Reprogramming of anaerobic metabolism by the FnrS Small RNA

Small RNAs (sRNA) that act by base pairing with trans-encoded mRNAs modulate metabolism in response to a variety of environmental stimuli. Here, we describe an Hfq-binding sRNA (FnrS) whose expression is induced upon a shift from aerobic to anaerobic conditions and which acts to down regulate the levels of a variety of mRNAs encoding metabolic enzymes. Anaerobic induction in minimal medium depends strongly on FNR but is also affected by ArcA and CRP. Whole genome expression analysis showed that the levels of at least 32 mRNAs are down regulated upon FnrS overexpression, 15 of which are predicted to base pair with FnrS by TargetRNA. The sRNA is highly conserved across its entire length in numerous enterobacteria, and mutation analysis revealed that two separate regions of FnrS base pair with different sets of target mRNAs. The majority of the target genes previously reported to be down regulated in an FNR-dependent manner lack recognizable FNR binding sites. We thus suggest that FnrS extends the FNR regulon and increases the efficiency of anaerobic metabolism by repressing the synthesis of enzymes that are not needed under these conditions. MG1655 carrying either pFnrS or the control vector pAZ3 was used in all experiments. Overnight bacterial cultures grown with shaking at 37˚C in LB media with ampicillin at a final concentration of 50 ug/mL were diluted 1000-fold into 10 ml of LB-ampicillin media and grown with shaking at 37˚C. When cultures reached an O.D.600 of 0.5, arabinose was added at a final concentration of 0.2%. Total RNA was extracted from cells at the indicated times using the hot phenol procedure.