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Khan NM, Ali A, Wan Y, Zhou G. Genome-wide identification of heavy-metal ATPases genes in Areca catechu: investigating their functionality under heavy metal exposure. BMC PLANT BIOLOGY 2024; 24:484. [PMID: 38822228 PMCID: PMC11141028 DOI: 10.1186/s12870-024-05201-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
Heavy-metal ATPases (HMAs) play a vital role in plants, helping to transport heavy metal ions across cell membranes.However, insufficient data exists concerning HMAs genes within the Arecaceae family.In this study, 12 AcHMA genes were identified within the genome of Areca catechu, grouped into two main clusters based on their phylogenetic relationships.Genomic distribution analysis reveals that the AcHMA genes were unevenly distributed across six chromosomes. We further analyzed their physicochemical properties, collinearity, and gene structure.Furthermore, RNA-seq data analysis exhibited varied expressions in different tissues of A. catechu and found that AcHMA1, AcHMA2, and AcHMA7 were highly expressed in roots, leaves, pericarp, and male/female flowers. A total of six AcHMA candidate genes were selected based on gene expression patterns, and their expression in the roots and leaves was determined using RT-qPCR under heavy metal stress. Results showed that the expression levels of AcHMA1 and AcHMA3 genes were significantly up-regulated under Cd2 + and Zn2 + stress. Similarly, in response to Cu2+, the AcHMA5 and AcHMA8 revealed the highest expression in roots and leaves, respectively. In conclusion, this study will offer a foundation for exploring the role of the HMAs gene family in dealing with heavy metal stress conditions in A. catechu.
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Affiliation(s)
- Noor Muhammad Khan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Akhtar Ali
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yinglang Wan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Guangzhen Zhou
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China.
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2
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Flores-Iga G, Lopez-Ortiz C, Gracia-Rodriguez C, Almeida A, Nimmakayala P, Reddy UK, Balagurusamy N. A Genome-Wide Identification and Comparative Analysis of the Heavy-Metal-Associated Gene Family in Cucurbitaceae Species and Their Role in Cucurbita pepo under Arsenic Stress. Genes (Basel) 2023; 14:1877. [PMID: 37895226 PMCID: PMC10606463 DOI: 10.3390/genes14101877] [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: 09/05/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The heavy-metal-associated (HMA) proteins are a class of PB1-type ATPases related to the intracellular transport and detoxification of metals. However, due to a lack of information regarding the HMA gene family in the Cucurbitaceae family, a comprehensive genome-wide analysis of the HMA family was performed in ten Cucurbitaceae species: Citrullus amarus, Citrullus colocynthis, Citrullus lanatus, Citrullus mucosospermus, Cucumis melo, Cucumis sativus, Cucurbita maxima, Cucurbita moschata, Cucurbita pepo, and Legenaria siceraria. We identified 103 Cucurbit HMA proteins with various members, ranging from 8 (Legenaria siceraria) to 14 (Cucurbita pepo) across species. The phylogenetic and structural analysis confirmed that the Cucurbitaceae HMA protein family could be further classified into two major clades: Zn/Co/Cd/Pb and Cu/Ag. The GO-annotation-based subcellular localization analysis predicted that all HMA gene family members were localized on membranes. Moreover, the analysis of conserved motifs and gene structure (intron/exon) revealed the functional divergence between clades. The interspecies microsynteny analysis demonstrated that maximum orthologous genes were found between species of the Citrullus genera. Finally, nine candidate HMA genes were selected, and their expression analysis was carried out via qRT-PCR in root, leaf, flower, and fruit tissues of C. pepo under arsenic stress. The expression pattern of the CpeHMA genes showed a distinct pattern of expression in root and shoot tissues, with a remarkable expression of CpeHMA6 and CpeHMA3 genes from the Cu/Ag clade. Overall, this study provides insights into the functional analysis of the HMA gene family in Cucurbitaceae species and lays down the basic knowledge to explore the role and mechanism of the HMA gene family to cope with arsenic stress conditions.
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Affiliation(s)
- Gerardo Flores-Iga
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Carlos Lopez-Ortiz
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Celeste Gracia-Rodriguez
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Aldo Almeida
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark;
| | - Padma Nimmakayala
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Umesh K. Reddy
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
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3
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Abeyrathna SS, Abeyrathna NS, Basak P, Irvine GW, Zhang L, Meloni G. Plastic recognition and electrogenic uniport translocation of 1 st-, 2 nd-, and 3 rd-row transition and post-transition metals by primary-active transmembrane P 1B-2-type ATPase pumps. Chem Sci 2023; 14:6059-6078. [PMID: 37293658 PMCID: PMC10246665 DOI: 10.1039/d3sc00347g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023] Open
Abstract
Transmembrane P1B-type ATPase pumps catalyze the extrusion of transition metal ions across cellular lipid membranes to maintain essential cellular metal homeostasis and detoxify toxic metals. Zn(ii)-pumps of the P1B-2-type subclass, in addition to Zn2+, select diverse metals (Pb2+, Cd2+ and Hg2+) at their transmembrane binding site and feature promiscuous metal-dependent ATP hydrolysis in the presence of these metals. Yet, a comprehensive understanding of the transport of these metals, their relative translocation rates, and transport mechanism remain elusive. We developed a platform for the characterization of primary-active Zn(ii)-pumps in proteoliposomes to study metal selectivity, translocation events and transport mechanism in real-time, employing a "multi-probe" approach with fluorescent sensors responsive to diverse stimuli (metals, pH and membrane potential). Together with atomic-resolution investigation of cargo selection by X-ray absorption spectroscopy (XAS), we demonstrate that Zn(ii)-pumps are electrogenic uniporters that preserve the transport mechanism with 1st-, 2nd- and 3rd-row transition metal substrates. Promiscuous coordination plasticity, guarantees diverse, yet defined, cargo selectivity coupled to their translocation.
