Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase

Elife. 2018 Dec 12;7:e42179. doi: 10.7554/eLife.42179.


Bacterial and eukaryotic nuclear RNA polymerases (RNAPs) cap RNA with the oxidized and reduced forms of the metabolic effector nicotinamide adenine dinucleotide, NAD+ and NADH, using NAD+ and NADH as non-canonical initiating nucleotides for transcription initiation. Here, we show that mitochondrial RNAPs (mtRNAPs) cap RNA with NAD+ and NADH, and do so more efficiently than nuclear RNAPs. Direct quantitation of NAD+- and NADH-capped RNA demonstrates remarkably high levels of capping in vivo: up to ~60% NAD+ and NADH capping of yeast mitochondrial transcripts, and up to ~15% NAD+ capping of human mitochondrial transcripts. The capping efficiency is determined by promoter sequence at, and upstream of, the transcription start site and, in yeast and human cells, by intracellular NAD+ and NADH levels. Our findings indicate mtRNAPs serve as both sensors and actuators in coupling cellular metabolism to mitochondrial transcriptional outputs, sensing NAD+ and NADH levels and adjusting transcriptional outputs accordingly.

Keywords: E. coli; RNA capping; RNA polymerase; S. cerevisiae; biochemistry; chemical biology; chromosomes; gene expression; human; metabolism; mitochondria; non-canonical initiating nucleotide; transcription initiation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cytoplasm / genetics
  • Cytoplasm / metabolism
  • DNA-Directed RNA Polymerases / genetics*
  • Humans
  • Mitochondria / genetics
  • NAD / genetics
  • Oxidation-Reduction
  • Promoter Regions, Genetic
  • RNA Caps / genetics*
  • RNA, Mitochondrial / genetics*
  • Saccharomyces cerevisiae / genetics
  • Transcription Initiation Site
  • Transcription, Genetic*


  • RNA Caps
  • RNA, Mitochondrial
  • NAD
  • DNA-Directed RNA Polymerases