Chapter

Laboratory Protocols in Fungal Biology

Part of the series Fungal Biology pp 545-557

Date:

Bioinformatic Protocols and the Knowledge-Base for Secretomes in Fungi

  • Gengkon LumAffiliated withDepartment of Computer Science and Information Systems, Youngstown State University
  • , Xiang Jia MinAffiliated withDepartment of Biological Sciences, Center for Applied Chemical Biology, Youngstown State University, One University Plaza Email author 

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Abstract

Fungal secreted proteins play important roles in cell signaling, metabolism, and regulation of fungal growth and development. The secretome refers to all secreted proteins in a proteome that are identified from completely sequenced genomes. The majority of secreted proteins are classical, signal peptide-dependent proteins that can be predicted using bioinformatics tools. In this chapter, we describe some commonly used tools for secreted protein prediction in fungi and propose a relatively accurate bioinformatic protocol for fungal secretome identification. The protocol combines multiple signal peptide or subcellular location predictors, including SignalP, WoLF PSORT, and Phobius, with TMHMM for removing transmembrane proteins and PROSITE PS-Scan for removing endoplasmic reticulum (ER) proteins. Applying this protocol, we have built the fungal secretome knowledge-base (FunSecKB). The utility of FunSecKB is described in detail. FunSecKB serves the community as a central portal for search and deposition of fungal secretome information.

Keywords

Secreted proteins Secretome Signal peptide Fungi Prediction Knowledge-base Database