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Affiliation(s)
- Sameera S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
| | - Nisansala S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
| | - Priyanka Basak
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
| | - Gordon W Irvine
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
| | - Limei Zhang
- Department of Biochemistry and Redox Biology Center and the Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln Lincoln NE 68588 USA
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
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Wang R, Zhu Z, Cheng W, Chang C, Song X, Huang F. Cadmium accumulation and isotope fractionation in typical protozoa Tetrahymena: A new perspective on remediation of Cd pollution in wastewater. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131517. [PMID: 37146330 DOI: 10.1016/j.jhazmat.2023.131517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 05/07/2023]
Abstract
Cadmium (Cd) pollution threatens water safety and human health, which has raised serious public concern. Tetrahymena is a model protozoan, possessing the potential to remediate Cd contaminated water given the rapid expression of thiols. However, the mechanism of Cd accumulation in Tetrahymena has not been well understood, which hinders its application in environmental remediation. This study elucidated the pathway of Cd accumulation in Tetrahymena using Cd isotope fractionation. Our results showed that Tetrahymena preferentially absorb light Cd isotopes, with Δ114/110CdTetrahymena-solution = -0.20 ± 0.02‰ ∼ - 0.29 ± 0.02‰, which implies that the intracellular Cd is probably in the form of Cd-S. The fractionation generated by Cd complexation with thiols is constant (Δ114/110CdTetrahymena-remaining solution ∼ -0.28 ± 0.02‰), which is not affected by the concentrations of Cd in intracellular and culture medium, nor by the physiological changes in cells. Furthermore, the detoxification process of Tetrahymena results in an increase in cellular Cd accumulation from 11.7% to 23.3% with the elevated Cd concentrations in batch Cd stress culture experiments. This study highlights the promising application of Cd isotope fractionation in Tetrahymena for the remediation of heavy metal pollution in water.
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Affiliation(s)
- Ruirui Wang
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhiqiang Zhu
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wenhan Cheng
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China; College of Resources and Environment, Anhui Agriculture University, Hefei, Anhui 230036, China
| | - Chuanyu Chang
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaoyuan Song
- Hefei National Research Center for Physical Sciences at the Microscale, MOE Key Laboratory of Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Fang Huang
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China; CAS Center for Excellence in Comparative Planetology, University of Science and Technology of China, Hefei, Anhui 230026, China.
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Interplay between Two-Component Regulatory Systems Is Involved in Control of Cupriavidus metallidurans Metal Resistance Genes. J Bacteriol 2023; 205:e0034322. [PMID: 36892288 PMCID: PMC10127602 DOI: 10.1128/jb.00343-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Metal resistance of Cupriavidus metallidurans is based on determinants that were acquired in the past by horizontal gene transfer during evolution. Some of these determinants encode transmembrane metal efflux systems. Expression of most of the respective genes is controlled by two-component regulatory systems composed of a membrane-bound sensor/sensory histidine kinase (HK) and a cytoplasmic, DNA-binding response regulator (RR). Here, we investigated the interplay between the three closely related two-component regulatory systems CzcRS, CzcR2S2, and AgrRS. All three systems regulate the response regulator CzcR, while the RRs AgrR and CzcR2 were not involved in czc regulation. Target promoters were czcNp and czcPp for genes upstream and downstream of the central czc gene region. The two systems together repressed CzcRS-dependent upregulation of czcP-lacZ at low zinc concentrations in the presence of CzcS but activated this signal transmission at higher zinc concentrations. AgrRS and CzcR2S2 interacted to quench CzcRS-mediated expression of czcNp-lacZ and czcPp-lacZ. Together, cross talk between the three two-component regulatory systems enhanced the capabilities of the Czc systems by controlling expression of the additional genes czcN and czcP. IMPORTANCE Bacteria are able to acquire genes encoding resistance to metals and antibiotics by horizontal gene transfer. To bestow an evolutionary advantage on their host cell, new genes must be expressed, and their expression should be regulated so that resistance-mediating proteins are produced only when needed. Newly acquired regulators may interfere with those already present in a host cell. Such an event was studied here in the metal-resistant bacterium Cupriavidus metallidurans. The results demonstrate how regulation by the acquired genes interacts with the host's extant regulatory network. This leads to emergence of a new system level of complexity that optimizes the response of the cell to periplasmic signals.
