FleQ DNA Binding Consensus Sequence Revealed by Studies of FleQ-Dependent Regulation of Biofilm Gene Expression in Pseudomonas aeruginosa
ABSTRACTThe transcription factor FleQ fromPseudomonas aeruginosaderepresses expression of genes involved in biofilm formation when intracellular levels of the second messenger cyclic diguanosine monophosphate (c-di-GMP) are high. FleQ also activates transcription of flagellar genes, and the expression of these genes is highest at low intracellular c-di-GMP. FleQ thus plays a central role in mediating the transition between planktonic and biofilm lifestyles ofP. aeruginosa. Previous work showed that FleQ controls expression of thepeloperon for Pel exopolysaccharide biosynthesis by converting from a repressor to an activator upon binding c-di-GMP. To explore the activity of FleQ further, we carried out DNase I footprinting at three additional biofilm gene promoters, those ofpsl,cdrAB, and PA2440. The expression ofcdrAB, encoding a cell surface adhesin, was sufficiently responsive to FleQ to allow us to carry outin vivopromoter assays. The results showed that, similarly to our observations with thepeloperon, FleQ switches from a repressor to an activator ofcdrABgene expression in response to c-di-GMP. From the footprinting data, we identified a FleQ DNA binding consensus sequence. A search for this conserved sequence in bacterial genome sequences led to the identification of FleQ binding sites in the promoters of thesiaABCDoperon, important for cell aggregation, and thebdlAgene, important for biofilm dispersal, inP. aeruginosa. We also identified FleQ binding sites upstream oflapA-like adhesin genes in otherPseudomonasspecies.IMPORTANCEThe transcription factor FleQ is widely distributed inPseudomonasspecies. In all species examined, it is a master regulator of flagellar gene expression. It also regulates diverse genes involved in biofilm formation inP. aeruginosawhen intracellular levels of the second messenger c-di-GMP are high. Unlike flagellar genes, biofilm-associated genes are not always easy to recognize in genome sequences. Here, we identified a consensus DNA binding sequence for FleQ. This allowed us to surveyPseudomonasstrains and find new genes that are likely regulated by FleQ and possibly involved in biofilm formation.