sakei regulated by σLsa H, the experimental system described abov

sakei regulated by σLsa H, the experimental system described above was used in a full-genome comparative transcriptome analysis of sigH(hy)* and sigH(wt)* after one hour induction with 30 μM CuSO4. Quantification and statistical analysis of the microarray data (see Methods for parameters) led to relatively few KU-57788 research buy differentially expressed candidate genes. The overexpressed sigH gene in sigH(hy)* was 11 ± 3 times induced compared to the WT strain in this microarray experiment; qPCR-based quantification of the same

RNA samples showed a 149 ± 42-fold greater expression relative to the WT strain, confirming the successful overexpression of sigH Lsa. Differences in fold ratios between microarray-profiling and qPCR analysis are not unusual but were high in our experiment; they might reflect a less efficient detection on microarray or an overestimation by qPCR especially

when genes are weakly expressed in one of the conditions, which seemed to be the case for the com genes. Based on statistical tests (P value < 0.05), our microarray analysis initially identified some 25 candidate genes whose expression was likely affected by sigH Lsa overexpression; behavior of several genes was confirmed by qPCR (Table 2). The known genes can be grouped into two main functional categories: competence (DNA uptake) and DNA metabolism. All the late competence (com) operons encoding structural elements of the DNA uptake machinery were highly activated by sigH Lsa overexpression. In contrast, transcription of ssb, regulated p38 MAPK inhibitors clinical trials as a late competence gene in B. subtilis [32], was nearly constant or only very weakly induced. Other genes involved in DNA metabolism, and known to be induced during the competence state in other species, i.e., recombination genes recA and dprA, both of which are involved in natural bacterial transformation in different species [33], gave a contrasted picture when their transcription was specifically measured by qPCR. Whereas recA was little activated, expression of dprA was highly induced in the sigH(hy)* context (Table 2). Table 2 Genome-wide transcriptome profiling of SigHLsa overexpression in L.sakei 23 K Functional category

and O-methylated flavonoid CDS Gene Name Product Pvalue (Bonferroni) common variance model Pvalue (FDR) varmixt model Expression sigH(hy)*/ ratio$ sigH(wt)*           microarray qPCR Competence LSA0492 comFA DNA uptake machinery § 1.54E-02 > threshold 1.5 ± 0.4 286 ± 88 LSA0493 comFC DNA uptake machinery 0 3.56E-03 2.2 ± 0.2   LSA1069 comEC DNA uptake machinery 9.52E-10 1.31E-02 1.9 ± 0.2   LSA1071 comEA DNA uptake machinery 0 7.23E-03 2.5 ± 0.3 261 ± 115 LSA1301 comGF DNA uptake machinery 0 2.71E-04 3 ± 2   LSA1302 comGE DNA uptake machinery 0 1.44E-06 3.7 ± 0.5   LSA1303 comGD DNA uptake machinery 0 2.21E-04 2.8 ± 0.3   LSA1304 comGC DNA uptake machinery 0 5.62E-12 7 ± 2 421 ± 104 LSA1305 comGB DNA uptake machinery 1.02E-10 3.57E-02 2.0 ± 0.3   LSA1306 comGA DNA uptake machinery 3.17E-09 7.25E-03 1.

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