Fig 1.
Conserved and diverged co-expression patterns of differentially regulated genes upon (hyper-) presence and/or absence of sigma factors.
(A) Hierarchical clustering based on Pearson correlation coefficients. 1504 genes (67.8%, vertically colored) were differentially regulated due to in trans expression and/or inactivation of a single sigma factor. Genes regulated by more than one sigma factor are shown in white. (B) The expression levels of 471 genes (21.2%) were influenced by two sigma factors (indicated by the two colored bars). (C) White balls highlight the (the number of) genes that are affected by the five most frequent sigma factor combinations.
Table 1.
Quantitative analysis of sigma factor regulons uncovered by mRNA profiling.
Fig 2.
De novo elucidated sigma factor binding motifs.
The MEME suite [53] was used to elucidate the sigma factor binding motifs (see Material and Methods section for details). For each sigma factor the motif representation is depicted and the average distance to the TSS is given.
Fig 3.
The P. aeruginosa strain PA14 sigma factor regulome.
The outer circle summarizes the distribution of the 2553 genes belonging to the primary PA14 sigmulome, including RpoD (depicted in green).Those genes that belong to more than one primary sigma factor regulon are indicated in brown. The second circle represents the PA14 core (blue) and accessory (orange) genome as previously defined [90]. The inner eleven circles highlight the genes associated with individual sigma factor primary regulons. The innermost diagram depicts the TOP 12 direct cross talks between the sigma factors. The figure was generated using Circos [91]. A high-resolution interactive image is available at https://bactome.helmholtz-hzi.de/.
Fig 4.
Functional characterization of primary sigma factor networks.
The PseudoCAP annotation [55] was used to categorize the members of the sigma factor networks (Fig. 3, S6 Table). For each category the enrichment factor based on the prevalence of the specified class in the regulon compared to the whole genome was calculated. The P values of the enriched categories are provided in S8 Table.
Table 2.
Quantitative analysis of primary sigma factor regulons.
Fig 5.
Functional profiling of the crosstalk among sigma factors in P. aeruginosa.
The PseudoCAP annotation [55] was used to categorize the members of the direct (violet bars) and indirect (light green bars) sigma factor crosstalk. The enrichment of specific gene classes is displayed. The P values of the enriched categories are provided in S10 Table.