Tracking the Elusive Function of <i>Bacillus subtilis</i> Hfq

<div><p>RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species including <i>Escherichia coli</i>, <i>Salmonella enterica</i> and <i>Vibrio cholera</i>. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive and somewhat controversial. In the present study, we have further addressed this point by comparing growth phenotypes and transcription profiles between wild-type and an <i>hfq</i> deletion mutant of the model Gram-positive bacterium, <i>Bacillus subtilis</i>. The absence of Hfq had no significant consequences on growth rates under nearly two thousand metabolic conditions and chemical treatments. The only phenotypic difference was a survival defect of <i>B</i>. <i>subtilis hfq</i> mutant in rich medium in stationary phase. Transcriptomic analysis correlated this phenotype with a change in the levels of nearly one hundred transcripts. Albeit a significant fraction of these RNAs (36%) encoded sporulation-related functions, analyses in a strain unable to sporulate ruled out sporulation <i>per se</i> as the basis of the <i>hfq</i> mutant’s stationary phase fitness defect. When expressed in <i>Salmonella</i>, <i>B</i>. <i>subtilis hfq</i> complemented the sharp loss of viability of a <i>degP hfq</i> double mutant, attenuating the chronic σ^E-activated phenotype of this strain. However, <i>B</i>. <i>subtilis hfq</i> did not complement other regulatory deficiencies resulting from loss of Hfq-dependent small RNA activity in <i>Salmonella</i> indicating a limited functional overlap between <i>Salmonella</i> and <i>B</i>. <i>subtilis</i> Hfqs. Overall, this study confirmed that, despite structural similarities with other Hfq proteins, <i>B</i>. <i>subtilis</i> Hfq does not play a central role in post-transcriptional regulation but might have a more specialized function connected with stationary phase physiology. This would account for the high degree of conservation of Hfq proteins in all 17 <i>B</i>. <i>subtilis</i> strains whose genomes have been sequenced.</p>