An expanded protein–protein interaction network in Bacillus subtilis reveals a group of hubs: Exploration by an integrative approach

Abstract

We have generated a protein-protein interaction network in Bacillus subtilis focused on several essential cellular processes such as cell division, cell responses to various stresses, the bacterial cytoskeleton, DNA replication and chromosome maintenance by careful application of the yeast two-hybrid approach. This network, composed of 793 interactions linking 287 proteins with an average connectivity of five interactions per protein, represents a valuable resource for future functional analyses. A striking feature of the network is a group of highly connected hubs (GoH) linking many different cellular processes. Most of the proteins of the GoH have unknown functions and are associated to the membrane. By the integration of available knowledge, in particular of transcriptome data sets, the GoH was decomposed into subgroups of party hubs corresponding to protein complexes or regulatory pathways expressed under different conditions. At a global level, the GoH might function as a very robust group of date hubs having partially redundant functions to integrate information from the different cellular pathways. Our analyses also provide a rational way to study the highly redundant functions of the GoH by a genetic approach.

Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported

“…We have also compared our D. vulgaris high confidence interactome and our revised version of the Hu et al (17) E. coli interactome to Y2H networks from six bacteria: E. coli (4), H. pylori (3), T. pallidum (9), C. jejuni (7), B. subtilis (6), and Synechocystis sp. (Fig.…”

“…Over the last 15 years, protein-protein "interactomes" have been characterized on a genome-wide scale in bacteria and eukaryotes by yeast 2-hybrid (Y2H) 1 and affinity purificationmass spectrometry (AP-MS) screens (1,(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). Y2H screens detect binary physical interactions between pairs of proteins expressed in a non-native host, whereas AP-MS detects proteins that co-purify with a tagged protein expressed in the native organism.…”

Metabolism Shapes the Cell

“…Another possibility is that UgtP and/or OpgH utilizes interactions with FtsZ to localize to regions in the cell where UDP-glucose is initially produced and metabolized. There are numerous protein-protein interaction and substrate channeling studies that certainly argue that bacteria are too clever to depend on diffusion alone to control metabolite flow (83)(84)(85)(86)(87)(88)(89)(90). Although the in vitro data argue for possible FtsZ-regulating mechanisms, especially for UgtP, any protein that interacts with an FtsZ surface may conceivably act as an inhibitor of FtsZ activity in vitro.…”

Function Annotation of Proteins in Eriocheir sinensis Based on the Protein-Protein Interaction Network

“…Given the significant importance of PINs, proteome-wide interaction networks based on protein interactions has been constructed for many organisms [10][11][12]. For example, Saccharomyces cerevisiae [13], Helicobacter pylori [14] and Bacillus subtilis [15]. In the decades-long development of PIN, interest has shifted from microbial systems [16,17] to mammalian [18] and a greater emphasis on more kinds of organisms [10].…”