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Metalloprotein-Specific or Critical Amino Acid Residues: Perspectives on Plant-Precise Detoxification and Recognition Mechanisms under Cadmium Stress. Int J Mol Sci 2022; 23:ijms23031734. [PMID: 35163656 PMCID: PMC8836122 DOI: 10.3390/ijms23031734] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 12/15/2022] Open
Abstract
Cadmium (Cd) pollution in cultivated land is caused by irresistible geological factors and human activities; intense diffusion and migration have seriously affected the safety of food crops. Plants have evolved mechanisms to control excessive influx of Cd in the environment, such as directional transport, chelation and detoxification. This is done by some specific metalloproteins, whose key amino acid motifs have been investigated by scientists one by one. The application of powerful cell biology, crystal structure science, and molecular probe targeted labeling technology has identified a series of protein families involved in the influx, transport and detoxification of the heavy metal Cd. This review summarizes them as influx proteins (NRAMP, ZIP), chelating proteins (MT, PDF), vacuolar proteins (CAX, ABCC, MTP), long-distance transport proteins (OPT, HMA) and efflux proteins (PCR, ABCG). We selected representative proteins from each family, and compared their amino acid sequence, motif structure, subcellular location, tissue specific distribution and other characteristics of differences and common points, so as to summarize the key residues of the Cd binding target. Then, we explain its special mechanism of action from the molecular structure. In conclusion, this review is expected to provide a reference for the exploration of key amino acid targets of Cd, and lay a foundation for the intelligent design and breeding of crops with high/low Cd accumulation.
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Chen J, Wang L, Li W, Zheng X, Li X. Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8. Front Microbiol 2022; 12:784575. [PMID: 35154027 PMCID: PMC8832061 DOI: 10.3389/fmicb.2021.784575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Our current knowledge on bacterial cadmium (Cd) resistance is mainly based on the functional exploration of specific Cd-resistance genes. In this study, we carried out a genomic study on Cd resistance of a newly isolated Cellulomonas strain with a MIC of 5 mM Cd. Full genome of the strain, with a genome size of 4.47 M bp and GC-content of 75.35%, was obtained through high-quality sequencing. Genome-wide annotations identified 54 heavy metal-related genes. Four potential Cd-resistance genes, namely zntAY8, copAY8, HMTY8, and czcDY8, were subjected to functional exploration. Quantitative PCR determination of in vivo expression showed that zntAY8, copAY8, and HMTY8 were strongly Cd-inducible. Expression of the three inducible genes against time and Cd concentrations were further quantified. It is found that zntAY8 responded more strongly to higher Cd concentrations, while expression of copAY8 and HMTY8 increased over time at lower Cd concentrations. Heterologous expression of the four genes in Cd-sensitive Escherichia coli led to different impacts on hosts’ Cd sorption, with an 87% reduction by zntAY8 and a 3.7-fold increase by HMTY8. In conclusion, a Cd-resistant Cellulomonas sp. strain was isolated, whose genome harbors a diverse panel of metal-resistance genes. Cd resistance in the strain is not controlled by a dedicated gene alone, but by several gene systems collectively whose roles are probably time- and dose-dependent. The plasmid-free, high-GC strain Y8 may provide a platform for exploring heavy metal genomics of the Cellulomonas genus.
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Affiliation(s)
- Jinghao Chen
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Likun Wang
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wenjun Li
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zheng
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Xiaofang Li
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- *Correspondence: Xiaofang Li,
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8
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Brown JB, Lee MA, Smith AT. Ins and Outs: Recent Advancements in Membrane Protein-Mediated Prokaryotic Ferrous Iron Transport. Biochemistry 2021; 60:3277-3291. [PMID: 34670078 DOI: 10.1021/acs.biochem.1c00586] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Iron is an essential nutrient for virtually every living organism, especially pathogenic prokaryotes. Despite its importance, however, both the acquisition and the export of this element require dedicated pathways that are dependent on oxidation state. Due to its solubility and kinetic lability, reduced ferrous iron (Fe2+) is useful to bacteria for import, chaperoning, and efflux. Once imported, ferrous iron may be loaded into apo and nascent enzymes and even sequestered into storage proteins under certain conditions. However, excess labile ferrous iron can impart toxicity as it may spuriously catalyze Fenton chemistry, thereby generating reactive oxygen species and leading to cellular damage. In response, it is becoming increasingly evident that bacteria have evolved Fe2+ efflux pumps to deal with conditions of ferrous iron excess and to prevent intracellular oxidative stress. In this work, we highlight recent structural and mechanistic advancements in our understanding of prokaryotic ferrous iron import and export systems, with a focus on the connection of these essential transport systems to pathogenesis. Given the connection of these pathways to the virulence of many increasingly antibiotic resistant bacterial strains, a greater understanding of the mechanistic details of ferrous iron cycling in pathogens could illuminate new pathways for future therapeutic developments.
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Affiliation(s)
- Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Mark A Lee
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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9
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Prediction of Metal Ion Binding Sites of Transmembrane Proteins. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:2327832. [PMID: 34721655 PMCID: PMC8556105 DOI: 10.1155/2021/2327832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/01/2021] [Indexed: 12/22/2022]
Abstract
The metal ion binding of transmembrane proteins (TMPs) plays a fundamental role in biological processes, pharmaceutics, and medicine, but it is hard to extract enough TMP structures in experimental techniques to discover their binding mechanism comprehensively. To predict the metal ion binding sites for TMPs on a large scale, we present a simple and effective two-stage prediction method TMP-MIBS, to identify the corresponding binding residues using TMP sequences. At present, there is no specific research on the metal ion binding prediction of TMPs. Thereby, we compared our model with the published tools which do not distinguish TMPs from water-soluble proteins. The results in the independent verification dataset show that TMP-MIBS has superior performance. This paper explores the interaction mechanism between TMPs and metal ions, which is helpful to understand the structure and function of TMPs and is of great significance to further construct transport mechanisms and identify potential drug targets.
