CsmR controls both, motility and cell shape, in Haloferax volcanii.

Archaea rely on motility and morphological plasticity to navigate their environments, yet the transcriptional regulation of these processes remains poorly understood. In Haloferax volcanii, archaellum-dependent motility is transcriptionally regulated, but an EarA-like central regulator for transcription of archaellum genes that is found in other Euryarchaeota like Methanococcus maripaludis or Pyrococcus furiosus, is absent. Here, we identify CsmR as a transcriptional regulator that controls archaellum biogenesis and cell-shape transitions in H. volcanii. Deletion of csmR abolished detectable motility, whereas overexpression increased motility and promoted a sustained rod-like morphology. Comparative transcriptomics defined a CsmR-associated regulon that includes archaellum and chemotaxis genes as well as cell-shape determinants (e.g., Sph3 and RdfA), and ChIP-seq identified promoter-proximal binding sites consistent with direct transcriptional control. Furthermore, csmR and cirA, a KaiC-like regulator, share extensive transcriptional overlap, with CirA potentially fine-tuning CsmR-mediated regulation through post-translational modification. These findings establish CsmR as a key regulator of archaellum gene expression and cell shape regulation in Haloferax volcanii, suggesting that haloarchaea coordinate these fundamental processes through an unidentified transcriptional network. Moreover, Northern blotting and cell shape observation suggest that transcription factor RosR is involved in the regulation of an regulatory RNA that shares extensive overlap with the cirA gene, possibly fine-tuning the effect of CirA on the regulation of the archaellum cluster and the rod shape determinants sph3 and rdfA. Understanding this interplay provides new insights into archaeal adaptability and may reveal broader regulatory principles in prokaryotic cell biology.