Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network
Fig 1
Bacteria integrate stimuli from the environment and decide whether to make biofilms or to move using the c-di-GMP network.
A: Bow-tie architecture of c-di-GMP signaling network: c-di-GMP is synthesized by diguanylate cyclase (DGC) proteins with GGDEF domains such as WspR, DipA, and SadC, and degraded by phosphodiesterases (PDE) proteins with EAL or HD-GYP domains such as BifA, and SadR. The DGCs and PDEs could sense stimuli—such as chemoattractants which could be a signal for motility, or mechanical contact with surfaces which could be a signal for biofilm formation—and change intracellular c-di-GMP levels in response; c-di-GMP effectors—such as c-di-GMP binding proteins and riboswitch RNAs—then sense c-di-GMP levels and control phenotype outputs such as biofilm formation, motility, virulence and cell division. B: At low levels of c-di-GMP the bacteria express flagella genes and go into motile mode. C: At high levels of c-di-GMP the bacteria repress flagella genes, express biofilm genes and go into biofilm mode.