Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates

The mitochondrial ribosome, which translates all mitochondrial DNA (mtDNA)-encoded proteins, should be tightly regulated pre- and post-transcriptionally. Recently, we found RNA-DNA differences (RDDs) at human mitochondrial 16S (large) rRNA position 947 that were indicative of post-transcriptional modification. Here, we show that these 16S rRNA RDDs result from a 1-methyladenosine (m1A) modification introduced by TRMT61B, thus being the first vertebrate methyltransferase that modifies both tRNA and rRNAs. m1A947 is conserved in humans and all vertebrates having adenine at the corresponding mtDNA position (90% of vertebrates). However, this mtDNA base is a thymine in 10% of the vertebrates and a guanine in the 23S rRNA of 95% of bacteria, suggesting alternative evolutionary solutions. m1A, uridine, or guanine may stabilize the local structure of mitochondrial and bacterial ribosomes. Experimental assessment of genome-edited Escherichia coli showed that unmodified adenine caused impaired protein synthesis and growth. Our findings revealed a conserved mechanism of rRNA modification that has been selected instead of DNA mutations to enable proper mitochondrial ribosome function.

[1]  Michael D. Wilson,et al.  The Evolutionary Landscape of Alternative Splicing in Vertebrate Species , 2012, Science.

[2]  D. Dressman,et al.  Heteroplasmic mitochondrial DNA mutations in normal and tumor cells , 2010, Nature.

[3]  Israel S. Fernández,et al.  Structure of the Mammalian Ribosome-Sec61 Complex to 3.4 Å Resolution , 2014, Cell.

[4]  N. Nomura,et al.  LRPPRC/SLIRP suppresses PNPase-mediated mRNA decay and promotes polyadenylation in human mitochondria , 2012, Nucleic acids research.

[5]  A. Bouskila,et al.  Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons , 2015, Genome biology and evolution.

[6]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[7]  V. Narry Kim,et al.  Emerging Roles of RNA Modification: m6A and U-Tail , 2014, Cell.

[8]  Zhiyu Peng,et al.  Lack of evidence for existence of noncanonical RNA editing , 2013, Nature Biotechnology.

[9]  V. Noireaux,et al.  Genetically expanded cell‐free protein synthesis using endogenous pyrrolysyl orthogonal translation system , 2015, Biotechnology and bioengineering.

[10]  Tsutomu Suzuki,et al.  Mass spectrometric identification and characterization of RNA-modifying enzymes. , 2007, Methods in enzymology.

[11]  Ruedi Aebersold,et al.  The complete structure of the large subunit of the mammalian mitochondrial ribosome , 2014, Nature.

[12]  Chuan He,et al.  RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation , 2015, Genes & development.

[13]  M. Mörl,et al.  Processing and Editing of Overlapping tRNAs in Human Mitochondria* , 1998, The Journal of Biological Chemistry.

[14]  A. Kundaje,et al.  Transcription Factors Bind Negatively Selected Sites within Human mtDNA Genes , 2014, Genome biology and evolution.

[15]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[16]  Hiroko Yamada,et al.  Human protein factory for converting the transcriptome into an in vitro–expressed proteome , 2008, Nature Methods.

[17]  Scott C. Blanchard,et al.  High-resolution structure of the Escherichia coli ribosome , 2015, Nature Structural &Molecular Biology.

[18]  Ahmet Kurdoglu,et al.  Alzheimer's disease is associated with altered expression of genes involved in immune response and mitochondrial processes in astrocytes , 2015, Neurobiology of Aging.

[19]  F. Buckner,et al.  Structure of Leishmania major methionyl-tRNA synthetase in complex with intermediate products methionyladenylate and pyrophosphate. , 2011, Biochimie.

[20]  A. Bergman,et al.  Disrupting Mitochondrial–Nuclear Coevolution Affects OXPHOS Complex I Integrity and Impacts Human Health , 2014, Genome biology and evolution.

