Megan M. McEvoy

Unusual Cu(I)/Ag(I) coordination of Escherichia coli CusF as revealed by atomic resolution crystallography and X-ray absorption spectroscopy.

Elevated levels of copper or silver ions in the environment are an immediate threat to many organisms. Escherichia coli is able to resist the toxic effects of these ions through strictly limiting intracellular levels of Cu(I) and Ag(I). The CusCFBA system is one system in E. coli responsible for copper/silver tolerance. A key component of this system is the periplasmic copper/silver‐binding protein, CusF. Here the X‐ray structure and XAS data on the CusF–Ag(I) and CusF–Cu(I) complexes, respectively, are reported. In the CusF–Ag(I) structure, Ag(I) is coordinated by two methionines and a histidine, with a nearby tryptophan capping the metal site. EXAFS measurements on the CusF–Cu(I) complex show a similar environment for Cu(I). The arrangement of ligands effectively sequesters the metal from its periplasmic environment and thus may play a role in protecting the cell from the toxic ion.

Direct Metal Transfer between Periplasmic Proteins Identifies a Bacterial Copper Chaperone

Transition metals require exquisite handling within cells to ensure that cells are not harmed by an excess of free metal species. In gram-negative bacteria, copper is required in only small amounts in the periplasm, not in the cytoplasm, so a key aspect of protection under excess metal conditions is to export copper from the periplasm. Additional protection could be conferred by a periplasmic chaperone to limit the free metal species prior to export. Using isothermal titration calorimetry, we have demonstrated that two periplasmic proteins, CusF and CusB, of the Escherichia coli Cu(I)/Ag(I) efflux system undergo a metal-dependent interaction. Through the development of a novel X-ray absorption spectroscopy approach using selenomethionine labeling to distinguish the metal sites of the two proteins, we have demonstrated transfer of Cu(I) occurs between CusF and CusB. The interaction between these proteins is highly specific, as a homologue of CusF with a 51% identical sequence and a similar affinity for metal, did not function in metal transfer. These experiments establish a metallochaperone activity for CusF in the periplasm of gram-negative bacteria, serving to protect the periplasm from metal-mediated damage.

Substrate-linked Conformational Change in the Periplasmic Component of a Cu(I)/Ag(I) Efflux System

Gram-negative bacteria utilize dual membrane resistance nodulation division-type efflux systems to export a variety of substrates. These systems contain an essential periplasmic component that is important for assembly of the protein complex. We show here that the periplasmic protein CusB from the Cus copper/silver efflux system has a critical role in Cu(I) and Ag(I) binding. Isothermal titration calorimetry experiments demonstrate that one Ag(I) ion is bound per CusB molecule with high affinity. X-ray absorption spectroscopy data indicate that the metal environment is an all-sulfur 3-coordinate environment. Candidates for the metal-coordinating residues were identified from sequence analysis, which showed four conserved methionine residues. Mutations of three of these methionine residues to isoleucine resulted in significant effects on CusB metal binding in vitro. Cells containing these CusB variants also show a decrease in their ability to grow on copper-containing plates, indicating an important functional role for metal binding by CusB. Gel filtration chromatography demonstrates that upon binding metal, CusB undergoes a conformational change to a more compact structure. Based on these structural and functional effects of metal binding, we propose that the periplasmic component of resistance nodulation division-type efflux systems plays an active role in export through substrate-linked conformational changes.

Switch or Funnel: How RND-Type Transport Systems Control Periplasmic Metal Homeostasis

Bacteria have evolved several transport mechanisms to maintain metal homeostasis and to detoxify the cell. One mechanism involves an RND (resistance-nodulation-cell division protein family)-driven tripartite protein complex to extrude a variety of toxic substrates to the extracellular milieu. These efflux systems are comprised of a central RND proton-substrate antiporter, a membrane fusion protein, and an outer membrane factor. The mechanism of substrate binding and subsequent efflux has yet to be elucidated. However, the resolution of recent protein crystal structures and genetic analyses of the components of the heavy-metal efflux family of RND proteins have allowed the developments of proposals for a substrate transport pathway. Here two models of substrate extrusion through RND protein complexes of the heavy-metal efflux protein family are described. The funnel model involves the shuttling of periplasmic substrate from the membrane fusion protein to the RND transporter and further on through the outer membrane factor to the extracellular space. Conversely, the switch model requires substrate binding to the membrane fusion protein, inducing a conformational change and creating an open-access state of the tripartite protein complex. The extrusion of periplasmic substrate bypasses the membrane fusion protein, enters the RND-transporter directly via its substrate-binding site, and is ultimately eliminated through the outer membrane channel. Evidence for and against the two models is described, and we propose that current data favor the switch model.

