genomewide characterization of host-pathogen interactions by ...

Maren Depke
Results
Pathogen Gene Expression Profiling
A
B
483 940 146
repressed
repressed
t 2
t 4
induced
258 77
induced
225
469
69
sequences differentially expressed
between stationary growth phase t 2
and exponential growth phase of
S. aureus RN1HG cultivated in pMEM
sequences differentially expressed
between stationary growth phase t 4
and exponential growth phase of
S. aureus RN1HG cultivated in pMEM
471
Fig. R.5.3: Comparison of the t 2 and t 4 stationary phase signatures of S. aureus RN1HG in pMEM.
Both stationary phase samples were compared to the baseline of exponential growth with statistical testing and multiple testing
correction (p* < 0.05), and a minimal absolute fold change cutoff of 2 was applied. The comparison of differentially expressed
sequences at the t 2 and t 4 time point was performed for all regulated sequences (A) and for induced and repressed sequences
separately (B).
Fractions of known genes and newly identified transcribed sequences included on the tiling
array and in the lists of differentially expressed sequences derived from the comparisons of
different growth phase samples
The 080604_SA_JH_Tiling array contains 3882 sequences of which 2825, corresponding to
73 %, are known transcripts and associated with a LocusTag number (SAOUHSC_*). The remaining
1057 sequences were identified as new transcripts in the tiling array analysis. These new
transcripts are expected to belong to all types of RNAs like mRNA and regulatory RNA, but also
formerly unknown transcribed fragments 5’ and 3’ to known genes might be included.
Furthermore, some artifacts might still be included. All sequences, known and new, were
included in statistical testing.
For the stationary phase-specific signature, 444 and 307 differentially expressed transcripts
belonged to the group of new transcripts at the t 2 and t 4 time point, respectively (Table R.5.2).
Table R.5.2: Fractions of known annotated and newly detected transcripts in the results of group comparisons with statistical testing
of different growth phase array data sets.
group comparison a
total number of
sequences with
absolute fold change
equal to or greater
than 2 AND significant
with p* < 0.05
number of known
transcribed sequences
with absolute fold
change equal to or
greater than 2 AND
significant with p* < 0.05
number of new
transcribed sequences
with absolute fold
change equal to or
greater than 2 AND
significant with p* < 0.05
stationary phase t 2 vs. exponential growth phase 1423 979 444
stationary phase t 4 vs. exponential growth phase 1086 779 307
a The 080604_SA_JH_Tiling array contains 3882 sequences of which 2825 are known transcripts. The remaining 1057 sequences were
identified as new transcripts in the tiling array analysis. All sequences were included in statistical testing.
Physiological aspects of stationary phase response
Stationary phase is characterized by a strongly reduced growth rate and by a reorganization of
the metabolic processes of the bacterial cell. Causative for these alterations is the consumption
of nutrients of the growth medium and the following starvation for the preferred carbon source.
Such changes have been published for S. aureus COL during growth in TSB in a global gel-based
and gel-free proteome study by Kohler et al. in 2005.
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