1
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Burgardt NI, Melian NA, González Flecha FL. Copper resistance in the cold: Genome analysis and characterisation of a P IB-1 ATPase in Bizionia argentinensis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13278. [PMID: 38943264 PMCID: PMC11213822 DOI: 10.1111/1758-2229.13278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/19/2024] [Indexed: 07/01/2024]
Abstract
Copper homeostasis is a fundamental process in organisms, characterised by unique pathways that have evolved to meet specific needs while preserving core resistance mechanisms. While these systems are well-documented in model bacteria, information on copper resistance in species adapted to cold environments is scarce. This study investigates the potential genes related to copper homeostasis in the genome of Bizionia argentinensis (JUB59-T), a psychrotolerant bacterium isolated from Antarctic seawater. We identified several genes encoding proteins analogous to those crucial for copper homeostasis, including three sequences of copper-transport P1B-type ATPases. One of these, referred to as BaCopA1, was chosen for cloning and expression in Saccharomyces cerevisiae. BaCopA1 was successfully integrated into yeast membranes and subsequently extracted with detergent. The purified BaCopA1 demonstrated the ability to catalyse ATP hydrolysis at low temperatures. Structural models of various BaCopA1 conformations were generated and compared with mesophilic and thermophilic homologous structures. The significant conservation of critical residues and structural similarity among these proteins suggest a shared reaction mechanism for copper transport. This study is the first to report a psychrotolerant P1B-ATPase that has been expressed and purified in a functional form.
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Affiliation(s)
- Noelia I. Burgardt
- Laboratorio de Biofísica Molecular, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica BiológicasUniversidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
- Present address:
Departamento de Ciencia y TecnologíaUniversidad Nacional de QuilmesBernalArgentina
| | - Noelia A. Melian
- Laboratorio de Biofísica Molecular, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica BiológicasUniversidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
| | - F. Luis González Flecha
- Laboratorio de Biofísica Molecular, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica BiológicasUniversidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
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2
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Gaschignard G, Millet M, Bruley A, Benzerara K, Dezi M, Skouri-Panet F, Duprat E, Callebaut I. AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily. Proteins 2024; 92:776-794. [PMID: 38258321 DOI: 10.1002/prot.26668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024]
Abstract
Three-dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) the use of AlphaFold2 3D structure models. Domains of this family were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most of them share conserved basic amino acids (hence their name CoBaHMA for Conserved Basic residues HMA), forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
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Affiliation(s)
- Geoffroy Gaschignard
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Manuela Dezi
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Feriel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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3
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Dmitriev OY, Patry J. Structure and mechanism of the human copper transporting ATPases: Fitting the pieces into a moving puzzle. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184306. [PMID: 38408697 DOI: 10.1016/j.bbamem.2024.184306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
Human copper transporters ATP7B and ATP7A deliver copper to biosynthetic pathways and maintain copper homeostasis in the cell. These enzymes combine several challenges for structural biology because they are large low abundance membrane proteins with many highly mobile domains and long disordered loops. No method has yet succeeded in solving the structure of the complete fully functional protein. Still, X-ray crystallography, Cryo-EM and NMR helped to piece together a structure based model of the enzyme activity and regulation by copper. We review the structures of ATP7B and ATP7A with an emphasis on the mechanistic insights into the unique aspects of the transport function and regulation of the human copper ATPases that have emerged from more than twenty years of research.
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Affiliation(s)
- Oleg Y Dmitriev
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Jaala Patry
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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4
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Bergmann L, Balzer Le S, Hageskal G, Preuss L, Han Y, Astafyeva Y, Loevenich S, Emmann S, Perez-Garcia P, Indenbirken D, Katzowitsch E, Thümmler F, Alawi M, Wentzel A, Streit WR, Krohn I. New dienelactone hydrolase from microalgae bacterial community-Antibiofilm activity against fish pathogens and potential applications for aquaculture. Sci Rep 2024; 14:377. [PMID: 38172513 PMCID: PMC10764354 DOI: 10.1038/s41598-023-50734-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/24/2023] [Indexed: 01/05/2024] Open
Abstract
Biofilms are resistant to many traditional antibiotics, which has led to search for new antimicrobials from different and unique sources. To harness the potential of aquatic microbial resources, we analyzed the meta-omics datasets of microalgae-bacteria communities and mined them for potential antimicrobial and quorum quenching enzymes. One of the most interesting candidates (Dlh3), a dienelactone hydrolase, is a α/β-protein with predicted eight α-helices and eight β-sheets. When it was applied to one of the major fish pathogens, Edwardsiella anguillarum, the biofilm development was reproducibly inhibited by up to 54.5%. The transcriptome dataset in presence of Dlh3 showed an upregulation in functions related to self-defense like active genes for export mechanisms and transport systems. The most interesting point regarding the biotechnological potential for aquaculture applications of Dlh3 are clear evidence of biofilm inhibition and that health and division of a relevant fish cell model (CHSE-214) was not impaired by the enzyme.
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Affiliation(s)
- Lutgardis Bergmann
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Simone Balzer Le
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Gunhild Hageskal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Lena Preuss
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yuchen Han
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yekaterina Astafyeva
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Simon Loevenich
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Sarah Emmann
- Molecular Microbiology, Institute for General Microbiology, Kiel University, Kiel, Germany
| | - Pablo Perez-Garcia
- Molecular Microbiology, Institute for General Microbiology, Kiel University, Kiel, Germany
| | | | - Elena Katzowitsch
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Fritz Thümmler
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Ines Krohn
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany.
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5
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Li W, Wang L, Li X, Zheng X, Cohen MF, Liu YX. Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1182-1194. [PMID: 36089219 PMCID: PMC11082258 DOI: 10.1016/j.gpb.2022.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.
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Affiliation(s)
- Wenjun Li
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Likun Wang
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaofang Li
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China.
| | - Xin Zheng
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Michael F Cohen
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
| | - Yong-Xin Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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6
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Fodor I, Yañez-Guerra LA, Kiss B, Büki G, Pirger Z. Copper-transporting ATPases throughout the animal evolution - From clinics to basal neuron-less animals. Gene 2023; 885:147720. [PMID: 37597707 DOI: 10.1016/j.gene.2023.147720] [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: 05/17/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Copper-transporting ATPases are a group of heavy metal-transporting proteins and which can be found in all living organisms. In animals, they are generally referred to as ATP7 proteins and are involved in many different physiological processes including the maintaining of copper homeostasis and the supply of copper to cuproenzymes. A single ATP7 gene is present in non-chordate animals while it is divided into ATP7A and ATP7B in chordates. In humans, dysfunction of ATP7 proteins can lead to severe genetic disorders, such as, Menkes disease and Wilson's disease, which are characterized by abnormal copper transport and accumulation, causing significant health complications. Therefore, there is a substantial amount of research on ATP7 genes and ATP7 proteins in humans and mice to understand pathophysiological conditions and find potential therapeutic interventions. Copper-transporting ATPases have also been investigated in some non-mammalian vertebrates, protostomes, single-cellular eukaryotes, prokaryotes, and archaea to gain useful evolutionary insights. However, ATP7 function in many animals has been somewhat neglected, particularly in non-bilaterians. Previous reviews on this topic only broadly summarized the available information on the function and evolution of ATP7 genes and ATP7 proteins and included only the classic vertebrate and invertebrate models. Given this, and the fact that a considerable amount of new information on this topic has been published in recent years, the present study was undertaken to provide an up-to-date, comprehensive summary of ATP7s/ATP7s and give new insights into their evolutionary relationships. Additionally, this work provides a framework for studying these genes and proteins in non-bilaterians. As early branching animals, they are important to understand the evolution of function of these proteins and their important role in copper homeostasis and neurotransmission.
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Affiliation(s)
- István Fodor
- Ecophysiological and Environmental Toxicological Research Group, Balaton Limnological Research Institute, H-8237 Tihany, Hungary.
| | | | - Bence Kiss
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Gergely Büki
- Department of Medical Genetics, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Zsolt Pirger
- Ecophysiological and Environmental Toxicological Research Group, Balaton Limnological Research Institute, H-8237 Tihany, Hungary
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7
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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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8
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Yang GM, Xu L, Wang RM, Tao X, Zheng ZW, Chang S, Ma D, Zhao C, Dong Y, Wu S, Guo J, Wu ZY. Structures of the human Wilson disease copper transporter ATP7B. Cell Rep 2023; 42:112417. [PMID: 37074913 DOI: 10.1016/j.celrep.2023.112417] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/22/2023] [Accepted: 04/05/2023] [Indexed: 04/20/2023] Open
Abstract
The P-type ATPase ATP7B exports cytosolic copper and plays an essential role in the regulation of cellular copper homeostasis. Mutants of ATP7B cause Wilson disease (WD), an autosomal recessive disorder of copper metabolism. Here, we present cryoelectron microscopy (cryo-EM) structures of human ATP7B in the E1 state in the apo, the putative copper-bound, and the putative cisplatin-bound forms. In ATP7B, the N-terminal sixth metal-binding domain (MBD6) binds at the cytosolic copper entry site of the transmembrane domain (TMD), facilitating the delivery of copper from the MBD6 to the TMD. The sulfur-containing residues in the TMD of ATP7B mark the copper transport pathway. By comparing structures of the E1 state human ATP7B and E2-Pi state frog ATP7B, we propose the ATP-driving copper transport model of ATP7B. These structures not only advance our understanding of the mechanisms of ATP7B-mediated copper export but can also guide the development of therapeutics for the treatment of WD.
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Affiliation(s)
- Guo-Min Yang
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Lingyi Xu
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Rou-Min Wang
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Xin Tao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zi-Wei Zheng
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Shenghai Chang
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Demin Ma
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Cheng Zhao
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yi Dong
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Shan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
| | - Jiangtao Guo
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Cardiology, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China.
| | - Zhi-Ying Wu
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China.