Chaperone-mediated copper handling in the periplasm

Covering: up to the end of 2009 Metal transport systems are broadly utilized to maintain low levels of metals to prevent cellular malfunction caused by an overabundance of metals. The CusCFBA Cu(I)/Ag(I) resistance system, commonly found in Gram-negative organisms, typically consists of a tripartite CBA transport complex that spans both the inner and outer membranes as well as a small periplasmic protein, CusF. In the CusCFBA system, CusF functions as a metallochaperone which transfers metal to the tripartite complex to aid in metal resistance. However, CusF-like proteins have also been observed in genomic contexts apart from the CBA-type transport systems, suggesting it could either play a role as a metallochaperone to other systems or have other roles than that of a metallochaperone. In this review, we focus on the molecular function of CusF in the CusCFBA transport system and discuss the metal transport pathway through this system. In addition we briefly discuss the potential functions of CusF-like proteins in other contexts.

Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry

The Escherichia coli periplasmic proteins CusF and CusB, as part of the CusCFBA efflux system, aid in the resistance of elevated levels of copper and silver by direct metal transfer between the metallochaperone CusF and the membrane fusion protein CusB before metal extrusion from the periplasm to the extracellular space. Although previous in vitro experiments have demonstrated highly specific interactions between CusF and CusB that are crucial for metal transfer to occur, the structural details of the interaction have not been determined. Here, the interactions between CusF and CusB are mapped through nuclear magnetic resonance (NMR) spectroscopy and chemical cross-linking coupled with high-resolution mass spectrometry to better understand how recognition and metal transfer occur between these proteins. The NMR (1)H-(15)N correlation spectra reveal that CusB interacts with the metal-binding face of CusF. In vitro chemical cross-linking with a 7.7 Å homobifunctional amine-reactive cross-linker, BS(2)G, was used to capture the CusF/CusB interaction site, and mass spectral data acquired on an LTQ-Orbitrap confirm the following two cross-links: CusF K31 to CusB K29 and CusF K58 to CusB K32, thus revealing that the N-terminal region of CusB interacts with the metal-binding face of CusF. The proteins transiently interact in a metal-dependent fashion, and contacts between CusF and CusB are localized to regions near their respective metal-binding sites.

Phosphohistidines in bacterial signaling

The movement of Gram-negative bacteria in response to nutrients in the environment is driven by two interlinked chemotaxis systems, the methyl-accepting chemotaxis protein (MCP)-mediated pathway, and the phosphoenolpyruvate: sugar phosphotransferase (PTS)-mediated pathway. The physical link connecting the two systems is unclear, but the common utilization of histidine-containing phosphocarrier proteins is an intriguing similarity. The recent structure determinations of several proteins from the PTS-mediated pathway, the phosphotransfer domain from the kinase CheA of the MCP-mediated chemotaxis pathway, and a homologous kinase, ArcB, enable the comparison of the histidine active sites of these systems. Overall, the tertiary folds of the proteins are quite different, as are the structural details of the histidine active sites within the proteins, and therefore there is not an obvious structural homolog via which the two pathways communicate, despite their similar chemical mechanisms.

Mechanism of ATPase-mediated Cu+ Export and Delivery to Periplasmic Chaperones: THE INTERACTION OF ESCHERICHIA COLI CopA AND CusF*