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10
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Andrei A, Di Renzo MA, Öztürk Y, Meisner A, Daum N, Frank F, Rauch J, Daldal F, Andrade SLA, Koch HG. The CopA2-Type P 1B-Type ATPase CcoI Serves as Central Hub for cbb 3-Type Cytochrome Oxidase Biogenesis. Front Microbiol 2021; 12:712465. [PMID: 34589071 PMCID: PMC8475189 DOI: 10.3389/fmicb.2021.712465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Copper (Cu)-transporting P1B-type ATPases are ubiquitous metal transporters and crucial for maintaining Cu homeostasis in all domains of life. In bacteria, the P1B-type ATPase CopA is required for Cu-detoxification and exports excess Cu(I) in an ATP-dependent reaction from the cytosol into the periplasm. CopA is a member of the CopA1-type ATPase family and has been biochemically and structurally characterized in detail. In contrast, less is known about members of the CopA2-type ATPase family, which are predicted to transport Cu(I) into the periplasm for cuproprotein maturation. One example is CcoI, which is required for the maturation of cbb 3-type cytochrome oxidase (cbb 3-Cox) in different species. Here, we reconstituted purified CcoI of Rhodobacter capsulatus into liposomes and determined Cu transport using solid-supported membrane electrophysiology. The data demonstrate ATP-dependent Cu(I) translocation by CcoI, while no transport is observed in the presence of a non-hydrolysable ATP analog. CcoI contains two cytosolically exposed N-terminal metal binding sites (N-MBSs), which are both important, but not essential for Cu delivery to cbb 3-Cox. CcoI and cbb 3-Cox activity assays in the presence of different Cu concentrations suggest that the glutaredoxin-like N-MBS1 is primarily involved in regulating the ATPase activity of CcoI, while the CopZ-like N-MBS2 is involved in Cu(I) acquisition. The interaction of CcoI with periplasmic Cu chaperones was analyzed by genetically fusing CcoI to the chaperone SenC. The CcoI-SenC fusion protein was fully functional in vivo and sufficient to provide Cu for cbb 3-Cox maturation. In summary, our data demonstrate that CcoI provides the link between the cytosolic and periplasmic Cu chaperone networks during cbb 3-Cox assembly.
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Affiliation(s)
- Andreea Andrei
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Maria Agostina Di Renzo
- Institute for Biochemistry, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Alexandra Meisner
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Noel Daum
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Fabian Frank
- Institute for Biochemistry, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Juna Rauch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Susana L A Andrade
- Institute for Biochemistry, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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11
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Herbert FC, Abeyrathna SS, Abeyrathna NS, Wijesundara YH, Brohlin OR, Carraro F, Amenitsch H, Falcaro P, Luzuriaga MA, Durand-Silva A, Diwakara SD, Smaldone RA, Meloni G, Gassensmith JJ. Stabilization of supramolecular membrane protein-lipid bilayer assemblies through immobilization in a crystalline exoskeleton. Nat Commun 2021; 12:2202. [PMID: 33850135 PMCID: PMC8044103 DOI: 10.1038/s41467-021-22285-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 11/09/2022] Open
Abstract
Artificial native-like lipid bilayer systems constructed from phospholipids assembling into unilamellar liposomes allow the reconstitution of detergent-solubilized transmembrane proteins into supramolecular lipid-protein assemblies called proteoliposomes, which mimic cellular membranes. Stabilization of these complexes remains challenging because of their chemical composition, the hydrophobicity and structural instability of membrane proteins, and the lability of interactions between protein, detergent, and lipids within micelles and lipid bilayers. In this work we demonstrate that metastable lipid, protein-detergent, and protein-lipid supramolecular complexes can be successfully generated and immobilized within zeolitic-imidazole framework (ZIF) to enhance their stability against chemical and physical stressors. Upon immobilization in ZIF bio-composites, blank liposomes, and model transmembrane metal transporters in detergent micelles or embedded in proteoliposomes resist elevated temperatures, exposure to chemical denaturants, aging, and mechanical stresses. Extensive morphological and functional characterization of the assemblies upon exfoliation reveal that all these complexes encapsulated within the framework maintain their native morphology, structure, and activity, which is otherwise lost rapidly without immobilization.
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Affiliation(s)
- Fabian C Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Sameera S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Nisansala S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Yalini H Wijesundara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Olivia R Brohlin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Francesco Carraro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Graz, Austria
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Graz, Austria
| | - Paolo Falcaro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Graz, Austria
| | - Michael A Luzuriaga
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Alejandra Durand-Silva
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Shashini D Diwakara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Ronald A Smaldone
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA.
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA.
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, USA.
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12
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Dulay H, Tabares M, Kashefi K, Reguera G. Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. Front Microbiol 2020; 11:600463. [PMID: 33324382 PMCID: PMC7726332 DOI: 10.3389/fmicb.2020.600463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.
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Affiliation(s)
- Hunter Dulay
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Marcela Tabares
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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13
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Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch HG. Cu Homeostasis in Bacteria: The Ins and Outs. MEMBRANES 2020; 10:E242. [PMID: 32962054 PMCID: PMC7558416 DOI: 10.3390/membranes10090242] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.
