Fig. 3: Overexpression of a small, horizontally-acquired, chromosomal operon.

A Schematic representation (left panel) and heatmap of the differential expression (log₂ fold change [FC], right panel) of a small chromosomal operon, comprised of the pfp and ifp genes, and the lysR transcriptional regulator gene that could control its expression (lysR-pfp-ifp cluster). Differential expression is performed by comparing the pOXA-48-carrying strains to their respective pOXA-48-free counterparts (see Methods). E. coli (C325, EC10 and MG1655) does not encode the lysR-pfp-ifp cluster, thus heatmap tiles are colored in gray. Significant log₂FC are indicated by a dot. Strains belonging to the same Sequence Type (ST) are indicated with shapes. B Unrooted phylogenetic tree of the concatenated alignments of the protein sequences of the lysR-pfp-ifp cluster genes in Proteobacteria (n = 698) (see Methods). Pie charts show the proportion of Proteobacteria strains belonging to the Gamma- (red), Beta- (yellow) or Alphaproteobacteria (blue) classes included below each of the indicated internal branches. Enterobacteriaceae strains that branch from the same node are shaded in gray; other Enterobacteriaceae species not branching from that node are indicated. Bootstrap values are represented with a color gradient in the branches of the tree: low (aprox. 8), medium (aprox. 46) and high (aprox. 100) bootstrap values are colored in red, yellow and gray, respectively. Tree scale represents the average number of substitutions per site. C Genomic neighborhood of the lysR-pfp-ifp cluster in a representative subset of Proteobacteria strains: Shewanella denitrificans, Serratia marcescens, E. coli, Salmonella enterica, C. freundii, K. pneumoniae, K. variicola and Enterobacter cloacae. Genes are color-coded as indicated at the top. Homologous genes between strains and their percentage of sequence identity are indicated with a gray shading.