How the Early Genetic Code Was Established?: Inference from the Analysis of Extant Animal Mitochondrial Decoding Systems Kimitsuna Watanabe and Shin-ichi Yokobori Contents 1 Introduction ................................................................................... 26 2 Comparison of Genetic Apparatus in Mitochondrial and Non-mitochondrial Decoding Systems ....................................................................................... 27 3 Characteristics of Mitochondrial Genetic Code Systems ................................... 28 4 The Codon–Anticodon Relationship in Animal Mitochondria ............................. 31 5 How Was the Mitochondrial Decoding System Generated? ................................ 32 6 The Early Genetic Code System ............................................................. 33 7 From the Early Decoding System to the Universal Decoding System ..................... 35 8 Concluding Remarks and Perspective ....................................................... 36 References ........................................................................................ 38 Abstract Mitochondria are intracellular organelles in eukaryotic cells that have their own genome and translational apparatus. The vertebrate mitochondrial decoding system is thought to be the simplest among all extant living systems and to have originated by retrogression from the universal decoding system, induced mainly by genome economisation and directional mutation pressure during mitochondrial evolution. Thus, it is reasonable to speculate that the vertebrate genetic code table is a typical model for the early genetic code table. In some metazoan mitochondrial decoding systems, it was found that unmodified anticodons of tRNA have the potential to base-pair with cognate codons K. Watanabe (*) Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan e-mail: kim-wata@toyaku.ac.jp; kwatanab@ft.catv.ne.jp S. Yokobori Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan V.A. Erdmann et al. (eds.), Chemical Biology of Nucleic Acids, RNA Technologies, DOI 10.1007/978-3-642-54452-1_2, © Springer-Verlag Berlin Heidelberg 2014 25