1. Biochemistry and Chemical Biology
  2. Chromosomes and Gene Expression

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

  1. Jeremy G Bird
  2. Urmimala Basu
  3. David Kuster
  4. Aparna Ramachandran
  5. Ewa Grudzien-Nogalska
  6. Atif Towheed
  7. Douglas C Wallace
  8. Megerditch Kiledjian
  9. Dmitry Temiakov
  10. Smita S Patel  Is a corresponding author
  11. Richard H Ebright  Is a corresponding author
  12. Bryce E Nickels  Is a corresponding author
  1. Rutgers University, United States
  2. Heidelberg University, Germany
  3. The Children's Hospital of Philadelphia, United States
  4. University of Pennsylvania, United States
  5. Thomas Jefferson University, United States
https://doi.org/10.7554/eLife.42179
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  1. Jeremy G Bird
  2. Urmimala Basu
  3. David Kuster
  4. Aparna Ramachandran
  5. Ewa Grudzien-Nogalska
  6. Atif Towheed
  7. Douglas C Wallace
  8. Megerditch Kiledjian
  9. Dmitry Temiakov
  10. Smita S Patel
  11. Richard H Ebright
  12. Bryce E Nickels
(2018)
Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase
eLife 7:e42179.
https://doi.org/10.7554/eLife.42179
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Abstract

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.

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All data generated or analysed during this study are included in the manuscript.

Article and author information

Author details

  1. Jeremy G Bird

    Department of Genetics, Rutgers University, Piscataway, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Urmimala Basu

    Department of Biochemistry and Molecular Biology, Rutgers University, Piscataway, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. David Kuster

    Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8157-9223

  4. Aparna Ramachandran

    Department of Biochemistry and Molecular Biology, Rutgers University, Piscataway, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Ewa Grudzien-Nogalska

    Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Atif Towheed

    Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Douglas C Wallace

    Center for Mitochondrial and Epigenomic Medicine, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Megerditch Kiledjian

    Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Dmitry Temiakov

    Department of Biochemistry & Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Smita S Patel

    Department of Biochemistry and Molecular Biology, Rutgers University, Piscataway, United States
    For correspondence
    patelss@rwjms.rutgers.edu
    Competing interests
    The authors declare that no competing interests exist.

  11. Richard H Ebright

    Department of Chemistry, Rutgers University, Piscataway, United States
    For correspondence
    ebright@waksman.rutgers.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8915-7140

  12. Bryce E Nickels

    Department of Genetics, Rutgers University, Piscataway, United States
    For correspondence
    bnickels@waksman.rutgers.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7449-8831

Funding

National Institutes of Health (GM126488)

  • Megerditch Kiledjian

American Heart Association (16PRE30400001)

  • Urmimala Basu

National Institutes of Health (GM118086)

  • Smita S Patel

National Institutes of Health (GM104231)

  • Dmitry Temiakov

National Institutes of Health (GM041376)

  • Richard H Ebright

National Institutes of Health (GM118059)

  • Bryce E Nickels

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Alan G Hinnebusch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States

Version history

  1. Received: September 19, 2018
  2. Accepted: December 10, 2018
  3. Accepted Manuscript published: December 10, 2018 (version 1)
  4. Accepted Manuscript updated: December 12, 2018 (version 2)
  5. Version of Record published: December 18, 2018 (version 3)

Copyright

© 2018, Bird et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Jeremy G Bird
  2. Urmimala Basu
  3. David Kuster
  4. Aparna Ramachandran
  5. Ewa Grudzien-Nogalska
  6. Atif Towheed
  7. Douglas C Wallace
  8. Megerditch Kiledjian
  9. Dmitry Temiakov
  10. Smita S Patel
  11. Richard H Ebright
  12. Bryce E Nickels
(2018)
Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase
eLife 7:e42179.
https://doi.org/10.7554/eLife.42179

Share this article

https://doi.org/10.7554/eLife.42179

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