Impact of the POLRMT inhibitor IMT1B on mitochondrial genome copy number in Caenorhabditis elegans
Data files
Feb 27, 2025 version files 44.42 KB
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POLRMT_alignment_clustalw.aln
26.83 KB
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README.md
1.66 KB
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Summary_qPCR_all___test_deltaCt.xlsx
15.93 KB
Abstract
POLRMT is the dedicated mitochondrial RNA polymerase in metazoans and is essential for priming mitochondrial DNA (mtDNA) synthesis. Aberrant POLRMT causes mitochondrial dysfunction and has previously been linked to human metabolic disease. The small molecule IMT1B is an allosteric inhibitor of POLRMT, and its use in diverse model organisms is informative about various aspects of mtDNA synthesis and transcription. Previously, this drug has been shown to be effective in perturbing mtDNA gene expression in human cells and mice. Moreover, a leucine to phenylalanine substitution at position 813 of human POLRMT is predicted to disrupt interaction with the drug. However, the effect of the F813L mutation on the efficacy of POLRMT inhibition (POLRMTi) has not been rigorously tested. Here, we determined by multiple sequence alignment and phylogenetic analysis that this mutation in POLRMT is common among invertebrates, including the model nematode Caenorhabditis elegans. AlphaFold analyses of metazoan POLRMT folding suggest that the F813L substitution alters the physicochemical features of the IMT1B binding pocket. Finally, we find that IMT1B treatment of larval Caenorhabditis elegans has little impact on mtDNA copy number, suggesting that POLRMTi via IMT1B may not be effective in this model organism.
https://doi.org/10.5061/dryad.dfn2z35cf
Corresponding investigator:
Samantha Lewis
University of California, Berkeley
Co-Investigators:
Eve Kakudji, M.S.
University of California, Berkeley
Description of the data and file structure
This dataset contains raw data, protocols, and analysis used to produce figures and conclusions associated with a poster presented at the American Society of Cell Biology conference in December 2024.
Multiple sequence alignments are provided as clustalw .aln files that can be opened in MEGA.
Quantitative PCR data is provided as an Excel file.
All other files are in Supplemental Information. Detailed description of the analysis methodology can be found in the Supplemental Information file ‘Methods_details_Kakudji.docx’. Inputs to AlphaFold used to produce the structure comparisons between POLRMT/polrmt-1 across metazoan are provided in the Supplemental Information file ‘Comparison of POLRMT structures via AlphaFold.docx’. The relevant poster is provided as a PDF.
File: POLRMT alignment clustalw.aln
Description: Aligned protein sequences.
File: Summary qPCR all
Description: Compiled mtDNA qPCR data from 3 replicates and mtDNA copy number calculations.
Sheet1: Calculation of absolute mtDNA copy number per cell normalized to single copy nuclear gene, from Delta Ct values.
Sheet2: Calculation of fold change mtDNA per treatment, from Delta Ct values.
Quantitative PCR; AlphaFold modeling; Phylogenetics