1
|
Marson NA, Gallio AE, Mandal SK, Laskowski RA, Raven EL. In silico prediction of heme binding in proteins. J Biol Chem 2024; 300:107250. [PMID: 38569935 PMCID: PMC11101860 DOI: 10.1016/j.jbc.2024.107250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
The process of heme binding to a protein is prevalent in almost all forms of life to control many important biological properties, such as O2-binding, electron transfer, gas sensing or to build catalytic power. In these cases, heme typically binds tightly (irreversibly) to a protein in a discrete heme binding pocket, with one or two heme ligands provided most commonly to the heme iron by His, Cys or Tyr residues. Heme binding can also be used as a regulatory mechanism, for example in transcriptional regulation or ion channel control. When used as a regulator, heme binds more weakly, with different heme ligations and without the need for a discrete heme pocket. This makes the characterization of heme regulatory proteins difficult, and new approaches are needed to predict and understand the heme-protein interactions. We apply a modified version of the ProFunc bioinformatics tool to identify heme-binding sites in a test set of heme-dependent regulatory proteins taken from the Protein Data Bank and AlphaFold models. The potential heme binding sites identified can be easily visualized in PyMol and, if necessary, optimized with RosettaDOCK. We demonstrate that the methodology can be used to identify heme-binding sites in proteins, including in cases where there is no crystal structure available, but the methodology is more accurate when the quality of the structural information is high. The ProFunc tool, with the modification used in this work, is publicly available at https://www.ebi.ac.uk/thornton-srv/databases/profunc and can be readily adopted for the examination of new heme binding targets.
Collapse
Affiliation(s)
- Noa A Marson
- School of Chemistry, University of Bristol, Bristol, UK
| | | | | | - Roman A Laskowski
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Cambridge, UK
| | - Emma L Raven
- School of Chemistry, University of Bristol, Bristol, UK.
| |
Collapse
|
2
|
Hopp MT, Ugurlar D, Pezeshkpoor B, Biswas A, Ramoji A, Neugebauer U, Oldenburg J, Imhof D. In-depth structure-function profiling of the complex formation between clotting factor VIII and heme. Thromb Res 2024; 237:184-195. [PMID: 38631156 DOI: 10.1016/j.thromres.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND AND AIMS Blood disorders, such as sickle cell disease, and other clinical conditions are often accompanied by intravascular hemolytic events along with the development of severe coagulopathies. Hemolysis, in turn, leads to the accumulation of Fe(II/III)-protoporphyrin IX (heme) in the intravascular compartment, which can trigger a variety of proinflammatory and prothrombotic reactions. As such, heme binding to the blood coagulation proteins factor VIII (FVIII), fibrinogen, and activated protein C with functional consequences has been demonstrated earlier. METHODS We herein present an in-depth characterization of the FVIII-heme interaction at the molecular level and its (patho-)physiological relevance through the application of biochemical, biophysical, structural biology, bioinformatic, and diagnostic tools. RESULTS FVIII has a great heme-binding capacity with seven heme molecules associating with the protein. The respective binding sites were identified by investigating heme binding to FVIII-derived peptides in combination with molecular docking and dynamic simulation studies of the complex as well as cryo-electron microscopy, revealing three high-affinity and four moderate heme-binding motifs (HBMs). Furthermore, the relevance of the FVIII-heme complex formation was characterized in physiologically relevant assay systems, revealing a ~ 50 % inhibition of the FVIII cofactor activity even in the protein-rich environment of blood plasma. CONCLUSION Our study provides not only novel molecular insights into the FVIII-heme interaction and its physiological relevance, but also strongly suggests the reduction of the intrinsic pathway and the accentuation of the final clotting step (by, for example, fibrinogen crosslinking) in hemolytic conditions as well as a future perspective in the context of FVIII substitution therapy of hemorrhagic events in hemophilia A patients.
