Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA
- Tek N. Lamichhane1,5,
- Aneeshkumar G. Arimbasseri1,
- Keshab Rijal1,
- James R. Iben2,
- Fan Yan Wei3,
- Kazuhito Tomizawa3 and
- Richard J. Maraia1,4
- 1Section on Molecular and Cell Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
- 2Molecular Genetics Laboratory, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
- 3Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 860-0862 Kumamoto, Japan
- 4Commissioned Corps, US Public Health Service, Rockville, Maryland 20016, USA
- Corresponding author: maraiar{at}mail.nih.gov
Abstract
tRNA-isopentenyl transferases (IPTases) are highly conserved enzymes that form isopentenyl-N6-A37 (i6A37) on subsets of tRNAs, enhancing their translation activity. Nuclear-encoded IPTases modify select cytosolic (cy-) and mitochondrial (mt-) tRNAs. Mutation in human IPTase, TRIT1, causes disease phenotypes characteristic of mitochondrial translation deficiency due to mt-tRNA dysfunction. Deletion of the Schizosaccharomyces pombe IPTase (tit1-Δ) causes slow growth in glycerol, as well as in rapamycin, an inhibitor of TOR kinase that maintains metabolic homeostasis. Schizosaccharomyces pombe IPTase modifies three different cy-tRNAsSer as well as cy-tRNATyr, cy-tRNATrp, and mt-tRNATrp. We show that lower ATP levels in tit1-Δ relative to tit1+ cells are also more decreased by an inhibitor of oxidative phosphorylation, indicative of mitochondrial dysfunction. Here we asked if the tit1-Δ phenotypes are due to hypomodification of cy-tRNA or mt-tRNA. A cytosol-specific IPTase that modifies cy-tRNA, but not mt-tRNA, fully rescues the tit1-Δ phenotypes. Moreover, overexpression of cy-tRNAs also rescues the phenotypes, and cy-tRNATyr alone substantially does so. Bioinformatics indicate that cy-tRNATyr is most limiting for codon demand in tit1-Δ cells and that the cytosolic mRNAs most loaded with Tyr codons encode carbon metabolilizing enzymes, many of which are known to localize to mitochondria. Thus, S. pombe i6A37 hypomodification-associated metabolic deficiency results from hypoactivity of cy-tRNA, mostly tRNATyr, and unlike human TRIT1-deficiency does not impair mitochondrial translation due to mt-tRNA hypomodification. We discuss species-specific aspects of i6A37. Specifically relevant to mitochondria, we show that its hypermodified version, ms2i6A37 (2-methylthiolated), which occurs on certain mammalian mt-tRNAs (but not cy-tRNAs), is not found in yeast.
Keywords
Footnotes
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Abbreviations: IPTase, isopentenyl tRNA transferase; TMS, tRNA-mediated suppression; PHA6, positive hybridization in the absence of i6A37
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.054064.115.
- Received August 19, 2015.
- Accepted December 28, 2015.
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