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Saura MLP, Cajachagua CL, Balan A, General IJ. Phosphate uptake in PhoX: Molecular mechanisms. Int J Biol Macromol 2024; 269:131993. [PMID: 38705335 DOI: 10.1016/j.ijbiomac.2024.131993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
PhoX is a high-affinity phosphate binding protein, present in Xanthomonas citri, a phytopathogen responsible for the citrus canker disease. Performing molecular dynamics simulations and different types of computational analyses, we study the molecular mechanisms at play in relation to phosphate binding, revealing the global functioning of the protein: PhoX naturally oscillates along its global normal modes, which allow it to explore both bound and unbound conformations, eventually attracting a nearby negative phosphate ion to the highly positive electrostatic potential on its surface, particularly close to the binding pocket. There, several hydrogen bonds are formed with the two main domains of the structure. Phosphate creates, in this way, a strong bridge that connects the domains, keeping itself between them, in a tight closed conformation, explaining its high binding affinity.
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Affiliation(s)
- María Luz Perez Saura
- School of Science and Technology, Universidad Nacional de San Martin, 25 de Mayo y Francia, San Martín 1650, Buenos Aires, Argentina
| | - Cindy Lee Cajachagua
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas II (ICBII), São Paulo,São Paulo, Brazil
| | - Andrea Balan
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas II (ICBII), São Paulo,São Paulo, Brazil
| | - Ignacio J General
- School of Science and Technology, Universidad Nacional de San Martin, ICIFI and CONICET, 25 de Mayo y Francia, San Martín 1650, Buenos Aires, Argentina.
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Zhao Q, Su X, Wang Y, Liu R, Bartlam M. Structural analysis of molybdate binding protein ModA from Klebsiella pneumoniae. Biochem Biophys Res Commun 2023; 681:41-46. [PMID: 37751633 DOI: 10.1016/j.bbrc.2023.09.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 09/20/2023] [Indexed: 09/28/2023]
Abstract
Klebsiella pneumoniae, a facultative anaerobe, relies on acquiring molybdenum to sustain growth in anaerobic conditions, a crucial factor for the pathogen to establish infections within host environments. Molybdenum plays a critical role in pathogenesis as it forms an essential component of cofactors for molybdoenzymes. K. pneumoniae utilizes the ABC (ATP-Binding-Cassette) transporter encoded by the modABC operon for uptake of the group VI elements molybdenum and tungsten. In this study, we determined the X-ray crystal structures of both the molybdenum-free and molybdenum-bound substrate-binding protein (SBP) ModA from Klebsiella pneumoniae to 2.00 Å and 1.77 Å resolution respectively. ModA crystallizes in the space group P222 with a single monomer in one asymmetric unit. The purified protein remained soluble and specifically bound molybdate and tungstate with Kd values of 6.3 nM and 5.2 nM, respectively. Tungstate competes with molybdate by binding to ModA, resulting in enhanced antimicrobial activity. These data provide a starting point for structural and functional analyses of molybdate transport in K. pneumoniae.
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Affiliation(s)
- Qi Zhao
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Xiaokang Su
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Yanan Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, 300071, China.
