Identification and functional characterization of mRNAs that exhibit stop codon readthrough in Arabidopsis thaliana

Sahoo, S and Singh, D and Singh, A and Pandit, M and Vasu, K and Som, S and Pullagurla, NJ and Laha, D and Eswarappa, SM (2022) Identification and functional characterization of mRNAs that exhibit stop codon readthrough in Arabidopsis thaliana. In: Journal of Biological Chemistry, 298 (8).

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Abstract

Stop codon readthrough (SCR) is the process of continuation of translation beyond the stop codon, generating protein isoforms with C-terminal extensions. SCR has been observed in viruses, fungi, and multicellular organisms, including mammals. However, SCR is largely unexplored in plants. In this study, we have analyzed ribosome profiling datasets to identify mRNAs that exhibit SCR in Arabidopsis thaliana. Analyses of the ribosome density, ribosome coverage, and three-nucleotide periodicity of the ribosome profiling reads in the mRNA region downstream of the stop codon provided strong evidence for SCR in mRNAs of 144 genes. We show that SCR generated putative evolutionarily conserved nuclear localization signals, transmembrane helices, and intrinsically disordered regions in the C-terminal extensions of several of these proteins. Furthermore, gene ontology functional enrichment analysis revealed that these 144 genes belong to three major functional groups—translation, photosynthesis, and abiotic stress tolerance. Using a luminescence-based readthrough assay, we experimentally demonstrated SCR in representative mRNAs belonging to each of these functional classes. Finally, using microscopy, we show that the SCR product of one gene that contains a nuclear localization signal at the C-terminal extension, CURT1B, localizes to the nucleus as predicted. Based on these observations, we propose that SCR plays an important role in plant physiology by regulating protein localization and function.

Item Type:	Journal Article
Publication:	Journal of Biological Chemistry
Publisher:	American Society for Biochemistry and Molecular Biology Inc.
Additional Information:	The copyright for this article belongs to the American Society for Biochemistry and Molecular Biology Inc.
Keywords:	Gene Ontology; Macromolecules; Mammals; Plants (botany); Proteins; Viruses, Arabidopsis; Arabidopsis thaliana; C-terminal extensions; Functional characterization; Nuclear localization signal; Protein isoforms; Readthrough; Ribosome; Stop codons; Translation, Genes
Department/Centre:	Division of Biological Sciences > Biochemistry UG Programme
Date Deposited:	04 Aug 2022 09:23
Last Modified:	04 Aug 2022 09:23
URI:	https://eprints.iisc.ac.in/id/eprint/75291

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