Exploring dynamic protein-protein interactions in cassava through the integrative interactome network

Abstract

Protein-protein interactions (PPIs) play an essential role in cellular regulatory processes. Despite, indepth studies to uncover the mystery of PPI-mediated regulations are still lacking. Here, an integrative interactome network (Meppi-Ux) was obtained by incorporating expression data into the improved genome-scale interactome network of cassava (MePPI-U). The MePPI-U, constructed by both interologand domain-based approaches, contained 3,638,916 interactions and 24,590 proteins (59% of proteins in the cassava AM560 genome version 6). After incorporating expression data as information of state, the MePPI-U rewired to represent condition-dependent PPIs (MePPI-Ux), enabling us to envisage dynamic PPIs (DPINs) that occur at specific conditions. The MePPI-Ux was exploited to demonstrate timely PPIs of cassava under various conditions, namely drought stress, brown streak virus (CBSV) infection, and starch biosynthesis in leaf/root tissues. MePPI-Ux drought and Meppi-Ux CBSV suggested involved ppis in response to stress. Meppi-Ux SB,leaf and Meppi-Ux SB,root suggested the involvement of interactions among transcription factor proteins in modulating how leaf or root starch is synthesized. These findings deepened our knowledge of the regulatory roles of PPIs in cassava and would undeniably assist targeted breeding efforts to improve starch quality and quantity. In cells, protein-protein interaction (PPI) is an important step that mediates the action of expressed proteins to function precisely in the regulatory process of signal transduction, homeostasis, and organ formation 1. Over 60 percent of entire proteins in genomes need to interact with their counterparts to achieve their functions, usually through post-translational modification (PTM) 2. The interaction between proteins might last lasting as in cases of stable multi-protein complexes. These interacting proteins are often found in cellular structures, e.g. binding of actin-cross-linking protein (CROLIN1) and F-actin protein to form actin structures in Arabiodopsis 3 , and are involved in the process of cell and organ formation, e.g. heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit in Starkeya novella involved in electron transfer of sulfite-oxidizing enzyme 4. The interactions could also be temporary, allowing transient mediation of regulatory states through changes in protein activity, stability, and localization across cellular compartments 5 , which are sources of dynamic regulation in cells. Some examples of transient protein interactions are the phosphorylation-dependent function of starch branching enzyme IIa (SBEIIa) in wheat, whereby the active form of SBEIIa is modulated by its interaction with kinase or phosphatase proteins; 6 the stability of autophagy protein 6 (ATG6) in Arabidopsis, which depends on its interaction with tumor necrosis factor receptor-associated factor TRAF1a and TRAF1b proteins; 7 and CSN1-induced COP1 nuclear localization in Arabidopsis, where the association of COP1 and signalsome COP9 (CSN...

Deciphering the Host–Pathogen Interactome of the Wheat–Common Bunt System: A Step towards Enhanced Resilience in Next Generation Wheat

“…In a study on Mycobacterium tuberculosis and Homo sapiens , researchers predicted HPIs by employing an e-value of 1e-10 and sequence identity of 30% [ 94 ]. Other researchers identified dynamic PPIs in cassava by using the following criteria: e-value ≤ 1 × 10 −10 , percent identity ≥ 60%, and percent coverage ≥ 80% in BLASTp sequence alignments [ 95 ].…”

Network organization of the plant immune system: from pathogen perception to robust defense induction

“…They were used in only one study to build a network based on 361 differentially expressed genes, co-occurrence, co-expression, and PPI data, and text mining (Ashrafi-Dehkordi et al, 2018). The cassava MePPi-U network constructed by Thanasomboon et al (2020) could be added to this group. However, the strategy used is different since a PPI network was first constructed and validated before integrating different RNA-seq datasets to infer the dynamics of PPIs and potentially those found in common under different abiotic or biotic stress conditions.…”

DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data

“…A protein-protein interaction network (shot for PPIN in the rest) is denoted as a undirected graph 𝐺 = (𝑉 , 𝐸), where each node represents a gene coding protein (shot for protein in the rest), each edge represents a protein-protein interaction [41], and matrix 𝑨 ∈ R 𝑛×𝑛 denotes the adjacency matrix encoding interactions of all nodes. Moreover, protein-protein interactions in a cell are usually dynamic and changing over time [9,24,26,43,44,50], and many efforts have been devoted into the dynamic PPIN construction [57,58,65,66], where a dynamic PPIN is represented as a sequence of observed snapshots G = {𝐺 (𝑡 ) } with 𝑡 ∈ {1, 2, . .…”