4%) of 2410 evaluated genes showed ≥ 2 fold changes at 43°C, among which 39 were down-regulated and 54 upregulated. More extensive changes were recorded at 48°C, since 532 (22%) transcript levels showed ≥ 2 fold changes, with 232 genes being down-regulated and 300 up-regulated. The distributions of the responding genes based on COG functional categories are shown
on Additional file 1. Since several COG functional categories included a mixture of annotated and poorly functionally characterized Trichostatin A order genes (e.g. transcription regulators), we listed all poorly characterized genes in the general function prediction only category (see also Additional file 2). To provide https://www.selleckchem.com/products/AZD2281(Olaparib).html some indication of basal gene activities under control conditions, we also provided (Additional file 3, 4 and 2) semi-quantitative estimates of normalized signal intensities recorded at 37°C, which were subdivided into four categories (see Methods).
Indeed, the highest-intensity signals (75th to 100th percentile) were well correlated with the most abundant transcript products of S. aureus predicted to be highly expressed from codon usage [34]. They also correlated quite well with the most abundant proteins revealed by S. aureus proteomic studies [35], in particular enzymes involved in DNA, RNA and protein transcription machineries, central metabolism and energy production. Conversely, the lowest intensity signals (25th percentile) recorded at 37°C were contributed by transcripts from poorly expressed genes, such as amino acid biosynthetic pathways known to be repressed by the presence of amino acids in the MHB medium [35]. Contribution of specific transcriptomic heat stress-responses As expected from previous studies of
heat-shock responses in gram-positive bacteria [13, 18, 19], all components of S. aureus HrcA and CtsR regulons [13] were strongly induced by up-shifts to both 43°C and 48°C (Additional file 3). Transcript levels of the genes regulated by CtsR only (ctsR, mcsA, mcsB, clpC, clpP, clpB) increased by ca. 3–5 fold at 43°C Phospholipase D1 and ca. 3–11 fold at 48°C. We also observed increased expression of genes simultaneously regulated by HrcA and CtsR (grpE, dnaK, dnaJ, prmA, groEL, groES) at both 43°C and 48°C heat-shock. At 48°C, several HSP transcripts were detected at saturating levels by the microarray setting and thus their increased expression was likely under-estimated. To circumvent this problem and also validate the microarray-determined, heat-induced changes, we tested up-regulation of HSP transcript levels by qRT-PCR. Indeed, several gene transcripts (ctsR, mcsA, mcsB, hrcA) whose levels were saturated in the microarray scanner after up-shift to 48°C were more highly increased (ca. 6–16-fold) when assayed by qRT-PCR (Additional file 3).