Cellular and Molecular Life Sciences

, Volume 74, Issue 14, pp 2663–2677 | Cite as

Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase

  • Yi-Hsueh Lee
  • Chia-Pei Chang
  • Yu-Ju Cheng
  • Yi-Yi Kuo
  • Yeong-Shin Lin
  • Chien-Chia Wang
Original Article


The discriminator base N73 is a key identity element of tRNAHis. In eukaryotes, N73 is an “A” in cytoplasmic tRNAHis and a “C” in mitochondrial tRNAHis. We present evidence herein that yeast histidyl-tRNA synthetase (HisRS) recognizes both A73 and C73, but somewhat prefers A73 even within the context of mitochondrial tRNAHis. In contrast, humans possess two distinct yet closely related HisRS homologues, with one encoding the cytoplasmic form (with an extra N-terminal WHEP domain) and the other encoding its mitochondrial counterpart (with an extra N-terminal mitochondrial targeting signal). Despite these two isoforms sharing high sequence similarities (81% identity), they strongly preferred different discriminator bases (A73 or C73). Moreover, only the mitochondrial form recognized the anticodon as a strong identity element. Most intriguingly, swapping the discriminator base between the cytoplasmic and mitochondrial tRNAHis isoacceptors conveniently switched their enzyme preferences. Similarly, swapping seven residues in the active site between the two isoforms readily switched their N73 preferences. This study suggests that the human HisRS genes, while descending from a common ancestor with dual function for both types of tRNAHis, have acquired highly specialized tRNA recognition properties through evolution.


Aminoacyl-tRNA synthetase Evolution Phylogenetic analysis Protein synthesis Subfunctionalization tRNA 



Aminoacyl-tRNA synthetase


Complementary DNA




5-Fluoroorotic acid


Green fluorescence protein


Histidyl-tRNA synthetase


Mitochondrial targeting signal


Open-reading frame


Polymerase chain reaction


Phosphoglycerate kinase


tRNAHis guanylyltransferase




Yeast extract peptone glycerol.



This work was supported by Grants MOST 103-2311-B-008-003-MY3, MOST 103-2923-B-008-001-MY3, and NSC 102-2311-B-008-004-MY3 (to C.C.W.) from the Ministry of Science and Technology (Taipei, Taiwan).

Supplementary material

18_2017_2491_MOESM1_ESM.phylip (132 kb)
Supplementary material 1 (PHYLIP 131 KB)


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Copyright information

© Springer International Publishing 2017

Authors and Affiliations

  • Yi-Hsueh Lee
    • 1
  • Chia-Pei Chang
    • 1
  • Yu-Ju Cheng
    • 1
  • Yi-Yi Kuo
    • 1
  • Yeong-Shin Lin
    • 2
  • Chien-Chia Wang
    • 1
  1. 1.Department of Life SciencesNational Central UniversityTaoyuanTaiwan
  2. 2.Institute of Bioinformatics and Systems BiologyNational Chiao Tung UniversityHsinchuTaiwan

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