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Akbari MS, Doran KS, Burcham LR. Metal Homeostasis in Pathogenic Streptococci. Microorganisms 2022; 10:microorganisms10081501. [PMID: 35893559 PMCID: PMC9331361 DOI: 10.3390/microorganisms10081501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 02/05/2023] Open
Abstract
Streptococcus spp. are an important genus of Gram-positive bacteria, many of which are opportunistic pathogens that are capable of causing invasive disease in a wide range of populations. Metals, especially transition metal ions, are an essential nutrient for all organisms. Therefore, to survive across dynamic host environments, Streptococci have evolved complex systems to withstand metal stress and maintain metal homeostasis, especially during colonization and infection. There are many different types of transport systems that are used by bacteria to import or export metals that can be highly specific or promiscuous. Focusing on the most well studied transition metals of zinc, manganese, iron, nickel, and copper, this review aims to summarize the current knowledge of metal homeostasis in pathogenic Streptococci, and their role in virulence.
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Mandal SK, Kanaujia SP. Structural and thermodynamic insights into a novel Mg 2+-citrate-binding protein from the ABC transporter superfamily. Acta Crystallogr D Struct Biol 2021; 77:1516-1534. [PMID: 34866608 DOI: 10.1107/s2059798321010457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/08/2021] [Indexed: 11/11/2022] Open
Abstract
More than one third of proteins require metal ions to accomplish their functions, making them obligatory for the growth and survival of microorganisms in varying environmental niches. In prokaryotes, besides their involvement in various cellular and physiological processes, metal ions stimulate the uptake of citrate molecules. Citrate is a source of carbon and energy and is reported to be transported by secondary transporters. In Gram-positive bacteria, citrate molecules are transported in complex with divalent metal ions, whereas in Gram-negative bacteria they are translocated by Na+/citrate symporters. In this study, the presence of a novel divalent-metal-ion-complexed citrate-uptake system that belongs to the primary active ABC transporter superfamily is reported. For uptake, the metal-ion-complexed citrate molecules are sequestered by substrate-binding proteins (SBPs) and transferred to transmembrane domains for their transport. This study reports crystal structures of an Mg2+-citrate-binding protein (MctA) from the Gram-negative thermophilic bacterium Thermus thermophilus HB8 in both apo and holo forms in the resolution range 1.63-2.50 Å. Despite binding various divalent metal ions, MctA possesses the coordination geometry to bind its physiological metal ion, Mg2+. The results also suggest an extended subclassification of cluster D SBPs, which are known to bind and transport divalent-metal-ion-complexed citrate molecules. Comparative assessment of the open and closed conformations of the wild-type and mutant MctA proteins suggests a gating mechanism of ligand entry following an `asymmetric domain movement' of the N-terminal domain for substrate binding.
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Affiliation(s)
- Suraj Kumar Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
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Davies JS, Currie MJ, Wright JD, Newton-Vesty MC, North RA, Mace PD, Allison JR, Dobson RCJ. Selective Nutrient Transport in Bacteria: Multicomponent Transporter Systems Reign Supreme. Front Mol Biosci 2021; 8:699222. [PMID: 34268334 PMCID: PMC8276074 DOI: 10.3389/fmolb.2021.699222] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
Multicomponent transporters are used by bacteria to transport a wide range of nutrients. These systems use a substrate-binding protein to bind the nutrient with high affinity and then deliver it to a membrane-bound transporter for uptake. Nutrient uptake pathways are linked to the colonisation potential and pathogenicity of bacteria in humans and may be candidates for antimicrobial targeting. Here we review current research into bacterial multicomponent transport systems, with an emphasis on the interaction at the membrane, as well as new perspectives on the role of lipids and higher oligomers in these complex systems.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael J Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Joshua D Wright
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jane R Allison
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, Digital Life Institute, University of Auckland, Auckland, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
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Identification and characterization of metal uptake ABC transporters in Mycobacterium tuberculosis unveil their ligand specificity. Int J Biol Macromol 2021; 185:324-337. [PMID: 34171249 DOI: 10.1016/j.ijbiomac.2021.06.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 01/09/2023]
Abstract
Mycobacterium tuberculosis, one of the major threats to mankind, requires micronutrients like metal ions for their survival and pathogenicity inside the host system. Intracellular pathogens such as M. tuberculosis have co-evolved to combat the nutritional immunity developed by the host. It has developed eminent mechanisms to sequester essential metal ions from the host system. One such prominent mechanism to scavenge metal ions to thrive in the host cell involves ATP-binding cassette (ABC) transporters, which transport metal ions (in free and/or complex forms) across the cell membrane. This study employs a high-throughput data mining analysis to identify open reading frames (ORFs) encoding metal uptake ABC transporters in M. tuberculosis H37Rv. In total, 19 ORFs resulting in seven ABC transport systems and two P-type ATPases were identified, which are potentially involved in the uptake of different metal ions. The results also suggest the existence of a subunit sharing mechanism in M. tuberculosis where the transmembrane and nucleotide binding domains are shared among different ABC transport systems indicating the import of multiple substrates via a single ABC transporter. Thus, this study reflects an overview of the repertoire of metal-specific ABC transport systems in M. tuberculosis H37Rv, providing potential therapeutic targets for the future.
