Do pathogenic bacteria encode more secreted proteins than their non-pathogenic relatives?

Abstract

Background Pathogenic and non-pathogenic bacteria secrete proteins for nutrient acquisition, cell-cell communication, and niche adaptation [1]. We hypothesized that pathogenic bacteria may encode larger fractions of secreted proteins (fsp) than their non-pathogenic relatives, assuming that pathogens might be under selective pressure to secrete virulence proteins involved in host immune evasion, invasion, and toxigenesis. To test this hypothesis, we compared the Sec-dependent fsp of various gram-positive and gram-negative bacteria and investigated the relation between the fsp and pathogenic potential of an organism. Methods We developed a pipeline that starts by a Perl script that truncates protein sequences to 70 amino acids or fewer followed by the application of existing signal prediction tools [2-4] and ends by the statistical analysis of the prediction data. For subsequent comparative secretome analyses, we used both the hidden Markov models- and the neural networks-based methods implemented in the SignalP 3.0 algorithm [2] (URL: http://www.cbs.dtu.dk/ services/SignalP) with modified thresholds. We used DataDesk (Data Description, Inc., Ithaca, NY; URL: http://www.datadesk.com) for all statistical analyses (including correlation analysis, analysis of variance, and multivariate analysis) and for plotting the results. Results