The oxidoreductase PYROXD1 uses NAD(P)+ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response

Igor Asanović; Emilia Strandback; Alena Kroupova; Djurdja Pasajlic; Anton Meinhart; Pai Tsung-Pin; Nemanja Djokovic; Dorothea Anrather; Thomas Schuetz; Marcin Józef Suskiewicz; Sirelin Sillamaa; Thomas Köcher; Rebecca Beveridge; Katarina Nikolic; Alexander Schleiffer; Martin Jinek; Markus Hartl; Tim Clausen; Josef Penninger; Peter Macheroux; Stefan Weitzer; Javier Martinez

doi:10.1016/j.molcel.2021.04.007

The oxidoreductase PYROXD1 uses NAD(P)⁺ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response

Igor Asanović, Emilia Strandback, Alena Kroupova, Djurdja Pasajlic, Anton Meinhart, Pai Tsung-Pin, Nemanja Djokovic, Dorothea Anrather, Thomas Schuetz, Marcin Józef Suskiewicz, Sirelin Sillamaa, Thomas Köcher, Rebecca Beveridge, Katarina Nikolic, Alexander Schleiffer, Martin Jinek, Markus Hartl, Tim Clausen, Josef Penninger, Peter MacherouxStefan Weitzer^*, Javier Martinez

^*Corresponding author for this work

Pure And Applied Chemistry

Research output: Contribution to journal › Article › peer-review

23 Citations (Scopus)

Abstract

The tRNA ligase complex (tRNA-LC) splices precursor tRNAs (pre-tRNA), and Xbp1-mRNA during the unfolded protein response (UPR). In aerobic conditions, a cysteine residue bound to two metal ions in its ancient, catalytic subunit RTCB could make the tRNA-LC susceptible to oxidative inactivation. Here, we confirm this hypothesis and reveal a co-evolutionary association between the tRNA-LC and PYROXD1, a conserved and essential oxidoreductase. We reveal that PYROXD1 preserves the activity of the mammalian tRNA-LC in pre-tRNA splicing and UPR. PYROXD1 binds the tRNA-LC in the presence of NAD(P)H and converts RTCB-bound NAD(P)H into NAD(P)⁺, a typical oxidative co-enzyme. However, NAD(P)⁺ here acts as an antioxidant and protects the tRNA-LC from oxidative inactivation, which is dependent on copper ions. Genetic variants of PYROXD1 that cause human myopathies only partially support tRNA-LC activity. Thus, we establish the tRNA-LC as an oxidation-sensitive metalloenzyme, safeguarded by the flavoprotein PYROXD1 through an unexpected redox mechanism.

Original language	English
Pages (from-to)	2520-2532.e16
Journal	Molecular Cell
Volume	81
Issue number	12
Early online date	29 Apr 2021
DOIs	https://doi.org/10.1016/j.molcel.2021.04.007
Publication status	Published - 17 Jun 2021

Funding

We thank Dhaarsini Koneswarakantha for help and advice, Johannes Popow for experimental suggestions, Sandra Cooper for fruitful discussions, and Life Science Editors for counseling in the writing of the manuscript. We also thank Andrzej Bylicki and Juliane Kley for advice and assistance in the initial crystallization trials, Karin Koch for advice and assistance in the initial pre-steady-state measurements, and Paola Hentges Pinto for assistance in the initial cloning of PYROXD1 for the overexpression in human cells. We want to express gratitude to Michael Riedelberger for advice on metal-ion related experiments. Furthermore, we thank Jutta Dammann, Daniela Zwolanek, Fabian Ackle, and Alessia Duerst for assistance in the purification of recombinant proteins. We also thank staff of beamlines at ESRF (Grenoble) for help during data collection. Work at the Martinez lab was funded by the Medical University of Vienna , the “ Fonds zur Förderung der wissenschaftlichen Forschung (FWF) ” as Stand-Alone Projects (P29888 and P32011) and through the RNA Biology Doctoral Program . I.A. and A.K. are funded by the Boehringer Ingelheim Fonds PhD Fellowship . Numerical simulations were run on the PARADOX-IV supercomputing facility at the Scientific Computing Laboratory, National Center of Excellence for the Study of Complex Systems, Institute of Physics Belgrade, supported in part by the Ministry of Education, Science and Technological Development of the Republic of Serbia . N.D. and K.N. acknowledge Ministry of Science and Technological Development of the Republic of Serbia contract no. 451-03-68/2020-14/200161 .

Keywords

copper
metalloenzyme
myopathy
NADH
NADPH
oxidative stress
oxidoreductase
pre-tRNA splicing
PYROXD1
RtcB
tRNA ligase complex
UPR

Access to Document

10.1016/j.molcel.2021.04.007

Cite this

Asanović, I., Strandback, E., Kroupova, A., Pasajlic, D., Meinhart, A., Tsung-Pin, P., Djokovic, N., Anrather, D., Schuetz, T., Suskiewicz, M. J., Sillamaa, S., Köcher, T., Beveridge, R., Nikolic, K., Schleiffer, A., Jinek, M., Hartl, M., Clausen, T., Penninger, J., ... Martinez, J. (2021). The oxidoreductase PYROXD1 uses NAD(P)⁺ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response. Molecular Cell, 81(12), 2520-2532.e16. https://doi.org/10.1016/j.molcel.2021.04.007

