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1.  Crystal structure of the CorA Mg2+ transporter 
Nature  2006;440(7085):10.1038/nature04642.
The magnesium ion, Mg2+, is essential for myriad biochemical processes and remains the only major biological ion whose transport mechanisms remain unknown. The CorA family of magnesium transporters is the primary Mg2+ uptake system of most prokaryotes1–3 and a functional homologue of the eukaryotic mitochondrial magnesium transporter4. Here we determine crystal structures of the full-length Thermotoga maritima CorA in an apparent closed state and its isolated cytoplasmic domain at 3.9 Å and 1.85Å resolution, respectively. The transporter is a funnel-shaped homopentamer with two transmembrane helices per monomer. The channel is formed by an inner group of five helices and putatively gated by bulky hydrophobic residues. The large cytoplasmic domain forms a funnel whose wide mouth points into the cell and whose walls are formed by five long helices that are extensions of the transmembrane helices. The cytoplasmic neck of the pore is surrounded, on the outside of the funnel, by a ring of highly conserved positively charged residues. Two negatively charged helices in the cytoplasmic domain extend back towards the membrane on the outside of the funnel and abut the ring of positive charge. An apparent Mg2+ ion was bound between monomers at a conserved site in the cytoplasmic domain, suggesting a mechanism to link gating of the pore to the intra-cellular concentration of Mg2+.
doi:10.1038/nature04642
PMCID: PMC3836678  PMID: 16598263
2.  Pseudomonas aeruginosa PA1006 Is a Persulfide-Modified Protein That Is Critical for Molybdenum Homeostasis 
PLoS ONE  2013;8(2):e55593.
A companion manuscript revealed that deletion of the Pseudomonas aeruginosa (Pae) PA1006 gene caused pleiotropic defects in metabolism including a loss of all nitrate reductase activities, biofilm maturation, and virulence. Herein, several complementary approaches indicate that PA1006 protein serves as a persulfide-modified protein that is critical for molybdenum homeostasis in Pae. Mutation of a highly conserved Cys22 to Ala or Ser resulted in a loss of PA1006 activity. Yeast-two-hybrid and a green-fluorescent protein fragment complementation assay (GFP-PFCA) in Pae itself revealed that PA1006 interacts with Pae PA3667/CsdA and PA3814/IscS Cys desulfurase enzymes. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) “top-down” analysis of PA1006 purified from Pae revealed that conserved Cys22 is post-translationally modified in vivo in the form a persulfide. Inductively-coupled-plasma (ICP)-MS analysis of ΔPA1006 mutant extracts revealed that the mutant cells contain significantly reduced levels of molybdenum compared to wild-type. GFP-PFCA also revealed that PA1006 interacts with several molybdenum cofactor (MoCo) biosynthesis proteins as well as nitrate reductase maturation factor NarJ and component NarH. These data indicate that a loss of PA1006 protein’s persulfide sulfur and a reduced availability of molybdenum contribute to the phenotype of a ΔPA1006 mutant.
doi:10.1371/journal.pone.0055593
PMCID: PMC3568144  PMID: 23409003
3.  dbVar and DGVa: public archives for genomic structural variation 
Nucleic Acids Research  2012;41(D1):D936-D941.
Much has changed in the last two years at DGVa (http://www.ebi.ac.uk/dgva) and dbVar (http://www.ncbi.nlm.nih.gov/dbvar). We are now processing direct submissions rather than only curating data from the literature and our joint study catalog includes data from over 100 studies in 11 organisms. Studies from human dominate with data from control and case populations, tumor samples as well as three large curated studies derived from multiple sources. During the processing of these data, we have made improvements to our data model, submission process and data representation. Additionally, we have made significant improvements in providing access to these data via web and FTP interfaces.
doi:10.1093/nar/gks1213
PMCID: PMC3531204  PMID: 23193291
4.  Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment 
BMC Microbiology  2012;12:186.
Background
Mangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood.
Results
Mangrove sediment was sampled from 0–5, 15–20 and 35–40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil), which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth.