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Saini G, Dalal V, Gupta DN, Sharma N, Kumar P, Sharma AK. A molecular docking and dynamic approach to screen inhibitors against ZnuA1 of Candidatus Liberibacter asiaticus. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1888948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Gunjan Saini
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vikram Dalal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Deena Nath Gupta
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Nidhi Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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Structure and Metal Binding Properties of Chlamydia trachomatis YtgA. J Bacteriol 2019; 202:JB.00580-19. [PMID: 31611288 DOI: 10.1128/jb.00580-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Abstract
The obligate intracellular pathogen Chlamydia trachomatis is a globally significant cause of sexually transmitted bacterial infections and the leading etiological agent of preventable blindness. The first-row transition metal iron (Fe) plays critical roles in chlamydial cell biology, and acquisition of this nutrient is essential for the survival and virulence of the pathogen. Nevertheless, how C. trachomatis acquires Fe from host cells is not well understood, since it lacks genes encoding known siderophore biosynthetic pathways, receptors for host Fe storage proteins, and the Fe acquisition machinery common to many bacteria. Recent studies have suggested that C. trachomatis directly acquires host Fe via the ATP-binding cassette permease YtgABCD. Here, we characterized YtgA, the periplasmic solute binding protein component of the transport pathway, which has been implicated in scavenging Fe(III) ions. The structure of Fe(III)-bound YtgA was determined at 2.0-Å resolution with the bound ion coordinated via a novel geometry (3 Ns, 2 Os [3N2O]). This unusual coordination suggested a highly plastic metal binding site in YtgA capable of interacting with other cations. Biochemical analyses showed that the metal binding site of YtgA was not restricted to interaction with only Fe(III) ions but could bind all transition metal ions examined. However, only Mn(II), Fe(II), and Ni(II) ions bound reversibly to YtgA, with Fe being the most abundant cellular transition metal in C. trachomatis Collectively, these findings show that YtgA is the metal-recruiting component of the YtgABCD permease and is most likely involved in the acquisition of Fe(II) and Mn(II) from host cells.IMPORTANCE Chlamydia trachomatis is the most common bacterial sexually transmitted infection in developed countries, with an estimated global prevalence of 4.2% in the 15- to 49-year age group. Although infection is asymptomatic in more than 80% of infected women, about 10% of cases result in serious disease. Infection by C. trachomatis is dependent on the ability to acquire essential nutrients, such as the transition metal iron, from host cells. In this study, we show that iron is the most abundant transition metal in C. trachomatis and report the structural and biochemical properties of the iron-recruiting protein YtgA. Knowledge of the high-resolution structure of YtgA will provide a platform for future structure-based antimicrobial design approaches.
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Mandal SK, Adhikari R, Sharma A, Chandravanshi M, Gogoi P, Kanaujia SP. Designating ligand specificities to metal uptake ABC transporters in Thermus thermophilus HB8. Metallomics 2019; 11:597-612. [DOI: 10.1039/c8mt00374b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acquisition of different metal ions by metal uptake ABC transporters of Thermus thermophilus HB8 for accomplishing its various cellular functions.
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Affiliation(s)
- Suraj Kumar Mandal
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Rahi Adhikari
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Anjaney Sharma
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Monika Chandravanshi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
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MntC-Dependent Manganese Transport Is Essential for Staphylococcus aureus Oxidative Stress Resistance and Virulence. mSphere 2018; 3:3/4/e00336-18. [PMID: 30021878 PMCID: PMC6052334 DOI: 10.1128/msphere.00336-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Work outlined in this report demonstrated that MntC-dependent manganese transport is required for S. aureus virulence. These study results support the model that MntC-specific antibodies elicited by a vaccine have the potential to disrupt S. aureus manganese transport and thus abrogate to its virulence. Staphylococcus aureus is a human pathogen that has developed several approaches to evade the immune system, including a strategy to resist oxidative killing by phagocytes. This resistance is mediated by production of superoxide dismutase (SOD) enzymes which use manganese as a cofactor. S. aureus encodes two manganese ion transporters, MntABC and MntH, and a possible Nramp family manganese transporter, exemplified by S. aureus N315 SA1432. Their relative contributions to manganese transport have not been well defined in clinically relevant isolates. For this purpose, insertional inactivation mutations were introduced into mntC, mntH, and SA1432 individually and in combination. mntC was necessary for full resistance to methyl viologen, a compound that generates intracellular free radicals. In contrast, strains with an intact mntH gene had a minimal increase in resistance that was revealed only in mntC strains, and no change was observed upon mutation of SA1432 in strains lacking both mntC and mntH. Similarly, MntC alone was required for high cellular SOD activity. In addition, mntC strains were attenuated in a murine sepsis model. To further link these observations to manganese transport, an S. aureus MntC protein lacking manganese binding activity was designed, expressed, and purified. While circular dichroism experiments demonstrated that the secondary and tertiary structures of this protein were unaltered, a defect in manganese binding was confirmed by isothermal titration calorimetry. Unlike complementation with wild-type mntC, introduction of the manganese-binding defective allele into the chromosome of an mntC strain did not restore resistance to oxidative stress or virulence. Collectively, these results underscore the importance of MntC-dependent manganese transport in S. aureus oxidative stress resistance and virulence. IMPORTANCE Work outlined in this report demonstrated that MntC-dependent manganese transport is required for S. aureus virulence. These study results support the model that MntC-specific antibodies elicited by a vaccine have the potential to disrupt S. aureus manganese transport and thus abrogate to its virulence.
