POSTER PRESENTATION Open Access
Do pathogenic bacteria encode more secreted
proteins than their non-pathogenic relatives?
Ahmed Abo-Bakr Mahmoud1, Ramy Karam Aziz2*
From UT-ORNL-KBRIN Bioinformatics Summit 2010
Cadiz, KY, USA. 19-21 March 2010
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 pre-
diction 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
We determined the theoretical secretomes of 176 chro-
mosomes and 115 plasmids in five gram-positive
and five gram-negative bacterial genera containing
* Correspondence: ramy.aziz@salmonella.org
2Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo
University, Cairo 11562, Egypt
Figure 1 Predicted fractions of secreted proteins by the chromosomes of ten bacterial genera with pathogenic and non-pathogenic
member. NN = neural networks method; HMM = hidden Markov models method.
Mahmoud and Aziz BMC Bioinformatics 2010, 11(Suppl 4):P28
http://www.biomedcentral.com/1471-2105/11/S4/P28
© 2010 Aziz and Mahmoud; licensee BioMed Central Ltd.

pathogenic and non-pathogenic members (Figure 1).
Our analysis showed significant differences in chromo-
somally encoded fsp between gram-positive and gram-
negative bacteria (chromosomes of gram-negative bac-
teria have larger fsp), while there was no particular pat-
tern in plasmid-encoded fsp. Whereas the overall
difference between pathogenic and non-pathogenic spe-
cies was not statistically significant, significant correla-
tion was observed between fsp and pathogenesis in
gram-positive cocci. For example, pathogenic Staphylo-
coccus aureus have higher fsp than other staphylococci,
while the non-pathogenic Streptococcus thermophilus
has the lowest fsp of all streptococci (Figure 2).
Conclusion
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.
Author details
1Maternity Governmental Hospital, Kuwait City, 85860, Kuwait. 2Department
of Microbiology and Immunology, Faculty of Pharmacy, Cairo University,
Cairo 11562, Egypt.
Published: 23 July 2010
References
1. Gennity JM, Inouye M: Protein secretion in bacteria. Curr Opin Biotechnol
1991, 2:661-667.
2. Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of
signal peptides: SignalP 3.0. J Mol Biol 2004, 340:783-795.
3. 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.
4. Zhou M, Boekhorst J, Francke C, Siezen RJ: LocateP: genome-scale
subcellular- location predictor for bacterial proteins. BMC Bioinformatics
2008, 9:173.
doi:10.1186/1471-2105-11-S4-P28
Cite this article as: Mahmoud and Aziz: Do pathogenic bacteria encode
more secreted proteins than their non-pathogenic relatives?. BMC
Bioinformatics 2010 11(Suppl 4):P28.
Figure 2 Pathogenic Gram-positive cocci encode larger fractions of secreted proteins than non-pathogenic relatives. NN = neural
networks method; HMM = hidden Markov models method. (A) Staphylococcal species (epid = epiderimidis; haemo = haemolyticus; sapro =
saprophyticus). (B) Streptococcal species (aga = agalactiae; pneu = pneumoniae; pyog = pyogenes; ther = thermophilus) P values: aureus vs. all:
P < 10-6; ther vs. all: P = 0.002 (NN), 0.0001 (HMM); agal vs. pyog: P = 0.012 (NN), 0.003 (HMM).
Mahmoud and Aziz BMC Bioinformatics 2010, 11(Suppl 4):P28
http://www.biomedcentral.com/1471-2105/11/S4/P28
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