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Comparative Transcriptomics Sheds Light on Remodeling of Gene Expression during Diazotrophy in the Thermophilic Methanogen Methanothermococcus thermolithotrophicus. mBio 2022; 13:e0244322. [PMID: 36409126 PMCID: PMC9765008 DOI: 10.1128/mbio.02443-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Some marine thermophilic methanogens are able to perform energy-consuming nitrogen fixation despite deriving only little energy from hydrogenotrophic methanogenesis. We studied this process in Methanothermococcus thermolithotrophicus DSM 2095, a methanogenic archaeon of the order Methanococcales that contributes to the nitrogen pool in some marine environments. We successfully grew this archaeon under diazotrophic conditions in both batch and fermenter cultures, reaching the highest cell density reported so far. Diazotrophic growth depended strictly on molybdenum and, in contrast to other diazotrophs, was not inhibited by tungstate or vanadium. This suggests an elaborate control of metal uptake and a specific metal recognition system for the insertion into the nitrogenase cofactor. Differential transcriptomics of M. thermolithotrophicus grown under diazotrophic conditions with ammonium-fed cultures as controls revealed upregulation of the nitrogenase machinery, including chaperones, regulators, and molybdate importers, as well as simultaneous upregulation of an ammonium transporter and a putative pathway for nitrate and nitrite utilization. The organism thus employs multiple synergistic strategies for uptake of nitrogen nutrients during the early exponential growth phase without altering transcription levels for genes involved in methanogenesis. As a counterpart, genes coding for transcription and translation processes were downregulated, highlighting the maintenance of an intricate metabolic balance to deal with energy constraints and nutrient limitations imposed by diazotrophy. This switch in the metabolic balance included unexpected processes, such as upregulation of the CRISPR-Cas system, probably caused by drastic changes in transcription levels of putative mobile and virus-like elements. IMPORTANCE The thermophilic anaerobic archaeon M. thermolithotrophicus is a particularly suitable model organism to study the coupling of methanogenesis to diazotrophy. Likewise, its capability of simultaneously reducing N2 and CO2 into NH3 and CH4 with H2 makes it a viable target for biofuel production. We optimized M. thermolithotrophicus cultivation, resulting in considerably higher cell yields and enabling the successful establishment of N2-fixing bioreactors. Improved understanding of the N2 fixation process would provide novel insights into metabolic adaptations that allow this energy-limited extremophile to thrive under diazotrophy, for instance, by investigating its physiology and uncharacterized nitrogenase. We demonstrated that diazotrophic growth of M. thermolithotrophicus is exclusively dependent on molybdenum, and complementary transcriptomics corroborated the expression of the molybdenum nitrogenase system. Further analyses of differentially expressed genes during diazotrophy across three cultivation time points revealed insights into the response to nitrogen limitation and the coordination of core metabolic processes.
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Maunders EA, Ngu DHY, Ganio K, Hossain SI, Lim BYJ, Leeming MG, Luo Z, Tan A, Deplazes E, Kobe B, McDevitt CA. The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis. Front Microbiol 2022; 13:903146. [PMID: 35685933 PMCID: PMC9171197 DOI: 10.3389/fmicb.2022.903146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/25/2022] [Indexed: 12/03/2022] Open
Abstract
Acquisition of the trace-element molybdenum via the high-affinity ATP-binding cassette permease ModABC is essential for Pseudomonas aeruginosa respiration in anaerobic and microaerophilic environments. This study determined the X-ray crystal structures of the molybdenum-recruiting solute-binding protein ModA from P. aeruginosa PAO1 in the metal-free state and bound to the group 6 metal oxyanions molybdate, tungstate, and chromate. Pseudomonas aeruginosa PAO1 ModA has a non-contiguous dual-hinged bilobal structure with a single metal-binding site positioned between the two domains. Metal binding results in a 22° relative rotation of the two lobes with the oxyanions coordinated by four residues, that contribute six hydrogen bonds, distinct from ModA orthologues that feature an additional oxyanion-binding residue. Analysis of 485 Pseudomonas ModA sequences revealed conservation of the metal-binding residues and β-sheet structural elements, highlighting their contribution to protein structure and function. Despite the capacity of ModA to bind chromate, deletion of modA did not affect P. aeruginosa PAO1 sensitivity to chromate toxicity nor impact cellular accumulation of chromate. Exposure to sub-inhibitory concentrations of chromate broadly perturbed P. aeruginosa metal homeostasis and, unexpectedly, was associated with an increase in ModA-mediated molybdenum uptake. Elemental analyses of the proteome from anaerobically grown P. aeruginosa revealed that, despite the increase in cellular molybdenum upon chromate exposure, distribution of the metal within the proteome was substantially perturbed. This suggested that molybdoprotein cofactor acquisition may be disrupted, consistent with the potent toxicity of chromate under anaerobic conditions. Collectively, these data reveal a complex relationship between chromate toxicity, molybdenum homeostasis and anaerobic respiration.