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Radka CD, Chen D, DeLucas LJ, Aller SG. The crystal structure of the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal. Acta Crystallogr D Struct Biol 2017; 73:921-939. [PMID: 29095164 PMCID: PMC5683015 DOI: 10.1107/s2059798317015236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/18/2017] [Indexed: 12/25/2022] Open
Abstract
Biological chelating molecules called siderophores are used to sequester iron and maintain its ferric state. Bacterial substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver these complexes to ATP-binding cassette (ABC) transporters for import into the cytoplasm, where the iron can be transferred from the siderophore to catalytic enzymes. In Yersinia pestis, the causative agent of plague, the Yersinia iron-uptake (Yiu) ABC transporter has been shown to improve iron acquisition under iron-chelated conditions. The Yiu transporter has been proposed to be an iron-siderophore transporter; however, the precise siderophore substrate is unknown. Therefore, the precise role of the Yiu transporter in Y. pestis survival remains uncharacterized. To better understand the function of the Yiu transporter, the crystal structure of YiuA (YPO1310/y2875), an SBP which functions to present the iron-siderophore substrate to the transporter for import into the cytoplasm, was determined. The 2.20 and 1.77 Å resolution X-ray crystal structures reveal a basic triad binding motif at the YiuA canonical substrate-binding site, indicative of a metal-chelate binding site. Structural alignment and computational docking studies support the function of YiuA in binding chelated metal. Additionally, YiuA contains two mobile helices, helix 5 and helix 10, that undergo 2-3 Å shifts across crystal forms and demonstrate structural breathing of the c-clamp architecture. The flexibility in both c-clamp lobes suggest that YiuA substrate transfer resembles the Venus flytrap mechanism that has been proposed for other SBPs.
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Affiliation(s)
- Christopher D. Radka
- Graduate Biomedical Sciences Microbiology Theme, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dongquan Chen
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lawrence J. DeLucas
- Office of the Provost, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Quantum chemical calculations of the active site of the solute-binding protein PsaA from Streptococcus pneumoniae explain electronic selectivity of metal binding. Struct Chem 2017. [DOI: 10.1007/s11224-017-1036-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Radka CD, DeLucas LJ, Wilson LS, Lawrenz MB, Perry RD, Aller SG. Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites. Acta Crystallogr D Struct Biol 2017; 73:557-572. [PMID: 28695856 PMCID: PMC5505154 DOI: 10.1107/s2059798317006349] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/26/2017] [Indexed: 01/05/2023] Open
Abstract
Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. In Yersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.
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Affiliation(s)
- Christopher D. Radka
- Graduate Biomedical Sciences Microbiology Theme, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lawrence J. DeLucas
- Office of the Provost, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Landon S. Wilson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Matthew B. Lawrenz
- Department of Microbiology and Immunology and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Robert D. Perry
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY 40536, USA
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Mandal SK, Chandravanshi M, Gogoi P, Kanaujia SP. In silico characterization of TTHA0596: A potential Zn 2+ binding protein of ATP-binding cassette transporter. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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L-glutamine Induces Expression of Listeria monocytogenes Virulence Genes. PLoS Pathog 2017; 13:e1006161. [PMID: 28114430 PMCID: PMC5289647 DOI: 10.1371/journal.ppat.1006161] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 02/02/2017] [Accepted: 12/30/2016] [Indexed: 12/27/2022] Open
Abstract
The high environmental adaptability of bacteria is contingent upon their ability to sense changes in their surroundings. Bacterial pathogen entry into host poses an abrupt and dramatic environmental change, during which successful pathogens gauge multiple parameters that signal host localization. The facultative human pathogen Listeria monocytogenes flourishes in soil, water and food, and in ~50 different animals, and serves as a model for intracellular infection. L. monocytogenes identifies host entry by sensing both physical (e.g., temperature) and chemical (e.g., metabolite concentrations) factors. We report here that L-glutamine, an abundant nitrogen source in host serum and cells, serves as an environmental indicator and inducer of virulence gene expression. In contrast, ammonia, which is the most abundant nitrogen source in soil and water, fully supports growth, but fails to activate virulence gene transcription. We demonstrate that induction of virulence genes only occurs when the Listerial intracellular concentration of L-glutamine crosses a certain threshold, acting as an on/off switch: off when L-glutamine concentrations are below the threshold, and fully on when the threshold is crossed. To turn on the switch, L-glutamine must be present, and the L-glutamine high affinity ABC transporter, GlnPQ, must be active. Inactivation of GlnPQ led to complete arrest of L-glutamine uptake, reduced type I interferon response in infected macrophages, dramatic reduction in expression of virulence genes, and attenuated virulence in a mouse infection model. These results may explain observations made with other pathogens correlating nitrogen metabolism and virulence, and suggest that gauging of L-glutamine as a means of ascertaining host localization may be a general mechanism.
