecoc rice Neurospora themoc ac metcoc ja C.elegans Zebrafish Human 0.1 Drosophila sch pombe Yeast Trptophan synthase (α and β) Bifurcated tree candida nodulisp spathosp neucra Halobacte coprinus Clostrid trametes arabidopsi Guillard oryza Nostoc Acantham haloferax buchnera Methanolob E.coli bacillis thet Methanosar Archaeog legionel Pseudomo 0.1 Rhodomic Caucre thermus zymonas Trptophan synthase (α and β) Collapse bifurcations nodulisp candida spathosp neucra Halobacte coprinus Clostrid trametes arabidopsi Guillard oryza Nostoc haloferax Acantham buchnera Methanolob thet E.coli Archaeog Methanosar bacillis legionel Pseudomo Rhodomic 0.1 Caucre thermus zymonas Arginine-tRNA ligase Chlorobium Thermot ma Thermo ac sulfolobusArchae fu Aeropyrum Pyrobac ae Pyroco-ab B.subtilis Aguifex Haloba ma Metpyr ka Metcoc ja Metthe th Metsar ma Zebra fish Human C.elegans D.melanoga Plasmodium Chlamy tr Synecococ Orzya HumanMt Neurospora E.coli Strep coe 0.1 CAUCR Yeast Sch.pombe Tryptophan-tRNA Ligase haloba su1 Plasmodium sulfolobus pyroco ab pyrobac ae metsar ma haloba su2 archae fu Aeropyrum methe th metcoc ja metpyr ka Neurospora schizop Rice Human Yeast strmy co E.col thermo ac B.subtilis C.elegans synecoc CAUCR 0.1 thermot ma Aquifex chlamy tr Chlorobium MutS protein family schpom seaurchin gallus ciona arabidopsi neucra zfish mouse human drosophila saccer oryza ecoli metbar thermmar plafal celegans dictyoste halmar clotet caucre natrpha bacanthstrpne 0.1 Whole matrix rate test comparing Ornithine carbamoyl and Aspartate carbamoyl Transferases Distance OCTase Distance ACTase 1 E.coli/Salmonella; Pea/arabidopsis 2 E.coli/Haemophilis; Yeast/neurospora 3 Plants/metazoa; plants/ fungi Whole matrix rate test comparing Tryptophan synthetase and Aspartate carbamoylTransferases Distance trpA Distance ACTase I have shown that the evolution for multiple genes in the tryptophan and arginine biosynthetic pathways, as well as their tRNA ligases show unusual phylogenies. If we discard functional constraint arguments (i.e. that some kind of peculiar protein chemistry is driving their evolution) then we can offer the following interpretation: These genes “found in the three kingdoms that are not just unusually highly conserved but whose topologies, when deduced from their sequences, strongly suggest that they evolved after Archaea, Bacteria and Eukaryotes had already diversified. In other words, these universal genes appear to be younger than the taxonomic groups in which they are found today “ That is to say, there was a time when Archaea, Bacteria and Eukaryotes existed but that they lacked the amino acids arginine and tryptophan. If so, then LUCA, if it ever existed, could not have had those two amino acids. Thus the current universal distribution of arginine and tryptophan is not explained by LUCA. Once we start down this road of reasoning there is no reason why we cannot imagine the the entire genetic code evolved within multiple demes that are linked together by Horizontal gene transfer. Possible outline for the emergence of tryptophan (W) tRNA ligase by duplication and horizontal spread of tyrosine (Y) tRNA ligase ?? Archaea Ytl ?? Eukarya Ytl Ytl Ytl + Wtl ?? Bacteria Ytl Ytl Ytl + Wtl Ytl + Wtl Ytl + Wtl Xianchi Dong, Minyun Zhou, Chen Zhong1, Bei Yang, Ning Shen and Jianping Ding (2010) “Crystal structure of Pyrococcus horikoshiitryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase” Nucleic Acids Research Volume 38, . 1401-1412 “Our results raise the possibility that present day tyrosyl- and tryptophanyl-tRNA synthetases appeared after the separation of nucleated cells from eubacteria.” Darwin’s notion of the Tree of Life “There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” ― Charles Darwin, The Origin of Species
