The wobble hypothesis revisited: Uridine-5-oxyacetic acid is critical for reading of G-ending codons

Abstract

According to Crick's wobble hypothesis, tRNAs with uridine at the wobble position (position 34) recognize A-and G-, but not U-or C-ending codons. However, U in the wobble position is almost always modified, and Salmonella enterica tRNAs containing the modified nucleoside uridine-5-oxyacetic acid (cmo 5 U34) at this position are predicted to recognize U-(but not C-) ending codons, in addition to A-and G-ending codons. We have constructed a set of S. enterica mutants with only the cmo 5 U-containing tRNA left to read all four codons in the proline, alanine, valine, and threonine family codon boxes. From the phenotypes of these mutants, we deduce that the proline, alanine, and valine tRNAs containing cmo 5 U read all four codons including the C-ending codons, while the corresponding threonine tRNA does not. A cmoB mutation, leading to cmo 5 U deficiency in tRNA, was introduced. Monitoring A-site selection rates in vivo revealed that the presence of cmo 5 U34 stimulated the reading of CCU and CCC (Pro), GCU (Ala), and GUC (Val) codons. Unexpectedly, cmo 5 U is critical for efficient decoding of G-ending Pro, Ala, and Val codons. Apparently, whereas G34 pairs with U in mRNA, the reverse pairing (U34-G) requires a modification of U34.

How the Early Genetic Code Was Established?: Inference from the Analysis of Extant Animal Mitochondrial Decoding Systems

“…In the last case, no structural study on the corresponding tRNA was performed, and no release factor (RF) relevant to the UAA codon was identified, so discussion on the codonanticodon relationship was not possible in this instance. There are 42 different anticodons and a total of 48 tRNAs with different body sequences in E. coli (Näsvall et al 2007) Modified nucleosides in the tRNA anticodons are associated with mitochondrial codon changes in all cases (Watanabe and Yokobori 2011): (1) The anticodon wobble position (the 34th) of tRNA Trp changes to 5-carboxymethyluridine (cmnm 5 U) in nematode mitochondria (Sakurai et al 2005) and to 5-taurinomethyluridine (τm 5 U) in ascidian (Suzuki et al 2011b), molluscan (Ohira et al 2013), and vertebrate (Suzuki et al 2002(Suzuki et al , 2011a mitochondria; (2) The anticodon wobble position of tRNA Met changes to 5-formylcytidine (f 5 C) in vertebrate (Moriya et al 1994), arthropod (Tomita et al 1999a), and nematode mitochondria (Watanabe et al 1994) and to τm 5 U in ascidian mitochondria (Suzuki et al 2011b); (3) The anticodon wobble nucleoside of tRNA Gly for AGR codons becomes τm 5 U in ascidian mitochondria (Suzuki et al 2011b). The anticodon wobble nucleoside of tRNA Ser becomes m 7 G in most invertebrate mitochondria (Matsuyama et al 1998;Tomita et al 1998) and unmodified U in nematode mitochondria (Watanabe et al 1994); (4) The starfish mitochondrial tRNA Asn that deciphers AAA as Asn possesses the anticodon GΨU (Ψ, pseudouridine) (Tomita et al 1999b); this is unusual in that it is a change at the second anticodon position.…”

Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon

“…Table 1 represents a situation found in some primitive bacteria and mitochondria, where N34-N3 base-pairing rules and degeneracy families match exactly (Bonitz et al 1980;Inagaki et al 1995;Suzuki 2005), meaning that the number of different tRNAs necessary for translation is at the minimum. As far as evolved genetic systems are concerned, some structural constraints require that more than one tRNA is usually necessary for the translation of all the codons in many codon families (Agris et al 2007;Näsvall et al 2007).…”

Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch

“…Also, the R⅐R and Y⅐Y mismatches had reversed acceptability compared with the translational rules derived by Lim and Curran (46). The T box system also exhibits a preference for G⅐U over U⅐G, which is the opposite of what is found in translation (47)(48)(49). However, as in translation (50,51), mismatches at position 2 were the most deleterious.…”