Conclusions
Analysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0–5 cm) being greater than in both deeper sediment layers (15–20 and 35–40 cm), which were similar to each other.
doi:10.1186/1471-2180-12-186
PMCID: PMC3579730  PMID: 22935169
Mangrove; Bacterial diversity; Anoxic sediment; Sulphate; Petroleum; Hydrocarbons
5.  X-ray Crystallography and Isothermal Titration Calorimetry Studies of the Salmonella Zinc Transporter ZntB 
SUMMARY
The ZntB Zn2+ efflux system is important for maintenance of Zn2+ homeostasis in Enterobacteria. We report crystal structures of ZntB cytoplasmic domains from Salmonella enterica serovar Typhimurium (StZntB) in dimeric and physiologically relevant homopentameric forms at 2.3 Å and 3.1 Å resolutions, respectively. The funnel-like structure is similar to that of the homologous Thermotoga maritima CorA Mg2+ channel and a Vibrio parahaemolyticus ZntB (VpZntB) soluble domain structure. However, the central α7 helix forming the inner wall of the StZntB funnel is oriented perpendicular to the membrane instead of the marked angle seen in CorA or VpZntB. Consequently, the StZntB funnel pore is cylindrical, not tapered, which may represent an “open” form of the ZntB soluble domain. Our crystal structures and isothermal titration calorimetry data indicate that there are three Zn2+ binding sites in the full-length ZntB, two of which could be involved in Zn2+ transport.
doi:10.1016/j.str.2011.02.011
PMCID: PMC3094545  PMID: 21565704
6.  The Phage Shock Protein PspA Facilitates Divalent Metal Transport and is Required for Virulence of Salmonella enterica sv. Typhimurium 
Molecular microbiology  2010;78(3):669-685.
SUMMARY
The phage shock protein (Psp) system is induced by extracytoplasmic stress and thought to be important for the maintenance of proton motive force (PMF). We investigated the contribution of PspA to Salmonella virulence. A pspA deletion mutation significantly attenuates the virulence of S. Typhimurium following intraperitoneal inoculation of C3H/HeN (Ityr) mice. PspA was found to be specifically required for virulence in mice expressing the Nramp1 (Slc11a1) divalent metal transporter, which restricts microbial growth by limiting the availability of essential divalent metals within the phagosome. Salmonella competes with Nramp1 by expressing multiple metal uptake systems including the Nramp-homolog MntH, the ABC transporter SitABCD, and the ZIP family transporter ZupT. PspA was found to facilitate Mn2+ transport by MntH and SitABCD, as well as Zn2+ and Mn2+ transport by ZupT. In vitro uptake of 54Mn2+ by MntH and ZupT was reduced in the absence of PspA. Transport-deficient mutants exhibit reduced viability in the absence of PspA when grown under metal-limited conditions. Moreover, the ZupT transporter is required for S. Typhimurium virulence in Nramp1-expressing mice. We propose that PspA promotes Salmonella virulence by maintaining PMF, which is required for the function of multiple transporters mediating bacterial divalent metal acquisition during infection.
doi:10.1111/j.1365-2958.2010.07357.x
PMCID: PMC2963695  PMID: 20807201
7.  Cation Selectivity by the CorA Mg2+ Channel Requires a Fully Hydrated Cation† 
Biochemistry  2010;49(29):5998-6008.
The CorA Mg2+ channel is the primary uptake system in about half of all bacteria and archaea. However, the basis for its Mg2+ selectivity is unknown. Previous data suggested that CorA binds a fully hydrated Mg2+ ion, unlike other ion channels. The crystal structure of Thermotoga maritima CorA shows a homopentamer with two transmembrane segments per monomer connected by a short periplasmic loop. This highly conserved loop, 281EFMPELKWS289 in Salmonella enterica serovar Typhimurium CorA, is the only portion of the channel outside of the cell, suggesting a role in cation selectivity. Mutation of charged residues in the loop, E281 and K287, to any of several amino acids had little effect, demonstrating that despite conservation, electrostatic interactions with these residues are not essential. While mutation of the universally conserved E285 gave a minimally functional channel, E285A and E285K mutants were the most functional, again indicating that the negative charge at this position is not a determining factor. Several mutations at K287 and W288 behaved anomalously in a transport assay. Analysis indicated that mutation of K287 and W288 disrupts cooperative interactions between distinct Mg2+ binding sites. Overall, these results are not compatible with electrostatic interaction of the Mg2+ ion with the periplasmic loop. Instead, the loop appears to form an initial binding site for hydrated Mg2+, not for the dehydrated cation. The loop residues may function to accelerate dehydration of the before entry of Mg2+ into the pore of the channel.
doi:10.1021/bi1005656
PMCID: PMC2912426  PMID: 20568735
8.  Improvements to services at the European Nucleotide Archive 
Nucleic Acids Research  2009;38(Database issue):D39-D45.
