genomewide characterization of host-pathogen interactions by ...

mean normalized intensity
Maren Depke
Results
Pathogen Gene Expression Profiling
A
14 5 675
B
genes containing Rex binding
sites in S. aureus according to
Pagels et al. 2010
genes containing Rex binding
sites in S. aureus according to
Pagels et al. 2010
sequences differentially
expressed in the comparison
“2.5 h anaerobic incubation”
vs. “1 h serum/CO 2 control”
Fig. R.5.12:
Expression of genes containing Rex binding sites.
A. Comparison of genes with Rex binding sites (according to
Pagels et al. 2010) and S. aureus RN1HG anaerobic gene
expression signature in the infection experiment study.
B. Comparison of genes with Rex binding sites (according to
Pagels et al. 2010) 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
19 genes containing Rex binding sites. 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 8 genes repressed in internalized staphylococci at the
2.5 h or 6.5 h time point, dark gray 5 genes differentially
expressed in at least one internalization time point and after
anaerobic incubation, and light gray marks the remaining 6
genes of which 3 possess a fold change value > 1.5 in the
anaerobic sample compared to baseline.
(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)
C
differentially expressed
sequences in “2.5 h
internalization” vs.
“1 h serum/CO 2 control”
10E+01 10.000
10E+00 1.000
10E-01 0.100
10E-02 0.010
10E-03 0.001
exp.
6
0 3
10
357 216
398
1 h
co.
2.5 h
int.
differentially expressed
sequences in “6.5 h
internalization” vs.
“1 h serum/CO 2 control”
OD 0.4 CO2 (serum) internalized internalized CO2 (serum) CO2 (serum) anaerobic
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
Genes of the SaeRS regulon exhibiting differential expression in internalized staphylococci
The two-component system SaeRS is known to positively regulate different virulence
associated genes, e. g. genes coding for adhesins or toxins. The induction of gene expression of
saeR was observed in internalized staphylococci 6.5 h after start of infection. Additionally, the
gene saeS for the histidine kinase sensor component was significantly different in 6.5 h
internalized staphylococci compared to baseline, but the fold change of 1.7 did not meet the
cutoff criterium of 2 (Fig. R.5.13 A). As the the two-component system SaeRS is known to be
subjected to positive autoinduction, the induction of saeR and trend for saeS provoked a detailed
analysis of genes known to be regulated by this system. In 2006, Rogasch et al. have published
transcriptome and secretome data of the SaeRS regulon in S. aureus strains COL and Newman
(Rogasch et al. 2006). Using a global microarray screening of saeRS mutants and parental strains,
Rogasch et al. defined 44 genes which were induced by the SaeRS two-component system, 40 of
which could be mapped to S. aureus NCTC8325 LocusTags (NCBI’s EntrezGenome Gene Plot;
http://www.ncbi.nlm.nih.gov/sutils/geneplot.cgi). For a first impression, the fraction of these
genes which were differentially expressed in 2.5 h and 6.5 h internalized staphylococci was
determined (Fig. R.5.13 B). At the 2.5 h time point, 4 genes with known regulation by SaeRS were
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