Control of gene expression by PdeL, a transcription regulator and c-di-GMP phosphodiesterase in Escherichia coli K12

PdeL is a transcription regulator and c-di-GMP specific phosphodiesterase in Escherichia coli. To address the transcription regulator function of PdeL we analyzed the transcriptomes of four E. coli K12 strains during the exponential growth phase by RNA-sequencing. These four strains included (1) wild-type E. coli K12 strain BW30270 carrying an empty vector control plasmid, (2) an isogenic pdeL deletion mutant carrying the control plasmid, as well as the pdeL mutant that was complemented with (3) a plasmid carrying pdeL under control of the IPTG-inducible tac promoter or (4) a plasmid encoding a fusion protein of the PdeL's DNA-binding domain and the C-terminal dimerization domain of phage Lambda cI repressor (PdeL-DBD_cI-C). Expression of plasmid-encoded pdeL and pdeL-DBD_cI-C, respectively, was induced by addition of IPTG for 15 minutes prior to RNA isolation. Analyses of the RNA-seq data revealed that plasmid-provided PdeL (and PdeL-DBD_cI-C) repress transcription of class II flagellar genes and presumably regulate the transcription of additional loci, while only little differences were observed between the transcriptomes of wild-type strain BW30270 and its isogenic pdeL mutant. Overall design: RNA-sequencing analyses were performed of three biological replicates (rep1, rep2, and rep3) of four different E. coli K12 strains, i.e. of a total of 12 RNA samples. The strains are E.coli K12 wild-type strain BW30270 carrying empty vector control plasmid (wt+ctrl), the delta-pdeL strain complemented with plasmidic pdeL (delta-pdeL+PdeL) or with the PdeL-cI fusion (delta-pdeL+PdeLDBD_cIc). The delta-pdeL strain carrying the empty vector control served as control (delta-pdeL+ctrl).