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe’s primary nucleotide sequence archival resource, safeguarding open nucleotide data access, engaging in worldwide collaborative data exchange and integrating with the scientific publication process. ENA has made significant contributions to the collaborative nucleotide archival arena as an active proponent of extending the traditional collaboration to cover capillary and next-generation sequencing information. We have continued to co-develop data and metadata representation formats with our collaborators for both data exchange and public data dissemination. In addition to the DDBJ/EMBL/GenBank feature table format, we share metadata formats for capillary and next-generation sequencing traces and are using and contributing to the NCBI SRA Toolkit for the long-term storage of the next-generation sequence traces. During the course of 2009, ENA has significantly improved sequence submission, search and access functionalities provided at EMBL–EBI. In this article, we briefly describe the content and scope of our archive and introduce major improvements to our services.
doi:10.1093/nar/gkp998
PMCID: PMC2808951  PMID: 19906712
9.  The Unique Nature of Mg2+ Channels 
Physiology (Bethesda, Md.)  2008;23:275-285.
Considering the biological abundance and importance of Mg2+, there is a surprising lack of information regarding the proteins that transport Mg2+, the mechanisms by which they do so, and their physiological roles within the cell. The best characterized Mg2+ channel to date is the bacterial protein CorA, present in a wide range of bacterial species. The CorA homolog Mrs2 forms the mitochondrial Mg2+ channel in all eukaryotes. Physiologically, CorA is involved in bacterial pathogenesis, and the Mrs2 eukaryotic homolog is essential for cell survival. A second Mg2+ channel widespread in bacteria is MgtE. Its eukaryotic homologs are the SLC41 family of carriers. Physiological roles for MgtE and its homologs have not been established. Recently, the crystal structures for the bacterial CorA and MgtE Mg2+ channels were solved, the first structures of any divalent cation channel. As befits the unique biological chemistry of Mg2+, both structures are unique, unlike that of any other channel or transporter. Although structurally quite different, both CorA and MgtE appear to be gated in a similar manner through multiple Mg2+ binding sites in the cytosolic domain of the channels. These sites essentially serve as Mg2+ “sensors” of cytosolic Mg2+ concentration. Many questions about these channels remain, however, including the molecular basis of Mg2+ selectivity and the physiological role(s) of their eukaryotic homologs.
doi:10.1152/physiol.00019.2008
PMCID: PMC2711038  PMID: 18927203
10.  Regulation of CorA Mg2+ Channel Function Affects the Virulence of Salmonella enterica Serovar Typhimurium ▿  
Journal of Bacteriology  2008;190(19):6509-6516.
The CorA Mg2+ channel is the primary source of intracellular Mg2+ in Salmonella enterica serovar Typhimurium. In another study, we found that a strain lacking corA was attenuated in mice and also defective for invasion and replication within Caco-2 epithelial cells (K. M. Papp-Wallace, M. Nartea, D. G. Kehres, S. Porwollik, M. McClelland, S. J. Libby, F. C. Fang, and M. E. Maguire, J. Bacteriol. 190:6517-6523, 2008). Therefore, we further examined Salmonella interaction with Caco-2 epithelial cells. Inhibiting CorA acutely or chronically with a high concentration of a selective inhibitor, Co(III) hexaammine, had no effect on S. enterica serovar Typhimurium invasion of Caco-2 epithelial cells. Complementing the corA mutation with corA from various species rescued the invasion defect only if the complementing allele was functional and if it was evolutionarily similar to S. enterica serovar Typhimurium CorA. One explanation for these results could be that regulation of CorA function is needed for optimal virulence. Further experiments examining corA transcription, CorA protein content, CorA transport, and cell Mg2+ content indicated that both CorA expression and CorA function are differentially regulated. Moreover, the rates of Mg2+ influx via CorA are not closely correlated with either protein levels or Mg2+ content. We conclude that loss of the CorA protein disrupts a regulatory network(s) with the ultimate phenotype of decreased virulence. This conclusion is compatible with the microarray results in our other study, which showed that loss of corA resulted in changes in transcription (and protein expression) in multiple metabolic pathways (Papp-Wallace et al., J. Bacteriol. 190:6517-6523, 2008). Further study of the regulation of CorA expression and function provides an opportunity to dissect the complexity of Mg2+ homeostasis and its ties to virulence within the bacterium.
doi:10.1128/JB.00144-08
PMCID: PMC2565989  PMID: 18676666
11.  The CorA Mg2+ Channel Is Required for the Virulence of Salmonella enterica Serovar Typhimurium▿ † 
Journal of Bacteriology  2008;190(19):6517-6523.
