基本HTML版本
Computational Molecular Biology 2014, Vol. 4, No. 7, 1-17
http://cmb.biopublisher.ca
1
Research Article Open Access
FunSecKB2: a fungal protein subcellular location knowledgebase
John Meinken
1,4
, David K. Asch
2,4
, Kofi A. Neizer-Ashun
3
, Guang-Hwa Chang
3
, Chester R.Cooper JR
2,4
, Xiang
Jia Min
2,4
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. Department of Mathematics & Statistics, Youngstown State University, Youngstown, OH 44555, USA
4. Center for Applied Chemical Biology, Youngstown State University, Youngstown, OH 44555, USA
Corresponding author email
Phone: (330) 941-1945 Fax: (330) 941-1483
Computational Molecular Biology, 2014, Vol.4, No.7 doi: 10.5376/cmb.2014.04.0007
Received: 05 Aug., 2014
Accepted: 21 Sep., 2014
Published: 22 Oct., 2014
© 2014 Meinken 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.
Preferred citation for this article:
Meinken et al., 2014,
FunSecKB2: a fungal protein subcellular location knowledgebase
,
Computational Molecular Biology, Vol.4, No.7, 1-17
(doi:
Abstract
FunSecKB2 is an improved and updated version of the fungal secretome and subcellular proteome, i. e. protein
subcellular location, knowledgebase. The fungal protein sequence data were retrieved from UniProtKB, consisting of nearly 2 million
entries with 167 species having a complete proteome. The assignments of protein subcellular locations were based on curated
information and prediction using seven computational tools. The tools used for subcellular location prediction include SignalP, WoLF
PSORT, Phobius, TargetP, TMHMM, FragAnchor, and PS-Scan. Secreted proteins, i.e. secretomes, along with 15 other subcellular
proteomes were predicted. The database can be searched by users using several different types of identifiers, gene name or
keyword(s). A subcellular proteome from a species can be searched or downloaded. BLAST searching whole fungal protein data or
secretomes is available. Community annotation of subcelluar locations based on experimental evidence is also supported. A primary
analysis revealed that the secretome size of a fungal species is one of the determining factors to its lifestyle. The Gene Ontology and
protein domain analysis of fungal secretomes revealed that fungal secretomes contain a large number of hydrolases, peptidases,
oxidoreductases, and lysases, which may have potential applications in bio-processing of chemical wastes or biofuel production. The
database provides an important and rich resource for the fungal community looking for protein subcellular location information and
performing comparative subcellular proteome analysis.
Database URL:
http://proteomics.ysu.edu/secretomes/fungi2/index.php
Keywords
Computational prediction; Fungi; Secreted protein; Secretome; Signal peptide; Subcellular location; Subcellular proteome
Introduction
Fungi play important roles in nature and in our daily
life. In nature, fungal species serve as decomposers of
biomass, which is critical for carbon and nutrient
cycling. In our daily life, edible mushrooms are
well-known examples of fungi.
Saccharomyces
cerevisiae
, known as a baker’s yeast, is widely used in
winemaking, baking and brewing. Some fungi are also
known as producers for drugs, such as antibiotics.
Fungal species are also important pathogens in insects,
animals, human and plants.
Fungi belong to one of the four kingdoms of
eukaryotic organisms. Fungal cells contain multiple
subcellular compartments for performing different
subcellular activities. For example, a mitochondrion,
which is a membrane-enclosed structure, is mainly
used to provide cellular energy; and a nucleus is a
place for storing genetic materials and a site for
controlling gene transcription. In this work, we define
a secretome as all proteins secreted outside the plasma
membrane in a species. These proteins include cell
wall proteins, extracellular matrix proteins, and
secreted soluble proteins that may serve as a hormone
or signal molecule or an enzyme. However, the
proteins in the secretory pathway machinery were not
included, which is slightly different form the original
definition of a secretome (Tjalsma et al., 2000; Lum
and Min, 2011a). Secreted proteins in biotrophic fungi
are identified as the main effectors responsible for