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Affiliation(s)
- Eve A. Maunders
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Dalton H. Y. Ngu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Sheikh I. Hossain
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Bryan Y. J. Lim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Michael G. Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Aimee Tan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Boštjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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Kang S, Kong F, Liang X, Li M, Yang N, Cao X, Yang M, Tao D, Yue X, Zheng Y. Label-Free Quantitative Proteomics Reveals the Multitargeted Antibacterial Mechanisms of Lactobionic Acid against Methicillin-Resistant Staphylococcus aureus (MRSA) using SWATH-MS Technology. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12322-12332. [PMID: 31638792 DOI: 10.1021/acs.jafc.9b06364] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The objective of the present study was to reveal the antibacterial mechanism of lactobionic acid (LBA) against methicillin-resistant Staphylococcus aureus (MRSA) using quantitative proteomics by sequential window acquisition of all theoretical mass spectra (SWATH-MS) to analyze 100 differentially expressed proteins after LBA treatment. Furthermore, multiple experiments were conducted to validate the results of the proteomic analysis including reactive oxygen species (ROS), virulence-associated gene expression, and the relative quantification of target proteins and genes by parallel reaction monitoring and quantitative real-time PCR. Combining the ultrastructure observations, proteomic analysis, and our previous research, the mode of LBA action against MRSA was speculated as cell wall damage and loss of membrane integrity; inhibition of DNA repair and protein synthesis; inhibition of virulence factors and biofilm production; induction of oxidative stress; and inhibition of metabolic pathways. These results suggest potential applications for LBA in food safety and pharmaceuticals, considering its multitarget effects against MRSA.
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Affiliation(s)
- Shimo Kang
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
| | - Fanhua Kong
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
| | - Xiaona Liang
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
| | - Mohan Li
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
| | - Ning Yang
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
| | - Xueyan Cao
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
| | - Mei Yang
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
| | - Dongbing Tao
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
| | - Xiqing Yue
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
| | - Yan Zheng
- College of Food Science , Shenyang Agricultural University , No. 120 Dongling Road , Shenyang , Liaoning 110161 , P.R. China
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Murray FJ, Sullivan FM, Hubbard SA, Hoberman AM, Carey S. A two-generation reproductive toxicity study of sodium molybdate dihydrate administered in drinking water or diet to Sprague-Dawley rats. Reprod Toxicol 2019; 84:75-92. [DOI: 10.1016/j.reprotox.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/07/2018] [Accepted: 11/26/2018] [Indexed: 11/29/2022]
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Abstract
Calcium ions are a kind of unavoidable ions in water. It has the deleterious effect on molybdenite flotation. High-calcium flotation wastewater (HCFW) was reused for flotation circuits after the pretreatment removing Ca2+ in from HCFW. The high cost of wastewater treatment limits HCFW reuse. In this paper, an efficient, innovative, low-cost and environmental-friendly flotation wastewater reuse technology was introduced. XLM, as a composite collector for molybdenite, is a mixture of diesel oil (DO) and polycyclic aromatic hydrocarbons (PAHs). It could reduce the deleterious effects of Ca2+ on the flotation of molybdenite in HCFW. Therefore, this was used to replace the pretreatment removing Ca2+ in from high Ca2+ wastewater and saved the cost of wastewater treatment. When XLM consists of 4 wt % PAHs and 96 wt % DO, it has better adaptability than DO in the different Ca2+ concentration of flotation water. The contact angle measurements indicated that PAHs, as a synergistic component of a composite collector, could adsorb on the edges of molybdenite in the presence of Ca2+ by forming PAHs-Ca2+-MoO42− structure to increase the contact angle of fine molybdenite particle and reduce the deleterious effects of Ca2+ on the flotation of molybdenite. The industrial-scale test further that demonstrated XLM can improve the molybdenite roughing recovery and grade by 1.8% and 3.46% compared with DO as the collector in high Ca2+ flotation wastewater. It is feasible and effective to replace high-cost wastewater treatment for molybdenum plants.
