Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons

Abstract

A stop or nonsense codon is an in-frame triplet within a messenger RNA that signals the termination of translation. One common feature shared among all three nonsense codons (UAA, UAG, and UGA) is a uridine present at the first codon position. It has been recently shown that the conversion of this uridine into pseudouridine (C) suppresses translation termination, both in vitro and in vivo. Furthermore, decoding of the pseudouridylated nonsense codons is accompanied by the incorporation of two specific amino acids in a nonsense codon-dependent fashion. C differs from uridine by a single N 1 H group at the C5 position; how C suppresses termination and, more importantly, enables selective decoding is poorly understood. Here, we provide molecular rationales for how pseudouridylated stop codons are selectively decoded. Our analysis applies crystal structures of ribosomes in varying states of translation to consider weakened interaction of C with release factor; thermodynamic and geometric considerations of the codon-anticodon base pairs to rank and to eliminate mRNA-tRNA pairs; the mechanism of fidelity check of the codon-anticodon pairing by the ribosome to evaluate noncanonical codon-anticodon base pairs and the role of water. We also consider certain tRNA modifications that interfere with the C-coordinated water in the major groove of the codon-anticodon mini-helix. Our analysis of nonsense codons enables prediction of potential decoding properties for C-modified sense codons, such as decoding CUU potentially as Cys and Tyr. Our results provide molecular rationale for the remarkable dynamics of ribosome decoding and insights on possible reprogramming of the genetic code using mRNA modifications.

Transcriptome-wide dynamics of RNA pseudouridylation

“…Molecular modelling data suggest a possibility that the pseudouridylation of specific codons may lead to altered tRNA–mRNA interactions; for example, pseudouridylation of the phenylalanine codon UUU (generating ψUU) could result in the incorporation of either cysteine or tyrosine 25 . Interestingly, when transfected into mammalian cells, in vitro -transcribed pseudouridine-containing mRNA is capable of generating a functional protein, suggesting that the decoding of sense codons is perhaps not grossly affected 26 .…”

Adaptive Translation as a Mechanism of Stress Response and Adaptation

“…Modification of U to Ψ in all three stop codons leads to high levels of stop codon readthrough, and each Ψ-modified stop codon specifically codes for two amino acids. Computational analysis suggests that Ψ-modified sense codons can be recoded; for example, the standard UUU codes for Phe, but ΨUU may be read as Cys/Tyr by the ribosome (55). Ψ is a major modification in tRNA, rRNA and spliceosomal RNA (8).…”

Structural Basis for Translation Termination on a Pseudouridylated Stop Codon

“…Substitution of the uridine to another nucleotide strongly reduces binding of release factors [17]. In line with this observation, recent computational analyses suggest that recognition of pseudouridine instead of uridine would require a conformational rearrangement of a stop codon [18]. The rearrangement was proposed to be necessary to align pseudouridine’s dipole moment (which is distinct from that of uridine) with the dipole moment of a release factor’s recognition helix α5 [18].…”