[21]  Tal Nagar,et al.  MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences. , 2011, Mitochondrion.

[22]  Alan Brown,et al.  The structure of the human mitochondrial ribosome , 2015, Science.

[23]  Richard M. Murray,et al.  Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology , 2013, Journal of visualized experiments : JoVE.

[24]  Ruedi Aebersold,et al.  Architecture of the large subunit of the mammalian mitochondrial ribosome , 2013, Nature.

[25]  Johann Holzmann,et al.  A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase—extensive moonlighting in mitochondrial tRNA biogenesis , 2012, Nucleic acids research.

[26]  J. Bujnicki,et al.  MODOMICS: a database of RNA modification pathways—2013 update , 2012, Nucleic Acids Res..

[27]  Tsutomu Suzuki,et al.  A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs , 2014, Nucleic acids research.

[28]  Leighton J. Core,et al.  RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II. , 2014, Cell reports.

[29]  O. Uhlenbeck,et al.  Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. , 1987, Nucleic acids research.

[30]  K. Watanabe,et al.  A Novel Wobble Rule Found in Starfish Mitochondria , 1998, The Journal of Biological Chemistry.

[31]  Tsutomu Suzuki,et al.  Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs. , 2012, RNA.

[32]  O. Nureki,et al.  Structural basis for anticodon recognition by methionyl-tRNA synthetase , 2005, Nature Structural &Molecular Biology.

[33]  Anton Nekrutenko,et al.  RNA–DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA , 2013, Genome research.

[34]  Ruedi Aebersold,et al.  The complete structure of the 55S mammalian mitochondrial ribosome , 2015, Science.

[35]  Sergey Melnikov,et al.  The Structure of the Eukaryotic Ribosome at 3.0 Å Resolution , 2011, Science.

[36]  Suzuki Tsutomu,et al.  Human mitochondrial diseases caused by lack of taurine modification in mitochondrial tRNAs , 2011 .

[37]  Takeo Suzuki,et al.  Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases. , 2011, Annual review of genetics.

[38]  M. A. Rubio,et al.  Unusual noncanonical intron editing is important for tRNA splicing in Trypanosoma brucei. , 2013, Molecules and Cells.

[39]  Gideon Rechavi,et al.  The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA , 2016, Nature.

[40]  Tsutomu Suzuki,et al.  A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. , 2013, Nature chemical biology.

[41]  Chengqi Yi,et al.  Transcriptome-wide dynamics of RNA pseudouridylation , 2015, Nature Reviews Molecular Cell Biology.

[42]  Alan Hodgkinson,et al.  High-Resolution Genomic Analysis of Human Mitochondrial RNA Sequence Variation , 2014, Science.

[43]  Hiroki Ueda,et al.  A biochemical landscape of A-to-I RNA editing in the human brain transcriptome , 2014, Genome research.

[44]  Tsutomu Suzuki,et al.  Single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly , 2015, Proceedings of the National Academy of Sciences.

[45]  B. Golinelli‐Pimpaneau,et al.  Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA. , 2008, Journal of molecular biology.

[46]  S. Bergmann,et al.  The evolution of gene expression levels in mammalian organs , 2011, Nature.

[47]  Gary L. Glish,et al.  Tandem Mass Spectrometry of Small, Multiply Charged Oligonucleotides , 1992, Journal of the American Society for Mass Spectrometry.

[48]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[49]  Andreas Hildebrandt,et al.  The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent , 2015, Nucleic acids research.

[50]  Steve Hoffmann,et al.  Traces of post-transcriptional RNA modifications in deep sequencing data , 2011, Biological chemistry.

[51]  Volker Knoop,et al.  When you can’t trust the DNA: RNA editing changes transcript sequences , 2011, Cellular and Molecular Life Sciences.

[52]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[53]  A. Benítez-Páez,et al.  The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. , 2012, RNA.

[54]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[55]  Alan Brown,et al.  Structure of the large ribosomal subunit from human mitochondria , 2014, Science.