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Bak DW, Weerapana E. Proteomic strategies to interrogate the Fe-S proteome. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119791. [PMID: 38925478 PMCID: PMC11365765 DOI: 10.1016/j.bbamcr.2024.119791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Iron‑sulfur (Fe-S) clusters, inorganic cofactors composed of iron and sulfide, participate in numerous essential redox, non-redox, structural, and regulatory biological processes within the cell. Though structurally and functionally diverse, the list of all proteins in an organism capable of binding one or more Fe-S clusters is referred to as its Fe-S proteome. Importantly, the Fe-S proteome is highly dynamic, with continuous cluster synthesis and delivery by complex Fe-S cluster biogenesis pathways. This cluster delivery is balanced out by processes that can result in loss of Fe-S cluster binding, such as redox state changes, iron availability, and oxygen sensitivity. Despite continued expansion of the Fe-S protein catalogue, it remains a challenge to reliably identify novel Fe-S proteins. As such, high-throughput techniques that can report on native Fe-S cluster binding are required to both identify new Fe-S proteins, as well as characterize the in vivo dynamics of Fe-S cluster binding. Due to the recent rapid growth in mass spectrometry, proteomics, and chemical biology, there has been a host of techniques developed that are applicable to the study of native Fe-S proteins. This review will detail both the current understanding of the Fe-S proteome and Fe-S cluster biology as well as describing state-of-the-art proteomic strategies for the study of Fe-S clusters within the context of a native proteome.
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Affiliation(s)
- Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
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2
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Liang F, Sun S, Zhou Y, Peng T, Xu X, Li B, Tan G. Escherichia coli alcohol dehydrogenase YahK is a protein that binds both iron and zinc. PeerJ 2024; 12:e18040. [PMID: 39282118 PMCID: PMC11397123 DOI: 10.7717/peerj.18040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 08/13/2024] [Indexed: 09/18/2024] Open
Abstract
Background Previous studies have highlighted the catalytic activity of Escherichia coli alcohol dehydrogenase YahK in the presence of coenzyme nicotinamide adenine dinucleotide (NAD) and metal zinc. Notably, competitive interaction between iron and zinc ligands has been shown to influence the catalytic efficiency of several key proteases. This study aims to unravel the intricate mechanisms underlying YahK's catalytic action, with a particular focus on the pivotal roles played by metal ions zinc and iron. Methods The purified YahK protein from E. coli cells cultivated in LB medium was utilized to investigate its metal-binding properties through UV-visible absorption measurements and determination of metal content. Subsequently, the effects of excess zinc and iron on the metal-binding ability and alcohol dehydrogenase activity of the YahK protein were explored using M9 minimal medium. Furthermore, site-directed mutagenesis technology was employed to determine the iron-binding site location within the YahK protein. Polyacrylamide gel electrophoresis was conducted to examine the relationship between iron and zinc with respect to the YahK protein. Results The study confirmed the presence of iron and zinc in the YahK protein, with the zinc-bound form exhibiting enhanced catalytic activity in alcohol dehydrogenation reactions. Conversely, the presence of iron appears to play a pivotal role in maintaining overall stability of the YahK protein. Furthermore, experimental findings indicate that excessive zinc within M9 minimal medium can competitively bind to iron-binding sites on YahK, thereby augmenting its alcohol dehydrogenase activity. Conclusion The dynamic binding of YahK to iron and zinc unveils its intricate regulatory mechanism as an alcohol dehydrogenase, thereby highlighting the possible physiological role of YahK in E. coli and its significance in governing cellular metabolic processes. This discovery provides a novel perspective for further investigating the specific impact of metal ion binding on YahK and E. coli cell metabolism.
