Table of Contents Author Guidelines Submit a Manuscript
Journal of Nucleic Acids
Volume 2011, Article ID 623095, 12 pages
http://dx.doi.org/10.4061/2011/623095
Review Article

tRNA Modification and Genetic Code Variations in Animal Mitochondria

1Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
2Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan

Received 31 May 2011; Accepted 4 July 2011

Academic Editor: Daisuke Miyoshi

Copyright © 2011 Kimitsuna Watanabe and Shin-ichi Yokobori. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Citations to this Article [34 citations]

The following is the list of published articles that have cited the current article.

  • Takeo Suzuki, Kenjyo Miyauchi, Tsutomu Suzuki, Shin-ichi Yokobori, Naoki Shigi, Akiko Kondow, Nono Takeuchi, Akihiko Yamagishi, and Kimitsuna Watanabe, “Taurine-containing Uridine Modifications in tRNA Anticodons Are Required to Decipher Non-universal Genetic Codes in Ascidian Mitochondria,” Journal Of Biological Chemistry, vol. 286, no. 41, pp. 35494–35498, 2011. View at Publisher · View at Google Scholar
  • Oliver Rackham, Timothy R. Mercer, and Aleksandra Filipovska, “The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression,” Wiley Interdisciplinary Reviews-Rna, vol. 3, no. 5, pp. 675–695, 2012. View at Publisher · View at Google Scholar
  • J. Ling, R. Daoud, M. J. Lajoie, G. M. Church, D. Soll, and B. F. Lang, “Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria,” Nucleic Acids Research, 2013. View at Publisher · View at Google Scholar
  • Sandra Wende, Edward G. Platzer, Frank Jühling, Joern Pütz, Catherine Florentz, Peter F. Stadler, and Mario Mörl, “Biological evidence for the world’s smallest tRNAs,” Biochimie, 2013. View at Publisher · View at Google Scholar
  • W. A. Cantara, F. V. Murphy, H. Demirci, and P. F. Agris, “Expanded use of sense codons is regulated by modified cytidines in tRNA,” Proceedings of the National Academy of Sciences, vol. 110, no. 27, pp. 10964–10969, 2013. View at Publisher · View at Google Scholar
  • S.-i. Yokobori, A. Kitamura, H. Grosjean, and Y. Bessho, “Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes,” Nucleic Acids Research, 2013. View at Publisher · View at Google Scholar
  • Takayuki Ohira, Takeo Suzuki, Kenjyo Miyauchi, Tsutomu Suzuki, Shin-ichi Yokobori, Akihiko Yamagishi, and Kimitsuna Watanabe, “Decoding Mechanism of Non-universal Genetic Codes in Loligo bleekeri Mitochondria,” Journal Of Biological Chemistry, vol. 288, no. 11, pp. 7645–7652, 2013. View at Publisher · View at Google Scholar
  • Peter F. Stadler, Matthias Bernt, Anke Braband, and Bernd Schierwater, “Genetic aspects of mitochondrial genome evolution,” Molecular Phylogenetics And Evolution, vol. 69, no. 2, pp. 328–338, 2013. View at Publisher · View at Google Scholar
  • David R. Wolstenholme, and C. Timothy Beagley, “Characterization and localization of mitochondrial DNA-encoded tRNAs and nuclear DNA-encoded tRNAs in the sea anemone Metridium senile,” Current Genetics, vol. 59, no. 3, pp. 139–152, 2013. View at Publisher · View at Google Scholar
  • Ilmo Hassinen, “Mitochondria and Energy Metabolism: Networks, Mechanisms, and Control,” Natural Biomarkers for Cellular Metabolism, pp. 3–40, 2014. View at Publisher · View at Google Scholar
  • S. Muhlhausen, and M. Kollmar, “Molecular Phylogeny of Sequenced Saccharomycetes Reveals Polyphyly of the Alternative Yeast Codon Usage,” Genome Biology and Evolution, vol. 6, no. 12, pp. 3222–3237, 2014. View at Publisher · View at Google Scholar
  • William J. Craigenpp. 287–297, 2014. View at Publisher · View at Google Scholar
  • Gabor L. Igloi, and Anne-Katrin Leisinger, “Identity elements for the aminoacylation of metazoan mitochondrial tRNA(Arg) have been widely conserved throughout evolution and ensure the fidelity o,” Rna Biology, vol. 11, no. 10, pp. 1313–1323, 2014. View at Publisher · View at Google Scholar
  • Yoshinori Kumazawa, Saaya Miura, Chiemi Yamada, and Yasuyuki Hashiguchi, “Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes,” Bmc Genomics, vol. 15, 2014. View at Publisher · View at Google Scholar
  • Kimitsuna Watanabe, and Shin-Ichi Yokoboripp. 25–40, 2014. View at Publisher · View at Google Scholar
  • M.J. Lajoie, D. Söll, and G.M. Church, “Overcoming challenges in engineering the genetic code,” Journal of Molecular Biology, 2015. View at Publisher · View at Google Scholar