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Pereira CT, Roesler C, Faria JN, Fessel MR, Balan A. Sulfate-Binding Protein (Sbp) from Xanthomonas citri: Structure and Functional Insights. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:578-588. [PMID: 28562158 DOI: 10.1094/mpmi-02-17-0032-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The uptake and transport of sulfate in bacteria is mediated by an ATP-binding cassette transporter (ABC transporter) encoded by sbpcysUWA genes, whose importance has been widely demonstrated due to their relevance in cysteine synthesis and bacterial growth. In Xanthomonas citri, the causative agent of canker disease, the expression of components from this ABC transporter and others related to uptake of organic sulfur sources has been shown during in vitro growth cultures. In this work, based on gene reporter and proteomics analyses, we showed the activation of the promoter that controls the sbpcysUWA operon in vitro and in vivo and the expression of sulfate-binding protein (Sbp), a periplasmic-binding protein, indicating that this protein plays an important function during growth and that the transport system is active during Citrus sinensis infection. To characterize Sbp, we solved its three-dimensional structure bound to sulfate at 1.14 Å resolution and performed biochemical and functional characterization. The results revealed that Sbp interacts with sulfate without structural changes, but the interaction induces a significant increasing of protein thermal stability. Altogether, the results presented in this study show the evidence of the functionality of the ABC transporter for sulfate in X. citri and its relevance during infection.
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Affiliation(s)
- Cristiane Tambascia Pereira
- 1 Laboratório Nacional de Biociências (LNBio), Centro de Pesquisas em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
- 2 Universidade de Campinas-UNICAMP, Instituto de Biologia, Campinas São Paulo, Brazil; and
- 3 Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Cássia Roesler
- 1 Laboratório Nacional de Biociências (LNBio), Centro de Pesquisas em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
- 2 Universidade de Campinas-UNICAMP, Instituto de Biologia, Campinas São Paulo, Brazil; and
| | - Jéssica Nascimento Faria
- 1 Laboratório Nacional de Biociências (LNBio), Centro de Pesquisas em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
- 2 Universidade de Campinas-UNICAMP, Instituto de Biologia, Campinas São Paulo, Brazil; and
| | - Melissa Regina Fessel
- 1 Laboratório Nacional de Biociências (LNBio), Centro de Pesquisas em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Andrea Balan
- 3 Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil
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The Influence of Ca2+ and pH on the Interaction between PAHs and Molybdenite Edges. MINERALS 2017. [DOI: 10.3390/min7060104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Sánchez-Arreguin JA, Hernandez-Oñate MA, León-Ramirez CG, Ruiz-Herrera J. Transcriptional analysis of the adaptation of Ustilago maydis during growth under nitrogen fixation conditions. J Basic Microbiol 2017; 57:597-604. [PMID: 28429489 DOI: 10.1002/jobm.201600660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/04/2017] [Indexed: 01/13/2023]
Abstract
Regulation of genes involved in nitrogen metabolism likely plays a role in the ability of fungi to exploit and survive under different environmental situations. To learn about the mechanism of adaptation of the biotrophic fungus Ustilago maydis from a medium containing a source of fixed nitrogen, to a medium depending on the ability to fix N2 by its bacterial endosymbiont, we explored gene expression profiles using RNA-Seq analyses under these two conditions. The differentially expressed (DE) fungal genes were analyzed, identifying 90 genes that were regulated 24 h after shifting the fungus to media lacking ammonium nitrate as a nitrogen source. From these, mRNA levels were increased for 49 genes, whereas 41 were down-regulated. The functional description associated to the regulated genes revealed that nine key pathways were represented, including, secondary metabolism, the metabolism of nitrogen, amino acid, fatty acid, amino sugar and nucleotide sugar, purine, peroxisome, and the regulation of actin cytoskeleton. These results suggest that the interplay of U. maydis with its N2 fixing bacterial endosymbiont is a flexible process that may be active during the adaptation of the fungus to the different nitrogen sources.
