Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS

Abstract

Strict L-chiral rejection through Gly-cisPro motif during chiral proofreading underlies inability of D-aminoacyl-tRNA deacylase (DTD) to discriminate between D-amino acids and achiral glycine. The consequent Gly-tRNAGly 'misediting paradox' is resolved by EF-Tu in the cell. Here, we show that DTD’s active site architecture can efficiently edit mischarged Gly-tRNAAla species four orders of magnitude more efficiently than even AlaRS, the only ubiquitous cellular checkpoint known for clearing the error. Also, DTD knockout in AlaRS editing-defective background causes pronounced toxicity in Escherichia coli even at low glycine levels which is alleviated by alanine supplementation. We further demonstrate that DTD positively selects the universally invariant tRNAAla-specific G3•U70. Moreover, DTD’s activity on non-cognate Gly-tRNAAla is conserved across all bacteria and eukaryotes, suggesting DTD’s key cellular role as a glycine deacylator. Our study thus reveals a hitherto unknown function of DTD in cracking the universal mechanistic dilemma encountered by AlaRS, and its physiological importance.

Article and author information

Author details

  1. Komal Ishwar Pawar

    CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    The authors declare that no competing interests exist.
  2. Katta Suma

    CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    The authors declare that no competing interests exist.
  3. Ayshwarya Seenivasan

    CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    The authors declare that no competing interests exist.
  4. Santosh Kumar Kuncha

    CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    The authors declare that no competing interests exist.
  5. Satya Brata Routh

    CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    The authors declare that no competing interests exist.
  6. Shobha P Kruparani

    CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    The authors declare that no competing interests exist.
  7. Rajan Sankaranarayanan

    CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
    For correspondence
    sankar@ccmb.res.in
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4524-9953

Funding

Council of Scientific and Industrial Research (12th Five Year Plan Project BSC0113)

  • Rajan Sankaranarayanan

Science and Engineering Research Board (JC Bose Fellowship)

  • Rajan Sankaranarayanan

Department of Biotechnology , Ministry of Science and Technology (Centre of Excellence)

  • Rajan Sankaranarayanan

Council of Scientific and Industrial Research (Research Fellowship)

  • Komal Ishwar Pawar
  • Satya Brata Routh

Department of Biotechnology , Ministry of Science and Technology (Research Associateship)

  • Katta Suma

Department of Biotechnology , Ministry of Science and Technology (INSPIRE Fellowship)

  • Santosh Kumar Kuncha

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Jonathan P Staley, University of Chicago, United States

Publication history

  1. Received: December 6, 2016
  2. Accepted: March 30, 2017
  3. Accepted Manuscript published: March 31, 2017 (version 1)
  4. Version of Record published: April 28, 2017 (version 2)

Copyright

© 2017, Pawar et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Komal Ishwar Pawar
  2. Katta Suma
  3. Ayshwarya Seenivasan
  4. Santosh Kumar Kuncha
  5. Satya Brata Routh
  6. Shobha P Kruparani
  7. Rajan Sankaranarayanan
(2017)
Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS
eLife 6:e24001.
https://doi.org/10.7554/eLife.24001

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