title: Phylogeny of genetic codes and punctuation codes within genetic codes.
abstract: Punctuation codons (starts, stops) delimit genes, reflect translation apparatus properties. Most codon reassignments involve punctuation. Here two complementary approaches classify natural genetic codes: (A) properties of amino acids assigned to codons (classical phylogeny), coding stops as X (A1, antitermination/suppressor tRNAs insert unknown residues), or as gaps (A2, no translation, classical stop); and (B) considering only punctuation status (start, stop and other codons coded as -1, 0 and 1 (B1); 0, -1 and 1 (B2, reflects ribosomal translational dynamics); and 1, -1, and 0 (B3, starts/stops as opposites)). All methods separate most mitochondrial codes from most nuclear codes; Gracilibacteria consistently cluster with metazoan mitochondria; mitochondria co-hosted with chloroplasts cluster with nuclear codes. Method A1 clusters the euplotid nuclear code with metazoan mitochondria; A2 separates euplotids from mitochondria. Firmicute bacteria Mycoplasma/Spiroplasma and Protozoan (and lower metazoan) mitochondria share codon-amino acid assignments. A1 clusters them with mitochondria, they cluster with the standard genetic code under A2: constraints on amino acid ambiguity versus punctuation-signaling produced the mitochondrial versus bacterial versions of this genetic code. Punctuation analysis B2 converges best with classical phylogenetic analyses, stressing the need for a unified theory of genetic code punctuation accounting for ribosomal constraints.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, Université de la Méditerranée, Marseille, France. Electronic address: varanuseremius@gmail.com.
authors.forename: Hervé
authors.initials: H
authors.lastname: Seligmann
mesh_terms: D000596:Amino Acids; D000818:Animals; D001419:Bacteria / Q000235:genetics; D018387:Codon, Initiator; D018388:Codon, Terminator; D018965:Frameshifting, Ribosomal; D005815:Genetic Code; D006801:Humans; D008928:Mitochondria; D010802:Phylogeny; D025341:Principal Component Analysis; D012343:RNA, Transfer
chemical_list: D000596:Amino Acids; D018387:Codon, Initiator; D018388:Codon, Terminator; D012343:RNA, Transfer
keywords: Circular code; Coding frame retrieval; Initiation codon; Natural circular code; Off frame stops; Principal component analyses; Ribosomal frameshift; Termination codon