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.
- Gennity JM, Inouye M: Protein secretion in bacteria. Curr Opin Biotechnol 1991, 2: 661–667. 10.1016/0958-1669(91)90031-YView ArticlePubMedGoogle Scholar
- Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340: 783–795. 10.1016/j.jmb.2004.05.028View ArticlePubMedGoogle Scholar
- Emanuelsson O, Brunak S, von Heijne G, Nielsen H: Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007, 2: 953–971. 10.1038/nprot.2007.131View ArticlePubMedGoogle Scholar
- Zhou M, Boekhorst J, Francke C, Siezen RJ: LocateP: genome-scale subcellular- location predictor for bacterial proteins. BMC Bioinformatics 2008, 9: 173. 10.1186/1471-2105-9-173PubMed CentralView ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd.