Proteomics

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Quantitative proteomics reveals extensive lysine ubiquitination in Arabidopsis thaliana

ABSTRACT: In this study, we describe an antibody-based approach to enrich ubiquitinated peptides from vegetative tissues for detection via peptide mass spectrometry. This enrichment method can be coupled with isobaric labeling to enable quantification from up to 18-multiplexed samples. This approach identified 19,740 ubiquitinated lysine sites arising from 5,936 proteins in Arabidopsis primary roots, seedlings and rosette leaves. Gene Ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. Proteins with altered abundance and ubiquitination state in roots upon bortezomib treatment included transporters, adaptors, and transcription factors.

INSTRUMENT(S): Q Exactive Plus, Orbitrap Exploris 480

ORGANISM(S): Arabidopsis Thaliana (ncbitaxon:3702)

SUBMITTER: Justin Walley  

PROVIDER: MSV000095496 | MassIVE | Wed Jul 31 09:06:00 BST 2024

SECONDARY ACCESSION(S): PXD054448

REPOSITORIES: MassIVE

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Quantitative proteomics reveals extensive lysine ubiquitination and transcription factor stability states in Arabidopsis.

Song Gaoyuan G   Montes Christian C   Olatunji Damilola D   Malik Shikha S   Ji Chonghui C   Clark Natalie M NM   Pu Yunting Y   Kelley Dior R DR   Walley Justin W JW  

The Plant cell 20241121

Protein activity, abundance, and stability can be regulated by posttranslational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function, yet we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich ubiquitinated peptides coupled with isobaric labeling to enable quantification of up to 18-multiplexed samples. This approac  ...[more]

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