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9
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Kalavacherla T, Buschmann S, Schleker ESM, Michel H, Reinhart C. Purification and characterization of eukaryotic ATP-dependent transporters homologously expressed in Pichia pastoris for structural studies by cryo-electron microscopy. Protein Expr Purif 2023; 204:106230. [PMID: 36632890 DOI: 10.1016/j.pep.2023.106230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 01/01/2023] [Indexed: 01/09/2023]
Abstract
Membrane proteins play an essential role in all living organisms. Although there have been numerous efforts in the past to elucidate the structure and function of eukaryotic primary active transporters, knowledge about the majority of these membrane proteins is still minimal. This is often due to their low availability and complex handling. In this study, we homologously expressed three ATP-dependent transport proteins, STE6-2p, NEO1-p, and YPK9-p, in Pichia pastoris and subsequently optimized the solubilization and purification processes. Sequential use of different mild detergents and utilization of hydrophilic matrices in the purification procedure allowed us to obtain all three transporters monodisperse and in high purity, enabling initial structural analysis by cryo-electron microscopy. Using the respective substrates, we determined the specific activity of all target proteins using an ATPase assay. This study opens the door to further functional and structural studies of this pharmacologically important class of membrane proteins.
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Affiliation(s)
- Tejaswi Kalavacherla
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany
| | - Sabine Buschmann
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany
| | - E Sabine M Schleker
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany
| | - Christoph Reinhart
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany.
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10
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Dao TH, Iverson A, Neville SL, Johnson MDL, McDevitt CA, Rosch JW. The role of CopA in Streptococcus pyogenes copper homeostasis and virulence. J Inorg Biochem 2023; 240:112122. [PMID: 36639322 PMCID: PMC10161136 DOI: 10.1016/j.jinorgbio.2023.112122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
Maintenance of intracellular metal homeostasis during interaction with host niches is critical to the success of bacterial pathogens. To prevent infection, the mammalian innate immune response employs metal-withholding and metal-intoxication mechanisms to limit bacterial propagation. The first-row transition metal ion copper serves critical roles at the host-pathogen interface and has been associated with antimicrobial activity since antiquity. Despite lacking any known copper-utilizing proteins, streptococci have been reported to accumulate significant levels of copper. Here, we report that loss of CopA, a copper-specific exporter, confers increased sensitivity to copper in Streptococcus pyogenes strain HSC5, with prolonged exposure to physiological levels of copper resulting in reduced viability during stationary phase cultivation. This defect in stationary phase survival was rescued by supplementation with exogeneous amino acids, indicating the pathogen had altered nutritional requirements during exposure to copper stress. Furthermore, S. pyogenes HSC5 ΔcopA was substantially attenuated during murine soft-tissue infection, demonstrating the importance of copper efflux at the host-pathogen interface. Collectively, these data indicate that copper can severely reduce the viability of stationary phase S. pyogenes and that active efflux mechanisms are required to survive copper stress in vitro and during infection.
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Affiliation(s)
- Tina H Dao
- St. Jude Children's Research Hospital, Department of Infectious Diseases, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Amy Iverson
- St. Jude Children's Research Hospital, Department of Infectious Diseases, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Stephanie L Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Michael D L Johnson
- St. Jude Children's Research Hospital, Department of Infectious Diseases, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Immunobiology, BIO5 Institute, Valley Fever Center for Excellence, and Asthma and Airway Disease Research Center, University of Arizona College of Medicine - Tucson, Tucson, AZ 85724, USA
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Jason W Rosch
- St. Jude Children's Research Hospital, Department of Infectious Diseases, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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11
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Pang J, Chen S, Gan W, Tang G, Jie Y, Li Z, Chong Y, Chen Y, Gong J, Li X, Mei Y. A novel nomogram based on routine clinical indicators for screening for Wilson's disease. LIVER RESEARCH 2023. [DOI: 10.1016/j.livres.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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12
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Mutations in troABCD against Copper Overload in a copA Mutant of Streptococcus suis. Appl Environ Microbiol 2023; 89:e0184122. [PMID: 36475883 PMCID: PMC9888204 DOI: 10.1128/aem.01841-22] [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: 12/12/2022] Open
Abstract
Streptococcus suis is a major swine pathogen that is increasingly recognized as a porcine zoonotic pathogen that threatens the health of both pigs and humans. Metal homeostasis plays a critical role during the process of bacterial infection. In this study, RNA sequencing was used to identify potential candidate genes involved in the maintenance of intracellular copper homeostasis. CopA was identified as the primary copper exporter in S. suis. The copA deletion mutant strain was found to be more sensitive to copper and accumulated more intracellular copper than the wild-type (WT) parent strain. In addition, adding manganese increased the ability of S. suis to resist copper, and the manganese transporter, TroABCD, was involved in tolerance to copper. The copA deletion mutant strain accumulated less copper when supplemented with manganese. Furthermore, when cultured with copper, the double deletion mutant (ΔcopAΔtroA) exhibited improved growth compared to the copA deletion mutant strain. In addition, the double deletion mutant (ΔcopAΔtroA) accumulated less copper than the copA deletion mutant strain. These data were consistent with a model wherein defective TroABCD resulted in decreased cellular copper accumulation and protected the strain against copper poisoning. IMPORTANCE Metal homeostasis plays a critical role during the process of bacterial infection. We identified three important potential candidate genes involved in maintenance of intracellular copper homeostasis. CopA was demonstrated to be the main copper exporter in Streptococcus suis, and manganese increased the tolerance of S. suis to copper. The double deletion mutant (ΔcopAΔtroA) improved growth ability over the copA deletion mutant strain in the presence of high concentrations of copper and accumulated less copper. These findings are consistent with a model wherein defective TroABCD resulted in decreased cellular accumulation of copper and protected the strain against copper poisoning.
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13
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Hu A, Zhang JW, Yang LY, Qiao PP, Lu D, Yu YF. Curcumin-loaded graphene oxide quantum dots enhance otoprotective effects via blocking cuproptosis. Front Bioeng Biotechnol 2023; 11:1183197. [PMID: 37152642 PMCID: PMC10154464 DOI: 10.3389/fbioe.2023.1183197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023] Open
Abstract
Background: Cisplatin (CIS) is widely used to treat various cancers but can cause ototoxicity and sensory hair cell loss in the inner ear. Copper induces an excessive production of reactive oxygen species (ROS) in hair cells, leading to the development of various antioxidants. Methods and results: This study aimed to evaluate the potential antioxidant properties of curcumin (CUR) in the inner ear organ of corti-1 cells (OC1) and animal models (zebrafish and guinea pigs). Graphene oxide quantum dots (GOQDs) enabled CUR to penetrate the round window membrane (RWM) and maintain the concentration in the perilymph after inner ear administration. The results showed that CUR/GOQDs had favorable biocompatibility and strongly affected ROS generation induced by CIS in OC1 cells. DCFHDA Green staining demonstrated that CUR/GOQDs successfully reversed the decrease in mitochondrial membrane potential induced by CIS in vitro and rescued cells from early cuproptosis, which was confirmed by FDX1 staining. Additionally, the experiment found that CUR decreased the expression of cuproptosis proteins (FDX1, LIAS, and LIPT1) and increased the expression of the Bcl-2 protein. Conclusion: The results demonstrate that CUR/GOQDs is a promising therapeutic agent that can prevent CIS-induced ototoxicity by blocking the cuproptosis signal pathway.
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Affiliation(s)
- An Hu
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Otolaryngology-Head and Neck Surgery, Gongli Hospital, Second Military Medical University, Shanghai, China
| | - Jian-Wei Zhang
- Department of Otolaryngology–Head and Neck Surgery, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Li-Yun Yang
- Department of Otolaryngology-Head and Neck Surgery, Gongli Hospital, Second Military Medical University, Shanghai, China
| | - Pei-Pei Qiao
- Department of Otolaryngology-Head and Neck Surgery, Gongli Hospital, Second Military Medical University, Shanghai, China
| | - Dan Lu
- Department of Otolaryngology-Head and Neck Surgery, Gongli Hospital, Second Military Medical University, Shanghai, China
| | - Ya-Feng Yu
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Ya-Feng Yu,
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14
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Tian P, Feng YX, Li CZ, Zhang P, Yu XZ. Transcriptional analysis of heavy metal P 1B-ATPases (HMAs) elucidates competitive interaction in metal transport between cadmium and mineral elements in rice plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:287-297. [PMID: 35900629 DOI: 10.1007/s11356-022-22243-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) pollution has become a major threat to crop production and quality globally. The heavy metal P1B-ATPases (HMAs) play a crucial role in metal transport in plants. In the present study, we investigated the interaction in metal transport by HMAs between Cd and mineral elements in rice plants. Rice seedlings were treated with cadmium nitrate either in the nutrient solution ("Cd+M") or in the ultrapure water ("Cd-M"). Result showed that phytotoxicity of Cd to rice seedlings was evident from both Cd treatments, judged by relative growth rate (RGR), where more severe repression (p < 0.05) of RGR was observed in the "Cd-M" treatments than the "Cd+M" treatments. More Cd (p < 0.05) was accumulated in rice tissues from the "Cd-M" treatments than the "Cd+M" treatments, while there is a significant difference (p < 0.05) in distribution and translocation of mineral elements in rice tissues between the "Cd+M" and the "Cd-M" treatments. RT-qPCR analysis displayed that the expression patterns of HMAs related genes were quite different between "Cd+M" and "Cd-M" treatments, suggesting their different regulatory effects during the transport of Cd and mineral elements within rice plants. The competition in metal transport by HMAs mainly occurs between Cd and micro-elements of Zn and Cu in rice tissues during Cd exposure. Overall, this study provides new evidence to clarify the different translocation mechanisms of HMAs in metal transport between Cd and mineral elements in rice seedlings during Cd exposure.
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Affiliation(s)
- Peng Tian
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Yu-Xi Feng
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Cheng-Zhi Li
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Ping Zhang
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Xiao-Zhang Yu
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China.
