Distal nucleotides affect the rate of stop codon read-through

Abstract

Background: A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position. However, it has been observed that ribosomes can misinterpret the stop codon and continue the translation in the 3′UTR region. This phenomenon is called stop codon read-through (SCR). It has been suggested that these events would occur on a programmed basis, but the underlying mechanisms are still not well understood.

Methods: Here, we present a strategy for the comprehensive identification of SCR events in the Drosophila melanogaster transcriptome by evaluating the ribosomal density profiles. The associated ribosomal leak rate was estimated for every event identified. A statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon in the sequences associated to SCR events was performed.

Results: The results show that the nucleotide usage pattern in transcripts with the UGA codon is different from the pattern for those transcripts ending in the UAA codon, suggesting the existence of at least two mechanisms that could alter the translational termination process. Furthermore, a linear regression models for each of the three stop codons was developed, and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon.

Conclusions: We report that distal nucleotides can affect the SCR rate in a stop-codon dependent manner.

Author summary

Sometimes ribosomes can misinterpret the stop codon and continue the translation to produce an extended protein. These events can occur by chance, as well as, by a programmed mechanism. However, the basis of this mechanism is still not known. In this paper, we report that the codon usage bias, at the end of the transcripts with UAA stop-codon, are a key determinant of the stop codon read-through. The non-optimal codon usage suggests that the canonical interpretation of the UAA codons might require ribosomal pause at the end of the coding region of the transcript.

Graphical abstract

Keywords

translational readthrough / stop codons / translational termination / ribosomal density profiles / nucleotide usage frequency

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DATA AVAILABILITY

Plots of the ribosomal density profile associated with all transcripts with SCR event can be found at Zenodo: Distal nucleotides affect the rate of stop codon read-through, zenodo.4633888. Data are available under the terms of the Creative Commons Attribution 4.0.

SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at https://doi.org/10.15302/ J-QB-022-0298.

AUTHOR CONTRIBUTIONS

LIE constructs ribosomal density profiles, participated in the statistical analysis and revised the manuscript. AMA carried out statistical analyses and modeling. JR conceived the study, coordinated the study and revised the manuscript. LD performs the divergence analysis, conceived the study and coordinated the study and wrote the draft of the manuscript. All authors read and approved the final manuscript.

ACKNOWLEDGEMENTS

LIE is funded by CONICET Ph.D. Fellowship. AMA and LD are researchers of CONICET (Argentina). JRR is Full Professor at the UNLP (Argentina). This work was supported by CONICET, Argentina (PIP2017-00059).

COMPLIANCE WITH ETHICS GUIDELINES

The authors Luciana I. Escobar, Andres M. Alonso, Jorge R. Ronderos and Luis Diambra declare that they have no conflict of interest or financial conflicts to disclose.

This article does not contain any studies with human or animal subjects performed by any of the authors.

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2022 The Author (s). Published by Higher Education Press.