gsrN ++ is the 4 gsrN overexpression strain described in Figure 2A and Figure 2-figure supplement 1A. Numbers indicate CCNA locus numbers of deleted genes. CFU of peroxide treated cultures were normalized by the CFU of the paired untreated culture. ( B) Quantification of relative hydrogen peroxide survival of strains presented in Figure 1E. σ T binding motif (bottom) generated from 21 σ T-dependent promoters using WebLogo ( Crooks et al., 2004). Promoters of both genes contain a consensus σ T binding site (nucleotides in red) ( Alvarez-Martinez et al., 2007 McGrath et al., 2007 Staroń et al., 2009). sigU is a well-characterized reporter of GSR transcription ( Foreman et al., 2012). ( A) Schematic of lacZ transcriptional fusions to the promoters of gsrN and sigU. GsrN does not affect transcription from a σ T-dependent reporter. GenBank locus ID is indicated for unnamed genes. ( E) Colony forming units (CFU) in dilution series (10 −1 to 10 −6 dilution factor) of wild-type and mutant Caulobacter strains after 0.2 mM hydrogen peroxide treatment for 1 hr. A gene encoding a small RNA, gsrN, was a top hit on the ranked list. Red intensity scales with the final rank weights ( Figure 1-source data 2). Final ranks were calculated using the stable solution of the iterative ranking algorithm (right). ![]() ( D) An initial correlation-weighted network was seeded with experimentally defined GSR regulatory genes (red, value = 1) (left). ( C) sigT and phyR transcript levels are correlated as a function of cell cycle progression, Pearson’s correlation coefficient r = 0.92. ![]() Data plotted from Figure 1-source data 1. The core GSR regulators, sigT and phyR, are highlighted in red and black, respectively. ( B) Normalized transcript levels from ( Fang et al., 2013) of known GSR regulated genes are plotted as a function of cell cycle time. ( A) Activation of general stress response (GSR) sigma factor, σ T, promotes transcription of genes that mitigate the effects of environmental stress and genes that regulate σ T activity.
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