title: Inferring the ancient history of the translation machinery and genetic code via recapitulation of ribosomal subunit assembly orders.
abstract: Universally conserved positions in ribosomal proteins have significant biases in amino acid usage, likely indicating the expansion of the genetic code at the time leading up to the most recent common ancestor(s) (MRCA). Here, we apply this principle to the evolutionary history of the ribosome before the MRCA. It has been proposed that the experimentally determined order of assembly for ribosomal subunits recapitulates their evolutionary chronology. Given this model, we produce a probabilistic evolutionary ordering of the universally conserved small subunit (SSU) and large subunit (LSU) ribosomal proteins. Optimizing the relative ordering of SSU and LSU evolutionary chronologies with respect to minimizing differences in amino acid usage bias, we find strong compositional evidence for a more ancient origin for early LSU proteins. Furthermore, we find that this ordering produces several trends in specific amino acid usages compatible with models of genetic code evolution.
authors.affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America. gregory.fournier@uconn.edu
authors.forename: Gregory P
authors.initials: GP
authors.lastname: Fournier
authors.forename: Justin E
authors.initials: JE
authors.lastname: Neumann
authors.forename: J Peter
authors.initials: JP
authors.lastname: Gogarten
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D019143:Evolution, Molecular; D005815:Genetic Code; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D014176:Protein Biosynthesis; D012269:Ribosomal Proteins / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism*; D017422:Sequence Analysis, DNA
chemical_list: D000596:Amino Acids; D012269:Ribosomal Proteins