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Affiliation(s)
- Feng Liang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Shujuan Sun
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi, Shandong, China
| | - YongGuang Zhou
- Laboratory of Molecular Medicine, Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tiantian Peng
- Laboratory of Molecular Medicine, Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xianxian Xu
- Laboratory of Molecular Medicine, Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Beibei Li
- Laboratory of Molecular Medicine, Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Guoqiang Tan
- Laboratory of Molecular Medicine, Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
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3
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Zeng X, Wei T, Wang X, Liu Y, Tan Z, Zhang Y, Feng T, Cheng Y, Wang F, Ma B, Qin W, Gao C, Xiao J, Wang C. Discovery of metal-binding proteins by thermal proteome profiling. Nat Chem Biol 2024; 20:770-778. [PMID: 38409364 DOI: 10.1038/s41589-024-01563-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
Metal-binding proteins (MBPs) have various and important biological roles in all living species and many human diseases are intricately linked to dysfunctional MBPs. Here, we report a chemoproteomic method named 'metal extraction-triggered agitation logged by thermal proteome profiling' (METAL-TPP) to globally profile MBPs in proteomes. The method involves the extraction of metals from MBPs using chelators and monitoring the resulting protein stability changes through thermal proteome profiling. Applying METAL-TPP to the human proteome with a broad-spectrum chelator, EDTA, revealed a group of proteins with reduced thermal stability that contained both previously known MBPs and currently unannotated MBP candidates. Biochemical characterization of one potential target, glutamine-fructose-6-phosphate transaminase 2 (GFPT2), showed that zinc bound the protein, inhibited its enzymatic activity and modulated the hexosamine biosynthesis pathway. METAL-TPP profiling with another chelator, TPEN, uncovered additional MBPs in proteomes. Collectively, this study developed a robust tool for proteomic discovery of MBPs and provides a rich resource for functional studies of metals in cell biology.
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Affiliation(s)
- Xin Zeng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Tiantian Wei
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xianghe Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Zhenshu Tan
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yihai Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Tianyu Feng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yao Cheng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Fengzhang Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Bin Ma
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Wei Qin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chuanping Gao
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Junyu Xiao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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4
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Coverdale JPC, Polepalli S, Arruda MAZ, da Silva ABS, Stewart AJ, Blindauer CA. Recent Advances in Metalloproteomics. Biomolecules 2024; 14:104. [PMID: 38254704 PMCID: PMC10813065 DOI: 10.3390/biom14010104] [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: 10/20/2023] [Revised: 11/17/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Interactions between proteins and metal ions and their complexes are important in many areas of the life sciences, including physiology, medicine, and toxicology. Despite the involvement of essential elements in all major processes necessary for sustaining life, metalloproteomes remain ill-defined. This is not only owing to the complexity of metalloproteomes, but also to the non-covalent character of the complexes that most essential metals form, which complicates analysis. Similar issues may also be encountered for some toxic metals. The review discusses recently developed approaches and current challenges for the study of interactions involving entire (sub-)proteomes with such labile metal ions. In the second part, transition metals from the fourth and fifth periods are examined, most of which are xenobiotic and also tend to form more stable and/or inert complexes. A large research area in this respect concerns metallodrug-protein interactions. Particular attention is paid to separation approaches, as these need to be adapted to the reactivity of the metal under consideration.
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Affiliation(s)
- James P. C. Coverdale
- School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Edgbaston B15 2TT, UK;
| | | | - Marco A. Z. Arruda
- Institute of Chemistry, Department of Analytical Chemistry, Universidade Estadual de Campinas, Campinas 13083-970, Brazil; (M.A.Z.A.); (A.B.S.d.S.)
| | - Ana B. Santos da Silva
- Institute of Chemistry, Department of Analytical Chemistry, Universidade Estadual de Campinas, Campinas 13083-970, Brazil; (M.A.Z.A.); (A.B.S.d.S.)
| | - Alan J. Stewart
- School of Medicine, University of St. Andrews, St Andrews KY16 9TF, UK
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5
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Hagen WR. The Development of Tungsten Biochemistry-A Personal Recollection. Molecules 2023; 28:molecules28104017. [PMID: 37241758 DOI: 10.3390/molecules28104017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The development of tungsten biochemistry is sketched from the viewpoint of personal participation. Following its identification as a bio-element, a catalogue of genes, enzymes, and reactions was built up. EPR spectroscopic monitoring of redox states was, and remains, a prominent tool in attempts to understand tungstopterin-based catalysis. A paucity of pre-steady-state data remains a hindrance to overcome to this day. Tungstate transport systems have been characterized and found to be very specific for W over Mo. Additional selectivity is presented by the biosynthetic machinery for tungstopterin enzymes. Metallomics analysis of hyperthermophilic archaeon Pyrococcus furiosus indicates a comprehensive inventory of tungsten proteins.
