A computational study of bacterial gene regulation and adaptation ...

transcriptional initiation by c-di-GMP via PilZ. Other effector proteins include those thatcontain degenerate active site motifs for the GGDEF or EAL domains that still retainsubstrate-binding ability (Christen et al. 2005; Kazmierczak et al. 2006). Interestingly, eventhose degenerate GGDEF and EAL proteins that have been characterised retain roles relatedto the control of motility and adhesion (Hengge 2009).Because of its structural similarity to nucleic acids, c-di-GMP was proposed to bind to RNAmolecules. This was experimentally verified later by the identification of riboswitches -regions in the 5’-UTR of certain mRNAs - that bind to c-di-GMP (Sudarsan et al. 2008). Thisparticular conserved RNA domain has been found in the mRNAs of GGDEF and EALproteins as well as some other proteins whose activities respond to c-di-GMP levels. This isan unequivocal example for post-transcriptional regulation of gene expression by this secondmessenger. Observation that c-di-GMP-sensing riboswitches, unlike those that sensemetabolic products, are found in phage genomes suggested that phages could sense‘physiological transformations’ in the bacterial cell by monitoring c-di-GMP levels.In spite of the above studies, data on both signal-response and effect-mediation involved in c-di-GMP signalling lag behind that on the enzymes involved in the molecule’s turnover. Weanticipate further research to expand our knowledge of these aspects of this novel, andimportant, signalling mechanism.21