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Affiliation(s)
- Andreea Andrei
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
- Fakultät für Biologie, Albert-Ludwigs Universität Freiburg; Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yavuz Öztürk
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Juna Rauch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | - Dorian Marckmann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
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14
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Environmetallomics: Systematically investigating metals in environmentally relevant media. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115875] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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15
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Abstract
Iron is essential for nearly every organism, and mismanagement of its intracellular concentrations (either deficiency or excess) contributes to diminished virulence in human pathogens, necessitating intricate metalloregulatory mechanisms. To date, although several metal-responsive riboswitches have been identified in bacteria, none has been shown to respond to FeII. The czcD riboswitch, present in numerous human gut microbiota and pathogens, was recently shown to respond to NiII and CoII but thought not to respond to FeII, on the basis of aerobic, in vitro assays; its function in vivo is not well understood. We constructed a fluorescent sensor using this riboswitch fused to the RNA aptamer, Spinach2. When assayed anaerobically, the resulting sensor responds in vitro to FeII, as well as to MnII, CoII, NiII, and ZnII, but only in the cases of FeII and MnII do the apparent Kd values (0.4 and 11 μM, respectively) fall within the range of labile metal concentrations maintained by known metalloregulators. We also show that the sensor-which is, to the best of our knowledge, the first reversible genetically encoded fluorescent sensor for FeII-responds to iron in Escherichia coli cells. Finally, we demonstrate that the putative metal exporters directly downstream of two czcD riboswitches efficiently rescue iron toxicity in a heterologous expression system. Together, our results indicate that iron merits consideration as a plausible physiological ligand for czcD riboswitches, although a response to general metal stress cannot be ruled out at present.
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Affiliation(s)
- Jiansong Xu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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16
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Kumar P, Dalal V, Sharma N, Kokane S, Ghosh DK, Kumar P, Sharma AK. Characterization of the heavy metal binding properties of periplasmic metal uptake protein CLas-ZnuA2. Metallomics 2020; 12:280-289. [DOI: 10.1039/c9mt00200f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Candidatus Liberibacter asiaticus (CLas), a phloem-limited unculturable Gram-negative bacterium, causes citrus greening disease.
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Affiliation(s)
- Pranav Kumar
- Department of Biotechnology
- Indian Institute of Technology Roorkee
- Roorkee-247 667
- India
| | - Vikram Dalal
- Department of Biotechnology
- Indian Institute of Technology Roorkee
- Roorkee-247 667
- India
| | - Nidhi Sharma
- Department of Biotechnology
- Indian Institute of Technology Roorkee
- Roorkee-247 667
- India
| | - Sunil Kokane
- 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
| | - 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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17
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Lewis BE, Mason Z, Rodrigues AV, Nuth M, Dizin E, Cowan JA, Stemmler TL. Unique roles of iron and zinc binding to the yeast Fe-S cluster scaffold assembly protein "Isu1". Metallomics 2019; 11:1820-1835. [PMID: 31532427 DOI: 10.1039/c9mt00172g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mitochondrial Fe-S cluster biosynthesis is accomplished within yeast utilizing the biophysical attributes of the "Isu1" scaffold assembly protein. As a member of a highly homologous protein family, Isu1 has sequence conservation between orthologs and a conserved ability to assemble [2Fe-2S] clusters. Regardless of species, scaffold orthologs have been shown to exist in both "disordered" and "structured" conformations, a structural architecture that is directly related to conformations utilized during Fe-S cluster assembly. During assembly, the scaffold helps direct the delivery and utilization of Fe(ii) and persulfide substrates to produce [2Fe-2S] clusters, however Zn(ii) binding alters the activity of the scaffold while at the same time stabilizes the protein in its structured state. Additional studies confirm Zn binds to the scaffold's Cys rich active site, and has an impact on the protein's ability to make Fe-S clusters. Understanding the interplay between Fe(ii) and Zn(ii) binding to Isu1 in vitro may help clarify metal loading events that occur during Fe-S cluster assembly in vivo. Here we determine the metal : protein stoichiometry for Isu1 Zn and Fe binding to be 1 : 1 and 2 : 1, respectively. As expected, while Zn binding shifts the Isu1 to its structured state, folding is not influenced by Fe(ii) binding. X-ray absorption spectroscopy (XAS) confirms Zn(ii) binds to the scaffold's cysteine rich active site but Fe(ii) binds at a location distinct from the active site. XAS results show Isu1 binding initially of either Fe(ii) or Zn(ii) does not significantly perturb the metal site structure of alternate metal. XAS confirmed that four scaffold orthologs bind iron as high-spin Fe(ii) at a site composed of ca. 6 oxygen and nitrogen nearest neighbor ligands. Finally, in our report Zn binding dramatically reduces the Fe-S cluster assembly activity of Isu1 even in the presence of frataxin. Given the Fe-binding activity we report for Isu1 and its orthologs here, a possible mechanism involving Fe(ii) transport to the scaffold's active site during cluster assembly has been considered.
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Affiliation(s)
- Brianne E Lewis
- Department of Pharmaceutical Science, Wayne State University, Detroit, MI 48201, USA.
| | - Zachary Mason
- Department of Pharmaceutical Science, Wayne State University, Detroit, MI 48201, USA.
| | - Andria V Rodrigues
- Department of Pharmaceutical Science, Wayne State University, Detroit, MI 48201, USA.
| | - Manunya Nuth
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Dizin
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - J A Cowan
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Science, Wayne State University, Detroit, MI 48201, USA.
