Phylogenetic footprinting and transcriptome profiling reveal new roles for two Bacillus cereus two-component systems

Members of the Bacillus cereus group can adapt to a wide range of environmental challenges. In bacteria, these challenges are often translated into a transcriptional response via the cognate response regulators (RRs) of specialized two-component systems (TCSs). We have previously developed a phylogenetic footprinting approach that was successfully implemented to predict specific binding sites (operators) and target genes for the RRs of B. cereus and related species. In this study, this footprinting approach was integrated with transcriptome analyses of two B. cereus TCS deletion mutants, involving the TCSs YvrHG and YufLM. Comparison of mutant versus wild-type transcriptomes revealed that the respective TCSs were significantly active during the exponential growth phase in rich medium and that the footprinting-based predictions were accurate for the two TCSs. Moreover, the predicted specific operators were used in combination with the transcriptome data to guide the identification of more extended TCS regulons. This revealed new roles for the respective TCSs, including the participation in an intricate transcriptional network involved in antibiotic resistance, including the confirmed resistance to oxolinic acid (YvrHG) and the confirmed uptake and metabolism of fumarate and the repression of fermentative pathways (YufLM). Two different comparisons were performed (both in duplo and Cy5-Cy3 dye-swapped): (1) B. cereus WT 30°C (mid-exponential) versus B. cereus delta-yufLM 30°C (mid-exponential) (2) B. cereus WT 30°C (mid-exponential) versus B. cereus delta-yvrHG 30°C (mid-exponential)