Collapse
Affiliation(s)
- Marie-T Hopp
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany; Department of Chemistry, Institute for Integrated Natural Sciences, University of Koblenz, Koblenz, Germany.
| | - Deniz Ugurlar
- Center for Electron Microscopy, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Behnaz Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Arijit Biswas
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Anuradha Ramoji
- Leibniz Institute of Photonic Technology, Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Ute Neugebauer
- Leibniz Institute of Photonic Technology, Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany; Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany.
| |
Collapse
|
3
|
Afsar A, Zhang L. Putative Molecular Mechanisms Underpinning the Inverse Roles of Mitochondrial Respiration and Heme Function in Lung Cancer and Alzheimer's Disease. BIOLOGY 2024; 13:185. [PMID: 38534454 DOI: 10.3390/biology13030185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
Mitochondria are the powerhouse of the cell. Mitochondria serve as the major source of oxidative stress. Impaired mitochondria produce less adenosine triphosphate (ATP) but generate more reactive oxygen species (ROS), which could be a major factor in the oxidative imbalance observed in Alzheimer's disease (AD). Well-balanced mitochondrial respiration is important for the proper functioning of cells and human health. Indeed, recent research has shown that elevated mitochondrial respiration underlies the development and therapy resistance of many types of cancer, whereas diminished mitochondrial respiration is linked to the pathogenesis of AD. Mitochondria govern several activities that are known to be changed in lung cancer, the largest cause of cancer-related mortality worldwide. Because of the significant dependence of lung cancer cells on mitochondrial respiration, numerous studies demonstrated that blocking mitochondrial activity is a potent strategy to treat lung cancer. Heme is a central factor in mitochondrial respiration/oxidative phosphorylation (OXPHOS), and its association with cancer is the subject of increased research in recent years. In neural cells, heme is a key component in mitochondrial respiration and the production of ATP. Here, we review the role of impaired heme metabolism in the etiology of AD. We discuss the numerous mitochondrial effects that may contribute to AD and cancer. In addition to emphasizing the significance of heme in the development of both AD and cancer, this review also identifies some possible biological connections between the development of the two diseases. This review explores shared biological mechanisms (Pin1, Wnt, and p53 signaling) in cancer and AD. In cancer, these mechanisms drive cell proliferation and tumorigenic functions, while in AD, they lead to cell death. Understanding these mechanisms may help advance treatments for both conditions. This review discusses precise information regarding common risk factors, such as aging, obesity, diabetes, and tobacco usage.
Collapse
Affiliation(s)
- Atefeh Afsar
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Li Zhang
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| |
Collapse
|
4
|
Dai Y, Fleischhacker AS, Liu L, Fayad S, Gunawan AL, Stuehr DJ, Ragsdale SW. Heme delivery to heme oxygenase-2 involves glyceraldehyde-3-phosphate dehydrogenase. Biol Chem 2022; 403:1043-1053. [PMID: 36302634 PMCID: PMC9661526 DOI: 10.1515/hsz-2022-0230] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022]
Abstract
Abstract
Heme regulatory motifs (HRMs) are found in a variety of proteins with diverse biological functions. In heme oxygenase-2 (HO2), heme binds to the HRMs and is readily transferred to the catalytic site in the core of the protein. To further define this heme transfer mechanism, we evaluated the ability of GAPDH, a known heme chaperone, to transfer heme to the HRMs and/or the catalytic core of HO2. Our results indicate GAPDH and HO2 form a complex in vitro. We have followed heme insertion at both sites by fluorescence quenching in HEK293 cells with HO2 reporter constructs. Upon mutation of residues essential for heme binding at each site in our reporter construct, we found that HO2 binds heme at the core and the HRMs in live cells and that heme delivery to HO2 is dependent on the presence of GAPDH that is competent for heme binding. In sum, GAPDH is involved in heme delivery to HO2 but, surprisingly, not to a specific site on HO2. Our results thus emphasize the importance of heme binding to both the core and the HRMs and the interplay of HO2 with the heme pool via GAPDH to maintain cellular heme homeostasis.
