A newfound signaling pathway employs a GGDEF enzyme with unique activity compared to the majority of homologs associated with bacterial cyclic di-GMP signaling. This system provides a rare opportunity to study how signaling proteins natively gain distinct function. Using genetic knockouts, riboswitch reporters, and RNA-Seq, we show that GacA, the Hypr GGDEF in Geobacter sulfurreducens, specifically regulates cyclic GMP-AMP (3′,3′-cGAMP) levels in vivo to stimulate gene expression associated with metal reduction separate from electricity production. To reconcile these in vivo findings with prior in vitro results that showed GacA was promiscuous, we developed a full kinetic model combining experimental data and mathematical modeling to reveal mechanisms that contribute to in vivo specificity. A 1.4 Å-resolution crystal structure of the Geobacter Hypr GGDEF domain was determined to understand the molecular basis for those mechanisms, including key cross-dimer interactions. Together these results demonstrate that specific signaling can result from a promiscuous enzyme.
Bibliographical noteFunding Information:
X-ray data were collected at Beamline 8.3.1 of the Lawrence Berkeley National Lab Advanced Light Source (ALS). We thank Professors Robert Bergman and Jennifer Doudna for helpful comments and discussion, Jason Peters for providing the Tn7 vectors and Jonathan Badalamenti for sequence analysis assistance and RNA-seq data management. This work was supported by NSF MCB collaborative grants 1716256 and 1714196 (to MCH and DRB), ONR grant N000141612194 (to DRB), NIH R01 GM124589 (to MCH), and NSF graduate fellowship (to ZFH).
© Hallberg et al.