CorA is the primary Mg2+ channel in Salmonella enterica serovar Typhimurium. A corA mutant is attenuated in mice and defective for invasion of and replication within epithelial cells. Microarray studies show that several virulence effectors are repressed in a corA mutant strain, which ultimately manifests itself as a decrease in virulence.
doi:10.1128/JB.00772-08
PMCID: PMC2566004  PMID: 18676664
12.  The MgtC Virulence Factor of Salmonella enterica Serovar Typhimurium Activates Na+,K+-ATPase 
Journal of Bacteriology  2006;188(15):5586-5594.
The mgtC gene of Salmonella enterica serovar Typhimurium encodes a membrane protein of unknown function that is important for full virulence in the mouse. Since mgtC is part of an operon with mgtB which encodes a Mg2+-transporting P-type ATPase, MgtC was hypothesized to function in ion transport, possibly in Mg2+ transport. Consequently, MgtC was expressed in Xenopus laevis oocytes, and its effect on ion transport was evaluated using ion selective electrodes. Oocytes expressing MgtC did not exhibit altered currents or membrane potentials in response to changes in extracellular H+, Mg2+, or Ca2+, thus ruling out a previously postulated function as a Mg2+/H+ antiporter. However, addition of extracellular K+ markedly hyperpolarized membrane potential instead of the expected depolarization. Addition of ouabain to block the oocyte Na+,K+-ATPase completely prevented hyperpolarization and restored the normal K+-induced depolarization response. These results suggested that the Na+,K+-ATPase was constitutively activated in the presence of MgtC resulting in a membrane potential largely dependent on Na+,K+-ATPase. Consistent with the involvement of Na+,K+-ATPase, oocytes expressing MgtC exhibited an increased rate of 86Rb+ uptake and had increased intracellular free [K+] and decreased free [Na+] and ATP. The free concentrations of Mg2+ and Ca2+ and cytosolic pH were unchanged, although the total intracellular Ca2+ content was slightly elevated. These results suggest that the serovar Typhimurium MgtC protein may be involved in regulating membrane potential but does not directly transport Mg2+ or another ion.
doi:10.1128/JB.00296-06
PMCID: PMC1540036  PMID: 16855249
13.  The Metal Permease ZupT from Escherichia coli Is a Transporter with a Broad Substrate Spectrum 
Journal of Bacteriology  2005;187(5):1604-1611.
The Escherichia coli zupT (formerly ygiE) gene encodes a cytoplasmic membrane protein (ZupT) related to members of the eukaryotic ZIP family of divalent metal ion transporters. Previously, ZupT was shown to be responsible for uptake of zinc. In this study, we show that ZupT is a divalent metal cation transporter of broad substrate specificity. An E. coli strain with a disruption in all known iron uptake systems could grow in the presence of chelators only if zupT was expressed. Heterologous expression of Arabidopsis thaliana ZIP1 could also alleviate iron deficiency in this E. coli strain, as could expression of indigenous mntH or feoABC. Transport studies with intact cells showed that ZupT facilitates uptake of 55Fe2+ similarly to uptake of MntH or Feo. Other divalent cations were also taken up by ZupT, as shown using 57Co2+. Expression of zupT rendered E. coli cells hypersensitive to Co2+ and sensitive to Mn2+. ZupT did not appear to be metal regulated: expression of a Φ(zupT-lacZ) operon fusion indicated that zupT is expressed constitutively at a low level.
doi:10.1128/JB.187.5.1604-1611.2005
PMCID: PMC1064025  PMID: 15716430
14.  Transcriptional Regulation of sitABCD of Salmonella enterica Serovar Typhimurium by MntR and Fur 
Journal of Bacteriology  2005;187(3):912-922.
Salmonella enterica serovar Typhimurium has two manganese transport systems, MntH and SitABCD. MntH is a bacterial homolog of the eukaryotic natural resistance-associated macrophage protein 1 (Nramp1), and SitABCD is an ABC-type transporter. Previously we showed that mntH is negatively controlled at the transcriptional level by the trans-acting regulatory factors, MntR and Fur. In this study, we examined the transcriptional regulation of sitABCD and compared it to the transcriptional regulation of mntH by constructing lacZ fusions to the promoter regions with and without mutations in putative MntR and/or Fur binding sites. The presence of Mn caused transcriptional repression of the sitABCD and mntH promoters primarily via MntR, but Fur was also capable of some repression in response to Mn. Likewise, Fe in the medium repressed transcription of both sit and mntH primarily via Fur, although MntR was also involved in this response. Transcriptional control by MntR and Fur was disrupted by site-specific mutations in the putative MntR and Fur binding sites, respectively. Transcription of the sit operon was also affected by the oxygen level and growth phase, but the increased expression observed under high oxygen conditions and higher cell densities is consistent with decreased availability of metals required for repression by the metalloregulatory proteins.