  • Ana Bezerra, Ana Guimarães, and Manuel Santos, “Non-Standard Genetic Codes Define New Concepts for Protein Engineering,” Life, vol. 5, no. 4, pp. 1610–1628, 2015. View at Publisher · View at Google Scholar
  • Dennis V. Lavrov, and Walker Pett, “Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages,” Genome Biology and Evolution, vol. 8, no. 9, pp. 2896–2913, 2016. View at Publisher · View at Google Scholar
  • Henri Grosjean, and Eric Westhof, “An integrated, structure- and energy-based view of the genetic code,” Nucleic Acids Research, pp. gkw608, 2016. View at Publisher · View at Google Scholar
  • Roxane-Marie Barthélémy, and Hervé Seligmann, “Cryptic tRNAs in chaetognath mitochondrial genomes,” Computational Biology and Chemistry, vol. 62, pp. 119–132, 2016. View at Publisher · View at Google Scholar
  • Markus Duechler, Grażyna Leszczyńska, Elzbieta Sochacka, and Barbara Nawrot, “Nucleoside modifications in the regulation of gene expression: focus on tRNA,” Cellular and Molecular Life Sciences, 2016. View at Publisher · View at Google Scholar
  • João Simões, Ana R. Bezerra, Gabriela R. Moura, Hugo Araújo, Ivo Gut, Mónica Bayes, and Manuel A. S. Santos, “The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons,” Frontiers in Microbiology, vol. 7, 2016. View at Publisher · View at Google Scholar
  • Yiwei Wang, and Roberta D. Brinton, “Triad of Risk for Late Onset Alzheimer’s: Mitochondrial Haplotype, APOE Genotype and Chromosomal Sex,” Frontiers in Aging Neuroscience, vol. 8, 2016. View at Publisher · View at Google Scholar
  • Sara Haag, Marina V Rodnina, Markus T Bohnsack, Katherine E Sloan, Jens Kretschmer, Sven Dennerlein, Peter Rehling, Claudia Höbartner, Namit Ranjan, Ahmed S Warda, Charlotte Blessing, Benedikt Hübner, and Jan Seikowski, “NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation,” EMBO Journal, vol. 35, no. 19, pp. 2104–2119, 2016. View at Publisher · View at Google Scholar
  • Asuteka Nagao, Mitsuhiro Ohara, Kenjyo Miyauchi, Shin-ichi Yokobori, Akihiko Yamagishi, Kimitsuna Watanabe, and Tsutomu Suzuki, “Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria,” Nature Structural & Molecular Biology, 2017. View at Publisher · View at Google Scholar
  • Emmanuel Noutahi, Virginie Calderon, Mathieu Blanchette, Franz B Lang, and Nadia El-Mabrouk, “CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes,” Bioinformatics, vol. 33, no. 21, pp. 3331–3339, 2017. View at Publisher · View at Google Scholar
  • Arif Uddin, Monisha Nath Choudhury, and Supriyo Chakraborty, “Factors influencing codon usage of mitochondrial ND1 gene in pisces, aves and mammals,” Mitochondrion, 2017. View at Publisher · View at Google Scholar
  • Martin Kollmar, and Stefanie Mühlhausen, “How tRNAs dictate nuclear codon reassignments: Only a few can capture non-cognate codons,” RNA Biology, pp. 1–7, 2017. View at Publisher · View at Google Scholar
  • Russell P. Saneto, “Genetics of Mitochondrial Disease,” 2017. View at Publisher · View at Google Scholar
  • Paul F. Agris, Amithi Narendran, Kathryn Sarachan, Ville Y.P. Väre, and Emily Eruysal, “The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity,” 2017. View at Publisher · View at Google Scholar
  • Jean Peccoud, Mohamed Amine Chebbi, Alexandre Cormier, Clément Gilbert, Isabelle Marcadé, Christopher Chandler, Richard Cordaux, and Bouziane Moumen, “Untangling heteroplasmy, structure, and evolution of an atypical mitochondrial genome by pacbio sequencing,” Genetics, vol. 207, no. 1, pp. 269–280, 2017. View at Publisher · View at Google Scholar
  • Chie Tomikawa, “7-Methylguanosine Modifications in Transfer RNA (tRNA),” International Journal of Molecular Sciences, vol. 19, no. 12, pp. 4080, 2018. View at Publisher · View at Google Scholar
  • Yuanning Li, Kevin M Kocot, Michael G Tassia, Johanna T Cannon, Matthias Bernt, and Kenneth M Halanych, “Mitogenomics Reveals a Novel Genetic Code in Hemichordata,” Genome Biology and Evolution, vol. 11, no. 1, pp. 29–40, 2018. View at Publisher · View at Google Scholar
  • Navanath M. Kumbhar, and Janhavi S. Gopal, “Structural significance of hypermodified nucleoside 5-carboxymethylaminomethyluridine (cmnm5U) from ‘wobble’ (34th) position of mitochondrial tRNAs: Molecular modeling and Markov state model studies,” Journal of Molecular Graphics and Modelling, 2018. View at Publisher · View at Google Scholar