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Li Y, Han S, Gao H. Heme homeostasis and its regulation by hemoproteins in bacteria. MLIFE 2024; 3:327-342. [PMID: 39359680 PMCID: PMC11442138 DOI: 10.1002/mlf2.12120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/08/2024] [Accepted: 02/23/2024] [Indexed: 10/04/2024]
Abstract
Heme is an important cofactor and a regulatory molecule involved in various physiological processes in virtually all living cellular organisms, and it can also serve as the primary iron source for many bacteria, particularly pathogens. However, excess heme is cytotoxic to cells. In order to meet physiological needs while preventing deleterious effects, bacteria have evolved sophisticated cellular mechanisms to maintain heme homeostasis. Recent advances in technologies have shaped our understanding of the molecular mechanisms that govern the biological processes crucial to heme homeostasis, including synthesis, acquisition, utilization, degradation, trafficking, and efflux, as well as their regulation. Central to these mechanisms is the regulation of the heme, by the heme, and for the heme. In this review, we present state-of-the-art findings covering the biochemical, physiological, and structural characterization of important, newly identified hemoproteins/systems involved in heme homeostasis.
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Affiliation(s)
- Yingxi Li
- Institute of Microbiology and College of Life SciencesZhejiang UniversityHangzhouChina
| | - Sirui Han
- Institute of Microbiology and College of Life SciencesZhejiang UniversityHangzhouChina
| | - Haichun Gao
- Institute of Microbiology and College of Life SciencesZhejiang UniversityHangzhouChina
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2
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Zhang C, Liu R, Kong X, Li H, Yu D, Fang X, Wu L, Wu Y. Adaptive Responses of a Peroxidase-like Polyoxometalate-Based Tri-Assembly to Bacterial Microenvironment (BME) Significantly Improved the Anti-Bacterial Effects. Int J Mol Sci 2023; 24:ijms24108858. [PMID: 37240203 DOI: 10.3390/ijms24108858] [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: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The present study presents the tertiary assembly of a POM, peptide, and biogenic amine, which is a concept to construct new hybrid bio-inorganic materials for antibacterial applications and will help to promote the development of antivirus agents in the future. To achieve this, a Eu-containing polyoxometalate (EuW10) was first co-assembled with a biogenic amine of spermine (Spm), which improved both the luminescence and antibacterial effect of EuW10. Further introduction of a basic peptide from HPV E6, GL-22, induced more extensive enhancements, both of them being attributed to the cooperation and synergistic effects between the constituents, particularly the adaptive responses of assembly to the bacterial microenvironment (BME). Further intrinsic mechanism investigations revealed in detail that the encapsulation of EuW10 in Spm and further GL-22 enhanced the uptake abilities of EuW10 in bacteria, which further improved the ROS generation in BME via the abundant H2O2 involved there and significantly promoted the antibacterial effects.
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Affiliation(s)
- Chunxia Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
| | - Rongrong Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
| | - Xueping Kong
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, No. 2 Liutiao Road, Changchun 130023, China
| | - Hongwei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, No. 2 Liutiao Road, Changchun 130023, China
| | - Dahai Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
| | - Xuexun Fang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
| | - Lixin Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
| | - Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, No. 2 Liutiao Road, Changchun 130023, China
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3
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Partipilo M, Yang G, Mascotti ML, Wijma HJ, Slotboom DJ, Fraaije MW. A conserved sequence motif in the Escherichia coli soluble FAD-containing pyridine nucleotide transhydrogenase is important for reaction efficiency. J Biol Chem 2022; 298:102304. [PMID: 35933012 PMCID: PMC9460512 DOI: 10.1016/j.jbc.2022.102304] [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: 05/18/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/06/2022] Open
Abstract
Soluble pyridine nucleotide transhydrogenases (STHs) are flavoenzymes involved in the redox homeostasis of the essential cofactors NAD(H) and NADP(H). They catalyze the reversible transfer of reducing equivalents between the two nicotinamide cofactors. The soluble transhydrogenase from Escherichia coli (SthA) has found wide use in both in vivo and in vitro applications to steer reducing equivalents toward NADPH-requiring reactions. However, mechanistic insight into SthA function is still lacking. In this work, we present a biochemical characterization of SthA, focusing for the first time on the reactivity of the flavoenzyme with molecular oxygen. We report on oxidase activity of SthA that takes place both during transhydrogenation and in the absence of an oxidized nicotinamide cofactor as an electron acceptor. We find that this reaction produces the reactive oxygen species hydrogen peroxide and superoxide anion. Furthermore, we explore the evolutionary significance of the well-conserved CXXXXT motif that distinguishes STHs from the related family of flavoprotein disulfide reductases in which a CXXXXC motif is conserved. Our mutational analysis revealed the cysteine and threonine combination in SthA leads to better coupling efficiency of transhydrogenation and reduced reactive oxygen species release compared to enzyme variants with mutated motifs. These results expand our mechanistic understanding of SthA by highlighting reactivity with molecular oxygen and the importance of the evolutionarily conserved sequence motif.
