Change of σ-factor mRNA levels as a function of growth phase.

<p>(A) Change in σ-factor mRNA levels (RNASeq data) comparing stationary and exponential CCUG^rfp cells cultivated in 7H9 medium. (B) Change in σ-factor mRNA levels (RNASeq data) comparing 2 weeks and 2 days old CCUG^rfp cells cultivated on 7H10 medium. (C) Change in σ-factor mRNA levels (qRT-PCR data) comparing stationary and exponential CCUG^rfp cells cultivated in 7H9 medium. Significant log₂-fold changes for <i>sigC</i>, <i>sigC_1</i>, <i>sigD</i>, <i>sig0975</i> and <i>sig3687</i> were 4.1, 2.8, 1.7, 0.2 and 2.5, respectively (p < 0.05). (D) Change in σ-factor mRNA levels (qRT-PCR data) comparing 2 weeks and 2 days old CCUG^rfp cells cultivated on 7H10 medium. Significant log₂-fold changes for <i>sigB</i>, <i>sigE</i>, <i>sigJ</i>, and <i>sigL</i> were 4.0, 3.0, 1.2, and 1.8, respectively (p < 0.05), while for <i>sigC</i>, <i>sigC_1</i>, <i>sigD</i>, and <i>sig 3687</i> the significant log₂-fold changes were 1.3, 2.0, 1.2, and 0.5, respectively (p < 0.05). With respect to <i>sigL</i> mRNA the significant log₂-fold change was higher, 1.8 (p < 0.05) <i>vs</i> < 0.1 (p < 0.05), when grown on 7H10 medium compared to growth in liquid 7H9 medium (Fig 3C). (E) Change in σ-factor mRNA levels (RNASeq data) comparing exponential and stationary DE4373 cells cultivated in 7H9 medium. The ratios of stationary <i>vs</i> exponential phase mRNA levels were plotted on a log₂ scale so that positive values indicate higher mRNA levels in late stages of growth. The different σ-factors are marked on the x-axis. The RNASeq data (GFOLD values; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139823#sec018" target="_blank">Materials and Methods</a>) are based on a single replicate, while the qRT-PCR data are based on at least 6 biological replicates for the exponential and two biological replicates for the stationary samples (except for <i>sigF</i> where it is based on three biological replicates). Statistically significant differences are indicated: * p < 0.05; ** p < 0.01; *** p < 0.001.