Deletion of an sRNA primes development in a multicellular bacterium

Small non-coding RNAs (sRNAs) regulate gene expression of many biological processes. During growth, some myxobacteria produce an sRNA — Pxr — that blocks fruiting-body development, an aggregative multicellular process typically triggered by starvation. Deleting the pxr gene allows Myxococcus xanthus to develop despite nutrient availability, but Pxr binding targets and the genes regulated by Pxr remain unknown. Here, after showing that Pxr controls the temporal dynamics of development, we compare the transcriptomes of vegetative M. xanthus cells possessing vs lacking pxr. Over half of the genes impacted by pxr deletion are linked to development, including known and previously undiscovered critical regulators. Pxr also positively regulates genes associated with general metabolic processes. Our study discovers phenotypic effects of Pxr regulation with ecological importance, identifies the suite of genes this sRNA controls during vegetative growth and reveals a previously unknown developmental regulator. These findings provide insights into the molecular mechanism controlling myxobacterial development. We generated and contrasted the transcriptional profiles of wild-type M. xanthus cells (GJV1, derived from DK1622) to those of cells lacking the small RNA pxr expression. The RNA was sampled from vegetative cells growing in liquid, allowing us to identify the potential gene targets of the sRNA Pxr in this bacterium.