An analysis of the Candida albicans genome database for soluble secreted proteins using computer‐based prediction algorithms

Abstract

We sought to identify all genes in the Candida albicans genome database whose deduced proteins would likely be soluble secreted proteins (the secretome). While certain C. albicans secretory proteins have been studied in detail, more data on the entire secretome is needed. One approach to rapidly predict the functions of an entire proteome is to utilize genomic database information and prediction algorithms. Thus, we used a set of prediction algorithms to computationally define a potential C. albicans secretome. We first assembled a validation set of 47 C. albicans proteins that are known to be secreted and 47 that are known not to be secreted. The presence or absence of an N-terminal signal peptide was correctly predicted by SignalP version 2.0 in 47 of 47 known secreted proteins and in 47 of 47 known nonsecreted proteins. When all 6165 C. albicans ORFs from CandidaDB were analysed with SignalP, 495 ORFs were predicted to encode proteins with N-terminal signal peptides. In the set of 495 deduced proteins with N-terminal signal peptides, 350 were predicted to have no transmembrane domains (or a single transmembrane domain at the extreme N-terminus) and 300 of these were predicted not to be GPI-anchored. TargetP was used to eliminate proteins with mitochondrial targeting signals, and the final computationally-predicted C. albicans secretome was estimated to consist of up to 283 ORFs. The C. albicans secretome database is available at http://info.med.yale.edu/intmed/infdis/candida/

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

“…Considering that CEP and CSEP genes constitute only 9.2% of the gene content, they were highly overrepresented in these presence-absence polymorphisms. CSEP analogs were described in fungal pathogens of humans and animals 21,22 , but specific loss of such genes has, to our knowledge, not been reported. It is possible that loss of CEP and/or CSEP genes reflects selective pressure resulting from breeding for pathogen resistance, which, unlike in animals and humans, is a normal process in crop plants (Supplementary Note).…”

Association Genetics Reveals Three Novel Avirulence Genes from the Rice Blast Fungal Pathogen Magnaporthe oryzae

“…The predicted proteome of 70-15 (11,109 proteins; magnaporthe_ grisea_2.3_proteins; http://www.broad.mit.edu/cgi-bin/ annotation/ magnaporthe/download_license.cgi) was screened using a previously described bioinformatics pipeline outlined in Methods (Lee et al, 2003;Torto et al, 2003), resulting in 1306 putative secreted proteins (see Supplemental Data Set 1 online).…”

Decoding Serological Response to Candida Cell Wall Immunome into Novel Diagnostic, Prognostic, and Therapeutic Candidates for Systemic Candidiasis by Proteomic and Bioinformatic Analyses

“…The strong immune response generated against Bgl2p may be attributable, at least in part, to its great abundance (22,27), loose association with cell wall (22,68,69), and secretory nature (27,70,71) because it could, therefore, be shed easily into the bloodstream and processed early by immunocompetent cells resulting in potent immune responses. Although no antigenic properties for this glucan 1,3-␤-glucosidase (Bgl2p) have been described so far in any Candida species, consistent evidence that antibodies against other fungal cell wallbound and extracellular ␤-glucosidases, like Histoplasma capsulatum H antigen (Hag1p), Coccidioides immitis tubeprecipitin antigen (TP/Bgl2p), or Paracoccidioides brasiliensis 43-kDa glycoprotein (gp43), are largely used in the serodiagnosis of active histoplasmosis (72), early coccidioidomycosis (73), or paracoccidioidomycosis (72,74), respectively, provides additional support for our finding that serum anti-Candida Bgl2p IgG antibodies may likewise be useful and complement Candida blood cultures for the early identification (seeing that these require several days to become positive (8)) for SC in high risk patients.…”