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Affiliation(s)
- Michele Partipilo
- Membrane Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Guang Yang
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Maria Laura Mascotti
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Hein J Wijma
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Membrane Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands.
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands.
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4
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Alsharabasy AM, Glynn S, Farràs P, Pandit A. Protein nitration induced by Hemin/NO: A complementary mechanism through the catalytic functions of hemin and NO-scavenging. Nitric Oxide 2022; 124:49-67. [PMID: 35513288 DOI: 10.1016/j.niox.2022.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/07/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022]
Abstract
Hemin and heme-peroxidases have been considered essential catalysts for the nitrite/hydrogen peroxide (H2O2)-mediated protein nitration in vitro, understood as one of the main pathways for protein modification in biological systems. However, the role of nitric oxide (●NO) in the heme/hemin-induced protein nitration has not been studied in-depth. This is despite its reductive nitrosylating effects following binding to hemin and the possible involvement of the reactive nitrogen species in the nitration of various functional proteins. Here, the ●NO-binding affinity of hemin has been studied along with the influence of ●NO on the internalization of hemin into MDA-MB-231 cells and the accompanying changes in the profile of intracellular nitrated proteins. Moreover, to further understand the mechanism involved, bovine serum albumin (BSA) nitration was studied after treatment with hemin and ●NO, with an investigation of the effects of pH of the reaction medium, generation of H2O2, and the oxidation of the tyrosine residues as the primary sites for the nitration. We demonstrated that hemin nitrosylation enhanced its cellular uptake and induced the one-electron oxidation and nitration of different intracellular proteins along with its ●NO-scavenging efficiency. Moreover, the hemin/NO-mediated BSA nitration was proved to be dependent on the concentration of ●NO and the pH of the reaction medium, with a vital role being played by the scavenging effects of protein for the free hemin molecules. Collectively, our results reaffirm the involvement of hemin and ●NO in the nitration mechanism, where the nitrosylation products can induce protein nitration while promoting the effects of the components of the nitrite/H2O2-mediated pathway.
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Affiliation(s)
- Amir M Alsharabasy
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Ireland
| | - Sharon Glynn
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Ireland; Discipline of Pathology, Lambe Institute for Translational Medicine, School of Medicine, National University of Ireland Galway, Ireland
| | - Pau Farràs
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Ireland; School of Chemistry, Ryan Institute, National University of Ireland Galway, Ireland
| | - Abhay Pandit
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Ireland.
