Expanded use of sense codons is regulated by modified cytidines in tRNA

Abstract

Codon use among the three domains of life is not confined to the universal genetic code. With only 22 tRNA genes in mammalian mitochondria, exceptions from the universal code are necessary for proper translation. A particularly interesting deviation is the decoding of the isoleucine AUA codon as methionine by the one mitochondrial-encoded tRNA Met . This tRNA decodes AUA and AUG in both the A-and P-sites of the metazoan mitochondrial ribosome. Enrichment of posttranscriptional modifications is a commonly appropriated mechanism for modulating decoding rules, enabling some tRNA functions while restraining others. In this case, a modification of cytidine, 5-formylcytidine (f

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA Met to expand codon recognition in mitochondrial translation

“…In combination with the generally lower efficiency of the alternative codons in the in vitro binding assays, only small differences between the binding of the unmodified, m 5 C‐ or f 5 C‐modified mt‐tRNA Met to AUA codons in the ribosomal A site were observed, while the binding of hm 5 C‐containing mt‐tRNA Met was less efficient. Previous reports with the unmodified or f 5 C34‐containing ASL of mt‐tRNA Met suggested that the formyl group might stabilise the non‐conventional basepairing of f 5 C34 with an adenosine in the third position of an AUA codon (Bilbille et al , 2011; Cantara et al , 2013). These studies also observed that binding of mt‐tRNA Met to alternative codons was weaker than to AUG and it is likely that ribosome interactions with mt‐tRNA Met outside of the ASL, that is with the tRNA body, further influence mt‐tRNA Met binding.…”

Celebrating wobble decoding: Half a century and still much is new

“…As an example, isoleucine shares a codon box with methionine where AUA, AUC, and AUU code for isoleucine, and AUG codes for methionine, with the exception of mitochondria where AUA also codes for methionine. 6,113,122 Two codons can be read by tRNA Ile GAU , but the AUA codon requires a different isoacceptor that would also not read AUG as isoleucine. Eukaryotes commonly have a tRNA Ile IAU which can read all three codons, but not AUG. 122 The genomes of bacteria and some eukaryotic organelles encode a tRNA Ile GAU and tRNA Ile LAU where L is lysidine (k 2 C).…”

“…5 Biophysical and biochemical experiments had suggested and continue to support the principle that some position 34 modifications structure the architecture of the anticodon stem and loop (ASL) to counter wobble whereas other modifications shape the ASL to enable a tRNA to decode three or even four synonymous codons (codons differing only in the wobble position N3). 6-10 …”

“…The modification of wobble position U 34 to s 2 U 34 alters tRNA's ability to wobble to G3; 5 the modification of C 32 to s 2 C 32 negates the ability of tRNAs with I 34 to decode A3 of the codon. 6 …”

Chemical synthesis of the 5-taurinomethyl(-2-thio)uridine modified anticodon arm of the human mitochondrial tRNALeu(UUR) and tRNALys

“…Chemically synthesized modified tRNA fragments, and in particular anticodon stem-loop hairpins (ASLs), have been widely utilized in model studies on the influence of posttranscriptional modification on molecule conformation/3D structure dynamics in solution (Duram et al 2005;Cantara et al 2012) as well as on conformation in the solid state (Weixlbaumer et al 2007;Cantara et al 2013). Recently, similar model studies on the impact of modification (f 5 C) on the structure/dynamics of the anticodon arm domain have been extended to hmt-tRNA specific for Met (Lusic et al 2008).…”