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Genome scale identification, structural analysis, and classification of periplasmic binding proteins from Mycobacterium tuberculosis. Curr Genet 2016; 63:553-576. [DOI: 10.1007/s00294-016-0664-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 01/26/2023]
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Sharma N, Selvakumar P, Saini G, Warghane A, Ghosh DK, Sharma AK. Crystal structure analysis in Zn 2+-bound state and biophysical characterization of CLas-ZnuA2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1649-1657. [PMID: 27570147 DOI: 10.1016/j.bbapap.2016.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 01/08/2023]
Abstract
A periplasmic solute binding protein from second of the two gene clusters of Znu system in CLA (CLas-ZnuA2) belong to Cluster A1 family of solute binding proteins (SBPs). The crystal structures in metal-free, intermediate and metal-bound states, in the previous study, revealed the unusual mechanism of metal binding and release for CLas-ZnuA2. Although CLas-ZnuA2 showed maximum sequence identity to the Mn/Fe-specific SBPs, the mechanistic resemblance seems to be closer to Zn-specific SBPs of Cluster A-I family. The present study reports the binding affinity studies using SPR and CD and crystal structure of CLas-ZnuA2 in Zn2+-bound state. Despite a similar overall structure, there are noticeable differences at the metal binding site. The SPR and CD analysis confirmed our previous observation that CLas-ZnuA2 exhibits a low metal-binding affinity. The low metal-binding affinity of CLas-ZnuA2 could be attributed to the presence of a proline in linker helix resulting in relatively higher bending and rigidity of the same. This structural feature fixes the C-domain similar to metal-bound states of related SBPs. Further, the binding of both Mn2+ and Zn2+ occurs pentavalently with square pyramidal geometry not preferred by either. The site-specific positive Darwinian selection analysis showed that the proline in linker helix is under purifying selection and might have diverged long ago. Our structural and evolutionary analyses suggest that CLasZnua2 might have evolved, particularly for plant pathogens, to facilitate transport of both Mn2+ and Zn2+, with reversible binding to Zn2+, unlike other Mn-binding SBPs (PsaA).
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Affiliation(s)
- Nidhi Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India
| | - Purushotham Selvakumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India
| | - Gunjan Saini
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India
| | - Ashish Warghane
- Plant Virology Laboratory, ICAR- Central Citrus Research Institute, Nagpur 440 010, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR- Central Citrus Research Institute, Nagpur 440 010, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India.
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16
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Abate F, Cozzi R, Maritan M, Lo Surdo P, Maione D, Malito E, Bottomley MJ. Crystal structure of FhuD at 1.6 Å resolution: a ferrichrome-binding protein from the animal and human pathogen Staphylococcus pseudintermedius. Acta Crystallogr F Struct Biol Commun 2016; 72:214-9. [PMID: 26919525 PMCID: PMC4774880 DOI: 10.1107/s2053230x16002272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 02/05/2016] [Indexed: 11/10/2022] Open
Abstract
Staphylococcus pseudintermedius is a leading cause of disease in dogs, and zoonosis causes human infections. Methicillin-resistant S. pseudintermedius strains are emerging, resembling the global health threat of S. aureus. Therefore, it is increasingly important to characterize potential targets for intervention against S. pseudintermedius. Here, FhuD, an S. pseudintermedius surface lipoprotein implicated in iron uptake, was characterized. It was found that FhuD bound ferrichrome in an iron-dependent manner, which increased the thermostability of FhuD by >15 °C. The crystal structure of ferrichrome-free FhuD was determined via molecular replacement at 1.6 Å resolution. FhuD exhibits the class III solute-binding protein (SBP) fold, with a ligand-binding cavity between the N- and C-terminal lobes, which is here occupied by a PEG molecule. The two lobes of FhuD were oriented in a closed conformation. These results provide the first detailed structural characterization of FhuD, a potential therapeutic target of S. pseudintermedius.
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Affiliation(s)
| | - Roberta Cozzi
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Martina Maritan
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Paola Lo Surdo
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Domenico Maione
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Enrico Malito
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
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Salmonella enterica serovar Typhimurium growth is inhibited by the concomitant binding of Zn(II) and a pyrrolyl-hydroxamate to ZnuA, the soluble component of the ZnuABC transporter. Biochim Biophys Acta Gen Subj 2015; 1860:534-41. [PMID: 26691136 DOI: 10.1016/j.bbagen.2015.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/04/2015] [Accepted: 12/11/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND Under conditions of Zn(II) deficiency, the most relevant high affinity Zn(II) transport system synthesized by many Gram-negative bacteria is the ZnuABC transporter. ZnuABC is absent in eukaryotes and plays an important role in bacterial virulence. Consequently, ZnuA, the periplasmic component of the transporter, appeared as a good target candidate to find new compounds able to contrast bacterial growth by interfering with Zn(II) uptake. METHODS Antibacterial activity assays on selected compounds from and in-house library against Salmonella enterica serovar Typhimurium ATCC14028 were performed. The X-ray structure of the complex formed by SeZnuA with an active compound was solved at 2.15Å resolution. RESULTS Two di-aryl pyrrole hydroxamic acids differing in the position of a chloride ion, RDS50 ([1-[(4-chlorophenyl)methyl]-4-phenyl-1H-pyrrol-3-hydroxamic acid]) and RDS51 (1-[(2-chlorophenyl)methyl]-4-phenyl-1H-pyrrol-3-hydroxamic acid) were able to inhibit Salmonella growth and its invasion ability of Caco-2 cells. The X-ray structure of SeZnuA containing RDS51 revealed its presence at the metal binding site concomitantly with Zn(II) which is coordinated by protein residues and the hydroxamate moiety of the compound. CONCLUSIONS Two molecules interfering with ZnuA-mediated Zn(II) transport in Salmonella have been identified for the first time. The resolution of the SeZnuA-RDS51 X-ray structure revealed that RDS51 is tightly bound both to the protein and to Zn(II) thereby inhibiting its release. These features pave the way to the rational design of new Zn(II)-binding drugs against Salmonella. GENERAL SIGNIFICANCE The data reported show that targeting the bacterial ZnuABC transporter can represent a good strategy to find new antibiotics against Gram-negative bacteria.
