Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

被引：137

作者：

Choi, Jaeyoung ^{[1
,2
,3
]}

Park, Jongsun ^{[1
,2
,3
,4
]}

Kim, Donghan ^{[1
,2
,3
]}

Jung, Kyongyong ^{[1
,2
,3
]}

Kang, Seogchan ^{[6
]}

Lee, Yong-Hwan ^{[1
,2
,3
,4
,5
]}

机构：

[1] Seoul Natl Univ, Fungal Bioinformat Lab, Seoul 151921, South Korea

[2] Seoul Natl Univ, Dept Agr Biotechnol, Seoul 151921, South Korea

[3] Seoul Natl Univ, Ctr Fungal Pathogenesis, Seoul 151921, South Korea

[4] Seoul Natl Univ, Ctr Fungal Genet Resources, Seoul 151921, South Korea

[5] Seoul Natl Univ, Ctr Agr Biomat, Seoul 151921, South Korea

[6] Penn State Univ, Dept Plant Pathol, University Pk, PA 16802 USA

来源：

BMC GENOMICS | 2010年 / 11卷

基金：

新加坡国家研究基金会;

关键词：

CANDIDA-ALBICANS GENOME; EXTRACELLULAR PROTEINS; SUBCELLULAR-LOCALIZATION; PROTEOMIC ANALYSIS; SIGNAL PEPTIDES; SEQUENCE; PLANT; YEAST; PHYTOPHTHORA; PREDICTION;

D O I：

10.1186/1471-2164-11-105

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background: Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD). Description: A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository. Conclusions: The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at http://fsd.snu.ac.kr/.

引用

页数：15

共 94 条

[1] Fungal degradation of wood:: initial proteomic analysis of extracellular proteins of Phanerochaete chrysosporium grown on oak substrate [J].

Abbas, A ;

Koc, H ;

Liu, F ;

Tien, M .

CURRENT GENETICS, 2005, 47 (01) :49-56

[2]

ABBAS KA, 2006, CELLULAR MOL IMMUNIL, P6

[3]

[Anonymous], THESIS U LEEDS

[4] Feature-based prediction of non-classical and leaderless protein secretion [J].

Bendtsen, JD ;

Jensen, LJ ;

Blom, N ;

von Heijne, G ;

Brunak, S .

PROTEIN ENGINEERING DESIGN & SELECTION, 2004, 17 (04) :349-356

[5] Improved prediction of signal peptides: SignalP 3.0 [J].

Bendtsen, JD ;

Nielsen, H ;

von Heijne, G ;

Brunak, S .

JOURNAL OF MOLECULAR BIOLOGY, 2004, 340 (04) :783-795

[6] Genomic Exploration of the Hemiascomycetous Yeasts:: 16.: Candida tropicalis [J].

Blandin, G ;

Ozier-Kalogeropoulos, O ;

Wincker, P ;

Artiguenave, F ;

Dujon, B .

FEBS LETTERS, 2000, 487 (01) :91-94

[7] Fungal secretomes - nature's toolbox for white biotechnology [J].

Bouws, Henning ;

Wattenberg, Andreas ;

Zorn, Holger .

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2008, 80 (03) :381-388

[8] Evolution of pathogenicity and sexual reproduction in eight Candida genomes [J].

Butler, Geraldine ;

Rasmussen, Matthew D. ;

Lin, Michael F. ;

Santos, Manuel A. S. ;

Sakthikumar, Sharadha ;

Munro, Carol A. ;

Rheinbay, Esther ;

Grabherr, Manfred ;

Forche, Anja ;

Reedy, Jennifer L. ;

Agrafioti, Ino ;

Arnaud, Martha B. ;

Bates, Steven ;

Brown, Alistair J. P. ;

Brunke, Sascha ;

Costanzo, Maria C. ;

Fitzpatrick, David A. ;

de Groot, Piet W. J. ;

Harris, David ;

Hoyer, Lois L. ;

Hube, Bernhard ;

Klis, Frans M. ;

Kodira, Chinnappa ;

Lennard, Nicola ;

Logue, Mary E. ;

Martin, Ronny ;

Neiman, Aaron M. ;

Nikolaou, Elissavet ;

Quail, Michael A. ;

Quinn, Janet ;

Santos, Maria C. ;

Schmitzberger, Florian F. ;

Sherlock, Gavin ;

Shah, Prachi ;

Silverstein, Kevin A. T. ;

Skrzypek, Marek S. ;

Soll, David ;

Staggs, Rodney ;

Stansfield, Ian ;

Stumpf, Michael P. H. ;

Sudbery, Peter E. ;

Srikantha, Thyagarajan ;

Zeng, Qiandong ;

Berman, Judith ;

Berriman, Matthew ;

Heitman, Joseph ;

Gow, Neil A. R. ;

Lorenz, Michael C. ;

Birren, Bruce W. ;

Kellis, Manolis .

NATURE, 2009, 459 (7247) :657-662

[9] Host-microbe interactions: Shaping the evolution of the plant immune response [J].

Chisholm, ST ;

Coaker, G ;

Day, B ;

Staskawicz, BJ .

CELL, 2006, 124 (04) :803-814

[10] Structure and dynamics of the fusion pores in live GH-secreting cells revealed using atomic force microscopy [J].

Cho, SJ ;

Jeftinija, K ;

Glavaski, A ;

Jeftinija, S ;

Jena, BP ;

Anderson, LL .

ENDOCRINOLOGY, 2002, 143 (03) :1144-1148

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