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18
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Antonucci I, Gallo G, Limauro D, Contursi P, Ribeiro AL, Blesa A, Berenguer J, Bartolucci S, Fiorentino G. Characterization of a promiscuous cadmium and arsenic resistance mechanism in Thermus thermophilus HB27 and potential application of a novel bioreporter system. Microb Cell Fact 2018; 17:78. [PMID: 29776370 PMCID: PMC5960188 DOI: 10.1186/s12934-018-0918-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/03/2018] [Indexed: 11/21/2022] Open
Abstract
Background The characterization of the molecular determinants of metal resistance has potential biotechnological application in biosensing and bioremediation. In this context, the bacterium Thermus thermophilus HB27 is a metal tolerant thermophile containing a set of genes involved in arsenic resistance which, differently from other microbes, are not organized into a single operon. They encode the proteins: arsenate reductase, TtArsC, arsenic efflux membrane transporter, TtArsX, and transcriptional repressor, TtSmtB. Results In this work we show that the arsenic efflux protein TtArsX and the arsenic responsive transcriptional repressor TtSmtB are required to provide resistance to cadmium. We analyzed the sensitivity to Cd(II) of mutants lacking TtArsX, finding that they are more sensitive to this metal than the wild type strain. In addition, using promoter probe reporter plasmids, we show that the transcription of TtarsX is also stimulated by the presence of Cd(II) in a TtSmtB-dependent way. Actually, a regulatory circuit composed of TtSmtB and a reporter gene expressed from the TtarsX promoter responds to variation in Cd(II), As(III) and As(V) concentrations. Conclusions Our results demonstrate that the system composed by TtSmtB and TtArsX is responsible for both the arsenic and cadmium resistance in T. thermophilus. The data also support the use of T. thermophilus as a suitable chassis for the design and development of As-Cd biosensors. Electronic supplementary material The online version of this article (10.1186/s12934-018-0918-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Immacolata Antonucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Giovanni Gallo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Danila Limauro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Patrizia Contursi
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Ana Luisa Ribeiro
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Alba Blesa
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy.
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19
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Cu +-specific CopB transporter: Revising P 1B-type ATPase classification. Proc Natl Acad Sci U S A 2018; 115:2108-2113. [PMID: 29440418 DOI: 10.1073/pnas.1721783115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The copper-transporting P1B-ATPases, which play a key role in cellular copper homeostasis, have been divided traditionally into two subfamilies, the P1B-1-ATPases or CopAs and the P1B-3-ATPases or CopBs. CopAs selectively export Cu+ whereas previous studies and bioinformatic analyses have suggested that CopBs are specific for Cu2+ export. Biochemical and spectroscopic characterization of Sphaerobacter thermophilus CopB (StCopB) show that, while it does bind Cu2+, the binding site is not the prototypical P1B-ATPase transmembrane site and does not involve sulfur coordination as proposed previously. Most important, StCopB exhibits metal-stimulated ATPase activity in response to Cu+, but not Cu2+, indicating that it is actually a Cu+ transporter. X-ray absorption spectroscopic studies indicate that Cu+ is coordinated by four sulfur ligands, likely derived from conserved cysteine and methionine residues. The histidine-rich N-terminal region of StCopB is required for maximal activity, but is inhibitory in the presence of divalent metal ions. Finally, reconsideration of the P1B-ATPase classification scheme suggests that the P1B-1- and P1B-3-ATPase subfamilies both comprise Cu+ transporters. These results are completely consistent with the known presence of only Cu+ within the reducing environment of the cytoplasm, which should eliminate the need for a Cu2+ P1B-ATPase.
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20
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Bozkurt E, Perez MAS, Hovius R, Browning NJ, Rothlisberger U. Genetic Algorithm Based Design and Experimental Characterization of a Highly Thermostable Metalloprotein. J Am Chem Soc 2018; 140:4517-4521. [DOI: 10.1021/jacs.7b10660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Esra Bozkurt
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marta A. S. Perez
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ruud Hovius
- Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicholas J. Browning
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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21
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Expression and purification of functionally active ferrous iron transporter FeoB from Klebsiella pneumoniae. Protein Expr Purif 2017; 142:1-7. [PMID: 28941825 DOI: 10.1016/j.pep.2017.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/13/2017] [Accepted: 09/17/2017] [Indexed: 12/26/2022]
Abstract
The acquisition of ferrous iron (Fe2+) is an important virulence factor utilized by several hospital-acquired (nosocomial) pathogens such as Klebsiella pneumoniae to establish infection within human hosts. Virtually all bacteria use the ferrous iron transport system (Feo) to acquire ferrous iron from their environments, which are often biological niches that stabilize Fe2+ relative to Fe3+. However, the details of this process remain poorly understood, likely owing to the few expression and purification systems capable of supplying sufficient quantities of the chief component of the Feo system, the integral membrane GTPase FeoB. This bottleneck has undoubtedly hampered efforts to understand this system in order to target it for therapeutic intervention. In this study, we describe the expression, solubilization, and purification of the Fe2+ transporter from K. pneumoniae, KpFeoB. We show that this protein may be heterologously overexpressed in Escherichia coli as the host organism. After testing several different commercially-available detergents, we have developed a solubilization and purification protocol that produces milligram quantities of KpFeoB with sufficient purity for enzymatic and biophysical analyses. Importantly, we demonstrate that KpFeoB displays robust GTP hydrolysis activity (kcatGTP of ∼10-1 s-1) in the absence of any additional stimulatory factors. Our findings suggest that K. pneumoniae may be capable of using its Feo system to drive Fe2+ import in an active manner.