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18
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Luo Z, Morey JR, McDevitt CA, Kobe B. Heterogeneous nucleation is required for crystallization of the ZnuA domain of pneumococcal AdcA. Acta Crystallogr F Struct Biol Commun 2015; 71:1459-64. [PMID: 26625286 PMCID: PMC4666472 DOI: 10.1107/s2053230x15021330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/10/2015] [Indexed: 01/17/2023] Open
Abstract
Zn(2+) is an essential nutrient for all known forms of life. In the major human pathogen Streptococcus pneumoniae, the acquisition of Zn(2+) is facilitated by two Zn(2+)-specific solute-binding proteins: AdcA and AdcAII. To date, there has been a paucity of structural information on AdcA, which has hindered a deeper understanding of the mechanism underlying pneumococcal Zn(2+) acquisition. Native AdcA consists of two domains: an N-terminal ZnuA domain and a C-terminal ZinT domain. In this study, the ZnuA domain of AdcA was crystallized. The initial crystals of the ZnuA-domain protein were obtained using dried seaweed as a heterogeneous nucleating agent. No crystals were obtained in the absence of the heterogeneous nucleating agent. These initial crystals were subsequently used as seeds to produce diffraction-quality crystals. The crystals diffracted to 2.03 Å resolution and had the symmetry of space group P1. This study demonstrates the utility of heterogeneous nucleation. The solution of the crystal structures will lead to further understanding of Zn(2+) acquisition by S. pneumoniae.
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Affiliation(s)
- Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Jacqueline R. Morey
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Christopher A. McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Boštjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
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19
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Manzoor I, Shafeeq S, Kuipers OP. Ni2+-Dependent and PsaR-Mediated Regulation of the Virulence Genes pcpA, psaBCA, and prtA in Streptococcus pneumoniae. PLoS One 2015; 10:e0142839. [PMID: 26562538 PMCID: PMC4643063 DOI: 10.1371/journal.pone.0142839] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/27/2015] [Indexed: 11/19/2022] Open
Abstract
Previous studies have shown that the transcriptional regulator PsaR regulates the expression of the PsaR regulon consisting of genes encoding choline binding protein (PcpA), the extracellular serine protease (PrtA), and the Mn2+-uptake system (PsaBCA), in the presence of manganese (Mn2+), zinc (Zn2+), and cobalt (Co2+). In this study, we explore the Ni2+-dependent regulation of the PsaR regulon. We have demonstrated by qRT-PCR analysis, metal accumulation assays, β-galactosidase assays, and electrophoretic mobility shift assays that an elevated concentration of Ni2+ leads to strong induction of the PsaR regulon. Our ICP-MS data show that the Ni2+-dependent expression of the PsaR regulon is directly linked to high, cell-associated, concentration of Ni2+, which reduces the cell-associated concentration of Mn2+. In vitro studies with the purified PsaR protein showed that Ni2+ diminishes the Mn2+-dependent interaction of PsaR to the promoter regions of its target genes, confirming an opposite effect of Mn2+ and Ni2+ in the regulation of the PsaR regulon. Additionally, the Ni2+-dependent role of PsaR in the regulation of the PsaR regulon was studied by transcriptome analysis.
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Affiliation(s)
- Irfan Manzoor
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sulman Shafeeq
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177, Stockholm, Sweden
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- * E-mail:
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20
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Deplazes E, Begg SL, van Wonderen JH, Campbell R, Kobe B, Paton JC, MacMillan F, McDevitt CA, O'Mara ML. Characterizing the conformational dynamics of metal-free PsaA using molecular dynamics simulations and electron paramagnetic resonance spectroscopy. Biophys Chem 2015; 207:51-60. [PMID: 26379256 DOI: 10.1016/j.bpc.2015.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 12/17/2022]
Abstract
Prokaryotic metal-ion receptor proteins, or solute-binding proteins, facilitate the acquisition of metal ions from the extracellular environment. Pneumococcal surface antigen A (PsaA) is the primary Mn(2+)-recruiting protein of the human pathogen Streptococcus pneumoniae and is essential for its in vivo colonization and virulence. The recently reported high-resolution structures of metal-free and metal-bound PsaA have provided the first insights into the mechanism of PsaA-facilitated metal binding. However, the conformational dynamics of metal-free PsaA in solution remain unknown. Here, we use continuous wave electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations to study the relative flexibility of the structural domains in metal-free PsaA and its distribution of conformations in solution. The results show that the crystal structure of metal-free PsaA is a good representation of the dominant conformation in solution, but the protein also samples structurally distinct conformations that are not captured by the crystal structure. Further, these results suggest that the metal binding site is both larger and more solvent exposed than indicated by the metal-free crystal structure. Collectively, this study provides atomic-resolution insight into the conformational dynamics of PsaA prior to metal binding and lays the groundwork for future EPR and MD based studies of PsaA in solution.