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Affiliation(s)
- José Alejandro Sánchez-Arreguin
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México.,Facultad de Ciencias Biológicas, Laboratorio de Micología y Fitopatología, Unidad de Manipulación Genética, Universidad Autónoma de Nuevo León, San Nicolas de Los Garza, Nuevo León, México
| | - Miguel Angel Hernandez-Oñate
- Cátedras-CONACYT-Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, México
| | - Claudia Geraldine León-Ramirez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
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TupA: a tungstate binding protein in the periplasm of Desulfovibrio alaskensis G20. Int J Mol Sci 2014; 15:11783-98. [PMID: 24992597 PMCID: PMC4139814 DOI: 10.3390/ijms150711783] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/29/2014] [Accepted: 05/29/2014] [Indexed: 11/17/2022] Open
Abstract
The TupABC system is involved in the cellular uptake of tungsten and belongs to the ABC (ATP binding cassette)-type transporter systems. The TupA component is a periplasmic protein that binds tungstate anions, which are then transported through the membrane by the TupB component using ATP hydrolysis as the energy source (the reaction catalyzed by the ModC component). We report the heterologous expression, purification, determination of affinity binding constants and crystallization of the Desulfovibrio alaskensis G20 TupA. The tupA gene (locus tag Dde_0234) was cloned in the pET46 Enterokinase/Ligation-Independent Cloning (LIC) expression vector, and the construct was used to transform BL21 (DE3) cells. TupA expression and purification were optimized to a final yield of 10 mg of soluble pure protein per liter of culture medium. Native polyacrylamide gel electrophoresis was carried out showing that TupA binds both tungstate and molybdate ions and has no significant interaction with sulfate, phosphate or perchlorate. Quantitative analysis of metal binding by isothermal titration calorimetry was in agreement with these results, but in addition, shows that TupA has higher affinity to tungstate than molybdate. The protein crystallizes in the presence of 30% (w/v) polyethylene glycol 3350 using the hanging-drop vapor diffusion method. The crystals diffract X-rays beyond 1.4 Å resolution and belong to the P21 space group, with cell parameters a = 52.25 Å, b = 42.50 Å, c = 54.71 Å, β = 95.43°. A molecular replacement solution was found, and the structure is currently under refinement.
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Luo L, Ke C, Guo X, Shi B, Huang M. Metal accumulation and differentially expressed proteins in gill of oyster (Crassostrea hongkongensis) exposed to long-term heavy metal-contaminated estuary. FISH & SHELLFISH IMMUNOLOGY 2014; 38:318-329. [PMID: 24698996 DOI: 10.1016/j.fsi.2014.03.029] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 02/23/2014] [Accepted: 03/07/2014] [Indexed: 06/03/2023]
Abstract
Bio-accumulation and bio-transmission of toxic metals and the toxicological responses of organisms exposed to toxic metals have been focused, due to heavy metal contaminations have critically threatened the ecosystem and food security. However, still few investigations focused on the responses of certain organisms exposed to the long term and severe heavy metal contamination in specific environments. In present investigation, the Hong Kong oyster, Crassostrea hongkongensis were obtained from 3 sites which were contaminated by different concentrations of heavy metals (such as zinc, copper, manganese and lead etc.), respectively. Heavy metal concentrations in the sea water samples collected from the 3 sites and the dissected tissues of the oysters with blue visceral mass were determinated to estimate the metal contamination levels in environments and the bio-accumulation ratios of the heavy metals in the different tissues of oysters. Moreover, Proteomic methods were employed to analyze the differentially expressed proteins in the gills of oysters exposed to long-term heavy metal contaminations. Results indicated that the Jiulong River estuary has been severely contaminated by Cu, Zn and slightly with Cr, Ni, Mn, etc, moreover, Zn and Cu were the major metals accumulated by oysters to phenomenally high concentrations (more than 3.0% of Zn and about 2.0% of Cu against what the dry weight of tissues were accumulated), and Cr, Ni, Mn, etc were also significantly accumulated. The differentially expressed proteins in the gills of oysters exposed to heavy metals participate in several cell processes, such as metal binding, transporting and saving, oxidative-reduction balance maintaining, stress response, signal transduction, etc. Significantly up-regulated expression (about 10 folds) of an important metal binding protein, metallothionein (MT) and granular cells was observed in the gills of oysters exposed to long-term and severely heavy-metal-contaminated estuary, it suggested that binding toxic metals with metallothionein-like proteins (MTLP) and storing toxic metals in metal-rich granules (MRG) with insoluble forms were the important strategies of oyster to detoxify the toxic metals and adapt to the high level of metal-contaminated environment. Most of the stress and immunity responsive proteins, such as heat shock proteins (HSP), extracellular superoxide dismutase (ECSOD) and cavortin, and the cellular redox reaction relative proteins such as 20G-Fe (II) oxygenase family oxidoreductase, aldehyde dehydrogenase and retinal dehydrogenase 2, were detected significantly down-regulated in the gills of oysters exposed to long term heavy metal contaminated environments, it indicated that long term exposure different from emergent exposure to heavy metal contamination may significantly suppress the stress and immunity response system of oysters. Moreover, Formin homology 2 domain containing protein (FH2). The only protein domain to directly nucleate actin monomers into unbranched filament polymers, by which will subsequently control gene expression and chromatin remodelling complexes, was also detected greatly up-regulated in the gills of oysters exposed to long-term heavy metal contaminations. It indicated that nuclear activity regulation may also be important for oyster to adapt to the long-term heavy-metal-contaminated environment.
