Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy

Christoph Loenarz, Rok Sekirnik, Armin Thalhammer, Wei Ge, Ekaterina Spivakovsky, Muhammad Mukram Mohamed Mackeen, Michael A. McDonough, Matthew E. Cockman, Benedikt M. Kessler, Peter J. Ratcliffe, Alexander Wolf, Christopher J. Schofield

Research output: Contribution to journalArticle

59 Citations (Scopus)

Abstract

The mechanisms by which gene expression is regulated by oxygen are of considerable interest from basic science and therapeutic perspectives. Using mass spectrometric analyses of Saccharomyces cerevisiae ribosomes, we found that the amino acid residue in closest proximity to the decoding center, Pro-64 of the 40S subunit ribosomal protein Rps23p (RPS23 Pro-62 in humans) undergoes posttranslational hydroxylation. We identify RPS23 hydroxylases as a highly conserved eukaryotic subfamily of Fe(II) and 2-oxoglutarate dependent oxygenases; their catalytic domain is closely related to transcription factor prolyl trans-4-hydroxylases that act as oxygen sensors in the hypoxic response in animals. The RPS23 hydroxylases in S. cerevisiae (Tpa1p), Schizosaccharomyces pombe and green algae catalyze an unprecedented dihydroxylation modification. This observation contrasts with higher eukaryotes, where RPS23 is monohydroxylated; the human Tpa1p homolog OGFOD1 catalyzes prolyl trans-3-hydroxylation. TPA1 deletion modulates termination efficiency up to ̃10-fold, including of pathophysiologically relevant sequences; we reveal Rps23p hydroxylation as its molecular basis. In contrast to most previously characterized accuracy modulators, including antibiotics and the prion state of the S. cerevisiae translation termination factor eRF3, Rps23p hydroxylation can either increase or decrease translational accuracy in a stop codon context-dependent manner. We identify conditions where Rps23p hydroxylation status determines viability as a consequence of nonsense codon suppression. The results reveal a direct link between oxygenase catalysis and the regulation of gene expression at the translational level. They will also aid in the development of small molecules altering translational accuracy for the treatment of genetic diseases linked to nonsense mutations.

Original languageEnglish
Pages (from-to)4019-4024
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume111
Issue number11
DOIs
Publication statusPublished - 18 Mar 2014

Fingerprint

Hydroxylation
Saccharomyces cerevisiae
Oxygenases
Nonsense Codon
Mixed Function Oxygenases
Oxygen
Prolyl Hydroxylases
Inborn Genetic Diseases
Chlorophyta
Schizosaccharomyces
Terminator Codon
Prions
Ribosomal Proteins
Gene Expression Regulation
Eukaryota
Catalysis
Ribosomes
Catalytic Domain
Transcription Factors
Anti-Bacterial Agents

Keywords

  • 2-oxoglutarate oxygenase
  • Hypoxia
  • Nonsense readthrough
  • Ribosomal hydroxylation
  • Translation

ASJC Scopus subject areas

  • General

Cite this

Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy. / Loenarz, Christoph; Sekirnik, Rok; Thalhammer, Armin; Ge, Wei; Spivakovsky, Ekaterina; Mohamed Mackeen, Muhammad Mukram; McDonough, Michael A.; Cockman, Matthew E.; Kessler, Benedikt M.; Ratcliffe, Peter J.; Wolf, Alexander; Schofield, Christopher J.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, No. 11, 18.03.2014, p. 4019-4024.

Research output: Contribution to journalArticle

Loenarz, C, Sekirnik, R, Thalhammer, A, Ge, W, Spivakovsky, E, Mohamed Mackeen, MM, McDonough, MA, Cockman, ME, Kessler, BM, Ratcliffe, PJ, Wolf, A & Schofield, CJ 2014, 'Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy', Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 11, pp. 4019-4024. https://doi.org/10.1073/pnas.1311750111
Loenarz, Christoph ; Sekirnik, Rok ; Thalhammer, Armin ; Ge, Wei ; Spivakovsky, Ekaterina ; Mohamed Mackeen, Muhammad Mukram ; McDonough, Michael A. ; Cockman, Matthew E. ; Kessler, Benedikt M. ; Ratcliffe, Peter J. ; Wolf, Alexander ; Schofield, Christopher J. / Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy. In: Proceedings of the National Academy of Sciences of the United States of America. 2014 ; Vol. 111, No. 11. pp. 4019-4024.
@article{60fb8f34c785484e8950821188090185,
title = "Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy",
abstract = "The mechanisms by which gene expression is regulated by oxygen are of considerable interest from basic science and therapeutic perspectives. Using mass spectrometric analyses of Saccharomyces cerevisiae ribosomes, we found that the amino acid residue in closest proximity to the decoding center, Pro-64 of the 40S subunit ribosomal protein Rps23p (RPS23 Pro-62 in humans) undergoes posttranslational hydroxylation. We identify RPS23 hydroxylases as a highly conserved eukaryotic subfamily of Fe(II) and 2-oxoglutarate dependent oxygenases; their catalytic domain is closely related to transcription factor prolyl trans-4-hydroxylases that act as oxygen sensors in the hypoxic response in animals. The RPS23 hydroxylases in S. cerevisiae (Tpa1p), Schizosaccharomyces pombe and green algae catalyze an unprecedented dihydroxylation modification. This observation contrasts with higher eukaryotes, where RPS23 is monohydroxylated; the human Tpa1p homolog OGFOD1 catalyzes prolyl trans-3-hydroxylation. TPA1 deletion modulates termination efficiency up to ̃10-fold, including of pathophysiologically relevant sequences; we reveal Rps23p hydroxylation as its molecular basis. In contrast to most previously characterized accuracy modulators, including antibiotics and the prion state of the S. cerevisiae translation termination factor eRF3, Rps23p hydroxylation can either increase or decrease translational accuracy in a stop codon context-dependent manner. We identify conditions where Rps23p hydroxylation status determines viability as a consequence of nonsense codon suppression. The results reveal a direct link between oxygenase catalysis and the regulation of gene expression at the translational level. They will also aid in the development of small molecules altering translational accuracy for the treatment of genetic diseases linked to nonsense mutations.",
keywords = "2-oxoglutarate oxygenase, Hypoxia, Nonsense readthrough, Ribosomal hydroxylation, Translation",
author = "Christoph Loenarz and Rok Sekirnik and Armin Thalhammer and Wei Ge and Ekaterina Spivakovsky and {Mohamed Mackeen}, {Muhammad Mukram} and McDonough, {Michael A.} and Cockman, {Matthew E.} and Kessler, {Benedikt M.} and Ratcliffe, {Peter J.} and Alexander Wolf and Schofield, {Christopher J.}",
year = "2014",
month = "3",
day = "18",
doi = "10.1073/pnas.1311750111",
language = "English",
volume = "111",
pages = "4019--4024",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "11",

