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Figure 1 Anticodon stem loops (ASLs) of well studied classical tRNAs. (A) Yeast tRNAPhe including m1G37, the natural precursor of the hypermodified wybutosine base found at position 37 of the fully matured native tRNA (compare Figure 2). (B) E.coli tRNAPhe ASL modification isoforms. The unmodified ASL displays (left) a hairpin structure with a small loop of three nucleotides and two extra base pairs U32-A38 and U33-A37. Introduction of i6A as sole nucleotide modification leads two the formation of the classical ASL-stem loop structure including a U-turn (middle). An ASL corresponding to that of the native tRNAPhe would include 32, 39 and ms2i6A modification (right). (C) tRNALys(NUU) from E.coli contains mnms2U (x = m) and t6A, while the tRNA from human cytosol contains mcms2U (x = c) and ms2t6A.The human mitochondrial tRNALys has a similar stem and an identical loop sequence (compare Figure 5) and contains m5U (x = ).
Figure 2 (A) Secondary structure of yeast tRNAPhe. Modified nucleotides are in bold. Tertiary interactions are indicated by dotted lines. (B) General architecture of classical elongator tRNAs. On the cloverleaf structure on the left, conserved residues important for elements of tertiary structure are indicated. R stands for conserved purine residues and Y stands for conserved pyrimidine residues. Frequently modified positions [>25%; according to reference (121)] in the anticodon are highlighted by circles. Frequently modified positions elsewhere in the tRNA are boxed. Tertiary interactions are indicated by dotted lines. In the representation on the right, acceptor and anticodon domains are arranged in an L-shape according to the 3D structure. (C) Reinforcement hypothesis. On the left, the unmodified tRNA forms a stable acceptor domain and a loosely structured anticodon domain (weak interactions are symbolized by grey dotted lines). Class I modification enzymes act on the acceptor domain and introduce modifications like T54, 55, m1A58, m5C48, m5C49 and/or others, as indicated by arrows. These modifications stabilize the T-loop structure and reinforce tertiary interactions with the D-loop. The formerly loose structure of the anticodon domain is thus better defined (symbolized by black lines) and now allows better substrate recognition by other modification enzymes.
Figure 3 Slight deviations from the classical tRNA structure. (A) Secondary structure of initiator from yeast. Modified nucleotides are in bold. Tertiary interactions are indicated by dotted lines. Note the absence of T54 and 55 and the additional tertiary interactions between the A20 and the T-loop as compared to tRNAPhe. R denotes a purine at position 59 of for which sequence data in the literature are contradictory (96,89). (B) Human mitochondrial tRNALeu(UUR). The secondary structure of the native tRNA including all modified bases is shown on the left. Modified nucleotides are in bold and tertiary interactions are indicated by dotted lines. The loose structure of the anticodon domain of the unmodified transcript (98) is shown on the right. Modified nucleotides are abbreviated according to references (96,122).
Figure 4 Rearrangements on the secondary structure level induced by double methylation of human cytosolic tRNAAsn. The calculated structure of the unmodified transcript on the left side features an aberrant D-stem without G10, but including G26. Double methylation on N6 of G26 impedes its Watson–Crick pairing with cytidines and thus renders the base pair G26-C11, which is highlighted by a box, impossible. The fully modified tRNAAsn may thus adopt the classical cloverleaf structure as shown on the right. U? denotes an unknown modified uridine, likely a derivative of ribothymidine, at position 54.
Figure 5 Methylation-induced rearrangement of human mitochondrial tRNALys. (A) Cloverleaf secondary structure of the fully modified human mitochondrial tRNALys. (B) The extended hairpin secondary structure of the unmodified transcript of human mitochondrial tRNALys (left) is converted to the cloverleaf by methylation on N1-A9, as evidenced in a chimeric tRNA containing m1A9 as single modified nucleotide (right). The methylation prevents an A9-U64 base pair (boxed) in the extended hairpin structure on the left. Modified nucleotides in bold are abbreviated according to references (96,122).
Figure 6 Possible influence of a conserved methylation pattern in rRNA. An unmodified oligoribonucleotide derived from helix 45 of a bacterial small subunit rRNA shows two alternative conformations in equilibrium, with K around 3, favouring the structure shown on the upper right. Introduction of several methyl groups restricts conformation space and results in the equilibrium being shifted almost completely to the structure shown on the lower left. Modified nucleotides are abbreviated according to reference (24).
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