doi:10.1128/JB.187.3.912-922.2005
PMCID: PMC545731  PMID: 15659669
15.  The CorA Mg2+ Transporter Does Not Transport Fe2+ 
Journal of Bacteriology  2004;186(22):7653-7658.
corA encodes the constitutively expressed primary Mg2+ uptake system of most eubacteria and many archaea. Recently, a mutation in corA was reported to make Salmonella enterica serovar Typhimurium markedly resistant to Fe2+-mediated toxicity. Mechanistically, this was hypothesized to be from an ability of CorA to mediate the influx of Fe2+. Consequently, we directly examined Fe2+ transport and toxicity in wild-type versus corA cells. As determined by direct transport assay, CorA cannot transport Fe2+ and Fe2+ does not potently inhibit CorA transport of 63Ni2+. Mg2+ can, relatively weakly, inhibit Fe2+ uptake, but inhibition is not dependent on the presence of a functional corA allele. Although excess Fe2+ was slightly toxic to S. enterica serovar Typhimurium, we were unable to elicit a significant differential sensitivity in a wild-type versus a corA strain. We conclude that CorA does not transport Fe2+ and that the relationship, if any, between iron toxicity and corA is indirect.
doi:10.1128/JB.186.22.7653-7658.2004
PMCID: PMC524906  PMID: 15516579
16.  The Salmonella enterica Serovar Typhimurium Divalent Cation Transport Systems MntH and SitABCD Are Essential for Virulence in an Nramp1G169 Murine Typhoid Model  
Infection and Immunity  2004;72(9):5522-5525.
Nramp1 is a transporter that pumps divalent cations from the vacuoles of phagocytic cells and is associated with the innate resistance of mice to diverse intracellular pathogens. We demonstrate that sitA and mntH, genes encoding high-affinity metal ion uptake systems in Salmonella enterica serovar Typhimurium, are upregulated when Salmonella is internalized by Nramp1-expressing macrophages and play an essential role in systemic infection of congenic Nramp1-expressing mice.
doi:10.1128/IAI.72.9.5522-5525.2004
PMCID: PMC517450  PMID: 15322058
17.  The CorA Mg2+ Transporter Is a Homotetramer 
Journal of Bacteriology  2004;186(14):4605-4612.
CorA is a primary Mg2+ transporter for Bacteria and Archaea. The C-terminal domain of ∼80 amino acids forms three transmembrane (TM) segments, which suggests that CorA is a homo-oligomer. A Cys residue was added to the cytoplasmic C terminus (C317) of Salmonella enterica serovar Typhimurium CorA with or without mutation of the single periplasmic Cys191 to Ser; each mutant retained function. Oxidation of the Cys191Ser Cys317 CorA gave a dimer. Oxidation of Cys317 CorA showed a dimer plus an additional band, apparently cross-linked via both Cys317 and C191. To determine oligomer order, intact cells or purified membranes were treated with formaldehyde or carbon disulfide. Higher-molecular-mass bands formed, consistent with the presence of a tetramer. Cross-linking of the Bacillus subtilis CorA expressed in Salmonella serovar Typhimurium similarly indicated a tetramer. CorA periplasmic soluble domains from both Salmonella serovar Typhimurium and the archaeon Methanococcus jannaschii were purified and shown to retain structure. Formaldehyde treatment showed formation of a tetramer. Finally, previous mutagenesis of the CorA membrane domain identified six intramembrane residues forming an apparent pore that interacts with Mg2+ during transport. Each was mutated to Cys. In mutants carrying a single intramembrane Cys residue, spontaneous disulfide bond formation that was enhanced by oxidation with Cu(II)-1,10-phenanthroline was observed between monomers, indicating that these Mg2+-interacting residues within the membrane are very close to their cognate residue on another monomer. Thus, CorA appears to be a homotetramer with a TM segment of one monomer physically close to the same TM segment of another monomer.
doi:10.1128/JB.186.14.4605-4612.2004
PMCID: PMC438605  PMID: 15231793
18.  Changes in Human Immunodeficiency Virus Type 1 Gag at Positions L449 and P453 Are Linked to I50V Protease Mutants In Vivo and Cause Reduction of Sensitivity to Amprenavir and Improved Viral Fitness In Vitro 
Journal of Virology  2002;76(15):7398-7406.
