genomewide characterization of host-pathogen interactions by ...

mean normalized intensity
Maren Depke
Results
Pathogen Gene Expression Profiling
Additionally, a high number of peptide/oligopeptide transporters were induced: peptide
transporters oppF and SAOUHSC_00169, oligopeptide transporters SAOUHSC_00926 and oppA,
and genes SAOUHSC_00923, oppC (SAOUHSC_00924), and oppD (SAOUHSC_00925) from the
same operon (SAOUHSC_00923 to SAOUHSC_00927). Also induced SAOUHSC_00928 gene codes
for an oligopeptide ABC transporter. In the same chromosomal region, a four-gene-operon
(SAOUHSC_00929 to SAOUHSC_00932) encodes oligopeptide ABC transporters appD, appF,
SAOUHSC_00931, and appC, but these were not induced in internalized staphylococci
(Fig. R.5.33).
Further example for induced transporter gene expression was another operon including msmX
(SAOUHSC_00175, multiple sugar-binding transport ATP-binding protein), SAOUHSC_00176
(bacterial extracellular solute-binding protein), SAOUHSC_00177 and SAOUHSC_00178 (both
maltose ABC transporter, permease proteins). Also opuD2 (osmoprotectant transporter), glnQ
(amino acid ABC transporter), SAOUHSC_02729 (amino acid ABC transporter-like protein), and
gntP (gluconate permease) were induced (Fig. R.5.34).
A
fold change in comparison to
baseline 1 h serum/CO 2 control
S. aureus
RN1HG
sample
conditions
and time
points
msmX SAOUHSC_
00176
SAOUHSC_
00177
SAOUHSC_
00178
opuD2 glnQ
SAOUHSC_
02729
exponential growth phase -1.3 -1.3 -1.2 -1.0 2.8 1.5 1.0 -1.0
2.5 h internalized 15.6 7.6 3.5 2.7 3.7 2.1 8.4 2.6
6.5 h internalized 8.2 5.6 2.8 1.8 2.9 -1.0 2.9 2.1
2.5 h serum/CO 2 control 1.4 -1.1 1.1 1.0 2.9 -1.2 -1.2 -1.2
6.5 h serum/CO 2 control 43.7 42.4 34.8 29.5 4.2 1.1 7.2 7.0
2.5 h anaerobic incubation 3.5 2.3 1.7 1.7 1.1 -1.1 1.2 -1.0
gntP
Fig. R.5.34: Sugar/maltose, osmoprotectant, amino acid,
and gluconate transporter or permease gene expression.
A. Overview on fold change values relative to the baseline
sample “1 h serum/CO 2 control” and on significance in
statistical group comparisons. The sample “6.5 h serum/CO 2
control” could not be included in statistical testing because
of small group size (n = 2).
B. Overview on mean normalized gene expression intensity.
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” (1 h co.). Although not being continuous data,
values were depicted as line graphs instead of bar charts for
better facility of inspection.
(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)
B
100.0
10.0
1.0
0.1
exp.
1 h
co.
2.5 h
int.
6.5 h
int.
2.5 h
co.
6.5 h
co.
2.5 h
anae.
S. aureus RN1HG sample conditions and time points
msmX
SAOUHSC_00176
SAOUHSC_00177
SAOUHSC_00178
opuD2
glnQ
SAOUHSC_02729
gntP
Gene expression changes in internalized staphylococci not occurring in the same way in any of
the control samples
Analysis of virulence associated or metabolic gene expression changes revealed a common
aspect of the internalization signature: For many genes, some of the control conditions or time
points exhibited a similar expression change as the internalized expression pattern. To get hints
on real specifically internalization dependent gene expression changes, a set of sequences, which
contained sequences with different expression in internalized staphylococci in comparison to all
other control samples, was defined in two steps. First, subsets of regulated sequences in
internalized staphylococci were constituted which were a) not regulated in 2.5 h serum/CO 2
control and b) not regulated in 2.5 h anaerobically incubated samples (each in reference to the
baseline sample of 1 h serum/CO 2 control with p* < 0.05 and a minimal absolute fold change of
2). In these sets, sequences were still included which possessed differing expression in the 6.5 h
serum/CO 2 control in comparison to the baseline samples.
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