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Readthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons

ABSTRACT: Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor transfer RNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of BASIC TRANSCRIPTION FACTOR 3. Furthermore, the SCR events exhibit non-conserved signature and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the unprecedented recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Oryza Sativa (rice) Arabidopsis Thaliana (mouse-ear Cress) Zea Mays (maize) Glycine Max

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Yuqian Zhang

LAB HEAD: Liuji Wu

PROVIDER: PXD035958 | Pride | 2024-02-02

REPOSITORIES: pride

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			Action	DRS
	Arabidopsis_P676-A-peptides.txt	Txt
	Arabidopsis_P676-A-proteinGroups.txt	Txt
	Arabidopsis_P676-C-peptides.txt	Txt
	Arabidopsis_P676-C-proteinGroups.txt	Txt
	Arabidopsis_P676-D-peptides.txt	Txt

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Readthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons

Project description:Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor transfer RNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of BASIC TRANSCRIPTION FACTOR 3. Furthermore, the SCR events exhibit non-conserved signature and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the unprecedented recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.

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Large-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline

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