title: Bioinformatic Analysis Reveals Archaeal tRNATyrand tRNATrpIdentities in Bacteria.
abstract: The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNATyrand tRNATrpgenes reveal bacterial or archaeal origins. We identified a trace of domain fusion and swapping in the archaeal-type TyrRS gene of a bacterial lineage, suggesting that CPR bacteria may have used this mechanism to create diverse proteins. Archaeal-type TrpRS of bacteria and a few TrpRS species of DPANN archaea represent a new phylogenetic clade (named TrpRS-A). The TrpRS-A open reading frames (ORFs) are always associated with another ORF (named ORF1) encoding an unknown protein without global sequence identity to any known protein. However, our protein structure prediction identified a putative HIGH-motif and KMSKS-motif as well as many α-helices that are characteristic of class I aminoacyl-tRNA synthetase (aaRS) homologs. These results provide another example of the diversity of molecular components that implement the genetic code and provide a clue to the early evolution of life and the genetic code.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. takahito.mukai@yale.edu.
authors.forename: Takahito
authors.initials: T
authors.lastname: Mukai
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. noah.reynolds@yale.edu.
authors.forename: Noah M
authors.initials: NM
authors.lastname: Reynolds
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. ana.crnkovic@yale.edu.
authors.forename: Ana
authors.initials: A
authors.lastname: Crnković
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. dieter.soll@yale.edu.|Department of Chemistry, Yale University, New Haven, CT 06520, USA. dieter.soll@yale.edu.
authors.forename: Dieter
authors.initials: D
authors.lastname: Söll
keywords: aaRS; evolution; genetic code; lateral gene transfer; tRNA