}

TY - JOUR

T1 - Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy

AU - Loenarz, Christoph

AU - Sekirnik, Rok

AU - Thalhammer, Armin

AU - Ge, Wei

AU - Spivakovsky, Ekaterina

AU - Mohamed Mackeen, Muhammad Mukram

AU - McDonough, Michael A.

AU - Cockman, Matthew E.

AU - Kessler, Benedikt M.

AU - Ratcliffe, Peter J.

AU - Wolf, Alexander

AU - Schofield, Christopher J.

PY - 2014/3/18

Y1 - 2014/3/18

N2 - The mechanisms by which gene expression is regulated by oxygen are of considerable interest from basic science and therapeutic perspectives. Using mass spectrometric analyses of Saccharomyces cerevisiae ribosomes, we found that the amino acid residue in closest proximity to the decoding center, Pro-64 of the 40S subunit ribosomal protein Rps23p (RPS23 Pro-62 in humans) undergoes posttranslational hydroxylation. We identify RPS23 hydroxylases as a highly conserved eukaryotic subfamily of Fe(II) and 2-oxoglutarate dependent oxygenases; their catalytic domain is closely related to transcription factor prolyl trans-4-hydroxylases that act as oxygen sensors in the hypoxic response in animals. The RPS23 hydroxylases in S. cerevisiae (Tpa1p), Schizosaccharomyces pombe and green algae catalyze an unprecedented dihydroxylation modification. This observation contrasts with higher eukaryotes, where RPS23 is monohydroxylated; the human Tpa1p homolog OGFOD1 catalyzes prolyl trans-3-hydroxylation. TPA1 deletion modulates termination efficiency up to ̃10-fold, including of pathophysiologically relevant sequences; we reveal Rps23p hydroxylation as its molecular basis. In contrast to most previously characterized accuracy modulators, including antibiotics and the prion state of the S. cerevisiae translation termination factor eRF3, Rps23p hydroxylation can either increase or decrease translational accuracy in a stop codon context-dependent manner. We identify conditions where Rps23p hydroxylation status determines viability as a consequence of nonsense codon suppression. The results reveal a direct link between oxygenase catalysis and the regulation of gene expression at the translational level. They will also aid in the development of small molecules altering translational accuracy for the treatment of genetic diseases linked to nonsense mutations.

AB - The mechanisms by which gene expression is regulated by oxygen are of considerable interest from basic science and therapeutic perspectives. Using mass spectrometric analyses of Saccharomyces cerevisiae ribosomes, we found that the amino acid residue in closest proximity to the decoding center, Pro-64 of the 40S subunit ribosomal protein Rps23p (RPS23 Pro-62 in humans) undergoes posttranslational hydroxylation. We identify RPS23 hydroxylases as a highly conserved eukaryotic subfamily of Fe(II) and 2-oxoglutarate dependent oxygenases; their catalytic domain is closely related to transcription factor prolyl trans-4-hydroxylases that act as oxygen sensors in the hypoxic response in animals. The RPS23 hydroxylases in S. cerevisiae (Tpa1p), Schizosaccharomyces pombe and green algae catalyze an unprecedented dihydroxylation modification. This observation contrasts with higher eukaryotes, where RPS23 is monohydroxylated; the human Tpa1p homolog OGFOD1 catalyzes prolyl trans-3-hydroxylation. TPA1 deletion modulates termination efficiency up to ̃10-fold, including of pathophysiologically relevant sequences; we reveal Rps23p hydroxylation as its molecular basis. In contrast to most previously characterized accuracy modulators, including antibiotics and the prion state of the S. cerevisiae translation termination factor eRF3, Rps23p hydroxylation can either increase or decrease translational accuracy in a stop codon context-dependent manner. We identify conditions where Rps23p hydroxylation status determines viability as a consequence of nonsense codon suppression. The results reveal a direct link between oxygenase catalysis and the regulation of gene expression at the translational level. They will also aid in the development of small molecules altering translational accuracy for the treatment of genetic diseases linked to nonsense mutations.

KW - 2-oxoglutarate oxygenase

KW - Hypoxia

KW - Nonsense readthrough

KW - Ribosomal hydroxylation

KW - Translation

UR - http://www.scopus.com/inward/record.url?scp=84896519650&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84896519650&partnerID=8YFLogxK

U2 - 10.1073/pnas.1311750111

DO - 10.1073/pnas.1311750111

M3 - Article

VL - 111

SP - 4019

EP - 4024

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 11

ER -