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5
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Krüger A, Keppel M, Sharma V, Frunzke J. The diversity of heme sensor systems - heme-responsive transcriptional regulation mediated by transient heme protein interactions. FEMS Microbiol Rev 2022; 46:6506450. [PMID: 35026033 DOI: 10.1093/femsre/fuac002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/21/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Heme is a versatile molecule that is vital for nearly all cellular life by serving as prosthetic group for various enzymes or as nutritional iron source for diverse microbial species. However, elevated levels of heme molecule are toxic to cells. The complexity of this stimulus has shaped the evolution of diverse heme sensor systems, which are involved in heme-dependent transcriptional regulation in eukaryotes and prokaryotes. The functions of these systems are manifold - ranging from the specific control of heme detoxification or uptake systems to the global integration of heme and iron homeostasis. This review focuses on heme sensor systems, regulating heme homeostasis by transient heme protein interaction. We provide an overview of known heme-binding motifs in prokaryotic and eukaryotic transcription factors. Besides the central ligands, the surrounding amino acid environment was shown to play a pivotal role in heme binding. The diversity of heme-regulatory systems therefore illustrates that prediction based on pure sequence information is hardly possible and requires careful experimental validation. Comprehensive understanding of heme-regulated processes is not only important for our understanding of cellular physiology, but also provides a basis for the development of novel antibacterial drugs and metabolic engineering strategies.
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Affiliation(s)
- Aileen Krüger
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Marc Keppel
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Vikas Sharma
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Julia Frunzke
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
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Grassmann AA, Zavala-Alvarado C, Bettin EB, Picardeau M, Benaroudj N, Caimano MJ. The FUR-like regulators PerRA and PerRB integrate a complex regulatory network that promotes mammalian host-adaptation and virulence of Leptospira interrogans. PLoS Pathog 2021; 17:e1009078. [PMID: 34855918 PMCID: PMC8638967 DOI: 10.1371/journal.ppat.1009078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/18/2021] [Indexed: 11/18/2022] Open
Abstract
Leptospira interrogans, the causative agent of most cases of human leptospirosis, must respond to myriad environmental signals during its free-living and pathogenic lifestyles. Previously, we compared L. interrogans cultivated in vitro and in vivo using a dialysis membrane chamber (DMC) peritoneal implant model. From these studies emerged the importance of genes encoding the Peroxide responsive regulators PerRA and PerRB. First described in in Bacillus subtilis, PerRs are widespread in Gram-negative and -positive bacteria, where regulate the expression of gene products involved in detoxification of reactive oxygen species and virulence. Using perRA and perRB single and double mutants, we establish that L. interrogans requires at least one functional PerR for infectivity and renal colonization in a reservoir host. Our finding that the perRA/B double mutant survives at wild-type levels in DMCs is noteworthy as it demonstrates that the loss of virulence is not due to a metabolic lesion (i.e., metal starvation) but instead reflects dysregulation of virulence-related gene products. Comparative RNA-Seq analyses of perRA, perRB and perRA/B mutants cultivated within DMCs identified 106 genes that are dysregulated in the double mutant, including ligA, ligB and lvrA/B sensory histidine kinases. Decreased expression of LigA and LigB in the perRA/B mutant was not due to loss of LvrAB signaling. The majority of genes in the perRA and perRB single and double mutant DMC regulons were differentially expressed only in vivo, highlighting the importance of host signals for regulating gene expression in L. interrogans. Importantly, the PerRA, PerRB and PerRA/B DMC regulons each contain multiple genes related to environmental sensing and/or transcriptional regulation. Collectively, our data suggest that PerRA and PerRB are part of a complex regulatory network that promotes host adaptation by L. interrogans within mammals.