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Affiliation(s)
- Lianzhong Luo
- Department of Pharmacy, Xiamen Medical College, Xiamen 361008, PR China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China; College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, PR China.
| | - Xiaoyu Guo
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, PR China
| | - Bo Shi
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, PR China
| | - Miaoqin Huang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, PR China
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Medrano FJ, de Souza CS, Romero A, Balan A. Structure determination of a sugar-binding protein from the phytopathogenic bacterium Xanthomonas citri. Acta Crystallogr F Struct Biol Commun 2014; 70:564-71. [PMID: 24817711 PMCID: PMC4014320 DOI: 10.1107/s2053230x14006578] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 03/25/2014] [Indexed: 02/05/2023] Open
Abstract
The uptake of maltose and related sugars in Gram-negative bacteria is mediated by an ABC transporter encompassing a periplasmic component (the maltose-binding protein or MalE), a pore-forming membrane protein (MalF and MalG) and a membrane-associated ATPase (MalK). In the present study, the structure determination of the apo form of the putative maltose/trehalose-binding protein (Xac-MalE) from the citrus pathogen Xanthomonas citri in space group P6522 is described. The crystals contained two protein molecules in the asymmetric unit and diffracted to 2.8 Å resolution. Xac-MalE conserves the structural and functional features of sugar-binding proteins and a ligand-binding pocket with similar characteristics to eight different orthologues, including the residues for maltose and trehalose interaction. This is the first structure of a sugar-binding protein from a phytopathogenic bacterium, which is highly conserved in all species from the Xanthomonas genus.
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Affiliation(s)
- Francisco Javier Medrano
- Department of Chemical and Physical Biology, Centro de Investigaciones Biologicas (CSIC), Madrid, Spain
| | - Cristiane Santos de Souza
- Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, Cidade Universitária, SP, Brazil
| | - Antonio Romero
- Department of Chemical and Physical Biology, Centro de Investigaciones Biologicas (CSIC), Madrid, Spain
| | - Andrea Balan
- Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, Cidade Universitária, SP, Brazil
- Laboratório Nacional de Biociências (LNBio), Centro de Pesquisas em Energia e Materiais (CNPEM), Campinas, SP, Brazil
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A specific interdomain interaction preserves the structural and binding properties of the ModA protein from the phytopathogen Xanthomonas citri domain interaction and transport in ModA. Arch Biochem Biophys 2013; 539:20-30. [PMID: 24035743 DOI: 10.1016/j.abb.2013.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 09/02/2013] [Accepted: 09/04/2013] [Indexed: 10/26/2022]
Abstract
The periplasmic-binding proteins in ATP-binding cassette systems (ABC Transporters) are responsible for the capture and delivery of ligands to their specific transporters, triggering a series of ATP-driven conformational changes that leads to the transport of the ligand. Structurally consisting of two lobes, the proteins change conformation after interaction with the ligand. The structure of the molybdate-binding protein (ModA) from Xanthomonas citri, bound to molybdate, was previously solved by our group and an interdomain interaction, mediated by a salt bridge between K127 and D59, apparently supports the binding properties and keeps the domains closed. To determinate the importance of this interaction, we built two ModA mutants, K127S and D59A, and analysed their functional and structural properties. Based on a set of spectroscopic experiments, crystallisation trials, structure determination and molecular dynamics (MD) simulations, we showed that the salt bridge is essential to maintain the structure and binding properties. Additionally, the MD simulations revealed that this mutant adopted a more compact structure that packed down the ligand-binding pocket. From the closed bound to open structure, the positioning of the helices forming the dipole and the salt bridge are essential to induce an intermediate state.