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22
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Smith AT, Ross MO, Hoffman BM, Rosenzweig AC. Metal Selectivity of a Cd-, Co-, and Zn-Transporting P 1B-type ATPase. Biochemistry 2016; 56:85-95. [PMID: 28001366 DOI: 10.1021/acs.biochem.6b01022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The P1B-ATPases, a family of transmembrane metal transporters important for transition metal homeostasis in all organisms, are subdivided into classes based on sequence conservation and metal specificity. The multifunctional P1B-4-ATPase CzcP is part of the cobalt, zinc, and cadmium resistance system from the metal-tolerant, model organism Cupriavidus metallidurans. Previous work revealed the presence of an unusual soluble metal-binding domain (MBD) at the CzcP N-terminus, but the nature, extent, and selectivity of the transmembrane metal-binding site (MBS) of CzcP have not been resolved. Using homology modeling, we show that four wholly conserved amino acids from the transmembrane (TM) domain (Met254, Ser474, Cys476, and His807) are logical candidates for the TM MBS, which may communicate with the MBD via interactions with the first TM helix. Metal-binding analyses indicate that wild-type (WT) CzcP has three MBSs, and data on N-terminally truncated (ΔMBD) CzcP suggest the presence of a single TM MBS. Electronic absorption and electron paramagnetic resonance spectroscopic analyses of ΔMBD CzcP and variant proteins thereof provide insight into the details of Co2+ coordination by the TM MBS. These spectroscopic data, combined with in vitro functional studies of WT and variant CzcP proteins, show that the side chains of Met254, Cys476, and His807 contribute to Cd2+, Co2+, and Zn2+ binding and transport, whereas the side chain of Ser474 appears to play a minimal role. By comparison to other P1B-4-ATPases, we suggest that an evolutionarily adapted flexibility in the TM region likely afforded CzcP the ability to transport Cd2+ and Zn2+ in addition to Co2+.
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Affiliation(s)
- Aaron T Smith
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Matthew O Ross
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Brian M Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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23
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Novel and efficient screening of PQQ high-yielding strains and subsequent cultivation optimization. Appl Microbiol Biotechnol 2016; 100:10321-10330. [PMID: 27464830 DOI: 10.1007/s00253-016-7739-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 10/21/2022]
Abstract
A novel and efficient screening method for pyrroloquinoline quinone (PQQ) high-yielding methylotrophic strains was developed by using glucose dehydrogenase apoenzyme (GDHA) which depended on PQQ as the cofactor. Using this high-throughput method, PQQ high-yielding strains were rapidly screened out from thousands of methylotrophic colonies at a time. The comprehensive phylogenetic analysis revealed that the highest PQQ-producing strain zju323 (CCTCC M 2016079) could be assigned to a novel species in the genus Methylobacillus of the Betaproteobacteria. After systematic optimization of different medium components and cultivation conditions, about 33.4 mg/L of PQQ was obtained after 48 h of cultivation with Methylobacillus sp. zju323 at the shake flask scale. Further cultivations of Methylobacillus sp. zju323 were carried out to investigate the biosynthesis of PQQ in 10-L bench-top fermenters. In the batch operation, the PQQ accumulation reached 78 mg/L in the broth after 53 h of cultivation. By adopting methanol feeding strategy, the highest PQQ concentration was improved up to 162.2 mg/L after 75 h of cultivation. This work developed a high-throughput strategy of screening PQQ-producing strains from soil samples and also demonstrated one potential bioprocess for large-scale PQQ production with the isolated PQQ strain.
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24
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Patel SJ, Lewis BE, Long JE, Nambi S, Sassetti CM, Stemmler TL, Argüello JM. Fine-tuning of Substrate Affinity Leads to Alternative Roles of Mycobacterium tuberculosis Fe2+-ATPases. J Biol Chem 2016; 291:11529-39. [PMID: 27022029 DOI: 10.1074/jbc.m116.718239] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 11/06/2022] Open
Abstract
Little is known about iron efflux transporters within bacterial systems. Recently, the participation of Bacillus subtilis PfeT, a P1B4-ATPase, in cytoplasmic Fe(2+) efflux has been proposed. We report here the distinct roles of mycobacterial P1B4-ATPases in the homeostasis of Co(2+) and Fe(2+) Mutation of Mycobacterium smegmatis ctpJ affects the homeostasis of both ions. Alternatively, an M. tuberculosis ctpJ mutant is more sensitive to Co(2+) than Fe(2+), whereas mutation of the homologous M. tuberculosis ctpD leads to Fe(2+) sensitivity but no alterations in Co(2+) homeostasis. In vitro, the three enzymes are activated by both Fe(2+) and Co(2+) and bind 1 eq of either ion at their transport site. However, equilibrium binding affinities and activity kinetics show that M. tuberculosis CtpD has higher affinity for Fe(2+) and twice the Fe(2+)-stimulated activity than the CtpJs. These parameters are paralleled by a lower activation and affinity for Co(2+) Analysis of Fe(2+) and Co(2+) binding to CtpD by x-ray absorption spectroscopy shows that both ions are five- to six-coordinate, constrained within oxygen/nitrogen environments with similar geometries. Mutagenesis studies suggest the involvement of invariant Ser, His, and Glu residues in metal coordination. Interestingly, replacement of the conserved Cys at the metal binding pocket leads to a large reduction in Fe(2+) but not Co(2+) binding affinity. We propose that CtpJ ATPases participate in the control of steady state Fe(2+) levels. CtpD, required for M. tuberculosis virulence, is a high affinity Fe(2+) transporter involved in the rapid response to iron dyshomeostasis generated upon redox stress.