Collapse
Affiliation(s)
- Yue Dai
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, NC-22, 9500 Euclid Avenue, Cleveland, OH44195, USA
| | - Angela S. Fleischhacker
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., 5301 MSRB III, Ann Arbor, MI48109, USA
| | - Liu Liu
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., 5301 MSRB III, Ann Arbor, MI48109, USA
| | - Sara Fayad
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., 5301 MSRB III, Ann Arbor, MI48109, USA
| | - Amanda L. Gunawan
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., 5301 MSRB III, Ann Arbor, MI48109, USA
| | - Dennis J. Stuehr
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, NC-22, 9500 Euclid Avenue, Cleveland, OH44195, USA
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., 5301 MSRB III, Ann Arbor, MI48109, USA
| |
Collapse
|
5
|
Jagadeesh ASV, Fang X, Kim SH, Guillen-Quispe YN, Zheng J, Surh YJ, Kim SJ. Non-canonical vs. Canonical Functions of Heme Oxygenase-1 in Cancer. J Cancer Prev 2022; 27:7-15. [PMID: 35419301 PMCID: PMC8984652 DOI: 10.15430/jcp.2022.27.1.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 01/18/2023] Open
Abstract
Heme oxygenase-1 (HO-1) is a critical stress-responsive enzyme that has antioxidant and anti-inflammatory functions. HO-1 catalyzes heme degradation, which gives rise to the formation of carbon monoxide (CO), biliverdin, and iron. The upregulation of HO-1 under pathological conditions associated with cellular stress represents an important cytoprotective defense mechanism by virtue of the anti-oxidant properties of the bilirubin and the anti-inflammatory effect of the CO produced. The same mechanism is hijacked by premalignant and cancerous cells. In recent years, however, there has been accumulating evidence supporting that the upregulation of HO-1 promotes cancer progression, independently of its catalytic activity. Such non-canonical functions of HO-1 are associated with its interaction with other proteins, particularly transcription factors. HO-1 also undergoes post-translational modifications that influence its stability, functional activity, cellular translocation, etc. HO-1 is normally present in the endoplasmic reticulum, but distinct subcellular localizations, especially in the nucleus, are observed in multiple cancers. The nuclear HO-1 modulates the activation of various transcription factors, which does not appear to be mediated by carbon monoxide and iron. This commentary summarizes the non-canonical functions of HO-1 in the context of cancer growth and progression and underlying regulatory mechanisms.
Collapse
Affiliation(s)
| | - Xizhu Fang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Seong Hoon Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Yanymee N. Guillen-Quispe
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Jie Zheng
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Young-Joon Surh
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Su-Jung Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| |
Collapse
|
6
|
Jagadeesh ASV, Fang X, Kim SH, Guillen-Quispe YN, Zheng J, Surh YJ, Kim SJ. Non-canonical vs. Canonical Functions of Heme Oxygenase-1 in Cancer. J Cancer Prev 2022. [PMID: 35419301 DOI: 10.15430/jcp.2022.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Heme oxygenase-1 (HO-1) is a critical stress-responsive enzyme that has antioxidant and anti-inflammatory functions. HO-1 catalyzes heme degradation, which gives rise to the formation of carbon monoxide (CO), biliverdin, and iron. The upregulation of HO-1 under pathological conditions associated with cellular stress represents an important cytoprotective defense mechanism by virtue of the anti-oxidant properties of the bilirubin and the anti-inflammatory effect of the CO produced. The same mechanism is hijacked by premalignant and cancerous cells. In recent years, however, there has been accumulating evidence supporting that the upregulation of HO-1 promotes cancer progression, independently of its catalytic activity. Such non-canonical functions of HO-1 are associated with its interaction with other proteins, particularly transcription factors. HO-1 also undergoes post-translational modifications that influence its stability, functional activity, cellular translocation, etc. HO-1 is normally present in the endoplasmic reticulum, but distinct subcellular localizations, especially in the nucleus, are observed in multiple cancers. The nuclear HO-1 modulates the activation of various transcription factors, which does not appear to be mediated by carbon monoxide and iron. This commentary summarizes the non-canonical functions of HO-1 in the context of cancer growth and progression and underlying regulatory mechanisms.
