Identity elements for the aminoacylation of metazoan mitochondrial tRNA^Arghave been widely conserved throughout evolution and ensure the fidelity of the AGR codon reassignment

Abstract

Eumetazoan mitochondrial tRNAs possess structures (identity elements) that require the specific recognition by their cognate nuclear-encoded aminoacyl-tRNA synthetases. The AGA (arginine) codon of the standard genetic code has been reassigned to serine/glycine/termination in eumetazoan organelles and is translated in some organisms by a mitochondrially encoded tRNASerUCU. One mechanism to prevent mistranslation of the AGA codon as arginine would require a set of tRNA identity elements distinct from those possessed by the cytoplasmic tRNAArg in which the major identity elements permit the arginylation of all 5 encoded isoacceptors. We have performed comparative in vitro aminoacylation using an insect mitochondrial arginyl-tRNA synthetase and tRNAArgUCG structural variants. The established identity elements are sufficient to maintain the fidelity of tRNASerUCU reassignment. tRNAs having a UCU anticodon cannot be arginylated but can be converted to arginine acceptance by identity element transplantation. We have examined the evolutionary distribution and functionality of these tRNA elements within metazoan taxa. We conclude that the identity elements that have evolved for the recognition of mitochondrial tRNAArgUCG by the nuclear encoded mitochondrial arginyl-tRNA synthetases of eumetazoans have been extensively, but not universally conserved, throughout this clade. They ensure that the AGR codon reassignment in eumetazoan mitochondria is not compromised by misaminoacylation. In contrast, in other metazoans, such as Porifera, whose mitochondrial translation is dictated by the universal genetic code, recognition of the 2 encoded tRNAArgUCG/UCU isoacceptors is achieved through structural features that resemble those employed by the yeast cytoplasmic system.

tRNA acceptor stem and anticodon bases form independent codes related to protein folding

“…Systematic analysis of their amino acid compositions and multiple sequence alignments may reveal patterns related to properties suggested here by tRNA acceptor stem coding. Evolution of tRNA identity elements is also important for understanding idiosyncratic coding, for example, as in plastids (34). The order in which predictors emerge in the stepwise regressions discussed above is similar, but not identical to, the series of decisions by which Delarue suggested that genetic coding actually became fixed (24).…”

Reassignment of a rare sense codon to a non-canonical amino acid inEscherichia coli

“…In the invertebrate mitochondria, the six ‘universal’ arginine codons are split into CGN for arginine and AGA/AGG for serine ( 51 ). The mitochondrial ArgRS does not mis-acylate tRNA Ser UCU , because it has a tRNA recognition mode slightly different from that of the nuclear ArgRS, and this altered recognition enables distinguishing between tRNA Ser UCU and tRNA Arg UCG ( 52 ). This case illuminates the importance of an adjustment in the endogenous tRNA―aaRS system for codon redefinition, as has been proposed ( 53 , 54 ) and shown with our engineering of a new tRNA system.…”

Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes

“…The positions of identity elements, and the charging/the progress of arginylation of the mitochondrial trnR genes of many Metazoa, in particular Porifera, has been analyzed in ( 14 ). A very important factor, the fact that trnR are remolded trnT , remained unnoticed within this study.…”

“…Identity elements of mitochondrial tRNAs have been analyzed in-vitro for trnR ( 14 ), trnD ( 15 ), trnY ( 15 , 16 ), trnL ( 17 ), trnS ( 18 , 19 ) and trnA ( 20 ). For the remaining tRNAs, identity elements have been analyzed in-silico through sequence and structural conservation studies, and comparisons to known identity elements of Escherichia coli ( 21 ).…”