Substrate-induced closing of the active site revealed by the crystal structure of pantothenate synthetase from Staphylococcus aureus.

Pantothenate synthetase (PS, EC 6.3.2.1) is the last enzyme in the pantothenate biosynthesis pathway, a metabolic pathway identified as a potential target for new antimicrobials. PS catalyzes the ATP-dependent condensation of pantoate and beta-alanine to form pantothenate. Here we report the overexpression, purification, enzyme assay, and tertiary structure of PS from Staphylococcus aureus. PS activity was experimentally confirmed, indicating a k(cat) value comparable to those of enzymes from other organisms. The structures of the apoenzyme and the reaction intermediate (pantoyl adenylate; PA) complex were determined by X-ray crystallography to resolutions of 2.5 and 1.85 A, respectively. Structural analysis indicated that the apoenzyme adopts an open and relatively mobile structure, while the complex structure is closed and entirely rigid. Structural comparison of the apoenzyme and the complex revealed how S. aureus PS undergoes open/close conformational change, and also determined the key interactions with the adenine ring of PA for a hinge bending domain closure. In the complex structure, PA and acetate are bound in the active site. We suggest that the acetate mimics the substrate beta-alanine. Therefore, the complex structure seems to represent a catalytic state poised for in-line nucleophilic attack on PA. These data also offer an alternative strategy for designing novel compounds that selectively inhibit PS activity.

Mutation of nfxB causes global changes in the physiology and metabolism of Pseudomonas aeruginosa.

Loss-of-function mutations in nfxB lead to up-regulation of mexCD-oprJ expression and, consequently, increased resistance to fluoroquinolone antibiotics. Such nfxB mutants have also been reported to exhibit altered virulence profiles, diminished type III secretion system-dependent cytotoxicity, and impaired fitness. However, it is not clear whether these phenotypes are directly linked to NfxB activity or whether inappropriate expression of the MexCD-OprJ pump has pleiotropic effects, thereby impacting indirectly on the phenotype of the cells. The aim of the current work is to investigate which of these possibilities is correct. We isolated a novel type of nfxB mutant generated by a spontaneous polygenic deletion and show that this mutant is rapidly out-competed when grown in a mixed culture with the wild-type progenitor. This competitive fitness defect only manifested itself during the stationary phase of growth. The endoproteome of the nfxB mutant, assessed using 2D-DiGE (difference gel electrophoresis), showed major alterations compared with the wild-type. Consistent with this, we found that the nfxB mutant was impaired in all forms of motility (swimming, swarming, and twitching) as well as in the production of siderophores, rhamnolipid, secreted protease, and pyocyanin. Further investigation showed that the exoproteome, endometabolome, and exometabolome of the nfxB mutant were all globally different compared with the wild-type. The exometabolome of the nfxB mutant was enriched in a selection of long chain fatty acids raising the possibility that these might be substrates for the MexCD-OprJ pump. The nfxB mutant metabotype could be complemented by expression of nfxB in trans and was abolished in an nfxB mexD double mutant, suggesting that inappropriate overexpression of a functional MexCD-OprJ efflux pump causes pleiotropic changes. Taken together, our data suggest that many of the nfxB mutant phenotypes are not caused by the direct effects of the NfxB regulator, but instead by inappropriate mexCD-oprJ expression. Furthermore, the pleiotropic nature of the phenotypes indicate that these may simply reflect the globally dysregulated physiology of the strain.

Variations on a theme: diverse N-acyl homoserine lactone-mediated quorum sensing mechanisms in gram-negative bacteria.

Many Gram-negative bacteria employ a mechanism of cell-cell communication known as quorum sensing (QS). The role of QS is to enable the cells in a culture to coordinate their gene expression profile with changes in the population cell density. The best characterized mechanisms of QS employ N-acylated homoserine lactones (AHLs) as signalling molecules. These AHLs are made by enzymes known as LuxI homologs, and accumulate in the culture supernatant at a rate proportional to the increase in cell density. Once the AHL concentration exceeds a certain threshold value, these ligands bind to intracellular receptors known as LuxR homologs. The latter are transcriptional regulators, whose activity alters upon binding the AHL ligand, thereby eliciting a change in gene transcription. Over the last five years, it has become increasingly obvious that this is a rather simplistic view of AHL-dependent QS, and that in fact, there is considerable diversity in the way in which LuxI-R homologs operate. The aim of the current review is to describe these variations on the basic theme, and to show how functional genomics is revolutionizing our understanding of QS-controlled regulons.