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Affiliation(s)
- Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Stephanie L Begg
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Jessica H van Wonderen
- Henry Wellcome Unit for Biological EPR, School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, UK
| | - Rebecca Campbell
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Fraser MacMillan
- Henry Wellcome Unit for Biological EPR, School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, UK
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia.
| | - Megan L O'Mara
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Research School of Chemistry, The Australian National University, Canberra, Australia. megan.o'
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21
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Gogoi P, Chandravanshi M, Mandal SK, Srivastava A, Kanaujia SP. Heterogeneous behavior of metalloproteins toward metal ion binding and selectivity: insights from molecular dynamics studies. J Biomol Struct Dyn 2015; 34:1470-85. [PMID: 26248730 DOI: 10.1080/07391102.2015.1080629] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. In this study, we used molecular dynamics (MD) simulations to investigate whether a cognate metal (bound to the structure) can be replaced with other similar metal ions. We have chosen seven different proteins (phospholipase A2, sucrose phosphatase, pyrazinamidase, cysteine dioxygenase (CDO), plastocyanin, monoclonal anti-CD4 antibody Q425, and synaptotagmin 1 C2B domain) bound to seven different divalent metal ions (Ca(2+), Mg(2+), Zn(2+), Fe(2+), Cu(2+), Ba(2+), and Sr(2+), respectively). In total, 49 MD simulations each of 50 ns were performed and each trajectory was analyzed independently. Results demonstrate that in some cases, cognate metal ions can be exchanged with similar metal ions. On the contrary, some proteins show binding affinity specifically to their cognate metal ions. Surprisingly, two proteins CDO and plastocyanin which are known to bind Fe(2+) and Cu(2+), respectively, do not exhibit binding affinity to any metal ion. Furthermore, the study reveals that in some cases, the active site topology remains rigid even without cognate metals, whereas, some require them for their active site stability. Thus, it will be interesting to experimentally verify the accuracy of these observations obtained computationally. Moreover, the study can help in designing novel active sites for proteins to sequester metal ions particularly of toxic nature.
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Affiliation(s)
- Prerana Gogoi
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Monika Chandravanshi
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Suraj Kumar Mandal
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Ambuj Srivastava
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Shankar Prasad Kanaujia
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
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22
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Pederick VG, Eijkelkamp BA, Begg SL, Ween MP, McAllister LJ, Paton JC, McDevitt CA. ZnuA and zinc homeostasis in Pseudomonas aeruginosa. Sci Rep 2015; 5:13139. [PMID: 26290475 PMCID: PMC4542158 DOI: 10.1038/srep13139] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/21/2015] [Indexed: 11/09/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous environmental bacterium and a clinically significant opportunistic human pathogen. Central to the ability of P. aeruginosa to colonise both environmental and host niches is the acquisition of zinc. Here we show that P. aeruginosa PAO1 acquires zinc via an ATP-binding cassette (ABC) permease in which ZnuA is the high affinity, zinc-specific binding protein. Zinc uptake in Gram-negative organisms predominantly occurs via an ABC permease, and consistent with this expectation a P. aeruginosa ΔznuA mutant strain showed an ~60% reduction in cellular zinc accumulation, while other metal ions were essentially unaffected. Despite the major reduction in zinc accumulation, minimal phenotypic differences were observed between the wild-type and ΔznuA mutant strains. However, the effect of zinc limitation on the transcriptome of P. aeruginosa PAO1 revealed significant changes in gene expression that enable adaptation to low-zinc conditions. Genes significantly up-regulated included non-zinc-requiring paralogs of zinc-dependent proteins and a number of novel import pathways associated with zinc acquisition. Collectively, this study provides new insight into the acquisition of zinc by P. aeruginosa PAO1, revealing a hitherto unrecognized complexity in zinc homeostasis that enables the bacterium to survive under zinc limitation.
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Affiliation(s)
- Victoria G Pederick
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Bart A Eijkelkamp
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Stephanie L Begg
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Miranda P Ween
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Lauren J McAllister
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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23
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Bajaj M, Mamidyala SK, Zuegg J, Begg SL, Ween MP, Luo Z, Huang JX, McEwan AG, Kobe B, Paton JC, McDevitt CA, Cooper MA. Discovery of novel pneumococcal surface antigen A (PsaA) inhibitors using a fragment-based drug design approach. ACS Chem Biol 2015; 10:1511-20. [PMID: 25786639 DOI: 10.1021/cb501032x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptococcus pneumoniae is a leading cause of life-threatening bacterial infections, especially in young children in developing countries. Pneumococcal infections can be treated with β-lactam antibiotics, but rapid emergence of multidrug-resistant strains of S. pneumoniae over the past two decades has emphasized the need to identify novel drug targets. Pneumococcal surface antigen A (PsaA) is one such target, found on the cell surface of S. pneumoniae. It functions as a high-affinity substrate-binding protein, facilitating acquisition of Mn(2+), which has an important role in protecting S. pneumoniae from reactive oxygen species and, hence, oxidative stress. Consequently, PsaA is essential for bacterial survival and an important virulence factor, which makes it a promising target for antibiotic drug development. To design novel PsaA inhibitors, we used a combination of de novo fragment-based drug discovery and in silico virtual screening methods. We profiled a collection of low molecular weight compounds that were selected based on their structural diversity and ability to bind to apo-PsaA in a virtual docking experiment. The screening resulted in two initial hits that were further optimized by structural variation to improve their potency while maintaining their ligand efficiency and favorable physicochemical properties. The optimized hits were validated using a cell-based assay and molecular dynamics simulations. We found that virtual screening substantially augmented fragment-based drug design approaches, leading to the identification of novel pneumococcal PsaA inhibitors.