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Affiliation(s)
- André A. Grassmann
- Department of Medicine, University of Connecticut Health, Farmington, Connecticut, United States of America
| | - Crispin Zavala-Alvarado
- Unité de Biologie des Spirochètes, Department of Microbiology, Institut Pasteur, Paris, France
- Université de Paris, Sorbonne Paris Cité, Communauté d’universités et d’établissements (COMUE), Bio Sorbonne Paris Cité (BioSPC), Paris, France
| | - Everton B. Bettin
- Department of Medicine, University of Connecticut Health, Farmington, Connecticut, United States of America
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sol, Brazil
| | - Mathieu Picardeau
- Unité de Biologie des Spirochètes, Department of Microbiology, Institut Pasteur, Paris, France
| | - Nadia Benaroudj
- Unité de Biologie des Spirochètes, Department of Microbiology, Institut Pasteur, Paris, France
| | - Melissa J. Caimano
- Department of Medicine, University of Connecticut Health, Farmington, Connecticut, United States of America
- Department of Pediatrics, University of Connecticut Health, Farmington, Connecticut, United States of America
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut, United States of America
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7
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Sevilla E, Bes MT, Peleato ML, Fillat MF. Fur-like proteins: Beyond the ferric uptake regulator (Fur) paralog. Arch Biochem Biophys 2021; 701:108770. [PMID: 33524404 DOI: 10.1016/j.abb.2021.108770] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/12/2021] [Accepted: 01/17/2021] [Indexed: 10/22/2022]
Abstract
Proteins belonging to the FUR (ferric uptake regulator) family are the cornerstone of metalloregulation in most prokaryotes. Although numerous reviews have been devoted to these proteins, these reports are mainly focused on the Fur paralog that gives name to the family. In the last years, the increasing knowledge on the other, less ubiquitous members of this family has evidenced their importance in bacterial metabolism. As the Fur paralog, the major regulator of iron homeostasis, Zur, Irr, BosR and PerR are tightly related to stress defenses and host-pathogen interaction being in many cases essential for virulence. Furthermore, the Nur and Mur paralogs largely contribute to control nickel and manganese homeostasis, which are cofactors of pivotal proteins for host colonization and bacterial redox homeostasis. The present review highlights the main features of FUR proteins that differ to the canonical Fur paralog either in the coregulatory metal, such as Zur, Nur and Mur, or in the action mechanism to control target genes, such as PerR, Irr and BosR.
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Affiliation(s)
- Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - M Teresa Bes
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - M Luisa Peleato
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - María F Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.
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8
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Nithichanon A, Tussakhon I, Samer W, Kewcharoenwong C, Ato M, Bancroft GJ, Lertmemongkolchai G. Immune responses in beta-thalassaemia: heme oxygenase 1 reduces cytokine production and bactericidal activity of human leucocytes. Sci Rep 2020; 10:10297. [PMID: 32581238 PMCID: PMC7314746 DOI: 10.1038/s41598-020-67346-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
Patients with beta-thalassaemia increase the risk of bacterial infections, particularly Burkholderia pseudomallei (Bp), the causative agent of melioidosis in Thailand. Impaired immune cell functions may be the cause of this susceptibility, but detailed mechanisms have not been defined. In this study, we observed impaired production of IFN-gamma and IL-10 by whole blood from beta-thalassaemia patients upon stimulation with a range of bacteria-derived stimuli. In contrast, IFN-gamma response via TCR and plasma IgG specific for Bp were still intact. Importantly, mRNA expression of heme oxygenase 1 (HO-1), a potential modulator of immune function, was increased in whole blood from beta-thalassaemia patients, either with or without stimulation with Bp in vitro. Induction of HO-1 by hemin or CoPP in vitro reduced production of IFN-gamma and IL-10 from healthy human PBMCs and decreased bacterial clearance activity of whole blood from healthy controls and beta-thalassaemia, while inhibition of HO-1 by SnPP enhanced both functions in healthy controls. These results were confirmed to some extent in purified human monocytes of healthy controls. Our results suggest a mechanism that excess hemin of beta-thalassaemia patients is a significant cause of immune suppression via HO-1 induction and may underlie the susceptibility of these individuals to severe bacterial infection.
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Affiliation(s)
- Arnone Nithichanon
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Inthira Tussakhon
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Waraporn Samer
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chidchamai Kewcharoenwong
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Gregory J Bancroft
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Ganjana Lertmemongkolchai
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand.
