Dysregulation of Streptococcus pneumoniae zinc homeostasis breaks ampicillin resistance in a pneumonia infection model.

Streptococcus pneumoniae is the primary cause of community-acquired bacterial pneumonia with rates of penicillin and multidrug-resistance exceeding 80% and 40%, respectively. The innate immune response generates a variety of antimicrobial agents to control infection, including zinc stress. Here, we characterize the impact of zinc intoxication on S. pneumoniae, observing disruptions in central carbon metabolism, lipid biogenesis, and peptidoglycan biosynthesis. Characterization of the pivotal peptidoglycan biosynthetic enzyme GlmU indicates a sensitivity to zinc inhibition. Disruption of the sole zinc efflux pathway, czcD, renders S. pneumoniae highly susceptible to ß-lactam antibiotics. To dysregulate zinc homeostasis in the wild-type strain, we investigated the safe-for-human-use ionophore 5,7-dichloro-2-[(dimethylamino)methyl]quinolin-8-ol (PBT2). PBT2 rendered wild-type S. pneumoniae strains sensitive to a range of antibiotics. Using an invasive ampicillin-resistant strain, we demonstrate in a murine pneumonia infection model the efficacy of PBT2 + ampicillin treatment. These findings present a therapeutic modality to break antibiotic resistance in multidrug-resistant S. pneumoniae.

Structural and functional characterizations of the C-terminal domains of CzcD proteins.

Zinc is a potent antimicrobial component of the innate immune response at the host-pathogen interface. Bacteria subvert or resist host zinc insults by metal efflux pathways that include cation diffusion facilitator (CDF) proteins. The structural and functional examination of this protein class has been limited, with only the structures of the zinc transporter YiiP proteins from E. coli and Shewanella oneidensis described to date. Here, we determine the metal binding properties, solution quaternary structures and three dimensional architectures of the C-terminal domains of the metal transporter CzcD proteins from Cupriavidus metallidurans, Pseudomonas aeruginosa and Thermotoga maritima. We reveal significant diversity in the metal-binding properties and structures of these proteins and discover a potential novel mechanism for metal-promoted dimerization for the Cupriavidus metallidurans and Pseudomonas aeruginosa proteins.

Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase of Staphylococcus aureus.

WalKR (YycFG) is the only essential two-component regulator in the human pathogen Staphylococcus aureus. WalKR regulates peptidoglycan synthesis, but this function alone does not explain its essentiality. Here, to further understand WalKR function, we investigate a suppressor mutant that arose when WalKR activity was impaired; a histidine to tyrosine substitution (H271Y) in the cytoplasmic Per-Arnt-Sim (PASCYT) domain of the histidine kinase WalK. Introducing the WalKH271Y mutation into wild-type S. aureus activates the WalKR regulon. Structural analyses of the WalK PASCYT domain reveal a metal-binding site, in which a zinc ion (Zn2+) is tetrahedrally-coordinated by four amino acids including H271. The WalKH271Y mutation abrogates metal binding, increasing WalK kinase activity and WalR phosphorylation. Thus, Zn2+-binding negatively regulates WalKR. Promoter-reporter experiments using S. aureus confirm Zn2+ sensing by this system. Identification of a metal ligand recognized by the WalKR system broadens our understanding of this critical S. aureus regulon.

The crystal structure of the CopC protein from Pseudomonas fluorescens reveals amended classifications for the CopC protein family.

The bacterial CopC family of proteins are periplasmic copper binding proteins that act in copper detoxification. These proteins contain Cu(I) and/or Cu(II) binding sites, with the family that binds Cu(II) only the most prevalent, based on sequence analyses. Here we present three crystal structures of the CopC protein from Pseudomonas fluorescens (Pf-CopC) that include the wild type protein bound to Cu(II) and two variant proteins, where Cu(II) coordinating ligands were mutated, in Cu-free states. We show that the Cu(II) atom in Pf-CopC is coordinated by two His residues, an Asp residue and the N-terminus of the protein (therefore a 3N + O site). This coordination structure is consistent with all structurally characterized proteins from the CopC family to date. Structural and sequence analyses of the CopC family allow a relationship between protein sequence and the Cu(II) binding affinity of these proteins to be proposed.

Crystal structure of bacterial succinate:quinone oxidoreductase flavoprotein SdhA in complex with its assembly factor SdhE.

Succinate:quinone oxidoreductase (SQR) functions in energy metabolism, coupling the tricarboxylic acid cycle and electron transport chain in bacteria and mitochondria. The biogenesis of flavinylated SdhA, the catalytic subunit of SQR, is assisted by a highly conserved assembly factor termed SdhE in bacteria via an unknown mechanism. By using X-ray crystallography, we have solved the structure of Escherichia coli SdhE in complex with SdhA to 2.15-Å resolution. Our structure shows that SdhE makes a direct interaction with the flavin adenine dinucleotide-linked residue His45 in SdhA and maintains the capping domain of SdhA in an "open" conformation. This displaces the catalytic residues of the succinate dehydrogenase active site by as much as 9.0 Å compared with SdhA in the assembled SQR complex. These data suggest that bacterial SdhE proteins, and their mitochondrial homologs, are assembly chaperones that constrain the conformation of SdhA to facilitate efficient flavinylation while regulating succinate dehydrogenase activity for productive biogenesis of SQR.

