DGCs can also be subject to allosteric product inhibition by c-di-GMP, which binds to a secondary site (I site) separated from the A site by 5 amino acids . This feedback MG-132 ic50 control helps to maintain adequate pools of c-di-GMP, avoiding excessive consumption of the GTP substrate and reducing stochastic perturbations in cellular c-di-GMP content [16, 17]. GGDEF and EAL proteins can also contain one or more transmembrane regions and signal
peptides that can anchor these proteins to the membrane, most probably allowing physical isolation of different GGDEF and EAL systems to unique microenvironments . In addition, some bacterial species can harbor multiple copies of proteins with GGDEF and EAL domains. Many of these copies may contain degenerate sites that are inactive and do not directly synthesize or degrade c-di-GMP but have adopted alternative functions, either as c-di-GMP binding effector proteins or through direct macromolecular interactions with no involvement of c-di-GMP at all . The diversity of sensor domains coupled to the multiplicity of these genes reveal a complex c-di-GMP network that integrates diverse environmental and cellular signals [16, 17]. This work was carried out to identify GGDEF and EAL domain-containing genes in three sequenced K. pneumoniae genomes. Searches were done
for the conserved GGDEF/EAL domains and the RxxD allosteric I site. Sensory domains associated with these proteins, as well as transmembrane helices and signal peptides were also identified. Bcl-w CHIR98014 clinical trial The results show that there are multiple copies of these genes in the sequenced genomes studied
and that some of these are shared while others are unique to a particular strain. Results and discussion Multiplicity of genes encoding GGDEF and EAL containing proteins To have an inventory of the number of genes coding for GGDEF and EAL domain-containing proteins, PSI-BLAST was used to identify the conserved GG(D/E)EF and E(A/V)L motifs in the three sequenced K. pneumoniae genomes. The genomes available at the time this analysis was done included one environmental strain, K. pneumoniae Kp342, a ACY-1215 price nitrogen-fixing endophyte isolated from corn , and two clinical isolates from the same subspecies: K. pneumoniae subsp. pneumoniae MGH 78578, isolated from a patient with nosocomial pneumonia , and K. pneumoniae subsp. pneumoniae NTUH-K2044, isolated from a patient with a hepatic abscess and meningitis . All genomes had multiple copies for proteins with GGDEF domains: 17 for NTUH-K2044, 18 for MGH 78578 and 21 for the environmental isolate Kp342 (Table 1). The majority of these proteins contained the GGEEF sequence motif and only 30% had GGDEF (Figure 1). A subset of the proteins (29%) had both GGDEF and EAL domains and more than 50% of these had GGDEF degenerate domains. Two GGDEF-only proteins (KPK_A0039 and KPN_pKPN3p05901) had GGDEF degenerate domains and were found on plasmids.