Myopathy-causing variants of PYROXD1 converge on impaired RNA ligation
- 1Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria.
Abstract
RNA ligation is critical for RNA processing pathways including pre-tRNA splicing. RTCB is the only essential RNA ligase in humans and the catalytic subunit of the tRNA ligase complex (tRNA-LC). Its active site is sensitive to oxidation and strictly depends on oxidoreductase PYROXD1, the only tRNA-LC subunit with multiple known pathogenic protein-coding variants. The role of RNA ligation in PYROXD1 myopathy remained contentious: loss of PYROXD1 primarily affects mitochondria, and ligation-linked readouts are inconsistent in existing assays. Here, we reveal that PYROXD1 is physically, genetically and functionally committed to the tRNA-LC. Selectively impairing RTCB activation reproduces hallmarks of PYROXD1 dysfunction, including mitochondrial deregulation. Using degron-based depletion of endogenous PYROXD1, we show that all six single amino acid variants reported in patients fail to sustain RNA ligation in proportion to their clinical severity. The variants segregate into three mechanistic classes: they lower protein stability, disrupt the NADPH-mediated conformational switch, or impair RTCB engagement by the C-terminal tail, a sequence unique to PYROXD1 and directly affected in the most severe variant D500N. Variant-level measurements in the degron model predict outcomes in homozygous and compound heterozygous patient fibroblasts. Together, these data establish impaired RNA ligation as the driver of PYROXD1 pathogenicity.
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BibTeX
@misc{guzmanperez2026myopathycausing,
title = {{Myopathy-causing variants of PYROXD1 converge on impaired RNA ligation}},
author = {S. Guzman-Perez and M. Kleinwaechter and M. S. Ozeren and A. Catharin and S. Weitzer and M. Milasinovic and M. B. Yaman and A. Gorbenkova and M. Hahn and R. Koglgruber and D. Hollenstein and J. M. Penninger and M. Hartl and S. T. Cooper and F. J. Evesson and J. Martinez and I. Asanovic},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.09.758034},
url = {https://www.biorxiv.org/content/10.64898/2026.10.09.758034v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Myopathy-causing variants of PYROXD1 converge on impaired RNA ligation
AU - S. Guzman-Perez
AU - M. Kleinwaechter
AU - M. S. Ozeren
AU - A. Catharin
AU - S. Weitzer
AU - M. Milasinovic
AU - M. B. Yaman
AU - A. Gorbenkova
AU - M. Hahn
AU - R. Koglgruber
AU - D. Hollenstein
AU - J. M. Penninger
AU - M. Hartl
AU - S. T. Cooper
AU - F. J. Evesson
AU - J. Martinez
AU - I. Asanovic
PY - 2026
DA - 2026/10/09
PB - bioRxiv
DO - 10.64898/2026.10.09.758034
UR - https://www.biorxiv.org/content/10.64898/2026.10.09.758034v1
AB - RNA ligation is critical for RNA processing pathways including pre-tRNA splicing. RTCB is the only essential RNA ligase in humans and the catalytic subunit of the tRNA ligase complex (tRNA-LC). Its active site is sensitive to oxidation and strictly depends on oxidoreductase PYROXD1, the only tRNA-LC subunit with multiple known pathogenic protein-coding variants. The role of RNA ligation in PYROXD1 myopathy remained contentious: loss of PYROXD1 primarily affects mitochondria, and ligation-linked readouts are inconsistent in existing assays. Here, we reveal that PYROXD1 is physically, genetically and functionally committed to the tRNA-LC. Selectively impairing RTCB activation reproduces hallmarks of PYROXD1 dysfunction, including mitochondrial deregulation. Using degron-based depletion of endogenous PYROXD1, we show that all six single amino acid variants reported in patients fail to sustain RNA ligation in proportion to their clinical severity. The variants segregate into three mechanistic classes: they lower protein stability, disrupt the NADPH-mediated conformational switch, or impair RTCB engagement by the C-terminal tail, a sequence unique to PYROXD1 and directly affected in the most severe variant D500N. Variant-level measurements in the degron model predict outcomes in homozygous and compound heterozygous patient fibroblasts. Together, these data establish impaired RNA ligation as the driver of PYROXD1 pathogenicity.
ER -