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DOI number:

10.1016/j.molp.2023.03.013

Journal:

Molecular Plant

Key Words:

4C interactomics; 4D biomolecular modulomes; CHAMPION; community; in vivo qXL-MS; nucleome

Abstract:

Nuclear proteins are major constituents and key regulators of nucleome topological organization and manipulators of nuclear events. To decipher the global connectivity of nuclear proteins and the hierarchically organized modules of their interactions, double chemical crosslinking coupled with mass spectrometry (in vivo XL-MS) analysis was integrated with the dimethyl labeling to generate a qXL-MS workflow, which enable the identification of 5340 crosslinked peptides (or crosslinks) from the nuclei of soybean seedlings. These crosslinks were converted into 1297 nuclear protein–protein interactions (PPIs), 1220 (94%) of which were non-confirmative (or novel) nuclear PPIs compared with those in repositories. There were 250 and 26 novel interactors of histones and the nucleolar box C/D small nucleolar ribonucleoprotein complex, respectively. Modulomic analysis of orthologous Arabidopsis PPIs produced 27 and 24 master nuclear PPI modules (NPIMs) that contain the condensate-forming protein(s) and the intrinsically disordered region–containing proteins, respectively. These NPIMs successfully captured previously reported nuclear protein complexes and nuclear bodies in the nucleus. Surprisingly, these NPIMs were hierarchically assorted into four higher-order communities in a nucleomic graph, including genome and nucleolus communities. This combinatorial pipeline of 4C quantitative interactomics and PPI network modularization revealed 17 ethylene-specific module variants that participate in a broad range of nuclear events. The pipeline was able to capture both nuclear protein complexes and nuclear bodies, construct the topological architectures of PPI modules and module variants in the nucleome, and probably map the protein compositions of biomolecular condensates.

Co-author:

Fengchao Yu, Guang Zhu, Wenhao Zhang, Haiteng Deng, Al Burlingame, Weichuan Yu, Tingliang Wang, Ning Li

First Author:

Shuaijian Dai#, Shichang Liu#, Chen Zhou#

Indexed by:

Journal paper

Document Type:

Article

Volume:

16

Issue:

5

Page Number:

930-961

ISSN No.:

1674-2052

Translation or Not:

no

Date of Publication:

2023-03-23