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9
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Nam D, Matsumoto Y, Uchida T, O'Brian MR, Ishimori K. Mechanistic insights into heme-mediated transcriptional regulation via a bacterial manganese-binding iron regulator, iron response regulator (Irr). J Biol Chem 2020; 295:11316-11325. [PMID: 32554810 DOI: 10.1074/jbc.ra119.011855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/15/2020] [Indexed: 11/06/2022] Open
Abstract
The transcription factor iron response regulator (Irr) is a key regulator of iron homeostasis in the nitrogen-fixating bacterium Bradyrhizobium japonicum Irr acts by binding to target genes, including the iron control element (ICE), and is degraded in response to heme binding. Here, we examined this binding activity using fluorescence anisotropy with a 6-carboxyfluorescein-labeled ICE-like oligomer (FAM-ICE). In the presence of Mn2+, Irr addition increased the fluorescence anisotropy, corresponding to formation of the Irr-ICE complex. The addition of EDTA to the Irr-ICE complex reduced fluorescence anisotropy, but fluorescence was recovered after Mn2+ addition, indicating that Mn2+ binding is a prerequisite for complex formation. Binding activity toward ICE was lost upon introduction of substitutions in a His-cluster region of Irr, revealing that Mn2+ binds to this region. We observed that the His-cluster region is also the heme binding site; results from fluorescence anisotropy and electrophoretic mobility shift analyses disclosed that the addition of a half-equivalent of heme dissociates Irr from ICE, likely because of Mn2+ release due to heme binding. We hypothesized that heme binding to another heme binding site, Cys-29, would also inhibit the formation of the Irr-ICE complex because it is proximal to the ICE binding site, which was supported by the loss of ICE binding activity in a Cys-29-mutated Irr. These results indicate that Irr requires Mn2+ binding to form the Irr-ICE complex and that the addition of heme dissociates Irr from ICE by replacing Mn2+ with heme or by heme binding to Cys-29.
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Affiliation(s)
- Dayeon Nam
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Yuki Matsumoto
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Mark R O'Brian
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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10
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Allen KE, Gumber D, Ostfeld RJ. Heart Failure and a Plant-Based Diet. A Case-Report and Literature Review. Front Nutr 2019; 6:82. [PMID: 31245377 PMCID: PMC6579888 DOI: 10.3389/fnut.2019.00082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 05/20/2019] [Indexed: 12/23/2022] Open
Abstract
A 54-year-old female with grade 3 obesity body mass index (BMI 45.2 kg/m2) and type II diabetes (hemoglobin A1c 8.1%) presented to her primary care physician in May 2017 with a chief complaint of left lower extremity edema. Work-up revealed heart failure with depressed left ventricular systolic function. Upon diagnosis, she substantially altered her lifestyle, changing her diet from a "healthy western" one to a whole food plant-based one. Guideline directed medical therapy for heart failure was also utilized. Over five and a half months, she lost 22.7 kg and reversed her diabetes without the use of diabetes medications. Her left ventricular systolic function normalized. Although causality cannot be determined, this case highlights the potential role of a plant-based diet in helping to reverse heart failure with reduced ejection fraction. This article will review how a minimally processed whole food plant-based dietary pattern and similar dietary patterns, such as the Dietary Approach to Stop Hypertension diet, may contribute to the reversal of left ventricular dysfunction.
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Affiliation(s)
- Kathleen E. Allen
- Department of Food and Nutrition, NewYork-Presbyterian, New York, NY, United States
| | - Divya Gumber
- Division of Cardiology, Montefiore Health System, Bronx, NY, United States
| | - Robert J. Ostfeld
- Division of Cardiology, Montefiore Health System, Bronx, NY, United States
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11
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Nishitani Y, Okutani H, Takeda Y, Uchida T, Iwai K, Ishimori K. Specific heme binding to heme regulatory motifs in iron regulatory proteins and its functional significance. J Inorg Biochem 2019; 198:110726. [PMID: 31220756 DOI: 10.1016/j.jinorgbio.2019.110726] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/07/2019] [Accepted: 05/27/2019] [Indexed: 12/31/2022]
Abstract
Iron regulatory proteins (IRPs) control iron metabolism in mammalian cells by binding to the iron-responsive element (IRE) in the target mRNA. Heme regulatory motifs (HRMs) are conserved in the two IRP homologues IRP1 and IRP2 that specifically bind to two and three heme equivalents, respectively; however, only the heme binding to the iron-dependent degradation (IDD) domain of IRP2 causes heme-mediated oxidation, which does not occur in IRP1. Therefore, the functional significance of conserved HRMs outside the IDD domain is yet unclear. In this study, spectroscopic heme titration with IRP mutants confirmed heme binding to each HRM in IRPs, and the effect of heme binding to HRMs on IRE binding was examined. Native polyacrylamide gel electrophoresis analysis revealed that heme binding to HRMs near the IRE binding site inhibits complex formation between IRPs and IRE without oxidative modification, indicating that the function of HRMs varies outside and within the IDD domain. However, the formation of a typical reactive oxygen species (ROS), hydrogen peroxide, was spectroscopically detected in both heme-bound IRPs. Comparing the heme environmental structures surrounding HRMs, the flexible conformation and many amino acid residues sensitive to ROS of the IDD domain were suggested to promote specific oxidation by the generated hydrogen peroxide. Thus, heme binding to HRM near the IRE binding site sterically interferes with IRE binding, while HRM in the IDD domain facilitates specific heme-mediated oxidation of the protein moiety and the protein degradation via the ubiquitin-proteasome system, resulting in the inhibition of IRE binding.
