As in other bacteria, the different sensor domains suggest a diverse range of environmental stimuli involved in regulatory responses in this bacterium [26, 27] (Table 1). In GGDEF proteins the most frequently H 89 found domain was GAF (18%) (cGMP phosphodiesterase, adenylyl cyclase), a cytoplasmic sensor domain

that can bind a number of small molecules including monocyclic nucleotides and oxygen and that is also BV-6 order common in signal transducing photoreceptor proteins such as phytochromes, which covalently link chromophores [28]. This was followed by HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain-containing proteins (14%). This domain has been found in many transmembrane receptors where it transmits signals from periplasmic sensor domains to cytoplasmic output domains via conformational changes [25, 29]. The PAS (PER, ARNT and SIM) domain was found only in 11% of the GGDEF proteins. PAS is structurally similar to GAF

and can bind small molecules such as heme, flavin, and adenine [29, 30]. Other domains were also found in smaller proportions. The membrane-embedded MASE (Membrane-associated sensor) BI 10773 clinical trial domain [25] was identified in 9% of the GGDEF proteins and 11% of the EAL proteins (Table 1), and the extracellular CHASE (cyclase/histidine kinases-associated sensing extracellular) and CACHE (Ca2+ channels and chemotaxis receptors) domains were found in 2% and 9% of the cases, respectively. The CHASE domain apparently recognizes short peptides and cytokines [25, 30, 31]. The CACHE domain is involved in binding small ligands such as amino acids, sugars and organic acids, and has been found in prokaryotic

chemotaxis receptors and animal ion channels [30, 31]. The most common sensor domain in EAL proteins was the CSS-motif (28%) of unknown function, followed by BLUF (for ‘sensing blue-light using FAD’) (12%), which is involved in sensing blue-light and possibly redox states [32]. Some sensor domains identified in other bacteria were not found in K. pneumoniae, as was the case for REC (receiving domain with phosphoacceptor site), which is implicated in activation of DGC proteins in organisms such as Caulobacter crescentus and Pseudomonas[27]. Predicted catalytic Galactosylceramidase activity in GGDEF-containing proteins Active DGCs consist of two subunits, each with an A site that binds a GTP molecule at the interface between the two subunits. The A site has the characteristic conserved GGDEF or GGEEF motif and point mutations that affect this sequence abolish enzymatic activity [17]. Many DGCs are also subject to allosteric inhibition, which involves binding of c-di-GMP to the I site characterized by the RxxD motif [16, 17]. Mutations of the R residue alter the inhibitory function and allosteric control, while mutations of the D amino acid do not [16]. In K.