Collapse
Affiliation(s)
| | - Xizhu Fang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Seong Hoon Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Yanymee N Guillen-Quispe
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Jie Zheng
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Young-Joon Surh
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Su-Jung Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| |
Collapse
|
7
|
Le VQ, Iacob RE, Zhao B, Su Y, Tian Y, Toohey C, Engen JR, Springer TA. Protection of the Prodomain α1-Helix Correlates with Latency in the Transforming Growth Factor-β Family. J Mol Biol 2022; 434:167439. [PMID: 34990654 PMCID: PMC8981510 DOI: 10.1016/j.jmb.2021.167439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/16/2021] [Accepted: 12/29/2021] [Indexed: 11/18/2022]
Abstract
The 33 members of the transforming growth factor beta (TGF-β) family are fundamentally important for organismal development and homeostasis. Family members are synthesized and secreted as pro-complexes of non-covalently associated prodomains and growth factors (GF). Pro-complexes from a subset of family members are latent and require activation steps to release the GF for signaling. Why some members are latent while others are non-latent is incompletely understood, particularly because of large family diversity. Here, we have examined representative family members in negative stain electron microscopy (nsEM) and hydrogen deuterium exchange (HDX) to identify features that differentiate latent from non-latent members. nsEM showed three overall pro-complex conformations that differed in prodomain arm domain orientation relative to the bound growth factor. Two cross-armed members, TGF-β1 and TGF-β2, were each latent. However, among V-armed members, GDF8 was latent whereas ActA was not. All open-armed members, BMP7, BMP9, and BMP10, were non-latent. Family members exhibited remarkably varying HDX patterns, consistent with large prodomain sequence divergence. A strong correlation emerged between latency and protection of the prodomain α1-helix from exchange. Furthermore, latency and protection from exchange correlated structurally with increased α1-helix buried surface area, hydrogen bonds, and cation-pi bonds. Moreover, a specific pattern of conserved basic and hydrophobic residues in the α1-helix and aromatic residues in the interacting fastener were found only in latent members. Thus, this first comparative survey of TGF-β family members reveals not only diversity in conformation and dynamics but also unique features that distinguish latent members.
Collapse
Affiliation(s)
- Viet Q Le
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, United States
| | - Bo Zhao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States; Department of Immunology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Yang Su
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Yuan Tian
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Cameron Toohey
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, United States. https://twitter.com/jrengen
| | - Timothy A Springer
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States.
| |
Collapse
|
8
|
Heme oxygenase-1, carbon monoxide, and malaria – The interplay of chemistry and biology. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
9
|
Fleischhacker AS, Sarkar A, Liu L, Ragsdale SW. Regulation of protein function and degradation by heme, heme responsive motifs, and CO. Crit Rev Biochem Mol Biol 2022; 57:16-47. [PMID: 34517731 PMCID: PMC8966953 DOI: 10.1080/10409238.2021.1961674] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Heme is an essential biomolecule and cofactor involved in a myriad of biological processes. In this review, we focus on how heme binding to heme regulatory motifs (HRMs), catalytic sites, and gas signaling molecules as well as how changes in the heme redox state regulate protein structure, function, and degradation. We also relate these heme-dependent changes to the affected metabolic processes. We center our discussion on two HRM-containing proteins: human heme oxygenase-2, a protein that binds and degrades heme (releasing Fe2+ and CO) in its catalytic core and binds Fe3+-heme at HRMs located within an unstructured region of the enzyme, and the transcriptional regulator Rev-erbβ, a protein that binds Fe3+-heme at an HRM and is involved in CO sensing. We will discuss these and other proteins as they relate to cellular heme composition, homeostasis, and trafficking. In addition, we will discuss the HRM-containing family of proteins and how the stability and activity of these proteins are regulated in a dependent manner through the HRMs. Then, after reviewing CO-mediated protein regulation of heme proteins, we turn our attention to the involvement of heme, HRMs, and CO in circadian rhythms. In sum, we stress the importance of understanding the various roles of heme and the distribution of the different heme pools as they relate to the heme redox state, CO, and heme binding affinities.