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Affiliation(s)
- Yudai Nishitani
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Hirotaka Okutani
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yukiko Takeda
- Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8561, Japan
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuhiro Iwai
- Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8561, Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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12
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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13
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Shimizu T, Lengalova A, Martínek V, Martínková M. Heme: emergent roles of heme in signal transduction, functional regulation and as catalytic centres. Chem Soc Rev 2019; 48:5624-5657. [DOI: 10.1039/c9cs00268e] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular mechanisms of unprecedented functions of exchangeable/labile heme and heme proteins including transcription, DNA binding, protein kinase activity, K+ channel functions, cis–trans isomerization, N–N bond formation, and other functions are described.
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Affiliation(s)
- Toru Shimizu
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Alzbeta Lengalova
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Václav Martínek
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Markéta Martínková
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
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14
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Fleischhacker AS, Carter EL, Ragsdale SW. Redox Regulation of Heme Oxygenase-2 and the Transcription Factor, Rev-Erb, Through Heme Regulatory Motifs. Antioxid Redox Signal 2018; 29:1841-1857. [PMID: 28990415 PMCID: PMC6217750 DOI: 10.1089/ars.2017.7368] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
SIGNIFICANCE Heme binds to and serves as a cofactor for a myriad of proteins that are involved in diverse biological processes. Hemoproteins also exhibit varying modes of heme binding, suggesting that the protein environment contributes to the functional versatility of this prosthetic group. The subject of this review is a subset of hemoproteins that contain at least one heme regulatory motif (HRM), which is a short sequence containing a Cys-Pro core that, in many cases, binds heme with the Cys acting as an axial ligand. Recent Advances: As more details about HRM-containing proteins are uncovered, some underlying commonalities are emerging, including a role in regulating protein stability. Further, the cysteines of some HRMs have been shown to form disulfide bonds. Because the cysteines must be in the reduced, dithiol form to act as a heme axial ligand, heme binds at these sites in a redox-regulated manner, as demonstrated for heme oxygenase-2 (HO2) and Rev-erbβ. CRITICAL ISSUES HRM-containing proteins have wide variations in heme affinity, utilize different axial ligand schemes, and exhibit differences in the ability to act as a redox sensor-all while having a wide variety of biological functions. Here, we highlight HO2 and Rev-erbβ to illustrate the similarities and differences between two hemoproteins that contain HRMs acting as redox sensors. FUTURE DIRECTIONS HRMs acting as redox sensors may be applicable to other HRM-containing proteins as many contain multiple HRMs and/or other cysteine residues, which may become more evident as the functional significance of HRMs is probed in additional proteins.
