Next Article in Journal
Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates
Next Article in Special Issue
Future of the Genetic Code
Previous Article in Journal / Special Issue
On the Uniqueness of the Standard Genetic Code
Article Menu

Export Article

Open AccessArticle

Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Department of Chemistry, Yale University, New Haven, CT 06520, USA
Author to whom correspondence should be addressed.
Academic Editor: Koji Tamura
Received: 16 January 2017 / Revised: 15 February 2017 / Accepted: 17 February 2017 / Published: 21 February 2017
Full-Text   |   PDF [2238 KB, uploaded 21 February 2017]   |  


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 tRNATyr and tRNATrp genes 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. View Full-Text
Keywords: tRNA; aaRS; genetic code; evolution; lateral gene transfer tRNA; aaRS; genetic code; evolution; lateral gene transfer

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Share & Cite This Article

MDPI and ACS Style

Mukai, T.; Reynolds, N.M.; Crnković, A.; Söll, D. Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria. Life 2017, 7, 8.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Life EISSN 2075-1729 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top