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Affiliation(s)
- Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Building 58, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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6
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Cheng Y, Wang H, Xu H, Liu Y, Ma B, Chen X, Zeng X, Wang X, Wang B, Shiau C, Ovchinnikov S, Su XD, Wang C. Co-evolution-based prediction of metal-binding sites in proteomes by machine learning. Nat Chem Biol 2023; 19:548-555. [PMID: 36593274 DOI: 10.1038/s41589-022-01223-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 11/08/2022] [Indexed: 01/03/2023]
Abstract
Metal ions have various important biological roles in proteins, including structural maintenance, molecular recognition and catalysis. Previous methods of predicting metal-binding sites in proteomes were based on either sequence or structural motifs. Here we developed a co-evolution-based pipeline named 'MetalNet' to systematically predict metal-binding sites in proteomes. We applied MetalNet to proteomes of four representative prokaryotic species and predicted 4,849 potential metalloproteins, which substantially expands the currently annotated metalloproteomes. We biochemically and structurally validated previously unannotated metal-binding sites in several proteins, including apo-citrate lyase phosphoribosyl-dephospho-CoA transferase citX, an Escherichia coli enzyme lacking structural or sequence homology to any known metalloprotein (Protein Data Bank (PDB) codes: 7DCM and 7DCN ). MetalNet also successfully recapitulated all known zinc-binding sites from the human spliceosome complex. The pipeline of MetalNet provides a unique and enabling tool for interrogating the hidden metalloproteome and studying metal biology.
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Affiliation(s)
- Yao Cheng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Haobo Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hua Xu
- State Key Laboratory of Protein and Plant Gene Research, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China.
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Bin Ma
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xuemin Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xin Zeng
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xianghe Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Bo Wang
- State Key Laboratory of Protein and Plant Gene Research, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
| | | | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellow, Harvard University, Cambridge, MA, USA
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China.
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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7
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Huynh TN, Stewart V. Purine catabolism by enterobacteria. Adv Microb Physiol 2023; 82:205-266. [PMID: 36948655 DOI: 10.1016/bs.ampbs.2023.01.001] [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] [Indexed: 02/13/2023]
Abstract
Purines are abundant among organic nitrogen sources and have high nitrogen content. Accordingly, microorganisms have evolved different pathways to catabolize purines and their metabolic products such as allantoin. Enterobacteria from the genera Escherichia, Klebsiella and Salmonella have three such pathways. First, the HPX pathway, found in the genus Klebsiella and very close relatives, catabolizes purines during aerobic growth, extracting all four nitrogen atoms in the process. This pathway includes several known or predicted enzymes not previously observed in other purine catabolic pathways. Second, the ALL pathway, found in strains from all three species, catabolizes allantoin during anaerobic growth in a branched pathway that also includes glyoxylate assimilation. This allantoin fermentation pathway originally was characterized in a gram-positive bacterium, and therefore is widespread. Third, the XDH pathway, found in strains from Escherichia and Klebsiella spp., at present is ill-defined but likely includes enzymes to catabolize purines during anaerobic growth. Critically, this pathway may include an enzyme system for anaerobic urate catabolism, a phenomenon not previously described. Documenting such a pathway would overturn the long-held assumption that urate catabolism requires oxygen. Overall, this broad capability for purine catabolism during either aerobic or anaerobic growth suggests that purines and their metabolites contribute to enterobacterial fitness in a variety of environments.
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Affiliation(s)
- TuAnh Ngoc Huynh
- Department of Food Science, University of Wisconsin, Madison, WI, United States
| | - Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, CA, United States.
