Comparative Network Biology Discovers Protein Complexes That Underline Cellular Differentiation in Anabaena sp

Unravelling the involvement of protein disorder in cyanobacterial stress responses

This study has explored the involvement of Intrinsically Disordered Proteins (IDPs) in cyanobacterial stress response. IDPs possess distinct physicochemical properties, which allow them to execute diverse functions. Anabaena PCC 7120, the model photosynthetic, nitrogen-fixing cyanobacterium encodes 688 proteins (11 % of the total proteome) with at least one intrinsically disordered region (IDR). Of these, 130 proteins that showed >30 % overall disorder were designated as IDPs. Physico-chemical analysis, showed these IDPs to adopt shapes ranging from 'globular' to 'tadpole-like'. Upon exposure to NaCl, 41 IDP-encoding genes were found to be differentially expressed. Surprisingly, most of these were induced, indicating the importance of IDP-accumulation in overcoming salt stress. Subsequently, six IDPs were identified to be induced by multiple stresses (salt, ammonium and selenite). Interestingly, the presence of these 6-multiple stress-induced IDPs was conserved in filamentous cyanobacteria. Utilizing the experimental proteomic data of Anabaena, these 6 IDPs were found to interact with many proteins involved in diverse pathways, underscoring their physiological importance as protein hubs. This study lays the framework for IDP-related research in Anabaena by (a) identifying, as well as physiochemically characterizing, all the disordered proteins and (b) uncovering a subset of IDPs that are likely to be critical in adaptation to environmental stresses.

Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry

We present CFdb, a harmonized resource of interaction proteomics data from 411 co-fractionation mass spectrometry (CF-MS) datasets spanning 21,703 fractions. Meta-analysis of this resource charts protein abundance, phosphorylation, and interactions throughout the tree of life, including a reference map of the human interactome. We show how large-scale CF-MS data can enhance analyses of individual CF-MS datasets, and exemplify this strategy by mapping the honey bee interactome.

CyanoMapDB: a database integrating experimentally validated protein-protein interactions in cyanobacteria

As one of the essential life forms in the biosphere, research on cyanobacteria has been growing remarkably for decades. Biological functions in organisms are often accomplished through protein-protein interactions (PPIs), which help to regulate interacting proteins or organize them into an integral machine. However, the study of PPIs in cyanobacteria falls far behind that in mammals and has not been integrated for ease of use. Thus, we built CyanoMapDB (http://www.cyanomapdb.msbio.pro/), a database providing cyanobacterial PPIs with experimental evidence, consisting of 52,304 PPIs among 6,789 proteins from 23 cyanobacterial species. We collected available data in UniProt, STRING, and IntAct, and mined numerous PPIs from co-fractionation MS data in cyanobacteria. The integrated data are accessible in CyanoMapDB (http://www.cyanomapdb.msbio.pro/), enabling users to easily query proteins of interest, investigate interacting proteins with evidence from different sources, and acquire a visual network of the target protein. We believe that CyanoMapDB will promote research involved with cyanobacteria and plants.