Dual regulatory role of cyclic di-GMP via the DgcY/HhmR complex in salt response of Halomonas hydrothermalis Y2

Bis-(3′−5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) is a key second messenger synthesized by diguanylate cyclases (DGCs) and regulates diverse bacterial behaviors. While many DGC modules are integrated within complex regulatory cassettes to ensure precise control of cellular processes, simpler DGC-containing cassettes are also widespread across bacteria, despite the regulative modes of their DGC activity remaining to be explored. In this study, we characterized a unique regulative network within a simple DGC cassette in Halomonas hydrothermalis Y2, DgcY, which comprises a six-transmembrane domain and a GGDEF domain lacking the canonical autoinhibitory site. In-frame deletion of dgcY significantly impaired the biofilm formation and strain growth under high-salt stress, particularly at lower temperatures. Notably, we uncovered a novel feedback inhibition mechanism in this strain, whereby c-di-GMP suppresses DgcY activity by facilitating the formation of a complex between DgcY and a LysR-type transcriptional regulator, HhmR. This interaction, mediated by the regulatory domain of HhmR, obviously reduced DgcY activity, especially in the presence of c-di-GMP. Functionally, the deletion of hhmR remarkably affected the swimming motility and biofilm formation of H. hydrothermalis Y2. Collectively, these findings revealed a collaborative feedback regulatory mode, in which c-di-GMP cooperates with a transcriptional regulator to modulate the DGC activity, thereby regulating signal transduction and bacterial adaptation to osmotic stress. IMPORTANCE Generally, c-di-GMP exerts negative feedback on DGC activity by binding to the autoinhibitory site of DGCs or functioning as a downstream effector for transcriptional regulators. In this study, we revealed a previously unrecognized mode of feedback inhibition, in which c-di-GMP indirectly suppresses DgcY activity by promoting complex formation between DgcY and a LysR-type transcriptional regulator. Moreover, this DGC-associated network contributed to bacterial adaptation under osmotic stress at low temperatures, providing new insight into how c-di-GMP signaling pathways are integrated in the cellular osmotic regulation.