Multi class intracellular protein targeting predictions in diatoms and other algae with complex plastids: ASAFind 2.0

Abstract

Cells of diatoms and related algae with complex plastids of red algal origin are highly compartmentalized. These plastids are surrounded by four envelope membranes, which also define the periplastidic compartment (PPC), the space between the second and third membranes. The PPC corresponds to the cytosol of the eukaryotic alga that was the ancestor of the complex plastid. Metabolic reactions as well as cell biological processes take place in this compartment; however, its exact function remains elusive. Automated predictions of protein locations proved useful for genome wide explorations of metabolism in the case of plastid proteins, but until now, no automated method for the prediction of PPC proteins was available. Here, we present an updated version of the plastid protein predictor ASAFind, which includes optional prediction of PPC proteins. The new ASAFind version also accepts the output of the most recent versions of SignalP (5.0) and TargetP (2.0) input data. Furthermore, we release a Python script to calculate custom scoring matrices for adjustment of the ASAFind method to other groups of algae, and included the option to run the predictions with custom scoring matrices in a simplified score cut-off mode.