Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome

0541499 - ÚMG 2021 RIV CH eng J - Journal Article
Sztacho, Martin - Šalovská, Barbora - Červenka, Jakub - Balaban, Can - Hoboth, Peter - Hozák, Pavel
Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome.
Cells. Roč. 10, č. 1 (2021), č. článku 68. E-ISSN 2073-4409
R&D Projects: GA ČR GA19-05608S; GA ČR(CZ) GA18-19714S; GA MŠMT LTC19048; GA MŠMT LTC20024; GA MŠMT(CZ) LM2018129; GA MŠMT(CZ) ED1.1.00/02.0109; GA MŠMT(CZ) EF16_013/0001775
Institutional support: RVO:68378050 ; RVO:67985904
Keywords : nucleus * limited proteolysis * mass spectrometry * phosphoinositides * phosphatidylinositol 4 * 5-bisphosphate
OECD category: Cell biology
Impact factor: 7.666, year: 2021
Method of publishing: Open access
https://www.mdpi.com/2073-4409/10/1/68

Specific nuclear sub-compartments that are regions of fundamental processes such as gene expression or DNA repair, contain phosphoinositides (PIPs). PIPs thus potentially represent signals for the localization of specific proteins into different nuclear functional domains. We performed limited proteolysis followed by label-free quantitative mass spectrometry and identified nuclear protein effectors of the most abundant PIP-phosphatidylinositol 4,5-bisphosphate (PIP2). We identified 515 proteins with PIP2-binding capacity of which 191 'exposed' proteins represent a direct PIP2 interactors and 324 'hidden' proteins, where PIP2 binding was increased upon trypsin treatment. Gene ontology analysis revealed that 'exposed' proteins are involved in the gene expression as regulators of Pol II, mRNA splicing, and cell cycle. They localize mainly to non-membrane bound organelles-nuclear speckles and nucleolus and are connected to the actin nucleoskeleton. 'Hidden' proteins are linked to the gene expression, RNA splicing and transport, cell cycle regulation, and response to heat or viral infection. These proteins localize to the nuclear envelope, nuclear pore complex, or chromatin. Bioinformatic analysis of peptides bound in both groups revealed that PIP2-binding motifs are in general hydrophilic. Our data provide an insight into the molecular mechanism of nuclear PIP2 protein interaction and advance the methodology applicable for further studies of PIPs or other protein ligands.
Permanent Link: http://hdl.handle.net/11104/0319063