Human immunodeficiency virus type 1 (HIV-1) Gag protease cleavage sites (CS) undergo sequence changes during the development of resistance to several protease inhibitors (PIs). We have analyzed the association of sequence variation at the p7/p1 and p1/p6 CS in conjunction with amprenavir (APV)-specific protease mutations following PI combination therapy with APV. Querying a central resistance data repository resulted in the detection of significant associations (P < 0.001) between the presence of APV protease signature mutations and Gag L449F (p1/p6 LP1′F) and P453L (p1/p6 PP5′L) CS changes. In population-based sequence analyses the I50V mutant was invariably linked to either L449F or P453L. Clonal analysis revealed that both CS mutations were never present in the same genome. Sequential plasma samples from one patient revealed a transition from I50V M46L P453L viruses at early time points to I50V M46I L449F viruses in later samples. Various combinations of the protease and Gag mutations were introduced into the HXB2 laboratory strain of HIV-1. In both single- and multiple-cycle assay systems and in the context of I50V, the L449F and P453L changes consistently increased the 50% inhibitory concentration of APV, while the CS changes alone had no measurable effect on inhibitor sensitivity. The decreased in vitro fitness of the I50V mutant was only partially improved by addition of either CS change (I50V M46I L449F mutant replicative capacity ≈ 16% of that of wild-type virus). Western blot analysis of Pr55 Gag precursor cleavage products from infected-cell cultures indicated accumulation of uncleaved Gag p1-p6 in all I50V viruses without coexisting CS changes. Purified I50V protease catalyzed cleavage of decapeptides incorporating the L449F or P453L change 10-fold and 22-fold more efficiently than cleavage of the wild-type substrate, respectively. HIV-1 protease CS changes are selected during PI therapy and can have effects on both viral fitness and phenotypic resistance to PIs.
doi:10.1128/JVI.76.15.7398-7406.2002
PMCID: PMC136352  PMID: 12097552
19.  Regulation of Salmonella enterica Serovar Typhimurium mntH Transcription by H2O2, Fe2+, and Mn2+ 
Journal of Bacteriology  2002;184(12):3151-3158.
MntH, a bacterial homolog of mammalian natural resistance associated macrophage protein 1 (Nramp1), is a primary transporter for Mn2+ influx in Salmonella enterica serovar Typhimurium and Escherichia coli. S. enterica serovar Typhimurium MntH contributes to H2O2 resistance and is important for full virulence. Consistent with its phenotype and function, mntH is regulated at the transcriptional level by both H2O2 and substrate cation. We have now identified three trans-acting regulatory factors and the three corresponding cis-acting mntH promoter motifs that mediate this regulation. In the presence of hydrogen peroxide, mntH is activated by OxyR, acting through an OxyR-binding motif centered just upstream of the likely −35 RNA polymerase-binding site. In the presence of Fe2+, mntH is repressed primarily by Fur, acting through a Fur-binding motif overlapping the −35 region. In the presence of Mn2+, mntH is repressed primarily by the Salmonella equivalent of E. coli b0817, a distant homolog of the Bacillus subtilis manganese transport repressor, MntR, acting through an inverted-repeat motif located between the likely −10 polymerase binding site and the ribosome binding site. E. coli b0817 was recently shown to bind the identical inverted-repeat motif in the E. coli mntH promoter and hence has been renamed MntR (S. I. Patzer and K. Hantke, J. Bacteriol. 183:4806-4813, 2001). Using Δfur, ΔmntR, and Δfur ΔmntR mutant strains as well as mutations in the Fur- and MntR-binding motif elements, we found that Fe2+ can also mediate repression through the Mn2+ repressor MntR.
doi:10.1128/JB.184.12.3151-3158.2002
PMCID: PMC135095  PMID: 12029030
20.  SitABCD Is the Alkaline Mn2+ Transporter of Salmonella enterica Serovar Typhimurium 
Journal of Bacteriology  2002;184(12):3159-3166.