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8
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van Dijk MC, de Kruijff RM, Hagedoorn PL. The Role of Iron in Staphylococcus aureus Infection and Human Disease: A Metal Tug of War at the Host—Microbe Interface. Front Cell Dev Biol 2022; 10:857237. [PMID: 35399529 PMCID: PMC8986978 DOI: 10.3389/fcell.2022.857237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/24/2022] [Indexed: 11/27/2022] Open
Abstract
Iron deficiency anemia can be treated with oral or intravenous Fe supplementation. Such supplementation has considerable effects on the human microbiome, and on opportunistic pathogenic micro-organisms. Molecular understanding of the control and regulation of Fe availability at the host-microbe interface is crucial to interpreting the side effects of Fe supplementation. Here, we provide a concise overview of the regulation of Fe by the opportunistic pathogen Staphylococcus aureus. Ferric uptake regulator (Fur) plays a central role in controlling Fe uptake, utilization and storage in order to maintain a required value. The micro-organism has a strong preference for heme iron as an Fe source, which is enabled by the Iron-regulated surface determinant (Isd) system. The strategies it employs to overcome Fe restriction imposed by the host include: hijacking host proteins, replacing metal cofactors, and replacing functions by non-metal dependent enzymes. We propose that integrated omics approaches, which include metalloproteomics, are necessary to provide a comprehensive understanding of the metal tug of war at the host-microbe interface down to the molecular level.
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Affiliation(s)
- Madeleine C. van Dijk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
- Department of Radiation Science and Technology, Delft University of Technology, Delft, Netherlands
| | - Robin M. de Kruijff
- Department of Radiation Science and Technology, Delft University of Technology, Delft, Netherlands
- *Correspondence: Robin M. de Kruijff, ; Peter-Leon Hagedoorn,
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
- *Correspondence: Robin M. de Kruijff, ; Peter-Leon Hagedoorn,
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9
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Abstract
Metalloproteins play diverse and critical functions in all living systems, and their dysfunctional forms are closely related to many human diseases. The development of methods that enable comprehensive mapping of metalloproteome is of great interest to help elucidate crucial roles of metalloproteins in both physiology and pathology, as well as to discover new metalloproteins. We herein briefly review recent progress in the field of metalloproteomics and provide future outlooks.
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Affiliation(s)
- Xin Zeng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yao Cheng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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10
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Brandis G. Reconstructing the Evolutionary History of a Highly Conserved Operon Cluster in Gammaproteobacteria and Bacilli. Genome Biol Evol 2021; 13:6156628. [PMID: 33677562 PMCID: PMC8046335 DOI: 10.1093/gbe/evab041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/01/2022] Open
Abstract
The evolution of gene order rearrangements within bacterial chromosomes is a fast process. Closely related species can have almost no conservation in long-range gene order. A prominent exception to this rule is a >40 kb long cluster of five core operons (secE-rpoBC-str-S10-spc-alpha) and three variable adjacent operons (cysS, tufB, and ecf) that together contain 57 genes of the transcriptional and translational machinery. Previous studies have indicated that at least part of this operon cluster might have been present in the last common ancestor of bacteria and archaea. Using 204 whole genome sequences, ∼2 Gy of evolution of the operon cluster were reconstructed back to the last common ancestors of the Gammaproteobacteria and of the Bacilli. A total of 163 independent evolutionary events were identified in which the operon cluster was altered. Further examination showed that the process of disconnecting two operons generally follows the same pattern. Initially, a small number of genes is inserted between the operons breaking the concatenation followed by a second event that fully disconnects the operons. While there is a general trend for loss of gene synteny over time, there are examples of increased alteration rates at specific branch points or within specific bacterial orders. This indicates the recurrence of relaxed selection on the gene order within bacterial chromosomes. The analysis of the alternation events indicates that segmental genome duplications and/or transposon-directed recombination play a crucial role in rearrangements of the operon cluster.
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Affiliation(s)
- Gerrit Brandis
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Sweden
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11
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Taher R, de Rosny E. A structure-function study of ZraP and ZraS provides new insights into the two-component system Zra. Biochim Biophys Acta Gen Subj 2020; 1865:129810. [PMID: 33309686 DOI: 10.1016/j.bbagen.2020.129810] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/16/2020] [Accepted: 12/07/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Zra belongs to the envelope stress response (ESR) two-component systems (TCS). It is atypical because of its third periplasmic repressor partner (ZraP), in addition to its histidine kinase sensor protein (ZraS) and its response regulator (ZraR) components. Furthermore, although it is activated by Zn2+, it is not involved in zinc homeostasis or protection against zinc toxicity. Here, we mainly focus on ZraS but also provide information on ZraP. METHODS The purified periplasmic domain of ZraS and ZraP were characterized using biophysical and biochemical technics: multi-angle laser light scattering (MALLS), circular dichroism (CD), differential scanning fluorescence (DSF), inductively coupled plasma atomic emission spectroscopy (ICP-AES), cross-linking and small-angle X-ray scattering (SAXS). In-vivo experiments were carried out to determine the redox state of the cysteine residue in ZraP and the consequences for the cell of an over-activation of the Zra system. RESULTS We show that ZraS binds one Zn2+ molecule with high affinity resulting in conformational changes of the periplasmic domain, consistent with a triggering function of the metal ion. We also demonstrate that, in the periplasm, the only cysteine residue of ZraP is at least partially reduced. Using SAXS, we conclude that the previously determined X-ray structure is different from the structure in solution. CONCLUSION Our results allow us to propose a general mechanism for the Zra system activation and to compare it to the homologous Cpx system. GENERAL SIGNIFICANCE We bring new input on the so far poorly described Zra system and notably on ZraS.
