Basic HTML Version
Computational Molecular Biology
2014, Vol.4, No.1, 1-17 http://cmb.sophiapublisher.com
Research Report
Open Access
PlantSecKB: the Plant Secretome and Subcellular Proteome KnowledgeBase
Gengkon Lum
1,3
, John Meinken
1
, Jessica Orr
2
, Stephanie Frazier
2
, Xiang Jia Min
2,3
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
Corresponding Author email: xmin@ysu.edu;
Author
Computational Molecular Biology, 2014, Vol.4, No.1 doi: 10.5376/cmb.2014.04.0001
Copyright
© 2014 Min et al. 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.
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
Introduction
Plants are the main contributors to the production of
biomass including carbohydrates, proteins, lipids,
cellulose and other biomaterials. Plant proteins
including enzymes, regulatory and structural proteins
play important biological roles in regulating plant
growth and development. Plant proteins are
synthesized within a cell and transported to different
subcellular locations including extracellular space or
matrix to perform their biological functions. This
process often is called protein sorting or targeting
(Foresti and Denecke, 2008; Rose and Lee, 2010).
Plant cells contain a cell wall, a plasma membrane,
choloroplasts, mitochondria, a large vacuole, a nucleus,
endoplasmic reticulum (ER), a Golgi apparatus,
peroxisomes, cytosol, etc. Membrane proteins can be
embedded or attached to plasma membrane, organelle
membrane or endomembrane systems.
Identification and analysis of protein subcellular
locations in eukaryotes is one of the important subjects
for annotating a proteome. In a plant species, proteins
secreted to the extracellular space or matrix, which
includes the cell wall, are collectively called a
“secretome” (Agrawal et al., 2010; Lum and Min, 2011a).
Computational
Molecular Biology
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)
Received: 04 Dec., 2013
|
Accepted: 24 Dec., 2013
|
Published: 24 Feb., 2014