Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase
Jeremy G Bird,
Urmimala Basu,
David Kuster,
Aparna Ramachandran,
Ewa Grudzien-Nogalska,
Atif Towheed,
Douglas C Wallace,
Megerditch Kiledjian,
Dmitry Temiakov,
Smita S Patel,
Richard H Ebright,
Bryce E Nickels
Affiliations
Jeremy G Bird
Department of Genetics and Waksman Institute, Rutgers University, United States; Department of Chemistry and Waksman Institute, Rutgers University, United States
Urmimala Basu
Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, United States; Biochemistry PhD Program, School of Graduate Studies, Rutgers University, United States
Department of Genetics and Waksman Institute, Rutgers University, United States; Department of Chemistry and Waksman Institute, Rutgers University, United States; Biochemistry Center Heidelberg, Heidelberg University, Germany
Aparna Ramachandran
Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, United States
Ewa Grudzien-Nogalska
Department of Cell Biology and Neuroscience, Rutgers University, United States
Atif Towheed
Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, United States
Douglas C Wallace
Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, United States; Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine, United States
Megerditch Kiledjian
Department of Cell Biology and Neuroscience, Rutgers University, United States
Dmitry Temiakov
Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, United States
Smita S Patel
Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, United States
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.