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Affiliation(s)
- Raleb Taher
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France; University of California, Irvine, Medical Science Building B, CA 92697, United States of America
| | - Eve de Rosny
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France.
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12
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Spanka DT, Konzer A, Edelmann D, Berghoff BA. High-Throughput Proteomics Identifies Proteins With Importance to Postantibiotic Recovery in Depolarized Persister Cells. Front Microbiol 2019; 10:378. [PMID: 30894840 PMCID: PMC6414554 DOI: 10.3389/fmicb.2019.00378] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial populations produce phenotypic variants called persisters to survive harmful conditions. Persisters are highly tolerant to antibiotics and repopulate environments after the stress has vanished. In order to resume growth, persisters have to recover from the persistent state, but the processes behind recovery remain mostly elusive. Deciphering these processes is an essential step toward understanding the persister phenomenon in its entirety. High-throughput proteomics by mass spectrometry is a valuable tool to assess persister physiology during any stage of the persister life cycle, and is expected to considerably contribute to our understanding of the recovery process. In the present study, an Escherichia coli strain, that overproduces the membrane-depolarizing toxin TisB, was established as a model for persistence by the use of high-throughput proteomics. Labeling of TisB persisters with stable isotope-containing amino acids (pulsed-SILAC) revealed an active translational response to ampicillin, including several RpoS-dependent proteins. Subsequent investigation of the persister proteome during postantibiotic recovery by label-free quantitative proteomics identified proteins with importance to the recovery process. Among them, AhpF, a component of alkyl hydroperoxide reductase, and the outer membrane porin OmpF were found to affect the persistence time of TisB persisters. Assessing the role of AhpF and OmpF in TisB-independent persisters demonstrated that the importance of a particular protein for the recovery process strongly depends on the physiological condition of a persister cell. Our study provides important insights into persister physiology and the processes behind recovery of depolarized cells.
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Affiliation(s)
- Daniel-Timon Spanka
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Daniel Edelmann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
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van der Weel L, As KS, Dekker WJ, van den Eijnden L, van Helmond W, Schiphorst C, Hagen WR, Hagedoorn PL. ZraP, the most prominent zinc protein under zinc stress conditions has no direct role in in-vivo zinc tolerance in Escherichia coli. J Inorg Biochem 2019; 192:98-106. [DOI: 10.1016/j.jinorgbio.2018.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/28/2018] [Accepted: 12/21/2018] [Indexed: 10/27/2022]
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14
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Abstract
Chemical speciation approaches is an inherent part of metallomics, once metals/metalloids and organic structures need to be currently evaluated for attaining metallomics studies. Then, this chapter focuses on the applications of the chemical speciation applied to the human health risk, food and human diet, drugs, forensic, nanoscience, and geological metallomics, also pointing out the advances in such area. Some aspects regarding sample preparation is commented along this chapter, and some strategies for maintaining the integrity of the metallomics information are also emphasized.
