PlantSecKB: the Plant Secretome and Subcellular Proteome KnowledgeBase  

Gengkon Lum1,3 , John Meinken1 , Jessica Orr2 , Stephanie Frazier2 , Xiang Jia Min2,3
1. Department of Computer Science and Information Systems, Youngstown State University, OH 44555, USA
2. Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
3. Center for Applied Chemical Biology, Youngstown State University, Youngstown, OH 44555, USA
Author    Correspondence author
Computational Molecular Biology, 2014, Vol. 4, No. 1   doi: 10.5376/cmb.2014.04.0001
Received: 04 Dec., 2013    Accepted: 24 Dec., 2013    Published: 24 Feb., 2014
© 2014 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Min et al., 2014, PlantSecKB: the Plant Secretome and Subcellular Proteome KnowledgeBase, Computational Molecular Biology, Vol.4, No.1 1-17 (doi: 10.5376/cmb.2014.04.0001)

Abstract

Prediction and curation of protein subcellular locations is essential for protein functional annotation. We developed the Plant Secretome and Subcellular Proteome KnowledgeBase (PlantSecKB) for the plant research community to access and curate plant protein subcellular locations, with a focus on secreted proteins. The database is constructed with all the available plant protein data retrieved from the UniProtKB database and plant protein sequences predicted from EST data assembled by the PlantGDB project. The database contains information collected from three sources: (1) subcellular locations that were curated or computationally predicted in the UniProtKB; (2) subcellular locations and features predicted by eight computational tools; (3) secreted proteins that were curated from recent literature. The categories of subcellular locations include secretome, mitochondria, chloroplast, cytosol, cytoskeleton, endoplasmic reticulum, Golgi apparatus, lysosome, peroxisome, nucleus, vacuole, and plasma membrane. The data can be searched by using UniProt accession number or ID, GenBank GI or RefSeq accession number, gene name, and keywords. Species specific secretome and subcellular proteomes can be searched and downloaded into a FASTA file.  BLAST is available to allow users to search the database based on protein sequences. Community curation for subcellular locations of plant proteins is also supported.  A primary analysis revealed that monocots and dicots had a similar proportion of secretomes, and monocots had a significantly higher proportion of proteins distributed to mitochondria (both membrane and non-membrane) and chloroplast membrane, while dicots had significantly more proteins distributed to cytosol and nucleus. This database aims to facilitate plant protein research and is available at http://proteomics.ysu.edu/secretomes/plant.php.

Keywords
Computational prediction; Expressed sequence tags; Plant; Secreted protein; Secretome; Signal peptide; Subcellular location; Subcellular proteome
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