Network Topological Analysis for the Identification of Novel Hubs in Plant Nutrition

Abstract

Network analysis is a systems biology-oriented approach based on graph theory that has been recently adopted in various fields of life sciences. Starting from mitochondrial proteomes purified from roots of Cucumis sativus plants grown under single or combined iron (Fe) and molybdenum (Mo) starvation, we reconstructed and analyzed at the topological level the protein–protein interaction (PPI) and co-expression networks. Besides formate dehydrogenase (FDH), already known to be involved in Fe and Mo nutrition, other potential mitochondrial hubs of Fe and Mo homeostasis could be identified, such as the voltage-dependent anion channel VDAC4, the beta-cyanoalanine synthase/cysteine synthase CYSC1, the aldehyde dehydrogenase ALDH2B7, and the fumaryl acetoacetate hydrolase. Network topological analysis, applied to plant proteomes profiled in different single or combined nutritional conditions, can therefore assist in identifying novel players involved in multiple homeostatic interactions.

Equine Mesenchymal Stem/Stromal Cells Freeze-Dried Secretome (Lyosecretome) for the Treatment of Musculoskeletal Diseases: Production Process Validation and Batch Release Test for Clinical Use

“…An Equus caballus protein-protein interaction (PPI) network was built by homology with Homo sapiens, as previously reported [55]. Proteins identified in at least 2 out of 7 replicate analysis were combined with the Homo sapiens PPI network retrieved from the STRING database [56].…”

CD4+ T-Cell Activation Prompts Suppressive Function by Extracellular Vesicle-Associated MicroRNAs

“…The list of transcripts differentially expressed following TCR stimulation was also used to reconstruct a PPI network by String Cytoscape’s App ( Doncheva et al, 2019 ); specifically, only Experiments (score >0.0031) and Databases (score >0.36) annotated interaction were considered. The reconstructed PPI network was finally processed at the topological level by Centiscape Cytoscape’s App ( Scardoni et al, 2014 ), to calculate the node Betweenness, Bridging, and Centroid centralities; nodes with centrality values above the average calculated on whole network were considered hubs, as previously reported ( Di Silvestre et al, 2021 ). In addition, statistical significance of topological results was tested by considering randomized network models ( Supplementary Figures 1C,D ): they were reconstructed and analyzed by an in-house R script based on VertexSort (to build random models), igraph (to compute centralities), and ggplot2 (to plot results) libraries; the results were visualized in the form of violin plots.…”

Presence of a Mitovirus Is Associated with Alteration of the Mitochondrial Proteome, as Revealed by Protein–Protein Interaction (PPI) and Co-Expression Network Models in Chenopodium quinoa Plants

“…All processing were performed by JMP15.2 SAS software. A Chenopodium quinoa PPI network model was reconstructed by homology with Arabidopsis thaliana, as previously reported [18]. Specifically, mitochondrial predicted or annotated Chenopodium quinoa protein sequences (n = 515) were submitted to STRING Cytoscape's App [30] aiming to homology with Arabidopsis thaliana proteins.…”

“…However, the number of studies focusing on PPIs prediction in plants is constantly increasing [ 15 , 16 , 17 ]. PPI network reconstruction often relies on orthologs in model plants, such as Arabidopsis thaliana [ 14 , 18 ]. Although this approach presents some limitations, ranging from false positives to poor coverage from associalogs, it represents a valuable strategy for a rapid PPI network inference in plant organisms [ 19 ].…”

“…Although this approach presents some limitations, ranging from false positives to poor coverage from associalogs, it represents a valuable strategy for a rapid PPI network inference in plant organisms [ 19 ]. Alternatively, and complementarily to PPI, Co-Exp models, reconstructed from experimental proteomic data, represent a way to model large-scale proteomic datasets of non-model plants as networks [ 18 , 20 ].…”