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The human mitochondrial mRNA structurome reveals mechanisms of gene expression

Affiliations
  • 1Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA.
  • 2University of Miami Medical Scientist Training Program, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA.
  • 3Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
  • 4Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA.
  • 5The Miami Veterans Affairs (VA) Medical System, 1201 NW 16th Street, Miami, FL 33125, USA.

Published on:

July 18, 2024

Abstract

The human mitochondrial genome encodes crucial oxidative phosphorylation system proteins, pivotal for aerobic energy transduction. They are translated from nine monocistronic and two bicistronic transcripts whose native structures remain unexplored, posing a gap in understanding mitochondrial gene expression. In this work, we devised the mitochondrial dimethyl sulfate mutational profiling with sequencing (mitoDMS-MaPseq) method and applied detection of RNA folding ensembles using expectation-maximization (DREEM) clustering to unravel the native mitochondrial messenger RNA (mt-mRNA) structurome in wild-type (WT) and leucine-rich pentatricopeptide repeat-containing protein (LRPPRC)-deficient cells. Our findings elucidate LRPPRC’s role as a holdase contributing to maintaining mt-mRNA folding and efficient translation. mt-mRNA structural insights in WT mitochondria, coupled with metabolic labeling, unveil potential mRNA-programmed translational pausing and a distinct programmed ribosomal frameshifting mechanism. Our data define a critical layer of mitochondrial gene expression regulation. These mt-mRNA folding maps provide a reference for studying mt-mRNA structures in diverse physiological and pathological contexts.

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