Background: It is unknown how soluble chaperones acquire Cu+ for delivery to metalloproteins and transporters. Results: Cu+ transfer from a Cu+ efflux ATPase to a periplasmic chaperone was observed. Conclusion: Specific transfer occurs after protein-protein recognition and interaction. Significance: These findings explain the requirement of multiple homologous transporters and chaperones for specificity in Cu+ delivery to alternative protein targets. Cellular copper homeostasis requires transmembrane transport and compartmental trafficking while maintaining the cell essentially free of uncomplexed Cu2+/+. In bacteria, soluble cytoplasmic and periplasmic chaperones bind and deliver Cu+ to target transporters or metalloenzymes. Transmembrane Cu+-ATPases couple the hydrolysis of ATP to the efflux of cytoplasmic Cu+. Cytosolic Cu+ chaperones (CopZ) interact with a structural platform in Cu+-ATPases (CopA) and deliver copper into the ion permeation path. CusF is a periplasmic Cu+ chaperone that supplies Cu+ to the CusCBA system for efflux to the extracellular milieu. In this report, using Escherichia coli CopA and CusF, direct Cu+ transfer from the ATPase to the periplasmic chaperone was observed. This required the specific interaction of the Cu+-bound form of CopA with apo-CusF for subsequent metal transfer upon ATP hydrolysis. As expected, the reverse Cu+ transfer from CusF to CopA was not observed. Mutation of CopA extracellular loops or the electropositive surface of CusF led to a decrease in Cu+ transfer efficiency. On the other hand, mutation of Met and Glu residues proposed to be part of the metal exit site in the ATPase yielded enzymes with lower turnover rates, although Cu+ transfer was minimally affected. These results show how soluble chaperones obtain Cu+ from transmembrane transporters. Furthermore, by explaining the movement of Cu+ from the cytoplasmic pool to the extracellular milieu, these data support a mechanism by which cytoplasmic Cu+ can be precisely directed to periplasmic targets via specific transporter-chaperone interactions.

Differing ability to transport nonmetal substrates by two RND‐type metal exporters

The metal-exporting systems CusCFBA of Escherichia coli and GesABC of Salmonella are resistance-nodulation-division (RND)-type multiprotein systems responsible for detoxification during metal stress. In this study, the substrate range was determined for each metal transport system and possible amino acid residues important in substrate specificity were identified. The Ges system, previously identified as a gold-efflux system, conferred resistance to the greatest number and variety of organic chemicals including chloramphenicol, not recognized previously as a substrate. Phylogenetic analysis showed that GesB is most closely related to a class of RND transporters including MexF that have been shown to be responsible for exporting fluoroquinolones, chloramphenicol, and biocides. However, many of the closest homologs of GesABC appear to play a role in metal resistance judging from the genetic context. In contrast, CusCFBA belongs to a distinct family of RND-type monovalent metal-exporter systems containing a number of essential metal-binding methionines, resulting in a much narrower substrate range.

Tracking metal ions through a Cu/Ag efflux pump assigns the functional roles of the periplasmic proteins

Significance Many bacteria produce large periplasmic efflux pumps that impart resistance to excess toxic metal ions. The CusC(F)BA Cu+/Ag+ efflux pump in Escherichia coli is one example. This pump’s mechanism is elusive because it is composed of four distinct proteins, three of which bind metal. By inserting a selenium probe sequentially into the metal-binding sites of the Cus proteins and loading them with Cu+ and Ag+, the bound metal ions could be tracked via X-ray absorption spectroscopy. We found that CusB activates the CusA pump and that CusF is a metallochaperone to CusA. We propose that CusB deactivates CusA once metal ion levels in the cell decrease. These results will aid in combating metal ion resistance by pathogenic bacteria. Copper is an essential nutrient for all aerobic organisms but is toxic in excess. At the host–pathogen interface, macrophages respond to bacterial infection by copper-dependent killing mechanisms, whereas the invading bacteria are thought to counter with an up-regulation of copper transporters and efflux pumps. The tripartite efflux pump CusCBA and its metallochaperone CusF are vital to the detoxification of copper and silver ions in the periplasm of Escherichia coli. However, the mechanism of efflux by this complex, which requires the activation of the inner membrane pump CusA, is poorly understood. Here, we use selenomethionine (SeM) active site labels in a series of biological X-ray absorption studies at the selenium, copper, and silver edges to establish a “switch” role for the membrane fusion protein CusB. We determine that metal-bound CusB is required for activation of cuprous ion transfer from CusF directly to a site in the CusA antiporter, showing for the first time (to our knowledge) the in vitro activation of the Cus efflux pump. This metal-binding site of CusA is unlike that observed in the crystal structures of the CusA protein and is composed of one oxygen and two sulfur ligands. Our results suggest that metal transfer occurs between CusF and apo-CusB, and that, when metal-loaded, CusB plays a role in the regulation of metal ion transfer from CusF to CusA in the periplasm.