$${\text{COSNet}}_i$$: ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes

Abstract

Background Upon environmental stimuli, ribosomes are surmised to undergo compositional rearrangements due to abundance changes among proteins assembled into the complex, leading to modulated structural and functional characteristics. Here, we present the ComplexOme-Structural Network Interpreter ($${\text{COSNet}}_i$$ COSNet i ), a computational method to allow testing whether ribosomal proteins (rProteins) that exhibit abundance changes under specific conditions are spatially confined to particular regions within the large ribosomal complex. Results $${\text{COSNet}}_i$$ COSNet i translates experimentally determined structures into graphs, with nodes representing proteins and edges the spatial proximity between them. In its first implementation, $${\text{COSNet}}_i$$ COSNet i considers rProteins and ignores rRNA and other objects. Spatial regions are defined using a random walk with restart methodology, followed by a procedure to obtain a minimum set of regions that cover all proteins in the complex. Structural coherence is achieved by applying weights to the edges reflecting the physical proximity between purportedly contacting proteins. The weighting probabilistically guides the random-walk path trajectory. Parameter tuning during region selection provides the option to tailor the method to specific biological questions by yielding regions of different sizes with minimum overlaps. In addition, other graph community detection algorithms may be used for the $${\text{COSNet}}_i$$ COSNet i workflow, considering that they yield different sized, non-overlapping regions. All tested algorithms result in the same node kernels under equivalent regions. Based on the defined regions, available abundance change information of proteins is mapped onto the graph and subsequently tested for enrichment in any of the defined spatial regions. We applied $${\text{COSNet}}_i$$ COSNet i to the cytosolic ribosome structures of Saccharomyces cerevisiae, Oryctolagus cuniculus, and Triticum aestivum using datasets with available quantitative protein abundance change information. We found that in yeast, substoichiometric rProteins depleted from translating polysomes are significantly constrained to a ribosomal region close to the tRNA entry and exit sites. Conclusions $${\text{COSNet}}_i$$ COSNet i offers a computational method to partition multi-protein complexes into structural regions and a statistical approach to test for spatial enrichments of any given subsets of proteins. $${\text{COSNet}}_i$$ COSNet i is applicable to any multi-protein complex given appropriate structural and abundance-change data. $${\text{COSNet}}_i$$ COSNet i is publicly available as a GitHub repository https://github.com/MSeidelFed/COSNet_i and can be installed using the python installer pip.

Protein interactome of 3′,5′‐cAMP reveals its role in regulating the actin cytoskeleton

“…Seven ribosomal proteins were identified among the significantly stabilized targets. Spatial statistics were performed using a Cryo‐EM wheat 80S ribosome structure (Armache et al., 2010a; Armache et al., 2010b) following previously published procedures (https://github.com/MSeidelFed/COSNet_i) (Martinez‐Seidel, Hsieh, et al., 2021) and tuning parameters (Martinez‐Seidel, Beine‐Golovchuk, et al., 2021). Coherent ribosomal regions were obtained and Fisher's exact test was used to statistically inquire whether the significantly stabilized ribosomal proteins were constrained to specific ribosomal regions or randomly scattered in the complex.…”