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15
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Orädd F, Steffen JH, Gourdon P, Andersson M. Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B. PLoS Comput Biol 2022; 18:e1010074. [PMID: 36070320 PMCID: PMC9484656 DOI: 10.1371/journal.pcbi.1010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/19/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022] Open
Abstract
ATP7B is a human copper-transporting P1B-type ATPase that is involved in copper homeostasis and resistance to platinum drugs in cancer cells. ATP7B consists of a copper-transporting core and a regulatory N-terminal tail that contains six metal-binding domains (MBD1-6) connected by linker regions. The MBDs can bind copper, which changes the dynamics of the regulatory domain and activates the protein, but the underlying mechanism remains unknown. To identify possible copper-specific structural dynamics involved in transport regulation, we constructed a model of ATP7B spanning the N-terminal tail and core catalytic domains and performed molecular dynamics (MD) simulations with (holo) and without (apo) copper ions bound to the MBDs. In the holo protein, MBD2, MBD3 and MBD5 showed enhanced mobilities, which resulted in a more extended N-terminal regulatory region. The observed separation of MBD2 and MBD3 from the core protein supports a mechanism where copper binding activates the ATP7B protein by reducing interactions among MBD1-3 and between MBD1-3 and the core protein. We also observed an increased interaction between MBD5 and the core protein that brought the copper-binding site of MBD5 closer to the high-affinity internal copper-binding site in the core protein. The simulation results assign specific, mechanistic roles to the metal-binding domains involved in ATP7B regulation that are testable in experimental settings. Living organisms depend upon active transport against gradients across biological membranes for survival. Such transport can be accomplished by ATP-dependent membrane protein transporters for which the activity must be regulated to maintain optimal concentrations in the cellular compartments. The regulatory mechanisms often involve structural responses inherent to the protein structure, which because of their dynamic nature can be hard to assess experimentally. A prime example is regulation of cellular copper levels by a copper-binding tail in the human copper transporter ATP7B. Dysregulation can cause severe diseases, for example the copper metabolism disorder Wilson’s disease, which is caused by mutations in ATP7B regulation machinery. Due to the practical difficulties in working with membrane proteins, most studies of ATP7B have been conducted in the absence of the membrane-bound protein core. Here, we used computer simulations of full-length ATP7B to study how structural dynamics in the regulatory tail differ between copper-bound and copper-free states. Copper induced increased dynamics in the tail, resulting in an overall movement towards the ion-binding site in the protein core. The simulations identified several, hitherto not reported, interactions between the regulatory tail and the protein core that can be targeted experimentally to enhance our understanding of this medically relevant regulatory mechanism.
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jonas Hyld Steffen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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16
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Salustros N, Grønberg C, Abeyrathna NS, Lyu P, Orädd F, Wang K, Andersson M, Meloni G, Gourdon P. Structural basis of ion uptake in copper-transporting P 1B-type ATPases. Nat Commun 2022; 13:5121. [PMID: 36045128 PMCID: PMC9433437 DOI: 10.1038/s41467-022-32751-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
Copper is essential for living cells, yet toxic at elevated concentrations. Class 1B P-type (P1B-) ATPases are present in all kingdoms of life, facilitating cellular export of transition metals including copper. P-type ATPases follow an alternating access mechanism, with inward-facing E1 and outward-facing E2 conformations. Nevertheless, no structural information on E1 states is available for P1B-ATPases, hampering mechanistic understanding. Here, we present structures that reach 2.7 Å resolution of a copper-specific P1B-ATPase in an E1 conformation, with complementing data and analyses. Our efforts reveal a domain arrangement that generates space for interaction with ion donating chaperones, and suggest a direct Cu+ transfer to the transmembrane core. A methionine serves a key role by assisting the release of the chaperone-bound ion and forming a cargo entry site together with the cysteines of the CPC signature motif. Collectively, the findings provide insights into P1B-mediated transport, likely applicable also to human P1B-members.
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Affiliation(s)
- Nina Salustros
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark
| | - Christina Grønberg
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark
| | - Nisansala S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800W Campbell Rd., Richardson, TX, 75080, USA
| | - Pin Lyu
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Fredrik Orädd
- Department of Chemistry, Umeå University, Linneaus Väg 10, SE-901 87, Umeå, Sweden
| | - Kaituo Wang
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark
| | - Magnus Andersson
- Department of Chemistry, Umeå University, Linneaus Väg 10, SE-901 87, Umeå, Sweden
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800W Campbell Rd., Richardson, TX, 75080, USA
| | - Pontus Gourdon
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark.
- Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84, Lund, Sweden.
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17
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Novoa-Aponte L, Argüello JM. Unique underlying principles shaping copper homeostasis networks. J Biol Inorg Chem 2022; 27:509-528. [PMID: 35802193 PMCID: PMC9470648 DOI: 10.1007/s00775-022-01947-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/27/2022] [Indexed: 12/27/2022]
Abstract
Abstract Copper is essential in cells as a cofactor for key redox enzymes. Bacteria have acquired molecular components that sense, uptake, distribute, and expel copper ensuring that cuproenzymes are metallated and steady-state metal levels are maintained. Toward preventing deleterious reactions, proteins bind copper ions with high affinities and transfer the metal via ligand exchange, warranting that copper ions are always complexed. Consequently, the directional copper distribution within cell compartments and across cell membranes requires specific dynamic interactions and metal exchange between cognate holo-apo protein partners. These metal exchange reactions are determined by thermodynamic and kinetics parameters and influenced by mass action. Then, copper distribution can be conceptualized as a molecular system of singular interacting elements that maintain a physiological copper homeostasis. This review focuses on the impact of copper high-affinity binding and exchange reactions on the homeostatic mechanisms, the conceptual models to describe the cell as a homeostatic system, the various molecule functions that contribute to copper homeostasis, and the alternative system architectures responsible for copper homeostasis in model bacteria. Graphical Abstract ![]()
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Affiliation(s)
- Lorena Novoa-Aponte
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St, Worcester, MA, 01605, USA.,Genetics and Metabolism Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St, Worcester, MA, 01605, USA.
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18
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Bitter RM, Oh S, Deng Z, Rahman S, Hite RK, Yuan P. Structure of the Wilson disease copper transporter ATP7B. SCIENCE ADVANCES 2022; 8:eabl5508. [PMID: 35245129 PMCID: PMC8896786 DOI: 10.1126/sciadv.abl5508] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/10/2022] [Indexed: 05/31/2023]
Abstract
ATP7A and ATP7B, two homologous copper-transporting P1B-type ATPases, play crucial roles in cellular copper homeostasis, and mutations cause Menkes and Wilson diseases, respectively. ATP7A/B contains a P-type ATPase core consisting of a membrane transport domain and three cytoplasmic domains, the A, P, and N domains, and a unique amino terminus comprising six consecutive metal-binding domains. Here, we present a cryo-electron microscopy structure of frog ATP7B in a copper-free state. Interacting with both the A and P domains, the metal-binding domains are poised to exert copper-dependent regulation of ATP hydrolysis coupled to transmembrane copper transport. A ring of negatively charged residues lines the cytoplasmic copper entrance that is presumably gated by a conserved basic residue sitting at the center. Within the membrane, a network of copper-coordinating ligands delineates a stepwise copper transport pathway. This work provides the first glimpse into the structure and function of ATP7 proteins and facilitates understanding of disease mechanisms and development of rational therapies.
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Affiliation(s)
- Ryan M. Bitter
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - SeCheol Oh
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suhaila Rahman
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Richard K. Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
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19
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Yang Z, Yang F, Liu JL, Wu HT, Yang H, Shi Y, Liu J, Zhang YF, Luo YR, Chen KM. Heavy metal transporters: Functional mechanisms, regulation, and application in phytoremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151099. [PMID: 34688763 DOI: 10.1016/j.scitotenv.2021.151099] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 05/22/2023]
Abstract
Heavy metal pollution in soil is a global problem with serious impacts on human health and ecological security. Phytoextraction in phytoremediation, in which plants uptake and transport heavy metals (HMs) to the tissues of aerial parts, is the most environmentally friendly method to reduce the total amount of HMs in soil and has wide application prospects. However, the molecular mechanism of phytoextraction is still under investigation. The uptake, translocation, and retention of HMs in plants are mainly mediated by a variety of transporter proteins. A better understanding of the accumulation strategy of HMs via transporters in plants is a prerequisite for the improvement of phytoextraction. In this review, the biochemical structure and functions of HM transporter families in plants are systematically summarized, with emphasis on their roles in phytoremediation. The accumulation mechanism and regulatory pathways related to hormones, regulators, and reactive oxygen species (ROS) of HMs concerning these transporters are described in detail. Scientific efforts and practices for phytoremediation carried out in recent years suggest that creation of hyperaccumulators by transgenic or gene editing techniques targeted to these transporters and their regulators is the ultimate powerful path for the phytoremediation of HM contaminated soils.
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Affiliation(s)
- Zi Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jia-Lan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hai-Tao Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hao Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yi Shi
- Guangdong Kaiyuan Environmental Technology Co., Ltd, Dongguan 523000, China
| | - Jie Liu
- Guangdong Kaiyuan Environmental Technology Co., Ltd, Dongguan 523000, China
| | - Yan-Feng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling 712100, Shaanxi, China
| | - Yan-Rong Luo
- Guangdong Kaiyuan Environmental Technology Co., Ltd, Dongguan 523000, China.
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
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20
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Placenti MA, Roman EA, González Flecha FL, González-Lebrero RM. Functional characterization of Legionella pneumophila Cu + transport ATPase. The activation by Cu + and ATP. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183822. [PMID: 34826402 DOI: 10.1016/j.bbamem.2021.183822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/08/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Cu+-ATPases are integral membrane proteins belonging to the IB subfamily of the P-type ATPases that couple Cu+ transport to the hydrolysis of ATP. As some structural and functional particularities arise for Cu+-ATPases, several authors suggest that some of the reaction steps of the Albers-Post model postulated for other P-ATPases may be different. In this work we describe a functional characterization of Legionella pneumophila Cu+-ATPase (LpCopA), the first PIB-ATPase whose structure was determined by X-ray crystallography. Cu+-ATPase activity of the enzyme presents a maximum at ∼37 °C and pH 6.6-6.8. Phospholipids enhance LpCopA Cu+-ATPase activity in a non-essential mode where optimal activity is achieved at an asolectin molar fraction of 0.15 and an amphiphile-protein ratio of ~30,000. As described for other P-ATPases, Mg2+ acts as an essential activator. Furthermore, Cu+-ATPase activity dependence on [Cu+] and [ATP] can both be described by a sum of two hyperbolic functions. Based on that, and the [Cu+] and [ATP] dependencies of the best fitting parameters of the hyperbolae pointed above, we propose a minimal reaction scheme for the catalytic mechanism that shares the basic reaction steps of the Albers-Post model for P-type ATPases. The reaction scheme postulated contemplates two different binding affinities for a single ATP (apparent affinities of 0.66 and 550 μM at [Cu+] → ∞) and binding of at least 2 Cu+ with different affinities as well (apparent affinities of 1.4 and 102.5 μM at [ATP] → ∞).
