Volume 11 Supplement 4
Do pathogenic bacteria encode more secreted proteins than their non-pathogenic relatives?
© Aziz and Mahmoud; licensee BioMed Central Ltd. 2010
Published: 23 July 2010
Pathogenic and non-pathogenic bacteria secrete proteins for nutrient acquisition, cell-cell communication, and niche adaptation . 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.
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  (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.
We developed a pipeline for the determination and comparison of fractions of secreted proteins in bacterial genomes, and observed significant differences between pathogenic and non-pathogenic species of staphylococci and streptococci.
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This article is published under license to BioMed Central Ltd.