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15
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Gonzalez PJ, Rivas MG, Mota CS, Brondino CD, Moura I, Moura JJ. Periplasmic nitrate reductases and formate dehydrogenases: Biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Aguilar-Barajas E, Díaz-Pérez C, Ramírez-Díaz MI, Riveros-Rosas H, Cervantes C. Bacterial transport of sulfate, molybdate, and related oxyanions. Biometals 2011; 24:687-707. [PMID: 21301930 DOI: 10.1007/s10534-011-9421-x] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 01/26/2011] [Indexed: 12/29/2022]
Affiliation(s)
- Esther Aguilar-Barajas
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Edificio B-3, Ciudad Universitaria, 58030 Morelia, Michoacan, Mexico
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18
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Oliveira ASF, Baptista AM, Soares CM. Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796. J Phys Chem B 2010; 114:5486-96. [PMID: 20369870 DOI: 10.1021/jp905735y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Despite the rapid advances in the study of ABC transporters, many fundamental questions linked to ATP binding/hydrolysis and its relation to the transport cycle remain unanswered. In particular, it is still neither clear nor consensual how the ATP energy is used by the nucleotide binding domains (NBDs) to produce mechanical work and drive the substrate translocation. The major conformational changes in the NBDs following ATP hydrolysis during the transport cycle and the role played by the conserved family motifs in harnessing the energy associated with nucleotide hydrolysis are yet unknown. Additionally, the way energy is transmitted from the catalytic to the membrane domains, in order to drive substrate translocation, is also a fundamental question that remains unanswered. Due to the high structure similarities of the NBD architecture throughout the whole ABC family, it is likely that the mechanism of ATP binding, hydrolysis, and communication with the transmembrane domains is similar in all family members, independently of the nature of the transported substrate. In this work, we focused our attention on the consequences of ATP hydrolysis in the NBDs, especially on the structural changes that occur during this process. For that, we use molecular dynamics simulation techniques taking as a starting point the X-ray structure of the MJ0796 dimer from Methanococcus jannaschii. Several potential intermediate states of the ATP hydrolytic cycle are investigated, each consisting of different combinations of nucleotide-bound forms. The results obtained allowed us to identify the conformational rearrangements induced by hydrolysis on the catalytic subunits, as well as the residues involved in this reorganization. The major changes are localized at specific regions of the protein, namely, involving segments 11-19 and 93-124. Additionally, our results together with the knowledge of complete ABC transporter X-ray structures suggest a possible NBD:TMD signal transmission interface.
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Affiliation(s)
- A Sofia F Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
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19
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Chan S, Giuroiu I, Chernishof I, Sawaya MR, Chiang J, Gunsalus RP, Arbing MA, Perry LJ. Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:242-50. [PMID: 20208152 PMCID: PMC2833028 DOI: 10.1107/s1744309109055158] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 12/22/2009] [Indexed: 11/10/2022]
Abstract
The trace-element oxyanion molybdate, which is required for the growth of many bacterial and archaeal species, is transported into the cell by an ATP-binding cassette (ABC) transporter superfamily uptake system called ModABC. ModABC consists of the ModA periplasmic solute-binding protein, the integral membrane-transport protein ModB and the ATP-binding and hydrolysis cassette protein ModC. In this study, X-ray crystal structures of ModA from the archaeon Methanosarcina acetivorans (MaModA) have been determined in the apoprotein conformation at 1.95 and 1.69 A resolution and in the molybdate-bound conformation at 2.25 and 2.45 A resolution. The overall domain structure of MaModA is similar to other ModA proteins in that it has a bilobal structure in which two mixed alpha/beta domains are linked by a hinge region. The apo MaModA is the first unliganded archaeal ModA structure to be determined: it exhibits a deep cleft between the two domains and confirms that upon binding ligand one domain is rotated towards the other by a hinge-bending motion, which is consistent with the 'Venus flytrap' model seen for bacterial-type periplasmic binding proteins. In contrast to the bacterial ModA structures, which have tetrahedral coordination of their metal substrates, molybdate-bound MaModA employs octahedral coordination of its substrate like other archaeal ModA proteins.