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Affiliation(s)
- M Agueda Placenti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - Ernesto A Roman
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Buenos Aires, Argentina
| | - F Luis González Flecha
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
| | - Rodolfo M González-Lebrero
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
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21
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Grønberg C, Hu Q, Mahato DR, Longhin E, Salustros N, Duelli A, Lyu P, Bågenholm V, Eriksson J, Rao KU, Henderson DI, Meloni G, Andersson M, Croll T, Godaly G, Wang K, Gourdon P. Structure and ion-release mechanism of P IB-4-type ATPases. eLife 2021; 10:73124. [PMID: 34951590 PMCID: PMC8880997 DOI: 10.7554/elife.73124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Transition metals, such as zinc, are essential micronutrients in all organisms, but also highly toxic in excessive amounts. Heavy-metal transporting P-type (PIB) ATPases are crucial for homeostasis, conferring cellular detoxification and redistribution through transport of these ions across cellular membranes. No structural information is available for the PIB-4-ATPases, the subclass with the broadest cargo scope, and hence even their topology remains elusive. Here we present structures and complementary functional analyses of an archetypal PIB‑4‑ATPase, sCoaT from Sulfitobacter sp. NAS14-1. The data disclose the architecture, devoid of classical so-called heavy metal binding domains, and provides fundamentally new insights into the mechanism and diversity of heavy-metal transporters. We reveal several novel P-type ATPase features, including a dual role in heavy-metal release and as an internal counter ion of an invariant histidine. We also establish that the turn-over of PIB‑ATPases is potassium independent, contrasting to many other P-type ATPases. Combined with new inhibitory compounds, our results open up for efforts in e.g. drug discovery, since PIB-4-ATPases function as virulence factors in many pathogens.
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Affiliation(s)
- Christina Grønberg
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Qiaoxia Hu
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Elena Longhin
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nina Salustros
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Pin Lyu
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Viktoria Bågenholm
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | | | | | | | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, United States
| | | | - Tristan Croll
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Gabriela Godaly
- Department of Laboratory Medicine, Umeå University, Umeå, Sweden
| | - Kaituo Wang
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
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22
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Roberts CS, Ni F, Mitra B. The Zinc and Iron Binuclear Transport Center of ZupT, a ZIP Transporter from Escherichia coli. Biochemistry 2021; 60:3738-3752. [PMID: 34793140 DOI: 10.1021/acs.biochem.1c00621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ZupT fromEscherichia coliis a member of the Zrt-/Irt-like Protein (ZIP) transporter family, which is responsible for zinc uptake during zinc-sufficient conditions. ZIP transporters have been shown to transport different divalent metal ions including zinc, iron, manganese, and cadmium. In this study, we show that ZupT has an asymmetric binuclear metal center in the transmembrane domain; one metal-binding site, M1, binds zinc, cadmium, and iron, while the other, M2, binds iron only and with higher affinity than M1. Using site-specific mutagenesis and transport activity measurements in whole cells and proteoliposomes, we show that zinc is transported from M1, while iron is transported from M2. The two sites share a common bridging ligand, a conserved glutamate residue. M1 and M2 have ligands from highly conserved motifs in transmembrane domains 4 and 5. Additionally, M2 has a ligand from transmembrane domain 6, a glutamate residue, which is conserved in the gufA subfamily of ZIP transporters, including ZupT and the human ZIP11. Unlike cadmium, iron transport from M2 does not inhibit the zinc transport activity but slightly stimulates it. This stimulation of activity is mediated through the bridging carboxylate ligand. The binuclear zinc-iron binding center in ZupT has likely evolved to enable the transport of essential metals from two different sites without competition; a similar mechanism of metal transport is likely to be found in the gufA subfamily of ZIP transporter proteins.
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Affiliation(s)
- Cameron S Roberts
- Department of Biochemistry, Microbiology and Immunology, School of Medicine, Wayne State University, Detroit, Michigan 48201, United States
| | - Fei Ni
- Department of Biochemistry, Microbiology and Immunology, School of Medicine, Wayne State University, Detroit, Michigan 48201, United States
| | - Bharati Mitra
- Department of Biochemistry, Microbiology and Immunology, School of Medicine, Wayne State University, Detroit, Michigan 48201, United States
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23
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Tomita A, Daiho T, Kusakizako T, Yamashita K, Ogasawara S, Murata T, Nishizawa T, Nureki O. Cryo-EM reveals mechanistic insights into lipid-facilitated polyamine export by human ATP13A2. Mol Cell 2021; 81:4799-4809.e5. [PMID: 34798056 DOI: 10.1016/j.molcel.2021.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/26/2021] [Accepted: 11/01/2021] [Indexed: 01/11/2023]
Abstract
The cytoplasmic polyamine maintains cellular homeostasis by chelating toxic metal cations, regulating transcriptional activity, and protecting DNA. ATP13A2 was identified as a lysosomal polyamine exporter responsible for polyamine release into the cytosol, and its dysfunction is associated with Alzheimer's disease and other neural degradation diseases. ATP13A2 belongs to the P5 subfamily of the P-type ATPase family, but its mechanisms remain unknown. Here, we report the cryoelectron microscopy (cryo-EM) structures of human ATP13A2 under four different conditions, revealing the structural coupling between the polyamine binding and the dephosphorylation. Polyamine is bound at the luminal tunnel and recognized through numerous electrostatic and π-cation interactions, explaining its broad specificity. The unique N-terminal domain is anchored to the lipid membrane to stabilize the E2P conformation, thereby accelerating the E1P-to-E2P transition. These findings reveal the distinct mechanism of P5B ATPases, thereby paving the way for neuroprotective therapy by activating ATP13A2.
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Affiliation(s)
- Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Daiho
- Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Tsurumi, Yokohama 230-0045, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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24
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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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25
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Uhlemann EME, Lee W, Tonelli M, Dmitriev OY. At sixes and sevens: cryptic domain in the metal binding chain of the human copper transporter ATP7A. Biophys J 2021; 120:4600-4607. [PMID: 34461106 DOI: 10.1016/j.bpj.2021.08.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/27/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022] Open
Abstract
ATP7A and ATP7B are structurally similar but functionally distinct active copper transporters that regulate copper levels in the human cells and deliver copper to the biosynthetic pathways. Both proteins have a chain of six cytosolic metal-binding domains (MBDs) believed to be involved in the copper-dependent regulation of the activity and intracellular localization of these enzymes. Although all the MBDs are quite similar in structure, their spacing differs markedly between ATP7A and ATP7B. We show by NMR that the long polypeptide between MBD1 and MBD2 of ATP7A forms an additional seventh metastable domain, which we called HMA1A (heavy metal associated domain 1A). The structure of HMA1A resembles the MBDs but contains no copper-binding site. The HMA1A domain, which is unique to ATP7A, may modulate regulatory interactions between MBD1-3, contributing to the distinct functional properties of ATP7A and ATP7B.
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Affiliation(s)
- Eva-Maria E Uhlemann
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Woonghee Lee
- Department of Chemistry, University of Colorado, Denver, Colorado
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin
| | - Oleg Y Dmitriev
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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26
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Maung MT, Carlson A, Olea-Flores M, Elkhadragy L, Schachtschneider KM, Navarro-Tito N, Padilla-Benavides T. The molecular and cellular basis of copper dysregulation and its relationship with human pathologies. FASEB J 2021; 35:e21810. [PMID: 34390520 DOI: 10.1096/fj.202100273rr] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/23/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022]
Abstract
Copper (Cu) is an essential micronutrient required for the activity of redox-active enzymes involved in critical metabolic reactions, signaling pathways, and biological functions. Transporters and chaperones control Cu ion levels and bioavailability to ensure proper subcellular and systemic Cu distribution. Intensive research has focused on understanding how mammalian cells maintain Cu homeostasis, and how molecular signals coordinate Cu acquisition and storage within organs. In humans, mutations of genes that regulate Cu homeostasis or facilitate interactions with Cu ions lead to numerous pathologic conditions. Malfunctions of the Cu+ -transporting ATPases ATP7A and ATP7B cause Menkes disease and Wilson disease, respectively. Additionally, defects in the mitochondrial and cellular distributions and homeostasis of Cu lead to severe neurodegenerative conditions, mitochondrial myopathies, and metabolic diseases. Cu has a dual nature in carcinogenesis as a promotor of tumor growth and an inducer of redox stress in cancer cells. Cu also plays role in cancer treatment as a component of drugs and a regulator of drug sensitivity and uptake. In this review, we provide an overview of the current knowledge of Cu metabolism and transport and its relation to various human pathologies.
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Affiliation(s)
- May T Maung
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT, USA
| | - Alyssa Carlson
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT, USA
| | - Monserrat Olea-Flores
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Guerrero, Mexico
| | - Lobna Elkhadragy
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Kyle M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA.,Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Napoleon Navarro-Tito
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Guerrero, Mexico
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Abeyrathna N, Abeyrathna S, Morgan MT, Fahrni CJ, Meloni G. Transmembrane Cu(I) P-type ATPase pumps are electrogenic uniporters. Dalton Trans 2021; 49:16082-16094. [PMID: 32469032 DOI: 10.1039/d0dt01380c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cu(i) P-type ATPases are transmembrane primary active ion pumps that catalyze the extrusion of copper ions across cellular membranes. Their activity is critical in controlling copper levels in all kingdoms of life. Biochemical and structural characterization established the structural framework by which Cu-pumps perform their function. However, the details of the overall mechanism of transport (uniporter vs. cotransporter) and electrogenicity still remain elusive. In this work, we developed a platform to reconstitute the model Cu(i)-pump from E. coli (EcCopA) in artificial lipid bilayer small unilamellar vesicles (SUVs) to quantitatively characterize the metal substrate, putative counter-ions and charge translocation. By encapsulating in the liposome lumen fluorescence detector probes (CTAP-3, pyranine and oxonol VI) responsive to diverse stimuli (Cu(i), pH and membrane potential), we correlated substrate, secondary-ion translocation and charge movement events in EcCopA proteoliposomes. This platform centered on multiple fluorescence reporters allowed study of the mechanism and translocation kinetic parameters in real-time for wild-type EcCopA and inactive mutants. The maximal initial Cu(i) transport rate of 165 nmol Cu(i) mg-1 min-1 and KM, Cu(I) = 0.15 ± 0.07 μM was determined with this analysis. We reveal that Cu(i) pumps are primary-active uniporters and electrogenic. The Cu(i) translocation cycle does not require proton counter-transport resulting in electrogenic generation of transmembrane potential upon translocation of one Cu(i) per ATP hydrolysis cycle. Thus, mechanistic differences between Cu(i) pumps and other better characterized P-type ATPases are discussed. The platform opens the venue to study translocation events and mechanisms of transport in other transition metal P-type ATPase pumps.
