GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP

Cyclic dinucleotides are an expanding class of signaling molecules that control many aspects of bacterial physiology. A synthase for cyclic AMP-GMP (cAG, also referenced as 3′-5′, 3′-5′ cGAMP) called DncV is associated with hyperinfectivity of Vibrio cholerae but has not been found in many bacteria, raising questions about the prevalence and function of cAG signaling. We have discovered that the environmental bacterium Geobacter sulfurreducens produces cAG and uses a subset of GEMM-I class riboswitches (GEMM-Ib, Genes for the Environment, Membranes, and Motility) as specific receptors for cAG. GEMM-Ib riboswitches regulate genes associated with extracellular electron transfer; thus cAG signaling may control aspects of bacterial electrophysiology. These findings expand the role of cAG beyond organisms that harbor DncV and beyond pathogenesis to microbial geochemistry, which is important to environmental remediation and microbial fuel cell development. Finally, we have developed an RNA-based fluorescent biosensor for live-cell imaging of cAG. This selective, genetically encodable biosensor will be useful to probe the biochemistry and cell biology of cAG signaling in diverse bacteria. Significance Bacteria are hidden forces of nature. For example, Geobacter bacteria play important roles in geochemistry by reducing metals in the environment. Scientists also are exploring the application of these bacteria toward toxic metal remediation and as “living batteries” that can generate electricity from biowaste. However, there is limited understanding of the signaling pathways that regulate this extracellular metal-reducing activity. Here we have discovered that Geobacter sulfurreducens use riboswitch sensors for a signaling molecule called cAG to regulate this process, which is an unexpected finding because cAG was previously associated only with pathogenic bacteria. Furthermore, we have adapted the riboswitch to generate a fluorescent biosensor that can be used to visualize cAG signaling in live bacteria.