title: Statistical evaluation of the Rodin-Ohno hypothesis: sense/antisense coding of ancestral class I and II aminoacyl-tRNA synthetases.
abstract: We tested the idea that ancestral class I and II aminoacyl-tRNA synthetases arose on opposite strands of the same gene. We assembled excerpted 94-residue Urgenes for class I tryptophanyl-tRNA synthetase (TrpRS) and class II Histidyl-tRNA synthetase (HisRS) from a diverse group of species, by identifying and catenating three blocks coding for secondary structures that position the most highly conserved, active-site residues. The codon middle-base pairing frequency was 0.35 ± 0.0002 in all-by-all sense/antisense alignments for 211 TrpRS and 207 HisRS sequences, compared with frequencies between 0.22 ± 0.0009 and 0.27 ± 0.0005 for eight different representations of the null hypothesis. Clustering algorithms demonstrate further that profiles of middle-base pairing in the synthetase antisense alignments are correlated along the sequences from one species-pair to another, whereas this is not the case for similar operations on sets representing the null hypothesis. Most probable reconstructed sequences for ancestral nodes of maximum likelihood trees show that middle-base pairing frequency increases to approximately 0.42 ± 0.002 as bacterial trees approach their roots; ancestral nodes from trees including archaeal sequences show a less pronounced increase. Thus, contemporary and reconstructed sequences all validate important bioinformatic predictions based on descent from opposite strands of the same ancestral gene. They further provide novel evidence for the hypothesis that bacteria lie closer than archaea to the origin of translation. Moreover, the inverse polarity of genetic coding, together with a priori α-helix propensities suggest that in-frame coding on opposite strands leads to similar secondary structures with opposite polarity, as observed in TrpRS and HisRS crystal structures.
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, USA.
authors.forename: Srinivas Niranj
authors.initials: SN
authors.lastname: Chandrasekaran
authors.forename: Galip Gürkan
authors.initials: GG
authors.lastname: Yardimci
authors.forename: Ozgün
authors.initials: O
authors.lastname: Erdogan
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Roach
authors.forename: Charles W
authors.initials: CW
authors.lastname: Carter
mesh_terms: D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics*; D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D020134:Catalytic Domain; D003062:Codon; D019143:Evolution, Molecular; D006643:Histidine-tRNA Ligase / Q000235:genetics*; D017433:Protein Structure, Secondary; D014369:Tryptophan-tRNA Ligase / Q000235:genetics*
chemical_list: D003062:Codon; D000604:Amino Acyl-tRNA Synthetases; D014369:Tryptophan-tRNA Ligase; D006643:Histidine-tRNA Ligase
keywords: aminoacyl-tRNA synthetases; ancestral gene reconstruction; multiple sequence alignment; multiple structure alignment; origin of translation; protein modularity; sense/antisense double open reading frames