MntH, a bacterial homolog of the mammalian natural resistance-associated macrophage protein 1 (Nramp1), is a primary Mn2+ transporter of Salmonella enterica serovar Typhimurium and Escherichia coli. S. enterica serovar Typhimurium MntH expression is important for full virulence; however, strains carrying an mntH deletion are only partially attenuated and display no obvious signs of Mn2+ deficiency. We noted that promoter sequences for mntH and for the putative Fe2+ transporter sitABCD appeared to have the same regulatory element responsive to Mn2+ and so hypothesized that sitABCD could transport Mn2+ with high affinity. We have now characterized transport by SitABCD in S. enterica serovar Typhimurium using 54Mn2+ and 55Fe2+ and compared its properties to those of MntH. SitABCD mediates the influx of Mn2+ with an apparent affinity (Ka) identical to that of MntH, 0.1 μM. It also transports Fe2+ but with a Ka 30 to 100 times lower, 3 to 10 μM. Inhibition of 54Mn2+ transport by Fe2+ and of 55Fe2+ transport by Mn2+ gave inhibition constants comparable to each cation's Ka for influx. Since micromolar concentrations of free Fe2+ are improbable in a biological system, we conclude that SitABCD functions physiologically as a Mn2+ transporter. The cation inhibition profiles of SitABCD and MntH are surprisingly similar for two structurally and energetically unrelated transporters, with a Cd2+ Ki of ≈1 μM and a Co2+ Ki of ≈20 μM and with Ni2+, Cu2+, and Fe3+ inhibiting both transporters only at concentrations of >0.1 mM. The one difference is that Zn2+ exhibits potent inhibition of SitABCD (Ki = 1 to 3 μM) but inhibits MntH weakly (Ki > 50 μM). We have previously shown that MntH transports Mn2+ most effectively under acidic conditions. In sharp contrast, SitABCD has almost no transport capacity at acid pHs and optimally transports Mn2+ at slightly alkaline pHs. Overall, coupled with evidence that each transporter is multiply but distinctly regulated at the transcriptional level, the distinct transport properties of MntH versus SitABCD suggest that each transporter may be specialized for Mn2+ uptake in different physiological environments.
doi:10.1128/JB.184.12.3159-3166.2002
PMCID: PMC135093  PMID: 12029031
21.  Emergence of Resistance to Protease Inhibitor Amprenavir in Human Immunodeficiency Virus Type 1-Infected Patients: Selection of Four Alternative Viral Protease Genotypes and Influence of Viral Susceptibility to Coadministered Reverse Transcriptase Nucleoside Inhibitors 
Previous data have indicated that the development of resistance to amprenavir, an inhibitor of the human immunodeficiency virus type 1 protease, is associated with the substitution of valine for isoleucine at residue 50 (I50V) in the viral protease. We present further findings from retrospective genotypic and phenotypic analyses of plasma samples from protease inhibitor-naïve and nucleoside reverse transcriptase inhibitor (NRTI)-experienced patients who experienced virological failure while participating in a clinical trial where they had been randomized to receive either amprenavir or indinavir in combination with NRTIs. Paired baseline and on-therapy isolates from 31 of 48 (65%) amprenavir-treated patients analyzed demonstrated the selection of protease mutations. These mutations fell into four distinct categories, characterized by the presence of either I50V, I54L/I54M, I84V, or V32I+I47V and often included accessory mutations, commonly M46I/L. The I50V and I84V genotypes displayed the greatest reductions in susceptibility to amprenavir, although each of the amprenavir-selected genotypes conferred little or no cross-resistance to other protease inhibitors. There was a significant association, for both amprenavir and indinavir, between preexisting baseline resistance to NRTIs subsequently received during the study and development of protease mutations (P = 0.014 and P = 0.031, respectively). Our data provide a comprehensive analysis of the mechanisms by which amprenavir resistance develops during clinical use and present evidence that resistance to concomitant agents in the treatment regimen predisposes to the development of mutations associated with protease inhibitor resistance and treatment failure.
doi:10.1128/AAC.46.3.731-738.2002
PMCID: PMC127503  PMID: 11850255
22.  The PPP-Family Protein Phosphatases PrpA and PrpB of Salmonella enterica Serovar Typhimurium Possess Distinct Biochemical Properties 
Journal of Bacteriology  2001;183(24):7053-7057.
