1. Biochemistry and Chemical Biology
  2. Microbiology and Infectious Disease
Download icon

Oxidation of cellular amino acid pools leads to cytotoxic mistranslation of the genetic code

  1. Tammy Bullwinkle
  2. Noah M Reynolds
  3. Medha Raina
  4. Adil B Moghal
  5. Eleftheria Matsa
  6. Andrei Rajkovic
  7. Huseyin Kayadibi
  8. Farbod Fazlollahi
  9. Christopher Ryan
  10. Nathaniel Howitz
  11. Kym F Faull
  12. Beth Lazazzera
  13. Michael Ibba  Is a corresponding author
  1. Ohio State University, United States
  2. Adana Military Hospital, Turkey
  3. Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, United States
  4. California Department of Toxic Substances Control, United States
  5. University of California, Los Angeles, United States
Research Article
  • Cited 54
  • Views 2,659
  • Annotations
Cite this article as: eLife 2014;3:e02501 doi: 10.7554/eLife.02501

Abstract

Aminoacyl-tRNA synthetases use a variety of mechanisms to ensure fidelity of the genetic code and ultimately select the correct amino acids to be used in protein synthesis. The physiological necessity of these quality control mechanisms in different environments remains unclear, as the cost versus benefit of accurate protein synthesis is difficult to predict. We show that in Escherichia coli, a non-coded amino acid produced through oxidative damage is a significant threat to the accuracy of protein synthesis and must be cleared by phenylalanine-tRNA synthetase in order to prevent cellular toxicity caused by mis-synthesized proteins. These findings demonstrate how stress can lead to the accumulation of non-canonical amino acids that must be excluded from the proteome in order to maintain cellular viability.

Article and author information

Author details

  1. Tammy Bullwinkle

    Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Noah M Reynolds

    Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Medha Raina

    Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Adil B Moghal

    Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Eleftheria Matsa

    Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Andrei Rajkovic

    Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Huseyin Kayadibi

    Adana Military Hospital, Adana, Turkey
    Competing interests
    The authors declare that no competing interests exist.

  8. Farbod Fazlollahi

    Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Christopher Ryan

    California Department of Toxic Substances Control, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Nathaniel Howitz

    University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  11. Kym F Faull

    Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  12. Beth Lazazzera

    University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  13. Michael Ibba

    Ohio State University, Columbus, United States
    For correspondence
    ibba.1@att.net
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Gisela Storz, National Institute of Child Health and Human Development, United States

Publication history

  1. Received: February 10, 2014
  2. Accepted: May 29, 2014
  3. Accepted Manuscript published: June 2, 2014 (version 1)
  4. Version of Record published: June 24, 2014 (version 2)

Copyright

© 2014, Bullwinkle 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.

Metrics

  • 2,659
    Page views
  • 257
    Downloads
  • 54
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Categories and tags

Research organisms

Further reading

    1. Biochemistry and Chemical Biology

    Myopalladin knockout mice develop cardiac dilation and show a maladaptive response to mechanical pressure overload

    Maria Carmela Filomena et al.
    Research Article

    Myopalladin (MYPN) is a striated muscle-specific immunoglobulin domain-containing protein located in the sarcomeric Z-line and I-band. MYPN gene mutations are causative for dilated (DCM), hypertrophic and restrictive cardiomyopathy. In a yeast two-hybrid screening, MYPN was found to bind to titin in the Z-line, which was confirmed by microscale thermophoresis. Cardiac analyses of MYPN knockout (MKO) mice showed the development of mild cardiac dilation and systolic dysfunction, associated with decreased myofibrillar isometric tension generation and increased resting tension at longer sarcomere lengths. MKO mice exhibited a normal hypertrophic response to transaortic constriction (TAC), but rapidly developed severe cardiac dilation and systolic dysfunction, associated with fibrosis, increased fetal gene expression, higher intercalated disc fold amplitude, decreased calsequestrin-2 protein levels, and increased desmoplakin and SORBS2 protein levels. Cardiomyocyte analyses showed delayed Ca2+ release and reuptake in unstressed MKO mice as well as reduced Ca2+ spark amplitude post-TAC, suggesting that altered Ca2+ handling may contribute to the development of DCM in MKO mice.

    1. Biochemistry and Chemical Biology

    Witnessing the structural evolution of an RNA enzyme

    Xavier Portillo et al.
    Research Article Updated

    An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.

    1. Biochemistry and Chemical Biology

    A universal pocket in fatty acyl-AMP ligases ensures redirection of fatty acid pool away from coenzyme A-based activation

    Gajanan S Patil et al.
    Research Article Updated

    Fatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4′-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and accept holo-ACP unlike other members of the ANL superfamily remains elusive. We show that FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3′,5′-bisphosphate-containing CoA from holo-ACP and thus FAALs can distinguish between CoA and holo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organizations. The universal distribution of FAALs suggests that they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.