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Affiliation(s)
- Megha Bajaj
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Australia
| | - Sreeman K. Mamidyala
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Australia
| | - Johannes Zuegg
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Australia
| | - Stephanie L. Begg
- Research
Centre for Infectious Diseases, School of Molecular and Biomedical
Science, University of Adelaide, Adelaide 5005, Australia
| | - Miranda P. Ween
- Research
Centre for Infectious Diseases, School of Molecular and Biomedical
Science, University of Adelaide, Adelaide 5005, Australia
| | - Zhenyao Luo
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, 4072, Australia
| | - Johnny X. Huang
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Australia
| | - Alastair G. McEwan
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, 4072, Australia
- Australian
Infectious Diseases Research Centre, The University of Queensland, St. Lucia, 4072, Australia
| | - Bostjan Kobe
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Australia
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, 4072, Australia
- Australian
Infectious Diseases Research Centre, The University of Queensland, St. Lucia, 4072, Australia
| | - James C. Paton
- Research
Centre for Infectious Diseases, School of Molecular and Biomedical
Science, University of Adelaide, Adelaide 5005, Australia
| | - Christopher A. McDevitt
- Research
Centre for Infectious Diseases, School of Molecular and Biomedical
Science, University of Adelaide, Adelaide 5005, Australia
| | - Matthew A. Cooper
- Institute
for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Australia
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24
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Morey JR, McDevitt CA, Kehl-Fie TE. Host-imposed manganese starvation of invading pathogens: two routes to the same destination. Biometals 2015; 28:509-19. [PMID: 25836716 PMCID: PMC4430393 DOI: 10.1007/s10534-015-9850-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/24/2015] [Indexed: 01/07/2023]
Abstract
During infection invading pathogens must acquire all essential nutrients, including first row transition metals, from the host. To combat invaders, the host exploits this fact and restricts the availability of these nutrients using a defense mechanism known as nutritional immunity. While iron sequestration is the most well-known aspect of this defense, recent work has revealed that the host restricts the availability of other essential elements, notably manganese (Mn), during infection. Furthermore, these studies have revealed that the host utilizes multiple strategies that extend beyond metal sequestration to prevent bacteria from obtaining these metals. This review will discuss the mechanisms by which bacteria attempt to obtain the essential first row transition metal ion Mn during infection, and the approaches utilized by the host to prevent this occurrence. In addition, this review will discuss the impact of host-imposed Mn starvation on invading bacteria.
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Affiliation(s)
- Jacqueline R. Morey
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Christopher A. McDevitt
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Thomas E. Kehl-Fie
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana IL, USA
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25
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Sharma N, Selvakumar P, Bhose S, Ghosh DK, Kumar P, Sharma AK. Crystal structure of a periplasmic solute binding protein in metal-free, intermediate and metal-bound states from Candidatus Liberibacter asiaticus. J Struct Biol 2015; 189:184-94. [PMID: 25641618 DOI: 10.1016/j.jsb.2015.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/30/2014] [Accepted: 01/23/2015] [Indexed: 12/23/2022]
Abstract
The Znu system, a member of ABC transporter family, is critical for survival and pathogenesis of Candidatus Liberibacter asiaticus (CLA). Two homologues of this system have been identified in CLA. Here, we report high resolution crystal structure of a periplasmic solute binding protein from second of the two gene clusters of Znu system in CLA (CLas-ZnuA2) in metal-free, intermediate and metal-bound states. CLas-ZnuA2 showed maximum sequence identity to the Mn/Fe-specific solute binding proteins (SBPs) of cluster A-I family. The overall fold of CLas-ZnuA2 is similar to the related cluster A-I family SBPs. The sequence and structure analysis revealed the unique features of CLas-ZnuA2. The comparison of CLas-ZnuA2 structure in three states showed that metal binding and release is facilitated by a large displacement along with a change in orientation of the side chain for one of the metal binding residue (His39) flipped away from metal binding site in metal-free form. The crystal structure captured in intermediate state of metal binding revealed the changes in conformation and interaction of the loop hosting His39 during the metal binding. A rigid body movement of C-domain along with partial unfolding of linker helix at its C-terminal during metal binding, as reported for PsaA, was not observed in CLas-ZnuA2. The present results suggest that despite showing maximum sequence identity to the Mn/Fe-specific SBPs, the mechanistic resemblance of CLas-ZnuA2 seems to be closer to Zn-specific SBPs of cluster A-I family.
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Affiliation(s)
- Nidhi Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India
| | - Purushotham Selvakumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India
| | - Sumit Bhose
- Plant Virology Laboratory, National Research Centre for Citrus, Indian Council of Agriculture Research (ICAR), Nagpur 440 010, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, National Research Centre for Citrus, Indian Council of Agriculture Research (ICAR), Nagpur 440 010, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667, India.