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Affiliation(s)
| | - Eric L Carter
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan
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15
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Ogura M, Endo R, Ishikawa H, Takeda Y, Uchida T, Iwai K, Kobayashi K, Ishimori K. Redox-dependent axial ligand replacement and its functional significance in heme-bound iron regulatory proteins. J Inorg Biochem 2018; 182:238-248. [PMID: 29449016 DOI: 10.1016/j.jinorgbio.2018.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/07/2017] [Accepted: 01/08/2018] [Indexed: 11/29/2022]
Abstract
Iron regulatory proteins (IRPs), regulators of iron metabolism in mammalian cells, control the translation of proteins involved in iron uptake, storage and utilization by binding to specific iron-responsive element (IRE) sequences of mRNAs. Two homologs of IRPs (IRP1 and IRP2) have a typical heme regulatory motif (HRM), a consensus sequence found in "heme-regulated proteins". However, specific heme binding to HRM has been reported only for IRP2, which is essential for oxidative modification and loss of binding to target mRNAs. In this paper, we confirmed that IRP1 also specifically binds two molar equivalents of heme, and found that the absorption and resonance Raman spectra of heme-bound IRP1 were quite similar to those of heme-bound IRP2. This shows that the heme environmental structures in IRP1 are close to those of proteins using heme as a regulatory molecule. Pulse radiolysis experiments, however, clearly revealed an axial ligand exchange from Cys to His immediately after the reduction of the heme iron to form a 5-coordinate His-ligated heme in heme-bound IRP2, whereas the 5-coordinate His-ligated heme was not observed after the reduction of heme-bound IRP1. Considering that the oxidative modification is only observed in heme-bound IRP2, but not IRP1, probably owing to the structural flexibility of IRP2, we propose that the transient 5-coordinate His-ligated heme is a prerequisite for oxidative modification of heme-bound IRP2, which functionally differentiates heme binding of IRP2 from that of IRP1.
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Affiliation(s)
- Mariko Ogura
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Ryosuke Endo
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8530, Japan
| | - Haruto Ishikawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8530, Japan
| | - Yukiko Takeda
- Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8561, Japan
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuhiro Iwai
- Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8561, Japan
| | - Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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16
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Kubota R, Takabe T, Arima K, Taniguchi H, Asayama S, Kawakami H. New class of artificial enzyme composed of Mn-porphyrin, imidazole, and cucurbit[10]uril toward use as a therapeutic antioxidant. J Mater Chem B 2018; 6:7050-7059. [DOI: 10.1039/c8tb01204k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this study, we investigated a new class of artificial enzymes composed of Mn-porphyrin, imidazole, and cucurbit[10]uril (CB[10]) toward therapeutic antioxidants.
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Affiliation(s)
- Riku Kubota
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Taiga Takabe
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Kohe Arima
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Hideaki Taniguchi
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Shoichiro Asayama
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Hiroyoshi Kawakami
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
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17
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Reed JH, Shi Y, Zhu Q, Chakraborty S, Mirts EN, Petrik ID, Bhagi-Damodaran A, Ross M, Moënne-Loccoz P, Zhang Y, Lu Y. Manganese and Cobalt in the Nonheme-Metal-Binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-Inactive Mechanism. J Am Chem Soc 2017; 139:12209-12218. [PMID: 28768416 PMCID: PMC5673108 DOI: 10.1021/jacs.7b05800] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The presence of a nonheme metal, such as copper and iron, in the heme-copper oxidase (HCO) superfamily is critical to the enzymatic activity of reducing O2 to H2O, but the exact mechanism the nonheme metal ion uses to confer and fine-tune the activity remains to be understood. We herein report that manganese and cobalt can bind to the same nonheme site and confer HCO activity in a heme-nonheme biosynthetic model in myoglobin. While the initial rates of O2 reduction by the Mn, Fe, and Co derivatives are similar, the percentages of reactive oxygen species (ROS) formation are 7%, 4%, and 1% and the total turnovers are 5.1 ± 1.1, 13.4 ± 0.7, and 82.5 ± 2.5, respectively. These results correlate with the trends of nonheme-metal-binding dissociation constants (35, 22, and 9 μM) closely, suggesting that tighter metal binding can prevent ROS release from the active site, lessen damage to the protein, and produce higher total turnover numbers. Detailed spectroscopic, electrochemical, and computational studies found no evidence of redox cycling of manganese or cobalt in the enzymatic reactions and suggest that structural and electronic effects related to the presence of different nonheme metals lead to the observed differences in reactivity. This study of the roles of nonheme metal ions beyond the Cu and Fe found in native enzymes has provided deeper insights into nature's choice of metal ion and reaction mechanism and allows for finer control of the enzymatic activity, which is a basis for the design of efficient catalysts for the oxygen reduction reaction in fuel cells.