Copper ATPase CopA from Escherichia coli: Quantitative Correlation between ATPase Activity and Vectorial Copper Transport.

Cu-ATPases are membrane copper transporters present in all kingdoms of life. They play a central role in Cu homeostasis by pumping Cu ions across cell membranes with energy derived from ATP hydrolysis. In this work, the Cu-ATPase CopA from Escherichia coli was expressed and purified in fully functional form and demonstrated to bind Cu(I) with subfemtomolar affinity. It was incorporated into the lipid membrane of giant unilamellar vesicles (GUVs) whose dimensions match those of eukaryotic cells. An 1H NMR approach provided a quantitative ATPase activity assay for the enzyme either dissolved in detergent or embedded in GUV membranes. The activity varied with the Cu(I) availability in an optimized assay solution for either environment, demonstrating a direct correlation between ATPase activity and Cu(I) transport. Quantitative analysis of the Cu content trapped by the GUVs is consistent with a Cu:ATP turnover ratio of 1.

Evaluation of quantitative probes for weaker Cu(i) binding sites completes a set of four capable of detecting Cu(i) affinities from nanomolar to attomolar.

Copper plays essential roles in biology, but abnormal interactions are damaging. Reliable quantification of copper-protein interactions will underpin the molecular understanding of copper nutrition and toxicity. We have previously established two high affinity probes, Bathocuproine disulfonate (Bcs) and Bicinchoninate (Bca) anions, that are capable of in vitro quantification of Cu(i) binding with affinities from pico- to atto-molar concentrations. Quantitative probes are required for Cu(i) binding of lower affinity for proteins and peptides typically associated with neurodegenerative diseases. The present work evaluates two classic Fe(ii) ligands Ferene S (Fs) and Ferrozine (Fz) as quantitative probes for Cu(i). Both react with Cu(i) quantitatively to yield well-defined complex anions [Cu(I)(Fs)2](3-) (λmax = 484 nm, ε = 6700 cm(-1) M(-1)) and [Cu(I)(Fz)2](3-) (λmax = 470 nm, ε = 4320 cm(-1) M(-1)). These complexes are sensitive to aerial oxidation (E1/2∼ +0.36 V vs. SHE) and to substitution by other ligands (e.g., Cl(-), MeCN). However, they can be protected effectively under anaerobic conditions by suitable reductants and an excess of the free probe ligands. Formation constants ß2 were determined by two approaches: direct metal ion titration and ligand competition. They provided estimates which differed by ∼3 orders of magnitude. The sources of these differences were examined carefully to consolidate the affinities of the two probes to a unified standard (10(15.1) M(-2) for Fz and 10(13.7) M(-2) for Fs). It is apparent that application of direct metal ion titrations to quantification of Cu(i) binding affinities is problematical and should be avoided. The four ligands Bcs, Bca, Fz and Fs in combination form a set of versatile probes for ligand competition experiments and are capable of detecting and differentiating an extended spectrum of Cu(i) binding affinities from nano- to atto-molar concentrations. Selected examples of quantification of weaker Cu(i) binding in proteins and peptides are provided, including that of an amyloid-ß peptide.

PcoE--a metal sponge expressed to the periplasm of copper resistance Escherichia coli. Implication of its function role in copper resistance.

Expression of the periplasmic protein PcoE of Escherichia coli is induced strongly by cupric salts under the control of the chromosomal copper tolerance system cusRS. Its isolation and study were complicated by de-amidation of Asn 54 and 103 at alkaline pH. Its apo form is essentially unstructured in solution and can be likened to a large unstructured multidentate ligand carrying multiple metal binding sites (15 Met; 10 His; 13 Asp, Glu; 10 Asn; 6 Lys). As expected, it binds multiple soft metal ions Cu(+) and Ag(+) non-cooperatively with the highest affinity for Cu(I) in the picomolar range (K(D)~10(-12) M). Binding of multiple soft ions induced dimerization and formation of some α-helical structure. PcoE also binds the harder metal ions Cu(2+) or Zn(2+) but with lower affinities and in smaller numbers. Cu(II) bound in PcoE is reduced readily to more tightly bound Cu(I). Overall, these properties mean that it is difficult to characterize individual species of defined metal content. Similar properties and difficulties have been reported for the homologous silver-binding protein SilE from Salmonella. However, the properties are consistent with a role for PcoE as a 'metal sponge' acting as a first line of defence against metal toxicity (under the control of the copper tolerance system cusRS) until the copper resistance operon pcoABCD is expressed.