Distal codons are key regulators in UAA codon read-through

LUCIANA INES ESCOBAR; ALONSO, ANDRES MARIANO; JORGE RAFAEL RONDEROS; L. DIAMBRA

Edinburgo

Workshop; Codon usage: Function, mechanism and evolution; 2022

EMBO

When the cellular machinery that translates the messenger RNA molecule into protein encounters a stop codon, it stops and releases the completed protein. Sometimes, however, the stop codon is not interpreted as a stop signal, and the translation of the messenger continues until another stop codon is encountered. This process is known as Stop Codon Read-through (SCR) [1], which gives rise to low abundance proteins with C-terminal extensions beyond the stop codon. SCR seems to play regulatory roles, but most immediately, diversifies the proteome by creating a pool of extended proteins. It has been suggested that these events would occur on a programmed basis, but the underlying mechanisms are still not well understood. Here, based on Ribo-seq data from Drosophila [2], we estimate ribosomal leak rate for 6739 transcripts. The examination of the 3'UTR region of these profiles allowed us to identify 1176 putative SCR events, with different ribosomal leak rates. We evaluated the nucleotides usage in a stop codon context region (60 pb) by means of the Kullback-Leibler divergence; which indicates differential nucleotide usage among two samples (transcripts with and without SCR) at each position. A descending ramp formed with slow codons is observed in almost all transcripts. The exception to this rule are those transcripts ending at UAA codon and which present SCR. We find a high frequency usage of nucleotides G or C (~75% against ~60% observed in the control group) in the third base of several codons of transcripts with the UAA stop codon and non-canonical termination. This result suggests that high ribosomal leakage rates in UAA ending transcripts could be associated with the lack of slow codons at the end of the coding region. This notable bias differs widely from that observed in UGA, indicating that the SCR mechanisms would be operating under patterns of differential usage of codons at distal positions for each type of stop codon [3].