Cross-regulation of (p)ppGpp and c-di-GMP pathways controls a cell-cycle transition

Bacteria must adapt their physiology to changing environments, a process often orchestrated by nucleotide messengers such as (p)ppGpp and cyclic di-GMP (c-di-GMP). While (p)ppGpp promotes survival under nutrient stress by suppressing growth, c-di-GMP supports sessile lifestyles and cell differentiation. In the -proteobacterium Caulobacter crescentus, these messengers have opposite effects on the cell cycle, suggesting potential cross-regulations. Here, we uncover direct molecular cross-talk between (p)ppGpp and c-di-GMP signaling pathways. Using biochemical, structural and genetic approaches, we show that (p)ppGpp binds to the diguanylate cyclase PleD and inhibits c-di-GMP synthesis by competing with GTP at the active site. This interaction prevents c-di-GMP accumulation under nutrient-limiting conditions, linking metabolic stress to inhibition of developmental progression. Our findings reveal a new paradigm for second messenger interplay, in which one messenger directly suppresses synthesis of another. This work provides insight into how bacteria integrate metabolic and developmental cues through small-molecule cross-talk to guide adaptive behavior.