Setting the Stage for an Interactive Map of Cytoskeletal Networks and Intracellular Transport Pathways

Abstract

The cytoskeletal and motor proteins belong to the most important components of eukaryotic cells. Most of them consist of diverse and huge protein families with general and very specific functions. They not only comprise the filament-forming proteins actin, intermediate filaments and microtubules, and the motor proteins myosin, kinesin and dynein, but all the regulatory and binding proteins. Here, we will present our progress towards designing an interactive map of the cytoskeletal network in eukaryotes and the pathways of active intracellular transport. The maps will be presented as interactive web application to assure accessibility and usability. The networks and transport functions are shown as cartoons. Depending on the taxon/organism, different cell types (single cell, muscle cell, neuron, root hair cells, etc.) and phases of the cell cycles will allow detailed investigation of all the members of the protein families involved. To construct these maps several prerequisites are necessary: A) Information about species and taxa; B) a complete list of the proteins involved including the resolution of ortholog/paralog relationships; C) a detailed review of the literature to reconstruct the cellular functions. A) and B) are currently stored in CyMoBase, the reference database for cytoskeletal and motor proteins. Data from newly sequenced species will be included through appropriate automatic software pipelines. C) will be implemented that the scientific community can update and refine known and newly determined functions. We hope that these networks and pathways will become useful tools in motility research and the basis for future experimental and computational studies.