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Affiliation(s)
- Nisansala Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
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28
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Koirala M, Shashikala HBM, Jeffries J, Wu B, Loftus SK, Zippin JH, Alexov E. Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease. Int J Mol Sci 2021; 22:ijms22158273. [PMID: 34361043 PMCID: PMC8347052 DOI: 10.3390/ijms22158273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Intravesicular pH plays a crucial role in melanosome maturation and function. Melanosomal pH changes during maturation from very acidic in the early stages to neutral in late stages. Neutral pH is critical for providing optimal conditions for the rate-limiting, pH-sensitive melanin-synthesizing enzyme tyrosinase (TYR). This dramatic change in pH is thought to result from the activity of several proteins that control melanosomal pH. Here, we computationally investigated the pH-dependent stability of several melanosomal membrane proteins and compared them to the pH dependence of the stability of TYR. We confirmed that the pH optimum of TYR is neutral, and we also found that proteins that are negative regulators of melanosomal pH are predicted to function optimally at neutral pH. In contrast, positive pH regulators were predicted to have an acidic pH optimum. We propose a competitive mechanism among positive and negative regulators that results in pH equilibrium. Our findings are consistent with previous work that demonstrated a correlation between the pH optima of stability and activity, and they are consistent with the expected activity of positive and negative regulators of melanosomal pH. Furthermore, our data suggest that disease-causing variants impact the pH dependence of melanosomal proteins; this is particularly prominent for the OCA2 protein. In conclusion, melanosomal pH appears to affect the activity of multiple melanosomal proteins.
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Affiliation(s)
- Mahesh Koirala
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - H. B. Mihiri Shashikala
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Jacob Jeffries
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Bohua Wu
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Stacie K. Loftus
- Genetic Disease Research Branch, National Human Genome Research Branch, National Institutes of Health, Bethesda, MD 22066, USA;
| | - Jonathan H. Zippin
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA;
| | - Emil Alexov
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
- Correspondence:
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Copper Toxicity Associated With an ATP7A-Related Complex Phenotype. Pediatr Neurol 2021; 119:40-44. [PMID: 33894639 DOI: 10.1016/j.pediatrneurol.2021.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/14/2021] [Accepted: 03/17/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND The ATP7A gene encodes a copper transporter whose mutations cause Menkes disease, occipital horn syndrome (OHS), and, less frequently, ATP7A-related distal hereditary motor neuropathy (dHMN). Here we describe a family with OHS caused by a novel mutation in the ATP7A gene, including a patient with a comorbid dHMN that worsened markedly after being treated with copper histidinate. METHODS We studied in detail the clinical features of the patients and performed a genomic analysis by using TruSight One Expanded Sequencing Panel. Subsequently, we determined the ATP7A and ATP7B expression levels, mitochondrial membrane potential, and redox balance in cultured fibroblasts of Patient 1. RESULTS We found a novel ATP7A late truncated mutation p.Lys1412AsnfsX15 in the two affected members of this family. The co-occurrence of OHS and dHMN in Patient 1 reveals the variable phenotypic expressivity of the variant. A severe clinical and neurophysiologic worsening was observed in the dHMN of Patient 1 when he was treated with copper replacement therapy, with a subsequent fast recovery after the copper histidinate was withdrawn. Functional studies revealed that the patient had low levels of both ATP7A and ATP7B, the other copper transporter, and high levels of superoxide ion in the mitochondria. CONCLUSIONS Our findings broaden the clinical spectrum of ATP7A-related disorders and demonstrate that two clinical phenotypes can occur in the same patient. The copper-induced toxicity and low levels of both ATP7A and ATP7B in our patient suggest that copper accumulation in motor neurons is the pathogenic mechanism in ATP7A-related dHMN.
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30
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Peng W, Yang X, Yan K, Chen H, Yuan F, Bei W. CopA Protects Actinobacillus pleuropneumoniae against Copper Toxicity. Vet Microbiol 2021; 258:109122. [PMID: 34052743 DOI: 10.1016/j.vetmic.2021.109122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 05/13/2021] [Indexed: 11/24/2022]
Abstract
Actinobacillus pleuropneumoniae is a Gram-negative bacterium causing porcine pleuropneumonia and severe economic losses in the global swine industry. The toxic trace element copper is required for many physiological and pathological processes in organisms. However, CopA, one of the most well-characterized P-type ATPases contributing to copper resistance, has not been characterized in A. pleuropneumoniae. We used quantitative PCR analysis to examine expression of the copA gene in A. pleuropneumoniae and investigated sequence conservation among serotypes and other Gram-negative bacteria. Growth characteristics were determined using growth curve analyses and spot dilution assays of the wild-type strain and a △copA mutant. We also used flame atomic absorption spectrophotometry to determine intracellular copper content and examined the virulence of the △copA mutant in a mouse model. The copA expression was induced by copper, and its nucleotide sequence was highly conserved among different serotypes of A. pleuropneumoniae. The amino acid sequence of CopA shared high identity with CopA sequences reported from several Gram-negative bacteria. Furthermore, the △copA mutant exhibited impaired growth and had higher intracellular copper content compared with the wild-type strain when supplemented with copper. The mouse model revealed that CopA had no influence on the virulence of A. pleuropneumoniae. In conclusion, these results demonstrated that CopA is required for resistance of A. pleuropneumoniae to copper and protects A. pleuropneumoniae against copper toxicity via copper efflux.
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Affiliation(s)
- Wei Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xia Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Kang Yan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Fangyan Yuan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China.
| | - Weicheng Bei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; State Key Laboratory of Genetically Engineered Veterinary Vaccines, Qingdao, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.
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31
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Martinez-Fierro ML, Cabral-Pacheco GA, Garza-Veloz I, Acuña-Quiñones J, Martinez-de-Villarreal LE, Ibarra-Ramirez M, Beuten J, Sanchez-Guerrero SE, Villarreal-Martinez L, Delgado-Enciso I, Rodriguez-Sanchez IP, Zuñiga-Ramirez VZ, Cardenas-Vargas E, Romero-Diaz V. Whole-Exome Sequencing, Proteome Landscape, and Immune Cell Migration Patterns in a Clinical Context of Menkes Disease. Genes (Basel) 2021; 12:genes12050744. [PMID: 34069220 PMCID: PMC8156642 DOI: 10.3390/genes12050744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 11/18/2022] Open
Abstract
Menkes disease (MD) is a rare and often lethal X-linked recessive syndrome, characterized by generalized alterations in copper transport and metabolism, linked to mutations in the ATPase copper transporting α (ATP7A) gene. Our objective was to identify genomic alterations and circulating proteomic profiles related to MD assessing their potential roles in the clinical features of the disease. We describe the case of a male patient of 8 months of age with silvery hair, tan skin color, hypotonia, alterations in neurodevelopment, presence of seizures, and low values of plasma ceruloplasmin. Trio-whole-exome sequencing (Trio-WES) analysis, plasma proteome screening, and blood cell migration assays were carried out. Trio-WES revealed a hemizygous change c.4190C > T (p.S1397F) in exon 22 of the ATP7A gene. Compared with his parents and with child controls, 11 plasma proteins were upregulated and 59 downregulated in the patient. According to their biological processes, 42 (71.2%) of downregulated proteins had a participation in cellular transport. The immune system process was represented by 35 (59.3%) downregulated proteins (p = 9.44 × 10−11). Additional studies are necessary to validate these findings as hallmarks of MD.
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Affiliation(s)
- Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S, Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6, Ejido la Escondida, Zacatecas 98160, Mexico; (G.A.C.-P.); (I.G.-V.); (J.A.-Q.); (V.Z.Z.-R.)
- Correspondence: ; Tel.: +52-(492)-925-6690 (ext. 4511)
| | - Griselda A. Cabral-Pacheco
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S, Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6, Ejido la Escondida, Zacatecas 98160, Mexico; (G.A.C.-P.); (I.G.-V.); (J.A.-Q.); (V.Z.Z.-R.)
