Abstract
Adhesion constitutes one of the initial stages of infection in microbial diseases and is mediated by adhesins. Hence, identification and comprehensive knowledge of adhesins and adhesin-like proteins is essential to understand adhesin mediated pathogenesis and how to exploit its therapeutic potential. However, the knowledge about fungal adhesins is rudimentary compared to that of bacterial adhesins. In addition to host cell attachment and mating, the fungal adhesins play a significant role in homotypic and xenotypic aggregation, foraging and biofilm formation. Experimental identification of fungal adhesins is labor- as well as time-intensive. In this work, we present a Support Vector Machine (SVM) based method for the prediction of fungal adhesins and adhesin-like proteins. The SVM models were trained with different compositional features, namely, amino acid, dipeptide, multiplet fractions, charge and hydrophobic compositions, as well as PSI-BLAST derived PSSM matrices. The best classifiers are based on compositional properties as well as PSSM and yield an overall accuracy of 86%. The prediction method based on best classifiers is freely accessible as a world wide web based server at http://bioinfo.icgeb.res.in/faap. This work will aid rapid and rational identification of fungal adhesins, expedite the pace of experimental characterization of novel fungal adhesins and enhance our knowledge about role of adhesins in fungal infections.
Highlights
Adhesins are cell surface proteins that confer upon the microbes the ability of attachment to cells, tissues and/or abiotic surfaces
We carried out the PSI-BLAST analysis on the non-redundant positive dataset of fungal adhesins in a manner like leave-one-out cross-validation (LOO CV), with the cut-off E-value (-e option of blastpgp) of 0.001 and the number of iterations as 3
We developed several Support Vector Machine (SVM)-based models using compositional properties as well as Position-Specific Scoring Matrix (PSSM) profiles to facilitate the identification of fungal adhesins
Summary
Adhesins are cell surface proteins that confer upon the microbes the ability of attachment to cells, tissues and/or abiotic surfaces. Adhesins pose as the first line of pathogen’s stratagem of host cell invasion and are indispensable determinant of its virulence. Apart from host cell attachment and mating, fungal adhesins are implicated in numerous other functions like social aggregation, foraging, biofilm formation on tissues, biomedical prosthesis and catheters [1] and xenotypic interactions with other microbes [2,3]. Differences in adhesion have been shown to be responsible for greater virulence/pathogenicity of one strain compared to the other in fungi [4,5]. The phenotypic variability and plasticity of adhesins poses as a remarkable stress-defense mechanism for fungi allowing them to alter their adhesion properties in response to different environments [6]
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