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15
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Proteome scale identification, classification and structural analysis of iron-binding proteins in bread wheat. J Inorg Biochem 2017; 170:63-74. [DOI: 10.1016/j.jinorgbio.2017.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/23/2017] [Accepted: 02/10/2017] [Indexed: 12/26/2022]
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16
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Wątły J, Potocki S, Rowińska-Żyrek M. Zinc Homeostasis at the Bacteria/Host Interface-From Coordination Chemistry to Nutritional Immunity. Chemistry 2016; 22:15992-16010. [DOI: 10.1002/chem.201602376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry; University of Wroclaw; F. Joliot-Curie 14 50-383 Wroclaw Poland
| | - Sławomir Potocki
- Faculty of Chemistry; University of Wroclaw; F. Joliot-Curie 14 50-383 Wroclaw Poland
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Tikhomirova A, Jiang D, Kidd SP. A new insight into the role of intracellular nickel levels for the stress response, surface properties and twitching motility by Haemophilus influenzae. Metallomics 2016; 7:650-61. [PMID: 25350148 DOI: 10.1039/c4mt00245h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nickel acts as a co-factor for a small number of enzymes in bacteria. Urease is one of the two nickel-dependent enzymes that have been identified in Haemophilus influenzae; glyoxalase I is the other. However, nickel has been suggested to have roles in H. influenzae that can not attributed to the function of these enzymes. We have previously shown that in the H. influenzae strain Rd KW20 the inability to acquire nickel led to alterations to the cell-type; an increased biofilm formation and changes in cell surface properties. Here we report the differences in the genome wide gene expression between Rd KW20 and a strain incapable of importing nickel (nikQ); revealing a link between intracellular nickel levels and genes involved in metabolic pathways, stress responses and genes associated with surface factors such as type IV pili. We have then taken a strain previously shown to use type IV pili both in biofilm formation and for twitching motility (86-028NP) and have shown its homologous genes (NTHI1417-1422; annotated as cobalt transporter, cbiKLMOQ) did import nickel and mutations in this locus had pleiotropic effects correlating to stress response and motility. Compared to wild type cells, the nickel depleted cells were more electronegativity charged, they aggregated and formed a biofilm. Correct intracellular nickel levels were also important for resistance to oxidative stress; the nickel depleted cells were more sensitive to oxidative stress. The nickel depleted cells were also non-motile, but the addition specifically of nickel returned these cells to a wild type motility state. We have also analysed the role of nickel uptake in a naturally, urease negative strain (the blood isolate R2866) and depleting intracellular nickel (a nikQ mutant) in this strain effected a similar range of cell functions. These data reveal a role for the capacity to acquire nickel from the environment and for the correct intracellular nickel levels as part of H. influenzae stress response and in signalling for a switch to a sessile bacterial lifestyle.
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Affiliation(s)
- Alexandra Tikhomirova
- Research Centre for Infectious Disease, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, 5005, Australia.
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18
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Hagedoorn PL. Microbial Metalloproteomics. Proteomes 2015; 3:424-439. [PMID: 28248278 PMCID: PMC5217388 DOI: 10.3390/proteomes3040424] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/04/2015] [Accepted: 11/23/2015] [Indexed: 12/12/2022] Open
Abstract
Metalloproteomics is a rapidly developing field of science that involves the comprehensive analysis of all metal-containing or metal-binding proteins in a biological sample. The purpose of this review is to offer a comprehensive overview of the research involving approaches that can be categorized as inductively coupled plasma (ICP)-MS based methods, X-ray absorption/fluorescence, radionuclide based methods and bioinformatics. Important discoveries in microbial proteomics will be reviewed, as well as the outlook to new emerging approaches and research areas.
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Affiliation(s)
- Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
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19
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Biophysical and physiological characterization of ZraP from Escherichia coli, the periplasmic accessory protein of the atypical ZraSR two-component system. Biochem J 2015; 472:205-16. [DOI: 10.1042/bj20150827] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022]
Abstract
ZraP is an octamer containing four interfacial metal-binding sites contributing to dimer stability. Zinc binding enhances its chaperone properties and zinc-bound ZraP represses the expression of the zraPSR operon. None of the Zra proteins are involved in zinc resistance.
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20
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Blindauer CA. Advances in the molecular understanding of biological zinc transport. Chem Commun (Camb) 2015; 51:4544-63. [DOI: 10.1039/c4cc10174j] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recognition of the importance of zinc homeostasis for health has driven a surge in structural data on major zinc-transporting proteins.