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S, Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6, Ejido la Escondida, Zacatecas 98160, Mexico; (G.A.C.-P.); (I.G.-V.); (J.A.-Q.); (V.Z.Z.-R.)
| | - Jesus Acuña-Quiñones
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S, Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6, Ejido la Escondida, Zacatecas 98160, Mexico; (G.A.C.-P.); (I.G.-V.); (J.A.-Q.); (V.Z.Z.-R.)
| | - Laura E. Martinez-de-Villarreal
- Departamento de Genética, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (L.E.M.-d.-V.); (M.I.-R.)
| | - Marisol Ibarra-Ramirez
- Departamento de Genética, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (L.E.M.-d.-V.); (M.I.-R.)
| | - Joke Beuten
- AiLife Diagnostics, 1920 Country Pl Pkwy Suite 100, Pearland, TX 77584, USA;
| | - Samantha E. Sanchez-Guerrero
- Hospital General Zacatecas “Luz González Cosío”, Servicios de Salud de Zacatecas, Zacatecas 98160, Mexico; (S.E.S.-G.); (E.C.-V.)
| | - Laura Villarreal-Martinez
- Hematology Service, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico;
| | - Ivan Delgado-Enciso
- Department of Molecular Medicine, School of Medicine, University of Colima, Colima 28040, Mexico;
| | - Iram P. Rodriguez-Sanchez
- Molecular and Structural Physiology Laboratory, School of Biological Sciences, Autonomous University of Nuevo León, Monterrey 64460, Mexico;
| | - Vania Z. Zuñiga-Ramirez
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S, Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km.6, Ejido la Escondida, Zacatecas 98160, Mexico; (G.A.C.-P.); (I.G.-V.); (J.A.-Q.); (V.Z.Z.-R.)
| | - Edith Cardenas-Vargas
- Hospital General Zacatecas “Luz González Cosío”, Servicios de Salud de Zacatecas, Zacatecas 98160, Mexico; (S.E.S.-G.); (E.C.-V.)
| | - Viktor Romero-Diaz
- Department of Histology, Universidad Autónoma de Nuevo León, Facultad de Medicina, Monterrey 64460, Mexico;
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Cation Transporters of Candida albicans-New Targets to Fight Candidiasis? Biomolecules 2021; 11:biom11040584. [PMID: 33923411 PMCID: PMC8073359 DOI: 10.3390/biom11040584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Candidiasis is the wide-spread fungal infection caused by numerous strains of yeast, with the prevalence of Candida albicans. The current treatment of candidiasis is becoming rather ineffective and costly owing to the emergence of resistant strains; hence, the exploration of new possible drug targets is necessary. The most promising route is the development of novel antibiotics targeting this pathogen. In this review, we summarize such candidates found in C. albicans and those involved in the transport of (metal) cations, as the latter are essential for numerous processes within the cell; hence, disruption of their fluxes can be fatal for C. albicans.
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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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Missel JW, Salustros N, Becares ER, Steffen JH, Laursen AG, Garcia AS, Garcia-Alai MM, Kolar Č, Gourdon P, Gotfryd K. Cyclohexyl-α maltoside as a highly efficient tool for membrane protein studies. Curr Res Struct Biol 2021; 3:85-94. [PMID: 34235488 PMCID: PMC8244287 DOI: 10.1016/j.crstbi.2021.03.002] [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: 12/22/2020] [Revised: 02/09/2021] [Accepted: 03/05/2021] [Indexed: 01/06/2023] Open
Abstract
Membrane proteins (MPs) constitute a large fraction of the proteome, but exhibit physicochemical characteristics that impose challenges for successful sample production crucial for subsequent biophysical studies. In particular, MPs have to be extracted from the membranes in a stable form. Reconstitution into detergent micelles represents the most common procedure in recovering MPs for subsequent analysis. n-dodecyl-β-D-maltoside (DDM) remains one of the most popular conventional detergents used in production of MPs. Here we characterize the novel DDM analogue 4-trans-(4-trans-propylcyclohexyl)-cyclohexyl α-maltoside (t-PCCαM), possessing a substantially lower critical micelle concentration (CMC) than the parental compound that represents an attractive feature when handling MPs. Using three different types of MPs of human and prokaryotic origin, i.e., a channel, a primary and a secondary active transporter, expressed in yeast and bacterial host systems, respectively, we investigate the performance of t-PCCαM in solubilization and affinity purification together with its capacity to preserve native fold and activity. Strikingly, t-PCCαM displays favorable behavior in extracting and stabilizing the three selected targets. Importantly, t-PCCαM promoted extraction of properly folded protein, enhanced thermostability and provided negatively-stained electron microscopy samples of promising quality. All-in-all, t-PCCαM emerges as competitive surfactant applicable to a broad portfolio of challenging MPs for downstream structure-function analysis.
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Affiliation(s)
- Julie Winkel Missel
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Nina Salustros
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Eva Ramos Becares
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Jonas Hyld Steffen
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Amalie Gerdt Laursen
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Maria M Garcia-Alai
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany.,Centre for Structural Systems Biology, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Čeněk Kolar
- Glycon Biochemicals GmbH, Im Biotechnologie Park TGZ 1, D-14943, Luckenwalde, Germany
| | - Pontus Gourdon
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark.,Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84, Lund, Sweden
| | - Kamil Gotfryd
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
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Orädd F, Andersson M. Tracking Membrane Protein Dynamics in Real Time. J Membr Biol 2021; 254:51-64. [PMID: 33409541 PMCID: PMC7936944 DOI: 10.1007/s00232-020-00165-8] [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: 09/21/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022]
Abstract
Abstract Membrane proteins govern critical cellular processes and are central to human health and associated disease. Understanding of membrane protein function is obscured by the vast ranges of structural dynamics—both in the spatial and time regime—displayed in the protein and surrounding membrane. The membrane lipids have emerged as allosteric modulators of membrane protein function, which further adds to the complexity. In this review, we discuss several examples of membrane dependency. A particular focus is on how molecular dynamics (MD) simulation have aided to map membrane protein dynamics and how enhanced sampling methods can enable observing the otherwise inaccessible biological time scale. Also, time-resolved X-ray scattering in solution is highlighted as a powerful tool to track membrane protein dynamics, in particular when combined with MD simulation to identify transient intermediate states. Finally, we discuss future directions of how to further develop this promising approach to determine structural dynamics of both the protein and the surrounding lipids. Graphic Abstract ![]()
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
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36
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Eiró LG, Ferreira MKM, Bittencourt LO, Aragão WAB, Souza MPCD, Silva MCF, Dionizio A, Buzalaf MAR, Crespo-López ME, Lima RR. Chronic methylmercury exposure causes spinal cord impairment: Proteomic modulation and oxidative stress. Food Chem Toxicol 2020; 146:111772. [DOI: 10.1016/j.fct.2020.111772] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
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Roberts CS, Muralidharan S, Ni F, Mitra B. Structural Role of the First Four Transmembrane Helices in ZntA, a P 1B-Type ATPase from Escherichia coli. Biochemistry 2020; 59:4488-4498. [PMID: 33190490 DOI: 10.1021/acs.biochem.0c00770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ZntA from Escherichia coli confers resistance to toxic concentrations of Pb2+, Zn2+, and Cd2+. It is a member of the P1B-ATPase transporter superfamily, which includes the human Cu+-transporting proteins ATP7A and ATP7B. P1B-type ATPases typically have a hydrophilic N-terminal metal-binding domain and eight transmembrane helices. A splice variant of ATP7B was reported, which has 100-fold higher night-specific expression in the pineal gland; it lacks the entire N-terminal domain and the first four transmembrane helices. Here, we report our findings with Δ231-ZntA, a similar truncation we created in ZntA. Δ231-ZntA has no in vivo and greatly reduced in vitro activity. It binds one metal ion per dimer at the transmembrane site, with a 15-19000-fold higher binding affinity, indicating highly significant changes in the dimer structure of Δ231-ZntA relative to that of ZntA. Cd2+ has the highest affinity for Δ231-ZntA, in contrast to ZntA, which has the highest affinity for Pb2+. Site-specific mutagenesis of the metal-binding residues, 392Cys, 394Cys, and 714Asp, showed that there is considerable flexibility at the metal-binding site, with any two of these three residues able to bind Zn2+ and Pb2+ unlike in ZntA. However, Cd2+ binds to only 392Cys and 714Asp, with 394Cys not involved in Cd2+ binding. Three-dimensional homology models show that there is a dramatic difference between the ZntA and Δ231-ZntA dimer structures, which help to explain these observations. Therefore, the first four transmembrane helices in ZntA and P1B-type ATPases play an important role in maintaining the correct dimer structure.
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Affiliation(s)
- Cameron S Roberts
- Department of Biochemistry, Microbiology and Immunology, School of Medicine, Wayne State University Detroit, Michigan 48201, United States
| | - Sandhya Muralidharan
- Department of Biochemistry, Microbiology and Immunology, School of Medicine, Wayne State University Detroit, Michigan 48201, United States
| | - Fei Ni
- Department of Biochemistry, Microbiology and Immunology, School of Medicine, Wayne State University Detroit, Michigan 48201, United States
| | - Bharati Mitra
- Department of Biochemistry, Microbiology and Immunology, School of Medicine, Wayne State University Detroit, Michigan 48201, United States
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Shanbhag VC, Gudekar N, Jasmer K, Papageorgiou C, Singh K, Petris MJ. Copper metabolism as a unique vulnerability in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118893. [PMID: 33091507 DOI: 10.1016/j.bbamcr.2020.118893] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023]
Abstract
The last 25 years have witnessed tremendous progress in identifying and characterizing proteins that regulate the uptake, intracellular trafficking and export of copper. Although dietary copper is required in trace amounts, sufficient quantities of this metal are needed to sustain growth and development in humans and other mammals. However, copper is also a rate-limiting nutrient for the growth and proliferation of cancer cells. Oral copper chelators taken with food have been shown to confer anti-neoplastic and anti-metastatic benefits in animals and humans. Recent studies have begun to identify specific roles for copper in pathways of oncogenic signaling and resistance to anti-neoplastic drugs. Here, we review the general mechanisms of cellular copper homeostasis and discuss roles of copper in cancer progression, highlighting metabolic vulnerabilities that may be targetable in the development of anticancer therapies.
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Affiliation(s)
- Vinit C Shanbhag
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, United States of America; The Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, United States of America
| | - Nikita Gudekar
- Genetics Area Program, University of Missouri, Columbia, MO 65211, United States of America; The Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, United States of America
| | - Kimberly Jasmer
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, United States of America; The Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, United States of America
| | - Christos Papageorgiou
- Department of Medicine, University of Missouri, Columbia, MO 65211, United States of America
| | - Kamal Singh
- The Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, United States of America; Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, United States of America
| | - Michael J Petris
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, United States of America; Department of Ophthalmology, University of Missouri, Columbia, MO 65211, United States of America; Genetics Area Program, University of Missouri, Columbia, MO 65211, United States of America; The Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, United States of America.