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Affiliation(s)
- Julian H. Reed
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yelu Shi
- Department of Biomedical Engineering, Chemistry, and Biological
Sciences, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Qianhong Zhu
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, Portland, OR,
97239, USA
| | - Saumen Chakraborty
- Department of Chemistry & Biochemistry, University of
Mississippi, Oxford, Mississippi, 38677, USA
| | - Evan N. Mirts
- Center for Biophysics and Quantitative Biology, University of
Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign,
Urbana, IL, 61801, USA
| | - Ambika Bhagi-Damodaran
- Department of Pharmaceutical Chemistry, University of California,
San Francisco, San Francisco, CA, 94143, USA
| | - Matthew Ross
- Department of Chemistry, Northwestern University, Evanston, IL,
60208, USA
| | - Pierre Moënne-Loccoz
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, Portland, OR,
97239, USA
| | - Yong Zhang
- Department of Biomedical Engineering, Chemistry, and Biological
Sciences, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of
Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign,
Urbana, IL, 61801, USA
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18
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Using a genome-scale metabolic network model to elucidate the mechanism of chloroquine action in Plasmodium falciparum. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2017; 7:138-146. [PMID: 28355531 PMCID: PMC5376308 DOI: 10.1016/j.ijpddr.2017.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 02/28/2017] [Accepted: 03/20/2017] [Indexed: 11/24/2022]
Abstract
Chloroquine, long the default first-line treatment against malaria, is now abandoned in large parts of the world because of widespread drug-resistance in Plasmodium falciparum. In spite of its importance as a cost-effective and efficient drug, a coherent understanding of the cellular mechanisms affected by chloroquine and how they influence the fitness and survival of the parasite remains elusive. Here, we used a systems biology approach to integrate genome-scale transcriptomics to map out the effects of chloroquine, identify targeted metabolic pathways, and translate these findings into mechanistic insights. Specifically, we first developed a method that integrates transcriptomic and metabolomic data, which we independently validated against a recently published set of such data for Krebs-cycle mutants of P. falciparum. We then used the method to calculate the effect of chloroquine treatment on the metabolic flux profiles of P. falciparum during the intraerythrocytic developmental cycle. The model predicted dose-dependent inhibition of DNA replication, in agreement with earlier experimental results for both drug-sensitive and drug-resistant P. falciparum strains. Our simulations also corroborated experimental findings that suggest differences in chloroquine sensitivity between ring- and schizont-stage P. falciparum. Our analysis also suggests that metabolic fluxes that govern reduced thioredoxin and phosphoenolpyruvate synthesis are significantly decreased and are pivotal to chloroquine-based inhibition of P. falciparum DNA replication. The consequences of impaired phosphoenolpyruvate synthesis and redox metabolism are reduced carbon fixation and increased oxidative stress, respectively, both of which eventually facilitate killing of the parasite. Our analysis suggests that a combination of chloroquine (or an analogue) and another drug, which inhibits carbon fixation and/or increases oxidative stress, should increase the clearance of P. falciparum from the host system.
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19
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Brewitz HH, Hagelueken G, Imhof D. Structural and functional diversity of transient heme binding to bacterial proteins. Biochim Biophys Acta Gen Subj 2017; 1861:683-697. [DOI: 10.1016/j.bbagen.2016.12.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 11/27/2022]
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20
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Kobayashi K, Nakagaki M, Ishikawa H, Iwai K, O’Brian MR, Ishimori K. Redox-Dependent Dynamics in Heme-Bound Bacterial Iron Response Regulator (Irr) Protein. Biochemistry 2016; 55:4047-54. [DOI: 10.1021/acs.biochem.6b00512] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuo Kobayashi
- The
Institute of Scientific and Industrial Research, Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Megumi Nakagaki
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Haruto Ishikawa
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Kazuhiro Iwai
- Molecular
and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8561, Japan
| | - Mark R. O’Brian
- Department
of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, New York 14214, United States
| | - Koichiro Ishimori
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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