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21
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Helmann JD. Specificity of metal sensing: iron and manganese homeostasis in Bacillus subtilis. J Biol Chem 2014; 289:28112-20. [PMID: 25160631 DOI: 10.1074/jbc.r114.587071] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Metalloregulatory proteins allow cells to sense metal ions and appropriately adjust the expression of metal uptake, storage, and efflux pathways. Bacillus subtilis provides a model for the coordinate regulation of iron and manganese homeostasis that involves three key regulators: Fur senses iron sufficiency, MntR senses manganese sufficiency, and PerR senses the intracellular Fe/Mn ratio. Here, I review the structural and physiological bases of selective metal perception, the effects of non-cognate metals, and mechanisms that may serve to coordinate iron and manganese homeostasis.
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Affiliation(s)
- John D Helmann
- From the Department of Microbiology, Cornell University, Ithaca, New York 14853-8101
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22
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Vogiatzis C, Zachariadis G. Tandem mass spectrometry in metallomics and the involving role of ICP-MS detection: A review. Anal Chim Acta 2014; 819:1-14. [DOI: 10.1016/j.aca.2014.01.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 01/05/2014] [Accepted: 01/10/2014] [Indexed: 01/02/2023]
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23
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Fu D, Finney L. Metalloproteomics: challenges and prospective for clinical research applications. Expert Rev Proteomics 2014; 11:13-9. [PMID: 24433146 DOI: 10.1586/14789450.2014.876365] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Metals are essential cofactors, utilized in many critical cellular processes. For example, zinc is important in insulin biosynthesis and may play a role in Alzheimer's disease, but much of how the zinc-mediated process remains unknown. Knowing which metal is in which protein at a given point in time would lead to new insights into how metals work in biological systems. New tools are being developed to investigate the biochemistry and cell biology of metals, with potential for biomedical applications. In this report, we consider the promise and limitations of metalloproteins detection techniques. We provide a brief overview of the techniques available and a discussion of the technical challenges to biomedical applications, with particular focus on what must be overcome for the potential of these approaches to be achieved.
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Affiliation(s)
- Dax Fu
- Department of Physiology, Johns Hopkins School of Medicine, 202 Physiology Building, 725 North Wolfe Street, Baltimore, MD 21205, USA
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24
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Barnett JP, Scanlan DJ, Blindauer CA. Identification of major zinc-binding proteins from a marine cyanobacterium: insight into metal uptake in oligotrophic environments. Metallomics 2014; 6:1254-68. [DOI: 10.1039/c4mt00048j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The open ocean cyanobacteriumSynechococcussp. WH8102 thrives at extremely low zinc concentrations. Metalloproteomics experiments have identified an outer-membrane bound porin with zinc-binding ability that is upregulated at low zinc levels, suggesting a role for porins in highly efficient zinc uptake.
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25
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Wang D, Fierke CA. The BaeSR regulon is involved in defense against zinc toxicity in E. coli. Metallomics 2013; 5:372-83. [PMID: 23446818 DOI: 10.1039/c3mt20217h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intracellular zinc homeostasis is regulated by an extensive network of transporters, ligands and transcription factors. The zinc detoxification functions of three transporters and a periplasmic protein regulated by the BaeSR two-component system were explored in this work by evaluating the effect of single gene knockouts in the BaeSR regulon on the cell growth rate, free zinc, total zinc and total copper after zinc shock. Two exporters, MdtABC and MdtD, and the periplasmic protein, Spy, are involved in zinc detoxification based on the growth defects at high cell density and increases in free (>1000-fold) and total zinc/copper (>2-fold) that were observed in the single knockout strains upon exposure to zinc. These proteins complement the ATP-driven zinc export mediated by ZntA in E. coli to limit zinc toxicity. These results highlight the functions of the BaeSR regulon in metal homeostasis.
