PXD038762

PXD038762 is an original dataset announced via ProteomeXchange.

Title	Readthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons
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.
HostingRepository	PRIDE
AnnounceDate	2024-02-02
AnnouncementXML	Submission_2024-02-02_01:04:50.013.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yuqian Zhang
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Glycine max; NCBI TaxID: 3847; scientific name: Oryza sativa (Rice); NCBI TaxID: 4530; scientific name: Zea mays (Maize); NCBI TaxID: 4577;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-12 22:27:41	ID requested
⏵ 1	2024-02-02 01:04:50	announced

10.1016/J.CELREP.2024.113723;

submitter keyword: proteogenomics, mass spectrometry,stop codon readthrough, recoding plasticity, amino acids, plants

Liuji Wu
contact affiliation	National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, China
contact email	wlj200120@163.com
lab head
Yuqian Zhang
contact affiliation	Henan Agricultural university
contact email	yqzhang0825@163.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD038762
     1. Label: PRIDE project
     2. Name: Readthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons