Dataset Information

Proteins identified by LC-MS/MS analysis to associate with RecJ4-StrepII (vs. empty vector).

ABSTRACT: RecJ4 association with RecJ3, RNase J and Cdc48A investigated by pullingown strep tagged-RecJ4 with its partner proteins

INSTRUMENT(S): LTQ Orbitrap XL

ORGANISM(S): Haloferax Volcanii Ds2

SUBMITTER: Swathi Dantuluri

LAB HEAD: Julie Maupin-Furlow

PROVIDER: PXD019933 | Pride | 2023-06-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Control-2889.raw	Raw
	Control-2889__F021050_.mzid.gz	Mzid
	Control-2889__F021050_.mzid_Control-2889__F021050_.MGF	Mzid
	OB-Control.raw	Raw
	OB-Control__F021051_.mzid.gz	Mzid

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Project description:Cellular functional pathways have evolved through selection based on fitness benefits conferred through protein intra- and inter-molecular interactions that comprise all protein conformational features and protein-protein interactions, collectively referred to as the interactome. While the interactome is regulated by proteome levels, it is also regulated independently by, post translational modification, co-factor, and ligand levels, as well as local protein environmental factors, such as osmolyte concentration, pH, ionic strength, temperature and others. In modern biomedical research, cultivatable cell lines have become an indispensable tool, with selection of optimal cell lines that exhibit specific functional profiles being critical for success in many cases. While it is clear that cell lines derived from different cell types have differential proteome levels, increased understanding of large-scale functional differences requires additional information beyond abundance level measurements, including how protein conformations and interactions are altered in certain cell types to shape functional landscapes. Here, we employed quantitative in vivo protein cross-linking coupled to mass spectrometry to probe large-scale protein conformational and interaction changes among three commonly employed human cell lines, HEK293, MCF-7, and HeLa cells. Isobaric quantitative Protein Interaction Reporter (iqPIR) technologies were used to obtain quantitative values of cross-linked peptides across three cell lines. These data illustrated highly reproducible (R2 values larger than 0.8 for all biological replicates) quantitative interactome levels across multiple biological replicates. We also measured protein abundance levels in these cells using data independent acquisition quantitative proteomics methods. Combining quantitative interactome and proteomics information allowed visualization of cell type-specific interactome changes mediated by proteome level adaptations as well as independently regulated interactome changes to gain deeper insight into possible drivers of these changes. Among the biggest detected alterations in protein interactions and conformations are changes in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, mitochondrial proteins, and others. Overall, these data demonstrate the utility and reproducibility of quantitative cross-linking to study systems-level interactome variations. Moreover, these results illustrate how combined quantitative interactomics and proteomics can provide unique insight on cellular functional landscapes.

Dataset Information

Proteins identified by LC-MS/MS analysis to associate with RecJ4-StrepII (vs. empty vector).

Dataset's files

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