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title = "The oxidoreductase PYROXD1 uses NAD(P)+ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response",

abstract = "The tRNA ligase complex (tRNA-LC) splices precursor tRNAs (pre-tRNA), and Xbp1-mRNA during the unfolded protein response (UPR). In aerobic conditions, a cysteine residue bound to two metal ions in its ancient, catalytic subunit RTCB could make the tRNA-LC susceptible to oxidative inactivation. Here, we confirm this hypothesis and reveal a co-evolutionary association between the tRNA-LC and PYROXD1, a conserved and essential oxidoreductase. We reveal that PYROXD1 preserves the activity of the mammalian tRNA-LC in pre-tRNA splicing and UPR. PYROXD1 binds the tRNA-LC in the presence of NAD(P)H and converts RTCB-bound NAD(P)H into NAD(P)+, a typical oxidative co-enzyme. However, NAD(P)+ here acts as an antioxidant and protects the tRNA-LC from oxidative inactivation, which is dependent on copper ions. Genetic variants of PYROXD1 that cause human myopathies only partially support tRNA-LC activity. Thus, we establish the tRNA-LC as an oxidation-sensitive metalloenzyme, safeguarded by the flavoprotein PYROXD1 through an unexpected redox mechanism.",

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Asanović, I, Strandback, E, Kroupova, A, Pasajlic, D, Meinhart, A, Tsung-Pin, P, Djokovic, N, Anrather, D, Schuetz, T, Suskiewicz, MJ, Sillamaa, S, Köcher, T, Beveridge, R, Nikolic, K, Schleiffer, A, Jinek, M, Hartl, M, Clausen, T, Penninger, J, Macheroux, P, Weitzer, S & Martinez, J 2021, 'The oxidoreductase PYROXD1 uses NAD(P)⁺ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response', Molecular Cell, vol. 81, no. 12, pp. 2520-2532.e16. https://doi.org/10.1016/j.molcel.2021.04.007

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T1 - The oxidoreductase PYROXD1 uses NAD(P)+ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response

AU - Asanović, Igor

AU - Strandback, Emilia

AU - Kroupova, Alena

AU - Pasajlic, Djurdja

AU - Meinhart, Anton

AU - Tsung-Pin, Pai

AU - Djokovic, Nemanja

AU - Anrather, Dorothea

AU - Schuetz, Thomas

AU - Suskiewicz, Marcin Józef

AU - Sillamaa, Sirelin

AU - Köcher, Thomas

AU - Beveridge, Rebecca

AU - Nikolic, Katarina

AU - Schleiffer, Alexander

AU - Jinek, Martin

AU - Hartl, Markus

AU - Clausen, Tim

AU - Penninger, Josef

AU - Macheroux, Peter

AU - Weitzer, Stefan

AU - Martinez, Javier

PY - 2021/6/17

Y1 - 2021/6/17

N2 - The tRNA ligase complex (tRNA-LC) splices precursor tRNAs (pre-tRNA), and Xbp1-mRNA during the unfolded protein response (UPR). In aerobic conditions, a cysteine residue bound to two metal ions in its ancient, catalytic subunit RTCB could make the tRNA-LC susceptible to oxidative inactivation. Here, we confirm this hypothesis and reveal a co-evolutionary association between the tRNA-LC and PYROXD1, a conserved and essential oxidoreductase. We reveal that PYROXD1 preserves the activity of the mammalian tRNA-LC in pre-tRNA splicing and UPR. PYROXD1 binds the tRNA-LC in the presence of NAD(P)H and converts RTCB-bound NAD(P)H into NAD(P)+, a typical oxidative co-enzyme. However, NAD(P)+ here acts as an antioxidant and protects the tRNA-LC from oxidative inactivation, which is dependent on copper ions. Genetic variants of PYROXD1 that cause human myopathies only partially support tRNA-LC activity. Thus, we establish the tRNA-LC as an oxidation-sensitive metalloenzyme, safeguarded by the flavoprotein PYROXD1 through an unexpected redox mechanism.

AB - The tRNA ligase complex (tRNA-LC) splices precursor tRNAs (pre-tRNA), and Xbp1-mRNA during the unfolded protein response (UPR). In aerobic conditions, a cysteine residue bound to two metal ions in its ancient, catalytic subunit RTCB could make the tRNA-LC susceptible to oxidative inactivation. Here, we confirm this hypothesis and reveal a co-evolutionary association between the tRNA-LC and PYROXD1, a conserved and essential oxidoreductase. We reveal that PYROXD1 preserves the activity of the mammalian tRNA-LC in pre-tRNA splicing and UPR. PYROXD1 binds the tRNA-LC in the presence of NAD(P)H and converts RTCB-bound NAD(P)H into NAD(P)+, a typical oxidative co-enzyme. However, NAD(P)+ here acts as an antioxidant and protects the tRNA-LC from oxidative inactivation, which is dependent on copper ions. Genetic variants of PYROXD1 that cause human myopathies only partially support tRNA-LC activity. Thus, we establish the tRNA-LC as an oxidation-sensitive metalloenzyme, safeguarded by the flavoprotein PYROXD1 through an unexpected redox mechanism.

KW - copper

KW - metalloenzyme

KW - myopathy

KW - NADH

KW - NADPH

KW - oxidative stress

KW - oxidoreductase

KW - pre-tRNA splicing

KW - PYROXD1

KW - RtcB

KW - tRNA ligase complex

KW - UPR

U2 - 10.1016/j.molcel.2021.04.007

DO - 10.1016/j.molcel.2021.04.007

M3 - Article

C2 - 33930333

AN - SCOPUS:85107908607

SN - 1097-2765

VL - 81

SP - 2520-2532.e16

JO - Molecular Cell

JF - Molecular Cell

IS - 12

ER -