Large-scale Top-down Proteomics of the Arabidopsis thaliana Leaf and Chloroplast Proteomes

ABSTRACT: We present a large-scale top-down proteomics study of plant leaf and chloroplast proteins, achieving the identification of over 4700 unique proteoforms. Using capillary zone electrophoresis coupled with tandem mass spectrometry analysis of offline size-exclusion chromatography fractions, we identify 3198 proteoforms for total leaf and 1836 proteoforms for chloroplast, with 1024 and 363 proteoforms having post-translational modifications (PTMs), respectively. The electrophoretic mobility prediction of CZE allowed us to validate PTMs that impact the charge state such as acetylation and phosphorylation. Identified PTMs included Trp (di)oxidation events on six chloroplast proteins that may represent novel targets of singlet oxygen sensing. Furthermore, our top-down proteomics data provides direct experimental evidence of the N- and C-terminal residues of numerous mature proteoforms from chloroplast, mitochondria, endoplasmic reticulum, and other sub-cellular localizations. With this information, we propose transit peptide cleavage sites and correct sub-cellular localization signal predictions. This large-scale analysis illustrates the power of top-down proteoform identification of PTMs and intact sequences that can benefit our understanding of both the structure and function of hundreds of plant proteins.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Liangliang Sun  

LAB HEAD: Liangliang Sun

PROVIDER: PXD034368 | Pride | 2023-01-05

REPOSITORIES: Pride