Salmonella enterica serovar Typhimurium requires Mn2+, but only a few Mn2+-dependent enzymes have been identified from bacteria. To characterize Mn2+-dependent enzymes from serovar Typhimurium, two putative PPP-family protein phosphatase genes were cloned from serovar Typhimurium and named prpA and prpB. Their DNA-derived amino acid sequences showed 61% identity to the corresponding Escherichia coli proteins and 41% identity to each other. Each phosphatase was expressed in E. coli and purified to near electrophoretic homogeneity. Both PrpA and PrpB absolutely required a divalent metal for activity. As with other phosphatases of this class, Mn2+ had the highest affinity and stimulated the greatest activity. The apparent Ka of PrpA for Mn2+ of 65 μM was comparable to that for other bacterial phosphatases, but PrpB had a much higher affinity for Mn2+ (1.3 μM). The pH optima were pH 6.5 for PrpA and pH 8 for PrpB, while the optimal temperatures were 45 to 55°C for PrpA and 30 to 37°C for PrpB. Each phosphatase could hydrolyze phosphorylated serine, threonine, or tyrosine residues, but their relative specific activities varied with the specific substrate tested. These differences suggest that each phosphatase is used by serovar Typhimurium under different growth or environmental conditions such as temperature or acidity.
doi:10.1128/JB.183.24.7053-7057.2001
PMCID: PMC95552  PMID: 11717262
23.  Magnesium and the Role of mgtC in Growth of Salmonella typhimurium 
Infection and Immunity  1998;66(8):3802-3809.
Salmonella typhimurium has three distinct transport systems for Mg2+: CorA, MgtA, and MgtB. The mgtCB operon encodes two proteins, MgtC, a hydrophobic protein with a predicted molecular mass of 22.5 kDa, and MgtB, a 102-kDa P-type ATPase Mg2+ transport protein. The mgtCB locus has been identified as part of a new Salmonella pathogenicity island, SPI-3. Transcription of mgtCB is regulated by extracellular Mg2+ via the two-component PhoPQ regulatory system important for virulence. To elucidate MgtC’s role in a low-Mg2+ environment, we looked at growth and transport in strains lacking the CorA and MgtA Mg2+ transporters but expressing MgtB, MgtC, or both. mgtC mgtB+ and mgtC+ mgtB+ strains exhibited growth in N minimal medium without added Mg2+ with a 1- to 2-h lag phase. An mgtC+ mgtB strain was also able to grow in N minimal medium without added Mg2+ but only after a 24-h lag phase. In N minimal medium containing 10 mM Mg2+, all strains grew after a short lag phase; the mgtC+ mgtB strain grew to a higher optical density at 600 nm than an mgtC+ mgtB+ strain and was comparable to wild type. The lengthy lag phase before growth in an mgtC+ mgtB strain was not due to lack of expression of MgtC. Western blot analysis indicated that substantial MgtC protein is present by 2 h after suspension in N minimal medium. Surprisingly, in an mgtC+ mgtB+ strain, MgtC was undetectable during Mg2+ starvation, although large amounts of MgtB were observed. The lack of expression of MgtC is not dependent on functional MgtB, since a strain carrying a nonfunctional MgtB with a mutation (D379A) also did not make MgtC. Since, during invasion of eukaryotic cells, S. typhimurium appears to be exposed to a low-pH as well as a low-Mg2+ environment, the growth of an mgtC+ mgtB strain was tested at low pH with and without added Mg2+. While significant quantities of MgtC could be detected after suspension at pH 5.2, the mgtC+ mgtB strain was unable to grow at pH 5.2 whether or not Mg2+ was present. Finally, using 63Ni2+ and 57Co2+ as alternative substrates for the unavailable 28Mg2+, cation uptake could not be detected in an mgtC+ mgtB strain after Mg2+ starvation. We conclude that MgtC is not a Mg2+ transporter and that it does not have a primary role in the survival of S. typhimurium at low pH.
PMCID: PMC108421  PMID: 9673265
24.  Functional Similarity between Archaeal and Bacterial CorA Magnesium Transporters 
Journal of Bacteriology  1998;180(10):2788-2791.
The constitutively expressed CorA Mg2+ transporter is the major Mg2+ influx system of Salmonella typhimurium and Escherichia coli. Genomic sequence data indicated the presence of a homolog in the archaeal organism Methanococcus jannaschii. The putative M. jannaschii CorA was expressed in an Mg2+-transport-deficient strain of S. typhimurium to determine its functional characteristics. The archaeal CorA homolog is a functional Mg2+ uptake system when expressed in S. typhimurium and has properties which are highly similar to those of the normal CorA transporter of S. typhimurium despite having a low level of sequence identity with the protein and being expressed in a lipid membrane of quite different composition than normal. This implies that the overall function of the proteins is the same and further suggests that their structures are very similar.
PMCID: PMC107238  PMID: 9573171

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