Collapse
Affiliation(s)
- Angela S. Fleischhacker
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anindita Sarkar
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Liu Liu
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| |
Collapse
|
10
|
Hanna DA, Moore CM, Liu L, Yuan X, Dominic IM, Fleischhacker AS, Hamza I, Ragsdale SW, Reddi AR. Heme oxygenase-2 (HO-2) binds and buffers labile ferric heme in human embryonic kidney cells. J Biol Chem 2021; 298:101549. [PMID: 34973332 PMCID: PMC8808069 DOI: 10.1016/j.jbc.2021.101549] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 01/13/2023] Open
Abstract
Heme oxygenases (HOs) detoxify heme by oxidatively degrading it into carbon monoxide, iron, and biliverdin, which is reduced to bilirubin and excreted. Humans express two isoforms of HO: the inducible HO-1, which is upregulated in response to excess heme and other stressors, and the constitutive HO-2. Much is known about the regulation and physiological function of HO-1, whereas comparatively little is known about the role of HO-2 in regulating heme homeostasis. The biochemical necessity for expressing constitutive HO-2 is dependent on whether heme is sufficiently abundant and accessible as a substrate under conditions in which HO-1 is not induced. By measuring labile heme, total heme, and bilirubin in human embryonic kidney HEK293 cells with silenced or overexpressed HO-2, as well as various HO-2 mutant alleles, we found that endogenous heme is too limiting a substrate to observe HO-2-dependent heme degradation. Rather, we discovered a novel role for HO-2 in the binding and buffering of heme. Taken together, in the absence of excess heme, we propose that HO-2 regulates heme homeostasis by acting as a heme buffering factor that controls heme bioavailability. When heme is in excess, HO-1 is induced, and both HO-2 and HO-1 can provide protection from heme toxicity via enzymatic degradation. Our results explain why catalytically inactive mutants of HO-2 are cytoprotective against oxidative stress. Moreover, the change in bioavailable heme due to HO-2 overexpression, which selectively binds ferric over ferrous heme, is consistent with labile heme being oxidized, thereby providing new insights into heme trafficking and signaling.
Collapse
Affiliation(s)
- David A. Hanna
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Courtney M. Moore
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Liu Liu
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Xiaojing Yuan
- Department of Animal and Avian Sciences, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Iramofu M. Dominic
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Iqbal Hamza
- Department of Animal and Avian Sciences, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Amit R. Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA,Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA,For correspondence: Amit R. Reddi
| |
Collapse
|
11
|
Takemoto M, Sakamoto H, Higashimoto Y, Taira J. Complex Formation of Heme Oxygenase-2 with Heme Is Competitively Inhibited by the Cytosolic Domain of Caveolin-1. Biochemistry 2021; 60:2300-2308. [PMID: 34223768 DOI: 10.1021/acs.biochem.1c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism and physiological functions of heme oxygenase-2 (HO-2)-mediated carbon monoxide (CO) production, accompanied by heme metabolism, have been studied intensively in recent years. The enzymatic activity of constitutively expressed HO-2 must be strictly controlled in terms of the toxicity and chemical stability of CO. In this study, the molecular interaction between HO-2 and caveolin-1 and its effect on HO action were evaluated. An enzyme kinetics assay with residues 82-101 of caveolin-1, also called the caveolin scaffold domain, inhibited HO-2 activity in a competitive manner. Analytical ultracentrifugation and a hemin titration assay suggested that the inhibitory effect was generated by direct binding of caveolin-1 to aromatic residues, which were defined as components of the caveolin-binding motif in the HO-2 heme pocket. Herein, we developed a HO-2-based fluorescence bioprobe, namely EGFP-Δ19/D159H, which was capable of quantifying heme binding by HO-2 as the initial step in the CO production. The fluorescence of EGFP-Δ19/D159H decreased in accordance with 5-aminolevulinic acid-facilitated heme biosynthesis in COS-7 cells. In contrast, expression of the N-terminal cytosolic domain of caveolin-1 (residues 1-101) increased the probe fluorescence, suggesting that the cytosolic domain of caveolin-1 potently inhibits the binding of heme to the heme pocket of EGFP-Δ19/D159H. Taken together, our results suggest that caveolin-1 is a negative regulator of HO-2 enzymatic action. Moreover, our bioprobe EGFP-Δ19/D159H represents a powerful tool for use in future studies addressing HO-2-mediated CO production.
