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Mapping Architecture of Protein complexes in Arabidopsis using XL-MS (Histone H2B turboID)

ABSTRACT: Capturing molecular machines in action is key to understanding protein complex architecture, cellular regulation, and gene function. Here, we present a cross-linking mass spectrometry (XL-MS) platform using the PhoX cross-linker to map proteome-wide interactions in Arabidopsis thaliana. By analyzing whole-cell lysates, chloroplasts, and nuclei, we identified 52,944 unique cross-links pairs, corresponding to 37,531 residue pairs captured across 5,064 proteins and 3,083 protein-protein interactions (2,385 heteromeric and 698 homomultimeric). Comparison with the STRING database showed that 676 interactions had scores ≥ 0.9 and 241 ranged from 0.7–0.9. Our dataset provides residue-level interfaces that complement existing interaction networks with experimental evidence of spatial proximity. XL-MS captured the spatial organization of protein complexes, including the chloroplast 70S ribosome stalk and intermediates in photosystem repair, and revealed both shared and distinct interaction patterns across photosystems, ribosomes, and chromatin-associated proteins. The data also suggest ribosome ubiquitination, supported by diGly proteomics, and are consistent with histone interaction patterns observed using histone-TurboID. In addition, we identified an O-acyltransferase associated with histones, suggesting a potential role in chromatin-related processes. Together, these results demonstrate the utility of XL-MS for system-level mapping of the plant proteome and provide a resource for further study.

INSTRUMENT(S):

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

TISSUE(S): Seedling

SUBMITTER: Shouling Xu

LAB HEAD: Shouling Xu

PROVIDER: PXD078284 | Pride | 2026-07-29

REPOSITORIES: Pride

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			Action	DRS
	Dataset_details_H2B_TD.txt	Txt
	E20260123_02.raw	Raw
	E20260123_03.raw	Raw
	E20260123_04.raw	Raw
	E20260123_06.raw	Raw

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Mapping Architecture of Protein complexes in Arabidopsis using XL-MS (Part I Cell lysate)

Project description:Capturing molecular machines in action is key to understanding protein complex architecture, cellular regulation, and gene function. Here, we present a cross-linking mass spectrometry (XL-MS) platform using the PhoX cross-linker to map proteome-wide interactions in Arabidopsis thaliana. By analyzing whole-cell lysates, chloroplasts, and nuclei, we identified 52,944 unique cross-links pairs, corresponding to 37,531 residue pairs captured across 5,064 proteins and 3,083 protein-protein interactions (2,385 heteromeric and 698 homomultimeric). Comparison with the STRING database showed that 676 interactions had scores ≥ 0.9 and 241 ranged from 0.7–0.9. Our dataset provides residue-level interfaces that complement existing interaction networks with experimental evidence of spatial proximity. XL-MS captured the spatial organization of protein complexes, including the chloroplast 70S ribosome stalk and intermediates in photosystem repair, and revealed both shared and distinct interaction patterns across photosystems, ribosomes, and chromatin-associated proteins. The data also suggest ribosome ubiquitination, supported by diGly proteomics, and are consistent with histone interaction patterns observed using histone-TurboID. In addition, we identified an O-acyltransferase associated with histones, suggesting a potential role in chromatin-related processes. Together, these results demonstrate the utility of XL-MS for system-level mapping of the plant proteome and provide a resource for further study.

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