Epigenetic control of the master regulator fumarate nitrate reductase (FNR) contributes to survival of Haemophilus influenzae during lung infection
Regulatory elements that dictate how Haemophilus influenzae adapts to the airways of COPD patients are poorly understood. In this work, global fitness profiling of H. influenzae mutants by transposon mutagenesis/sequencing (Tn-seq) within the mouse lung identified Dam methyltransferase as an in vivo requirement, even though dam mutants grow normally during in vitro culture. In turn, methylation sequencing found that genome-wide Dam methylation patterns were undermethylated at GATC motifs with putative regulatory elements. This was confirmed for the htpG heat-shock chaperone gene, making it the first case of phenotypic variation controlled by variable Dam methylation for H. influenzae. Moreover, RNA sequencing revealed a novel multifactorial regulatory network, in which Dam methyltransferase activity is coordinated with the FNR and Fur transcriptional regulators to control the expression anaerobic defences against host-produced reactive species. Our results indicate key bacterial pathways for survival in diseased environments with high nitrosative stress, where damage to the airways reduces the amount of oxygen in the lungs as is encountered in COPD. Overall design: To study how H. influenzae adapts to the airways of COPD patients. A key factor, Dam methyltransferase, was studied in aerobic and anaerobic conditions with the comparison of gene expression (RNA-seq) of wild type samples and Dam mutants.