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Affiliation(s)
- Da Wang
- Department of Chemistry, The University of Michigan, 930 N University Ave, Ann Arbor, MI 48109, USA
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26
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Hu L, Cheng T, He B, Li L, Wang Y, Lai YT, Jiang G, Sun H. Identification of Metal-Associated Proteins in Cells by Using Continuous-Flow Gel Electrophoresis and Inductively Coupled Plasma Mass Spectrometry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300794] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Hu L, Cheng T, He B, Li L, Wang Y, Lai YT, Jiang G, Sun H. Identification of metal-associated proteins in cells by using continuous-flow gel electrophoresis and inductively coupled plasma mass spectrometry. Angew Chem Int Ed Engl 2013; 52:4916-20. [PMID: 23553936 DOI: 10.1002/anie.201300794] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Ligang Hu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, P. R. China
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28
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Saito S, Kawashima M, Ohshima H, Enomoto K, Sato M, Yoshimura H, Yoshimoto K, Maeda M, Shibukawa M. Separation of metalloproteins using a novel metal ion contaminant sweeping technique and detection of protein-bound copper by a metal ion probe in polyacrylamide gel electrophoresis: distribution of copper in human serum. Analyst 2013; 138:6097-105. [DOI: 10.1039/c3an01107k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Abstract
Zinc(II) ions are catalytic, structural, and regulatory cofactors in proteins. In contrast to painstakingly collecting the pieces by isolating and characterizing zinc proteins, 'omics' approaches are now allowing us to tease out information about zinc proteins from genomes and to piece together the information to a broader knowledge and appreciation of the role of zinc in biology. Estimates for the number of zinc proteins in the human genome and in genomes of other organisms have been derived from a bioinformatics approach: mining sequence databases for homologies of known zinc-coordination motifs with characteristic ligand signatures for metal binding and combining this information with the knowledge about metal-binding domains of proteins. This approach resulted in an impressive number of almost 3000 human zinc proteins and made major contributions to our understanding of the composition of the zinc proteome and the functions of zinc proteins. However, the impact of zinc on protein science is even greater. Predictions do not include yet undiscovered ligand signatures, coordination environments that employ complex binding patterns with nonsequential binding of ligands and ligand bridges, zinc/protein interactions at protein interfaces, and transient interactions of zinc(II) ions with proteins that are not known to be zinc proteins. All this information and recent discoveries of how cellular zinc is controlled and how zinc(II) ions function as signaling ions add an hitherto unrecognized dimension to the zinc proteome of multicellular eukaryotic organisms. Zinc proteomics employs a combination of approaches from different disciplines, such as bioinformatics, biology, inorganic biochemistry, and significantly, analytical and structural chemistry. It provides crucial large-scale datasets for interpreting the roles of zinc in health and disease at both a molecular and a global, systems biology, level.
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Affiliation(s)
- Wolfgang Maret
- King's College London, School of Medicine, Diabetes and Nutritional Sciences Division, Metal Metabolism Group, London, SE1 9NH, UK,
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Iobbi-Nivol C, Leimkühler S. Molybdenum enzymes, their maturation and molybdenum cofactor biosynthesis in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012. [PMID: 23201473 DOI: 10.1016/j.bbabio.2012.11.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molybdenum cofactor (Moco) biosynthesis is an ancient, ubiquitous, and highly conserved pathway leading to the biochemical activation of molybdenum. Moco is the essential component of a group of redox enzymes, which are diverse in terms of their phylogenetic distribution and their architectures, both at the overall level and in their catalytic geometry. A wide variety of transformations are catalyzed by these enzymes at carbon, sulfur and nitrogen atoms, which include the transfer of an oxo group or two electrons to or from the substrate. More than 50 molybdoenzymes were identified in bacteria to date. In molybdoenzymes Mo is coordinated to a dithiolene group on the 6-alkyl side chain of a pterin called molybdopterin (MPT). The biosynthesis of Moco can be divided into four general steps in bacteria: 1) formation of the cyclic pyranopterin monophosphate, 2) formation of MPT, 3) insertion of molybdenum into molybdopterin to form Moco, and 4) additional modification of Moco with the attachment of GMP or CMP to the phosphate group of MPT, forming the dinucleotide variant of Moco. This review will focus on molybdoenzymes, the biosynthesis of Moco, and its incorporation into specific target proteins focusing on Escherichia coli. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Chantal Iobbi-Nivol
- Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Marseille, France
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33
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Sevcenco AM, Hagen WR, Hagedoorn PL. Microbial Metalloproteomes Explored Using MIRAGE. Chem Biodivers 2012; 9:1967-80. [DOI: 10.1002/cbdv.201100412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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34
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Raimunda D, Khare T, Giometti C, Vogt S, Argüello JM, Finney L. Identifying metalloproteins through X-ray fluorescence mapping and mass spectrometry. Metallomics 2012; 4:921-7. [DOI: 10.1039/c2mt20095c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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