genomewide characterization of host-pathogen interactions by ...

mean normalized intensity
mean normalized intensity
mean normalized intensity
mean normalized intensity
Maren Depke
Results
Pathogen Gene Expression Profiling
A
fold change in comparison to
baseline 1 h serum/CO 2 control
tyrS leuS thrS pheS pheT serS aspS hisS ileS alaS metS asnS gltX trpS valS glyS cysS argS proS lysS
S. aureus
RN1HG
sample
conditions
and time
points
exponential growth phase -1.1 -1.0 -1.4 -1.2 -1.3 -1.2 -1.3 -1.2 -1.2 -1.2 -1.1 -1.1 -1.1 1.2 -1.2 3.3 -1.0 -1.1 -1.1 -1.0
2.5 h internalized -2.7 -2.0 -2.1 -2.5 -2.7 -2.2 -1.6 -1.8 -1.5 -1.3 -1.6 -2.0 -1.5 -1.4 -1.1 -1.1 1.5 -1.3 -1.0 -1.2
6.5 h internalized -3.3 -2.3 -2.4 -3.4 -3.5 -2.4 -2.1 -2.3 -1.8 -1.5 -1.4 -1.8 -1.2 -1.3 1.6 1.9 -1.1 -1.2 1.1 -1.0
2.5 h serum/CO 2 control -5.1 -3.0 -2.8 -3.8 -3.9 -2.9 -4.6 -4.5 -3.3 -1.8 -1.2 -1.7 -1.2 1.1 -2.4 2.3 1.2 1.2 -1.6 -1.5
6.5 h serum/CO 2 control -11.2 -5.0 -3.6 -6.2 -4.8 -3.2 -7.5 -8.8 -4.4 -1.8 -1.5 -2.1 -1.3 -1.0 -2.3 1.6 2.0 1.1 -2.0 -1.6
2.5 h anaerobic incubation -3.9 -2.0 -1.5 -2.1 -2.3 -1.9 -3.8 -3.5 -2.9 -1.8 -1.2 -1.5 -1.4 1.0 -2.0 2.1 1.1 1.1 -1.9 -1.9
B
C
10.0
10.0
tyrS
ileS
leuS
alaS
thrS
metS
1.0
pheS
pheT
serS
1.0
asnS
gltX
trpS
aspS
hisS
0.1
0.1
D
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
E
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
10.0
10.0
1.0
valS
glyS
cysS
1.0
argS
proS
lysS
0.1
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
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
Fig. R.5.27: tRNA synthetase 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-E. 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.
Twenty tRNA synthetase genes were assigned to four groups: genes repressed in at least one time point of internalization (B), genes
with trend of repression in at least one time point of internalization with p* < 0.05, but an absolute fold change of less than 2 (C),
genes with trend of induction in one time point of internalization (D), and genes exhibiting no change in expression (E).
(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)
After having observed the described changes in metabolic gene expression, the possible
differential expression of transporter genes was addressed directly. Here, two groups could be
distinguished. The first group consisted of transporter genes with repressed gene expression in at
least one analyzed time point of internalized staphylococci. The urea transporter
SAOUHSC_02557 belonged to this group. Noticeably, the adjacent urease operon
SAOUHSC_02558 to SAOUHSC_02565 (ureABCEFGD) possessed a similar expression pattern,
although not all genes were detected as differentially expressed (Fig. R.5.28).
161