Collapse
Affiliation(s)
- Misaki Takemoto
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka 820-8502, Japan
| | - Hiroshi Sakamoto
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka 820-8502, Japan
| | - Yuichiro Higashimoto
- Department of Chemistry, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Junichi Taira
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka 820-8502, Japan.,Department of Chemistry, Kurume University School of Medicine, Kurume 830-0011, Japan
| |
Collapse
|
12
|
Pethő D, Hendrik Z, Nagy A, Beke L, Patsalos A, Nagy L, Póliska S, Méhes G, Tóth C, Potor L, Eaton JW, Jacob HS, Balla G, Balla J, Gáll T. Heme cytotoxicity is the consequence of endoplasmic reticulum stress in atherosclerotic plaque progression. Sci Rep 2021; 11:10435. [PMID: 34001932 PMCID: PMC8129109 DOI: 10.1038/s41598-021-89713-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023] Open
Abstract
Hemorrhage and hemolysis with subsequent heme release are implicated in many pathologies. Endothelial cells (ECs) encounter large amount of free heme after hemolysis and are at risk of damage from exogenous heme. Here we show that hemorrhage aggravates endoplasmic reticulum (ER) stress in human carotid artery plaques compared to healthy controls or atheromas without hemorrhage as demonstrated by RNA sequencing and immunohistochemistry. In EC cultures, heme also induces ER stress. In contrast, if cultured ECs are pulsed with heme arginate, cells become resistant to heme-induced ER (HIER) stress that is associated with heme oxygenase-1 (HO-1) and ferritin induction. Knocking down HO-1, HO-2, biliverdin reductase, and ferritin show that HO-1 is the ultimate cytoprotectant in acute HIER stress. Carbon monoxide-releasing molecules (CORMs) but not bilirubin protects cultured ECs from HIER stress via HO-1 induction, at least in part. Knocking down HO-1 aggravates heme-induced cell death that cannot be counterbalanced with any known cell death inhibitors. We conclude that endothelium and perhaps other cell types can be protected from HIER stress by induction of HO-1, and heme-induced cell death occurs via HIER stress that is potentially involved in the pathogenesis of diverse pathologies with hemolysis and hemorrhage including atherosclerosis.
Collapse
|
13
|
Fernández-Fierro A, Funes SC, Rios M, Covián C, González J, Kalergis AM. Immune Modulation by Inhibitors of the HO System. Int J Mol Sci 2020; 22:ijms22010294. [PMID: 33396647 PMCID: PMC7794909 DOI: 10.3390/ijms22010294] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/23/2022] Open
Abstract
The heme oxygenase (HO) system involves three isoforms of this enzyme, HO-1, HO-2, and HO-3. The three of them display the same catalytic activity, oxidating the heme group to produce biliverdin, ferrous iron, and carbon monoxide (CO). HO-1 is the isoform most widely studied in proinflammatory diseases because treatments that overexpress this enzyme promote the generation of anti-inflammatory products. However, neonatal jaundice (hyperbilirubinemia) derived from HO overexpression led to the development of inhibitors, such as those based on metaloproto- and meso-porphyrins inhibitors with competitive activity. Further, non-competitive inhibitors have also been identified, such as synthetic and natural imidazole-dioxolane-based, small synthetic molecules, inhibitors of the enzyme regulation pathway, and genetic engineering using iRNA or CRISPR cas9. Despite most of the applications of the HO inhibitors being related to metabolic diseases, the beneficial effects of these molecules in immune-mediated diseases have also emerged. Different medical implications, including cancer, Alzheimer´s disease, and infections, are discussed in this article and as to how the selective inhibition of HO isoforms may contribute to the treatment of these ailments.