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26
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Eijkelkamp BA, Morey JR, Ween MP, Ong CLY, McEwan AG, Paton JC, McDevitt CA. Extracellular zinc competitively inhibits manganese uptake and compromises oxidative stress management in Streptococcus pneumoniae. PLoS One 2014; 9:e89427. [PMID: 24558498 PMCID: PMC3928430 DOI: 10.1371/journal.pone.0089427] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/22/2014] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae requires manganese for colonization of the human host, but the underlying molecular basis for this requirement has not been elucidated. Recently, it was shown that zinc could compromise manganese uptake and that zinc levels increased during infection by S. pneumoniae in all the niches that it colonized. Here we show, by quantitative means, that extracellular zinc acts in a dose dependent manner to competitively inhibit manganese uptake by S. pneumoniae, with an EC50 of 30.2 µM for zinc in cation-defined media. By exploiting the ability to directly manipulate S. pneumoniae accumulation of manganese, we analyzed the connection between manganese and superoxide dismutase (SodA), a primary source of protection for S. pneumoniae against oxidative stress. We show that manganese starvation led to a decrease in sodA transcription indicating that expression of sodA was regulated through an unknown manganese responsive pathway. Intriguingly, examination of recombinant SodA revealed that the enzyme was potentially a cambialistic superoxide dismutase with an iron/manganese cofactor. SodA was also shown to provide the majority of protection against oxidative stress as a S. pneumoniae ΔsodA mutant strain was found to be hypersensitive to oxidative stress, despite having wild-type manganese levels, indicating that the metal ion alone was not sufficiently protective. Collectively, these results provide a quantitative assessment of the competitive effect of zinc upon manganese uptake and provide a molecular basis for how extracellular zinc exerts a ‘toxic’ effect on bacterial pathogens, such as S. pneumoniae.
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Affiliation(s)
- Bart A. Eijkelkamp
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, South Australia, Australia
| | - Jacqueline R. Morey
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, South Australia, Australia
| | - Miranda P. Ween
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, South Australia, Australia
| | - Cheryl-lynn Y. Ong
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Alastair G. McEwan
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - James C. Paton
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, South Australia, Australia
| | - Christopher A. McDevitt
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, South Australia, Australia
- * E-mail:
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27
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Plumptre CD, Eijkelkamp BA, Morey JR, Behr F, Couñago RM, Ogunniyi AD, Kobe B, O'Mara ML, Paton JC, McDevitt CA. AdcA and AdcAII employ distinct zinc acquisition mechanisms and contribute additively to zinc homeostasis inStreptococcus pneumoniae. Mol Microbiol 2014; 91:834-51. [DOI: 10.1111/mmi.12504] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Charles D. Plumptre
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Bart A. Eijkelkamp
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Jacqueline R. Morey
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Felix Behr
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Rafael M. Couñago
- School of Chemistry and Molecular Biosciences; University of Queensland; Brisbane Queensland Australia
- Australian Infectious Diseases Research Centre; University of Queensland; Brisbane Queensland Australia
- Institute for Molecular Bioscience; University of Queensland; Brisbane Queensland Australia
| | - Abiodun D. Ogunniyi
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences; University of Queensland; Brisbane Queensland Australia
- Australian Infectious Diseases Research Centre; University of Queensland; Brisbane Queensland Australia
- Institute for Molecular Bioscience; University of Queensland; Brisbane Queensland Australia
| | - Megan L. O'Mara
- School of Chemistry and Molecular Biosciences; University of Queensland; Brisbane Queensland Australia
- School of Mathematics and Physics; University of Queensland; Brisbane Queensland Australia
| | - James C. Paton
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Christopher A. McDevitt
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
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Cerasi M, Ammendola S, Battistoni A. Competition for zinc binding in the host-pathogen interaction. Front Cell Infect Microbiol 2013; 3:108. [PMID: 24400228 PMCID: PMC3872050 DOI: 10.3389/fcimb.2013.00108] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/11/2013] [Indexed: 11/13/2022] Open
Abstract
Due to its favorable chemical properties, zinc is used as a structural or catalytic cofactor in a very large number of proteins. Despite the apparent abundance of this metal in all cell types, the intracellular pool of loosely bound zinc ions available for biological exchanges is in the picomolar range and nearly all zinc is tightly bound to proteins. In addition, to limit bacterial growth, some zinc-sequestering proteins are produced by eukaryotic hosts in response to infections. Therefore, to grow and multiply in the infected host, bacterial pathogens must produce high affinity zinc importers, such as the ZnuABC transporter which is present in most Gram-negative bacteria. Studies carried in different bacterial species have established that disruption of ZnuABC is usually associated with a remarkable loss of pathogenicity. The critical involvement of zinc in a plethora of metabolic and virulence pathways and the presence of very low number of zinc importers in most bacterial species mark zinc homeostasis as a very promising target for the development of novel antimicrobial strategies.
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Affiliation(s)
- Mauro Cerasi
- Dipartimento di Biologia, Università di Roma Tor Vergata Rome, Italy
| | - Serena Ammendola
- Dipartimento di Biologia, Università di Roma Tor Vergata Rome, Italy
| | - Andrea Battistoni
- Dipartimento di Biologia, Università di Roma Tor Vergata Rome, Italy ; Istituto Nazionale Biostrutture e Biosistemi, Consorzio Interuniversitario Rome, Italy
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Couñago RM, Ween MP, Begg SL, Bajaj M, Zuegg J, O'Mara ML, Cooper MA, McEwan AG, Paton JC, Kobe B, McDevitt CA. Imperfect coordination chemistry facilitates metal ion release in the Psa permease. Nat Chem Biol 2013; 10:35-41. [DOI: 10.1038/nchembio.1382] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/19/2013] [Indexed: 12/21/2022]
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