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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: 45] [Impact Index Per Article: 11.3] [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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40
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Tadini-Buoninsegni F. Protein Adsorption on Solid Supported Membranes: Monitoring the Transport Activity of P-Type ATPases. Molecules 2020; 25:molecules25184167. [PMID: 32933017 PMCID: PMC7570688 DOI: 10.3390/molecules25184167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
P-type ATPases are a large family of membrane transporters that are found in all forms of life. These enzymes couple ATP hydrolysis to the transport of various ions or phospholipids across cellular membranes, thereby generating and maintaining crucial electrochemical potential gradients. P-type ATPases have been studied by a variety of methods that have provided a wealth of information about the structure, function, and regulation of this class of enzymes. Among the many techniques used to investigate P-type ATPases, the electrical method based on solid supported membranes (SSM) was employed to investigate the transport mechanism of various ion pumps. In particular, the SSM method allows the direct measurement of charge movements generated by the ATPase following adsorption of the membrane-bound enzyme on the SSM surface and chemical activation by a substrate concentration jump. This kind of measurement was useful to identify electrogenic partial reactions and localize ion translocation in the reaction cycle of the membrane transporter. In the present review, we discuss how the SSM method has contributed to investigate some key features of the transport mechanism of P-type ATPases, with a special focus on sarcoplasmic reticulum Ca2+-ATPase, mammalian Cu+-ATPases (ATP7A and ATP7B), and phospholipid flippase ATP8A2.
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Mhaske A, Dileep K, Kumar M, Poojary M, Pandhare K, Zhang KY, Scaria V, Binukumar B. ATP7A Clinical Genetics Resource - A comprehensive clinically annotated database and resource for genetic variants in ATP7A gene. Comput Struct Biotechnol J 2020; 18:2347-2356. [PMID: 32994893 PMCID: PMC7501406 DOI: 10.1016/j.csbj.2020.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022] Open
Abstract
ATP7A is a critical copper transporter involved in Menkes Disease, Occipital horn Syndrome and X-linked distal spinal muscular atrophy type 3 which are X linked genetic disorders. These are rare diseases and their genetic epidemiology of the diseases is unknown. A number of genetic variants in the genes have been reported in published literature as well as databases, however, understanding the pathogenicity of variants and genetic epidemiology requires the data to be compiled in a unified format. To this end, we systematically compiled genetic variants from published literature and datasets. Each of the variants were systematically evaluated for evidences with respect to their pathogenicity and classified as per the American College of Medical Genetics and the Association of Molecular Pathologists (ACMG-AMP) guidelines into Pathogenic, Likely Pathogenic, Benign, Likely Benign and Variants of Uncertain Significance. Additional integrative analysis of population genomic datasets provides insights into the genetic epidemiology of the disease through estimation of carrier frequencies in global populations. To deliver a mechanistic explanation for the pathogenicity of selected variants, we also performed molecular modeling studies. Our modeling studies concluded that the small structural distortions observed in the local structures of the protein may lead to the destabilization of the global structure. To the best of our knowledge, ATP7A Clinical Genetics Resource is one of the most comprehensive compendium of variants in the gene providing clinically relevant annotations in gene.
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Affiliation(s)
- Aditi Mhaske
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - K.V. Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mukesh Kumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Mukta Poojary
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kam Y.J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
| | - B.K. Binukumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
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Inoue M, Sakuta N, Watanabe S, Zhang Y, Yoshikaie K, Tanaka Y, Ushioda R, Kato Y, Takagi J, Tsukazaki T, Nagata K, Inaba K. Structural Basis of Sarco/Endoplasmic Reticulum Ca 2+-ATPase 2b Regulation via Transmembrane Helix Interplay. Cell Rep 2020; 27:1221-1230.e3. [PMID: 31018135 DOI: 10.1016/j.celrep.2019.03.106] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/28/2019] [Accepted: 03/27/2019] [Indexed: 12/31/2022] Open
Abstract
Sarco/endoplasmic reticulum (ER) Ca2+-ATPase 2b (SERCA2b) is a ubiquitously expressed membrane protein that facilitates Ca2+ uptake from the cytosol to the ER. SERCA2b includes a characteristic 11th transmembrane helix (TM11) followed by a luminal tail, but the structural basis of SERCA regulation by these C-terminal segments remains unclear. Here, we determined the crystal structures of SERCA2b and its C-terminal splicing variant SERCA2a, both in the E1-2Ca2+-adenylyl methylenediphosphonate (AMPPCP) state. Despite discrepancies with the previously reported structural model of SERCA2b, TM11 was found to be located adjacent to TM10 and to interact weakly with a part of the L8/9 loop and the N-terminal end of TM10, thereby inhibiting the SERCA2b catalytic cycle. Accordingly, mutational disruption of the interactions between TM11 and its neighboring residues caused SERCA2b to display SERCA2a-like ATPase activity. We propose that TM11 serves as a key modulator of SERCA2b activity by fine-tuning the intramolecular interactions with other transmembrane regions.
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Affiliation(s)
- Michio Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Nanami Sakuta
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Satoshi Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Yuxia Zhang
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Kunihito Yoshikaie
- Graduate School of Biological Sciences, NARA Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Yoshiki Tanaka
- Graduate School of Biological Sciences, NARA Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Ryo Ushioda
- Graduate School of Biological Sciences, NARA Institute of Science and Technology, Ikoma 630-0192, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Yukinari Kato
- Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan
| | - Tomoya Tsukazaki
- Graduate School of Biological Sciences, NARA Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kazuhiro Nagata
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan.
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Early-onset Wilson disease caused by ATP7B exon skipping associated with intronic variant. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005306. [PMID: 32532881 PMCID: PMC7304350 DOI: 10.1101/mcs.a005306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/08/2020] [Indexed: 12/15/2022] Open
Abstract
Wilson disease is a medically actionable rare autosomal recessive disorder of defective copper excretion caused by mutations in ATP7B, one of two highly evolutionarily conserved copper-transporting ATPases. Hundreds of disease-causing variants in ATP7B have been reported to public databases; more than half of these are missense changes, and a significant proportion are presumed unequivocal loss-of-function variants (nonsense, frameshift, and canonical splice site). Current molecular genetic testing includes sequencing all coding exons (±10 bp) as well as deletion/duplication testing, with reported sensitivity of >98%. We report a proband from a consanguineous family with a biochemical phenotype consistent with early-onset Wilson disease who tested negative on conventional molecular genetic testing. Using a combination of whole-genome sequencing and transcriptome sequencing, we found that the proband's disease is due to skipping of exons 6–7 of the ATP7B gene associated with a novel intronic variant (NM_000053.4:c.1947-19T > A) that alters a putative splicing enhancer element. This variant was also homozygous in the proband's younger sister, whose subsequent clinical evaluations revealed biochemical evidence of Wilson disease. Our work adds to emerging evidence that ATP7B exon skipping from deep intronic variants outside typical splice junctions is an important mechanism of Wilson disease; the variants responsible may elude standard genetic testing.
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Leng Y, Li P, Zhou L, Xiao L, Liu Y, Zheng Z, Qin F, Hao Q, Xu H, Yao S, Dong B. Long-Term Correction of Copper Metabolism in Wilson's Disease Mice with AAV8 Vector Delivering Truncated ATP7B. Hum Gene Ther 2020; 30:1494-1504. [PMID: 31668086 DOI: 10.1089/hum.2019.148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Wilson's disease (WD) is an autosomal recessive disorder of copper metabolism caused by mutations in the ATP7B gene encoding a liver active copper transport enzyme. Gene therapy with adeno-associated virus (AAV) carrying full-length ATP7B, which is about 4.4 kb, was shown to rescue copper metabolism disorder in WD mouse model. However, due to its relatively large size, the AAV vector containing full-length ATP7B could be oversized for its packaging capacity, which could lead to inefficient packaging. To this purpose, we engineered a truncated ATP7B mutant (tATP7B) that is about 3.3 kb in length and used for AAV gene therapy for WD mice. In vitro test showed that the excretion of copper outside the cells could be achieved with tATP7B as efficient as the full-length ATP7B. In vivo delivery of tATP7B to WD mice by AAV8 vectors corrected their copper metabolisms and significantly rescued copper accumulation-related syndromes, including reduced urinary copper excretion, increased serum ceruloplasmin, and improved liver damages. Thus, our study demonstrated that AAV gene therapy based on truncated ATP7B is a promising strategy in the treatment of WD.
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Affiliation(s)
- Yingying Leng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ping Li
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lifang Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Xiao
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Liu
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhaoyue Zheng
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fengming Qin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qiukui Hao
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Heng Xu
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shaohua Yao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Biao Dong
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Adamczyk-Szabela D, Lisowska K, Romanowska-Duda Z, Wolf WM. Combined cadmium-zinc interactions alter manganese, lead, copper uptake by Melissa officinalis. Sci Rep 2020; 10:1675. [PMID: 32015369 PMCID: PMC6997233 DOI: 10.1038/s41598-020-58491-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/10/2020] [Indexed: 11/08/2022] Open
Abstract
Farmland soil typical for the Polish rural environment was used in pot experiment to estimate the impact of cadmium and zinc on the manganese, lead and copper uptake by lemon balm (Melissa officinalis L). Bioavailable and total forms of investigated metals in soil and metal concentrations in plants were determined by atomic absorption spectrometry. The plant photosynthesis indicators were also examined. Intensification of photosynthesis upon the high zinc and cadmium soil supplementation was observed. This effect was not detected at low metal concentrations. ANOVA proved that cadmium and zinc treatments influenced manganese, lead and copper transfer from soil and their concentration in plants. Zinc uptake and accumulation in either roots or above-ground parts in plant was inversely proportional to cadmium concentration in soil. Manganese concentration in roots decreased upon the soil supplementation with either zinc or cadmium. It suggests that the latter ions are transported via symplastic pathways and compete with manganese for similar transporters. The opposite situation was observed for lead and copper. Soil supplementation with cadmium and zinc affects manganese, lead and copper concentrations and photosynthesis intensity in lemon balm plant. The following combined interactions in either normal or stress conditions are important indicators of the migration pathways.