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Affiliation(s)
- Sarju J Patel
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Brianne E Lewis
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Jarukit E Long
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, and
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, and
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, and Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - José M Argüello
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609,
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Zhang J, Zhang M, Shohag MJI, Tian S, Song H, Feng Y, Yang X. Enhanced expression of SaHMA3 plays critical roles in Cd hyperaccumulation and hypertolerance in Cd hyperaccumulator Sedum alfredii Hance. PLANTA 2016; 243:577-89. [PMID: 26547194 DOI: 10.1007/s00425-015-2429-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/28/2015] [Indexed: 05/08/2023]
Abstract
The enhanced expression of a P 1B -type ATPase gene ( SaHMA3 ) is essential for Cd hyperaccumulation and hypertolerance in Sedum alfredii Hance. A functional understanding of the mechanism through which hyperaccumulator plants accumulate and tolerate extremely toxic metals is a prerequisite for the development of novel strategies for improving phytoremediation using engineered plants or natural hyperaccumulators as well as biofortification and food crop safety. Most hyperaccumulator species, however, are small and slow-growing, and their potential for large-scale decontamination of polluted soils is limited. Sedum alfredii Hance, the only one metal hyperaccumulator from the Crassulaceae family, is an ideal candidate for gaining a functional understanding of the intra-family hyperaccumulation mechanisms as well as their potential applications. In the present study, we isolated and functionally characterized a P1B-type ATPase gene (SaHMA3) from S. alfredii Hance. SaHMA3 alleles from a hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) were constitutively expressed in both shoot and root and encoded tonoplast-localized proteins, but showed differences in transport substrate specificity and expression level. SaHMA3 h from the HE plant was a Cd transporter. In contrast, SaHMA3n from NHE plants was able to transport both Zn and Cd. SaHMA3 showed a significantly higher constitutive expression level in HE plants than in NHE plants. Furthermore, the expression level of SaHMA3 in the shoots of HE plants was considerably higher than in the roots. Overexpression of SaHMA3h in tobacco plants significantly enhanced Cd tolerance and accumulation and greatly increased the root sequestration of Cd. In summary, our data suggested that SaHMA3 plays critical roles in Cd hyperaccumulation and hypertolerance in Cd hyperaccumulator S. alfredii Hance.
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Affiliation(s)
- Jie Zhang
- MOE Key Laboratory of Environment Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Min Zhang
- MOE Key Laboratory of Environment Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Md Jahidul Islam Shohag
- MOE Key Laboratory of Environment Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shengke Tian
- MOE Key Laboratory of Environment Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Haiyan Song
- MOE Key Laboratory of Environment Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ying Feng
- MOE Key Laboratory of Environment Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoe Yang
- MOE Key Laboratory of Environment Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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Fu Y, Bruce KE, Wu H, Giedroc DP. The S2 Cu(i) site in CupA from Streptococcus pneumoniae is required for cellular copper resistance. Metallomics 2016; 8:61-70. [PMID: 26346139 PMCID: PMC4720546 DOI: 10.1039/c5mt00221d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pathogenic bacteria have evolved copper homeostasis and resistance systems for fighting copper toxicity imposed by the human immune system. Streptococcus pneumoniae is a respiratory pathogen that encodes an obligatorily membrane-anchored Cu(i) binding protein, CupA, and a P1B-type ATPase efflux transporter, CopA. The soluble, cytoplasmic domain of CupA (sCupA) contains a binuclear Cu(i) cluster consisting of S1 and S2 Cu(i) ions. The NMR solution structure of apo-sCupA reveals the same cupredoxin fold of Cu2-sCupA, except that the Cu(i) binding loop (residues 112-116, harboring S2 Cu ligands M113 and M115) is highly dynamic as documented by both backbone and side chain methionine methyl order parameters. In contrast to the more solvent exposed, lower affinity S2 Cu site, the high affinity S1 Cu-coordinating cysteines (C74, C111) are pre-organized in the apo-sCupA structure. Biological experiments reveal that the S1 site is largely dispensable for cellular Cu resistance and may be involved in buffering low cytoplasmic Cu(i). In contrast, the S2 site is essential for Cu resistance. Expression of a chimeric CopZ chaperone fused to the CupA transmembrane helix does not protect S. pneumoniae from copper toxicity and substitution of a predicted cytoplasm-facing Cu(i) entry metal-binding site (MBS) on CopA also gives rise to a Cu-sensitivity phenotype. These findings suggest that CupA and CopA may interact and filling of the CupA S2 site with Cu(i) results in stimulation of cellular copper efflux by CopA.
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Affiliation(s)
- Yue Fu
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA. and Graduate Program in Biochemistry, Indiana University, Bloomington, Indiana 47405-7102, USA
| | - Kevin E Bruce
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Hongwei Wu
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA.
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA.
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