Collapse
Affiliation(s)
- Ayleen Fernández-Fierro
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
| | - Samanta C. Funes
- Instituto Multidisciplinario de Investigaciones Biológicas-San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas—Universidad Nacional de San Luis, 5700 San Luis, Argentina;
| | - Mariana Rios
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
| | - Camila Covián
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
| | - Jorge González
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
| | - Alexis M. Kalergis
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
- Correspondence: ; Tel.: +56-22-686-2842
| |
Collapse
|
14
|
Liu L, Dumbrepatil AB, Fleischhacker AS, Marsh ENG, Ragsdale SW. Heme oxygenase-2 is post-translationally regulated by heme occupancy in the catalytic site. J Biol Chem 2020; 295:17227-17240. [PMID: 33051205 PMCID: PMC7863905 DOI: 10.1074/jbc.ra120.014919] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/08/2020] [Indexed: 01/01/2023] Open
Abstract
Heme oxygenase-2 (HO2) and -1 (HO1) catalyze heme degradation to biliverdin, CO, and iron, forming an essential link in the heme metabolism network. Tight regulation of the cellular levels and catalytic activities of HO1 and HO2 is important for maintaining heme homeostasis. HO1 expression is transcriptionally regulated; however, HO2 expression is constitutive. How the cellular levels and activity of HO2 are regulated remains unclear. Here, we elucidate the mechanism of post-translational regulation of cellular HO2 levels by heme. We find that, under heme-deficient conditions, HO2 is destabilized and targeted for degradation, suggesting that heme plays a direct role in HO2 regulation. HO2 has three heme binding sites: one at its catalytic site and the others at its two heme regulatory motifs (HRMs). We report that, in contrast to other HRM-containing proteins, the cellular protein level and degradation rate of HO2 are independent of heme binding to the HRMs. Rather, under heme deficiency, loss of heme binding to the catalytic site destabilizes HO2. Consistently, an HO2 catalytic site variant that is unable to bind heme exhibits a constant low protein level and an enhanced protein degradation rate compared with the WT HO2. Finally, HO2 is degraded by the lysosome through chaperone-mediated autophagy, distinct from other HRM-containing proteins and HO1, which are degraded by the proteasome. These results reveal a novel aspect of HO2 regulation and deepen our understanding of HO2's role in maintaining heme homeostasis, paving the way for future investigation into HO2's pathophysiological role in heme deficiency response.
Collapse
Affiliation(s)
- Liu Liu
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Arti B Dumbrepatil
- Department of Chemistry, College of Literature, Science and Arts, University of Michigan, Ann Arbor, Michigan, USA
| | | | - E Neil G Marsh
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Department of Chemistry, College of Literature, Science and Arts, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| |
Collapse
|
15
|
Fleischhacker AS, Gunawan AL, Kochert BA, Liu L, Wales TE, Borowy MC, Engen JR, Ragsdale SW. The heme-regulatory motifs of heme oxygenase-2 contribute to the transfer of heme to the catalytic site for degradation. J Biol Chem 2020; 295:5177-5191. [PMID: 32152224 PMCID: PMC7170523 DOI: 10.1074/jbc.ra120.012803] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/03/2020] [Indexed: 11/06/2022] Open
Abstract
Heme-regulatory motifs (HRMs) are present in many proteins that are involved in diverse biological functions. The C-terminal tail region of human heme oxygenase-2 (HO2) contains two HRMs whose cysteine residues form a disulfide bond; when reduced, these cysteines are available to bind Fe3+-heme. Heme binding to the HRMs occurs independently of the HO2 catalytic active site in the core of the protein, where heme binds with high affinity and is degraded to biliverdin. Here, we describe the reversible, protein-mediated transfer of heme between the HRMs and the HO2 core. Using hydrogen-deuterium exchange (HDX)-MS to monitor the dynamics of HO2 with and without Fe3+-heme bound to the HRMs and to the core, we detected conformational changes in the catalytic core only in one state of the catalytic cycle-when Fe3+-heme is bound to the HRMs and the core is in the apo state. These conformational changes were consistent with transfer of heme between binding sites. Indeed, we observed that HRM-bound Fe3+-heme is transferred to the apo-core either upon independent expression of the core and of a construct spanning the HRM-containing tail or after a single turnover of heme at the core. Moreover, we observed transfer of heme from the core to the HRMs and equilibration of heme between the core and HRMs. We therefore propose an Fe3+-heme transfer model in which HRM-bound heme is readily transferred to the catalytic site for degradation to facilitate turnover but can also equilibrate between the sites to maintain heme homeostasis.
Collapse
Affiliation(s)
- Angela S Fleischhacker
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - Amanda L Gunawan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - Brent A Kochert
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Liu Liu
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Maelyn C Borowy
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|