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Affiliation(s)
- Dorota Adamczyk-Szabela
- Lodz University of Technology, Institute of General and Ecological Chemistry, 90-924, Lodz, Zeromskiego 116, Poland.
| | - Katarzyna Lisowska
- Lodz University of Technology, Institute of General and Ecological Chemistry, 90-924, Lodz, Zeromskiego 116, Poland
| | - Zdzisława Romanowska-Duda
- University of Lodz, Laboratory of Plants Ecophysiology. Faculty of Biology and Environmental Protection, 90-237, Lodz, Banacha 12/16, Poland
| | - Wojciech M Wolf
- Lodz University of Technology, Institute of General and Ecological Chemistry, 90-924, Lodz, Zeromskiego 116, Poland
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Tang N, Sandahl TD, Ott P, Kepp KP. Computing the Pathogenicity of Wilson's Disease ATP7B Mutations: Implications for Disease Prevalence. J Chem Inf Model 2019; 59:5230-5243. [PMID: 31751128 DOI: 10.1021/acs.jcim.9b00852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genetic variations in the gene encoding the copper-transport protein ATP7B are the primary cause of Wilson's disease. Controversially, clinical prevalence seems much smaller than the prevalence estimated by genetic screening tools, causing fear that many people are undiagnosed, although early diagnosis and treatment is essential. To address this issue, we benchmarked 16 state-of-the-art computational disease-prediction methods against established data of missense ATP7B mutations. Our results show that the quality of the methods varies widely. We show the importance of optimizing the threshold of the methods used to distinguish pathogenic from nonpathogenic mutations against data of clinically confirmed pathogenic and nonpathogenic mutations. We find that most methods use thresholds that predict too many ATP7B mutations to be pathogenic. Thus, our findings explain the current controversy on Wilson's disease prevalence because meta-analysis and text search methods include many computational estimates that lead to higher disease prevalence than clinically observed. As proteins and diseases differ widely, a one-size-fits-all threshold cannot distinguish pathogenic and nonpathogenic mutations efficiently, as shown here. We also show that amino acid changes with small evolutionary substitution probability, mainly due to amino acid volume, are more associated with the disease, implying a pathological effect on the conformational state of the protein, which could affect copper transport or adenosine triphosphate recognition and hydrolysis. These findings may be a first step toward a more quantitative genotype-phenotype relationship of Wilson's disease.
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Affiliation(s)
- Ning Tang
- DTU Chemistry , Technical University of Denmark , Kemitorvet 206 , 2800 Kongens Lyngby , Denmark
| | - Thomas D Sandahl
- Department of Hepatology and Gastroenterology , Aarhus University Hospital , 8200 Aarhus , Denmark
| | - Peter Ott
- Department of Hepatology and Gastroenterology , Aarhus University Hospital , 8200 Aarhus , Denmark
| | - Kasper P Kepp
- DTU Chemistry , Technical University of Denmark , Kemitorvet 206 , 2800 Kongens Lyngby , Denmark
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Han Y, Wang T, Chen G, Pu Q, Liu Q, Zhang Y, Xu L, Wu M, Liang H. A Pseudomonas aeruginosa type VI secretion system regulated by CueR facilitates copper acquisition. PLoS Pathog 2019; 15:e1008198. [PMID: 31790504 PMCID: PMC6907878 DOI: 10.1371/journal.ppat.1008198] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 12/12/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022] Open
Abstract
The type VI secretion system (T6SS) is widely distributed in Gram-negative bacteria, whose function is known to translocate substrates to eukaryotic and prokaryotic target cells to cause host damage or as a weapon for interbacterial competition. Pseudomonas aeruginosa encodes three distinct T6SS clusters (H1-, H2-, and H3-T6SS). The H1-T6SS-dependent substrates have been identified and well characterized; however, only limited information is available for the H2- and H3-T6SSs since relatively fewer substrates for them have yet been established. Here, we obtained P. aeruginosa H2-T6SS-dependent secretomes and further characterized the H2-T6SS-dependent copper (Cu2+)-binding effector azurin (Azu). Our data showed that both azu and H2-T6SS were repressed by CueR and were induced by low concentrations of Cu2+. We also identified the Azu-interacting partner OprC, a Cu2+-specific TonB-dependent outer membrane transporter. Similar to H2-T6SS genes and azu, expression of oprC was directly regulated by CueR and was induced by low Cu2+. In addition, the Azu-OprC-mediated Cu2+ transport system is critical for P. aeruginosa cells in bacterial competition and virulence. Our findings provide insights for understanding the diverse functions of T6SSs and the role of metal ions for P. aeruginosa in bacteria-bacteria competition. The type VI secretion system (T6SS) is a specific macromolecular protein export apparatus, and widely distributed in Gram-negative bacteria. T6SS plays an important role in anti-bacterial competition or delivers effector proteins to both eukaryotic and prokaryotic cells. In the present study, we performed secretomes analysis and identified 21 substrates of P. aeruginosa H2-T6SS-dependent. Specifically, we report a Cu2+-scavenging pathway consisting of a copper transporter, OprC, and a type VI secretion system (H2-T6SS)-secreted Cu2+-binding protein, Azu. Both of them are under control of the transcriptional regulator CueR. Indeed, the Azu-OprC-mediated Cu2+ transport system is critical for P. aeruginosa cells in bacterial competition and virulence. These findings exemplify how P. aeruginosa deploys this metal system to adapt to the complex environment during evolution.
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Affiliation(s)
- Yuying Han
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Tietao Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Gukui Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Qinqin Pu
- Department of Basic Science, School of Medicine and Health Science, University of North Dakota, Grand Forks, North Dakota, United States of America
| | - Qiong Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, GuangDong, China
| | - Yani Zhang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Linghui Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, GuangDong, China
| | - Min Wu
- Department of Basic Science, School of Medicine and Health Science, University of North Dakota, Grand Forks, North Dakota, United States of America
| | - Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
- * E-mail:
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Alwan KB, Welch EF, Blackburn NJ. Catalytic M Center of Copper Monooxygenases Probed by Rational Design. Effects of Selenomethionine and Histidine Substitution on Structure and Reactivity. Biochemistry 2019; 58:4436-4446. [PMID: 31626532 DOI: 10.1021/acs.biochem.9b00823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The M centers of the mononuclear monooxygenases peptidylglycine monooxygenase (PHM) and dopamine β-monooxygenase bind and activate dioxygen en route to substrate hydroxylation. Recently, we reported the rational design of a protein-based model in which the CusF metallochaperone was repurposed via a His to Met mutation to act as a structural and spectroscopic biomimic. The PHM M site exhibits a number of unusual attributes, including a His2Met ligand set, a fluxional Cu(I)-S(Met) bond, tight binding of exogenous ligands CO and N3-, and complete coupling of oxygen reduction to substrate hydroxylation even at extremely low turnover rates. In particular, mutation of the Met ligand to His completely eliminates the catalytic activity despite the propensity of CuI-His3 centers to bind and activate dioxygen in other metalloenzyme systems. Here, we further develop the CusF-based model to explore methionine variants in which Met is replaced by selenomethionine (SeM) and histidine. We examine the effects on coordinate structure and exogenous ligand binding via X-ray absorption spectroscopy and electron paramagnetic resonance and probe the consequences of mutations on redox chemistry via studies of the reduction by ascorbate and oxidation via molecular oxygen. The M-site model is three-coordinate in the Cu(I) state and binds CO to form a four-coordinate carbonyl. In the oxidized forms, the coordination changes to tetragonal five-coordinate with a long axial Met ligand that like the enzymes is undetectable at either the Cu or Se K edges. The EXAFS data at the Se K edge of the SeM variant provide unique information about the nature of the Cu-methionine bond that is likewise weak and fluxional. Kinetic studies document the sluggish reactivity of the Cu(I) complexes with molecular oxygen and rapid rates of reduction of the Cu(II) complexes by ascorbate, indicating a remarkable stability of the Cu(I) state in all three derivatives. The results show little difference between the Met ligand and its SeM and His congeners and suggest that the Met contributes to catalysis in ways that are more complex than simple perturbation of the redox chemistry. Overall, the results stimulate a critical re-examination of the canonical reaction mechanisms of the mononuclear copper monooxygenases.
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Affiliation(s)
- Katherine B Alwan
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Evan F Welch
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
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Petruzzelli R, Polishchuk RS. Activity and Trafficking of Copper-Transporting ATPases in Tumor Development and Defense against Platinum-Based Drugs. Cells 2019; 8:E1080. [PMID: 31540259 PMCID: PMC6769697 DOI: 10.3390/cells8091080] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
Membrane trafficking pathways emanating from the Golgi regulate a wide range of cellular processes. One of these is the maintenance of copper (Cu) homeostasis operated by the Golgi-localized Cu-transporting ATPases ATP7A and ATP7B. At the Golgi, these proteins supply Cu to newly synthesized enzymes which use this metal as a cofactor to catalyze a number of vitally important biochemical reactions. However, in response to elevated Cu, the Golgi exports ATP7A/B to post-Golgi sites where they promote sequestration and efflux of excess Cu to limit its potential toxicity. Growing tumors actively consume Cu and employ ATP7A/B to regulate the availability of this metal for oncogenic enzymes such as LOX and LOX-like proteins, which confer higher invasiveness to malignant cells. Furthermore, ATP7A/B activity and trafficking allow tumor cells to detoxify platinum (Pt)-based drugs (like cisplatin), which are used for the chemotherapy of different solid tumors. Despite these noted activities of ATP7A/B that favor oncogenic processes, the mechanisms that regulate the expression and trafficking of Cu ATPases in malignant cells are far from being completely understood. This review summarizes current data on the role of ATP7A/B in the regulation of Cu and Pt metabolism in malignant cells and outlines questions and challenges that should be addressed to understand how ATP7A and ATP7B trafficking mechanisms might be targeted to counteract tumor development.
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Affiliation(s)
- Raffaella Petruzzelli
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy.
| | - Roman S Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy.
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Abstract
Copper is a redox-active transition metal ion required for the function of many essential human proteins. For biosynthesis of proteins coordinating copper, the metal may bind before, during or after folding of the polypeptide. If the metal binds to unfolded or partially folded structures of the protein, such coordination may modulate the folding reaction. The molecular understanding of how copper is incorporated into proteins requires descriptions of chemical, thermodynamic, kinetic and structural parameters involved in the formation of protein-metal complexes. Because free copper ions are toxic, living systems have elaborate copper-transport systems that include particular proteins that facilitate efficient and specific delivery of copper ions to target proteins. Therefore, these pathways become an integral part of copper protein folding in vivo. This review summarizes biophysical-molecular in vitro work assessing the role of copper in folding and stability of copper-binding proteins as well as protein-protein copper exchange reactions between human copper transport proteins. We also describe some recent findings about the participation of copper ions and copper proteins in protein misfolding and aggregation reactions in vitro.
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