genomewide characterization of host-pathogen interactions by ...

mean normalized intensity
mean normalized intensity
Maren Depke
Results
Pathogen Gene Expression Profiling
differentially expressed, 10 further genes were found to be regulated specifically after 6.5 h,
whereas another 10 genes were regulated in both internalization time points. Of these 4, 10, and
10 genes, the numbers of 3, 9, and 9 genes were increased in expression. The remaining gene of
each group exhibited repression (Fig. R.5.13 C, Table R.5.7).
A
33
B
genes regulated by SaeRS
according to Rogasch et al. 2006
22
16
11
saeR
saeS
00
OD 0.4 CO2 (serum) internalized internalized CO2 (serum) CO2 (serum) anaerobic
exp.
1 h
co.
2.5 h
int.
6.5 h
int.
2.5 h
co.
6.5 h
co.
2.5 h
anae.
0 h 1 h 2.5 h 6.5 h 2.5 h 6.5 h 2.5 h
S. aureus RN1HG sample conditions and time points
differentially expressed
sequences in “2.5 h
internalization” vs.
“1 h serum/CO 2 control”
4 10
10
353 209
398
differentially expressed
sequences in “6.5 h
internalization” vs.
“1 h serum/CO 2 control”
Fig. R.5.13:
Expression of genes known to be regulated by SaeRS.
A. Expression of saeR and saeS in S. aureus RN1HG during
the S9 infection experiment. Induction of both genes was
significant in statistical testing for the 6.5 h time point of
internalization, but did not pass the two-fold cutoff for
saeS.
B. Comparison of genes known to be regulated by SaeRS
(according to Rogasch et al. 2006) and S. aureus RN1HG S9
internalization gene expression signature 2.5 h and 6.5 h
after start of infection.
C. Overview on mean normalized gene expression intensity
for 24 genes known to be regulated by SaeRS. After the
global normalization by inter-chip scaling and detrending,
each individual gene has been normalized to the
expression level of the baseline sample “1 h serum/CO 2
control”. Although not being continuous data, values were
depicted as line graphs instead of bar charts for better
facility of inspection. Black indicates 9 genes induced in
internalized staphylococci at the 2.5 h or 6.5 h time point,
dark gray 9 genes induced at 6.5 h and 3 genes induced at
2.5 h after start of infection, and light gray marks the
remaining 3 genes of which one was repressed at both
time points, another specifically 2.5 h and the third
specifically 6.5 h after start of infection.
C
10E+02 100.000
10E+01 10.000
10E+00 1.000
10E-01 0.100
10E-02 0.010
OD 0.4 CO2 (serum) internalized internalized CO2 (serum) CO2 (serum) anaerobic
exp.
1 h
co.
2.5 h
int.
6.5 h
int.
2.5 h
co.
6.5 h
co.
2.5 h
anae.
0 h 1 h 2.5 h 6.5 h 2.5 h 6.5 h 2.5 h
S. aureus RN1HG sample conditions and time points
(exp. − exponential growth phase; 1 h co. – 1 h serum/CO 2 control;
2.5 h int. − 2.5 h internalization; 6.5 h int. − 6.5 h internalization;
2.5 h co. − 2.5 h serum/CO 2 control; 6.5 h co. − 6.5 h serum/CO 2
control; 2.5 h anae. − 2.5 h anaerobic incubation)
The set of 21 SaeRS regulated genes, which exhibited differential expression in at least one of
the two analyzed internalization time points, included certain functional groups of virulence
factors, and some could even be assigned to more than one group. Membrane bound
adhesins/MSCRAMMS were represented by the fibrinogen binding proteins A and B (fnbA, fnbB),
soluble adhesins/SERAMs were covered e. g. by extracellular adherence protein (eap), toxins
were included with the examples of different hemolysins, chemotaxis inhibitory protein (chp)
served as example for immune-evasive proteins, and finally, also secreted enzymes like serine
protease (spl) were listed. Thus, further data mining was performed in consideration of functional
groups of virulence factors.
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