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Affiliation(s)
- Sum Chan
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Iulia Giuroiu
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Irina Chernishof
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Janet Chiang
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Robert P. Gunsalus
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
- The Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Mark A. Arbing
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - L. Jeanne Perry
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
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Smart JP, Cliff MJ, Kelly DJ. A role for tungsten in the biology of Campylobacter jejuni: tungstate stimulates formate dehydrogenase activity and is transported via an ultra-high affinity ABC system distinct from the molybdate transporter. Mol Microbiol 2009; 74:742-57. [PMID: 19818021 DOI: 10.1111/j.1365-2958.2009.06902.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The food-borne pathogen Campylobacter jejuni possesses no known tungstoenzymes, yet encodes two ABC transporters (Cj0300-0303 and Cj1538-1540) homologous to bacterial molybdate (ModABC) uptake systems and the tungstate transporter (TupABC) of Eubacterium acidaminophilum respectively. The actual substrates and physiological role of these transporters were investigated. Tryptophan fluorescence spectroscopy and isothermal titration calorimetry of the purified periplasmic binding proteins of each system revealed that while Cj0303 is unable to discriminate between molybdate and tungstate (K(D) values for both ligands of 4-8 nM), Cj1540 binds tungstate with a K(D) of 1.0 +/- 0.2 pM; 50 000-fold more tightly than molybdate. Induction-coupled plasma mass spectroscopy of single and double mutants showed that this large difference in affinity is reflected in a lower cellular tungsten content in a cj1540 (tupA) mutant compared with a cj0303c (modA) mutant. Surprisingly, formate dehydrogenase (FDH) activity was decreased approximately 50% in the tupA strain, and supplementation of the growth medium with tungstate significantly increased FDH activity in the wild type, while inhibiting known molybdoenzymes. Our data suggest that C. jejuni possesses a specific, ultra-high affinity tungstate transporter that supplies tungsten for incorporation into FDH. Furthermore, possession of two MoeA paralogues may explain the formation of both molybdopterin and tungstopterin in this bacterium.
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Affiliation(s)
- Jonathan P Smart
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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21
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Duhme‐Klair A. From Siderophores and Self‐Assembly to Luminescent Sensors: The Binding of Molybdenum by Catecholamides. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900416] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Hollenstein K, Comellas-Bigler M, Bevers LE, Feiters MC, Meyer-Klaucke W, Hagedoorn PL, Locher KP. Distorted octahedral coordination of tungstate in a subfamily of specific binding proteins. J Biol Inorg Chem 2009; 14:663-72. [PMID: 19234723 DOI: 10.1007/s00775-009-0479-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 02/04/2009] [Indexed: 11/30/2022]
Abstract
Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). These substrates are captured by an external, high-affinity binding protein, and delivered to ATP binding cassette transporters, which move them across the cell membrane. We have recently reported a crystal structure of the molybdate/tungstate binding protein ModA/WtpA from Archaeoglobus fulgidus, which revealed an octahedrally coordinated central metal atom. By contrast, the previously determined structures of three bacterial homologs showed tetracoordinate molybdenum and tungsten atoms in their binding pockets. Until then, coordination numbers above four had only been found for molybdenum/tungsten in metalloenzymes where these metal atoms are part of the catalytic cofactors and coordinated by mostly non-oxygen ligands. We now report a high-resolution structure of A. fulgidus ModA/WtpA, as well as crystal structures of four additional homologs, all bound to tungstate. These crystal structures match X-ray absorption spectroscopy measurements from soluble, tungstate-bound protein, and reveal the details of the distorted octahedral coordination. Our results demonstrate that the distorted octahedral geometry is not an exclusive feature of the A. fulgidus protein, and suggest distinct binding modes of the binding proteins from archaea and bacteria.
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Affiliation(s)
- Kaspar Hollenstein
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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