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Zhou HL, Grimmett ZW, Venetos NM, Stomberski CT, Qian Z, McLaughlin PJ, Bansal PK, Zhang R, Reynolds JD, Premont RT, Stamler JS. An enzyme that selectively S-nitrosylates proteins to regulate insulin signaling. Cell 2023; 186:5812-5825.e21. [PMID: 38056462 PMCID: PMC10794992 DOI: 10.1016/j.cell.2023.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/01/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023]
Abstract
Acyl-coenzyme A (acyl-CoA) species are cofactors for numerous enzymes that acylate thousands of proteins. Here, we describe an enzyme that uses S-nitroso-CoA (SNO-CoA) as its cofactor to S-nitrosylate multiple proteins (SNO-CoA-assisted nitrosylase, SCAN). Separate domains in SCAN mediate SNO-CoA and substrate binding, allowing SCAN to selectively catalyze SNO transfer from SNO-CoA to SCAN to multiple protein targets, including the insulin receptor (INSR) and insulin receptor substrate 1 (IRS1). Insulin-stimulated S-nitrosylation of INSR/IRS1 by SCAN reduces insulin signaling physiologically, whereas increased SCAN activity in obesity causes INSR/IRS1 hypernitrosylation and insulin resistance. SCAN-deficient mice are thus protected from diabetes. In human skeletal muscle and adipose tissue, SCAN expression increases with body mass index and correlates with INSR S-nitrosylation. S-nitrosylation by SCAN/SNO-CoA thus defines a new enzyme class, a unique mode of receptor tyrosine kinase regulation, and a revised paradigm for NO function in physiology and disease.
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Affiliation(s)
- Hua-Lin Zhou
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zachary W Grimmett
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nicholas M Venetos
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Colin T Stomberski
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zhaoxia Qian
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Precious J McLaughlin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Puneet K Bansal
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rongli Zhang
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - James D Reynolds
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Anesthesiology and Perioperative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Richard T Premont
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jonathan S Stamler
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
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2
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Takemoto K, Tsurugi-Sakurada A, Moriuchi R, Yoneda Y, Kawai S. Cloning and characterization of NADPH-dependent double-bond reductases from Alnus sieboldiana that recognize linear diarylheptanoids as substrates. Phytochemistry 2023; 215:113850. [PMID: 37659705 DOI: 10.1016/j.phytochem.2023.113850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
Diarylheptanoids are secondary metabolites of plants that comprise a C6-C7-C6 scaffold. They can be broadly classified into linear-type and cyclic-type diarylheptanoids based on their chemical structures. Actinorhizal trees, such as Casuarina, Alnus, and Myrica, which form nodule symbiosis with actinomycetes Frankia, produce cyclic diarylheptanoids (CDHs); in Alnus sieboldiana Matsum. in particular, we have reported that the addition of CDHs leads to an increase in the number of nodules. However, the information available on the biosynthesis of CDHs is scarce. A greater number of plants CDHs (including those isolated from actinorhizal trees) with a saturated heptane chain have been isolated compared with linear, non-cyclic diarylheptanoids. To identify the genes involved in the synthesis of these compounds, genes with significant sequence similarity to existing plant double-bond reductases were screened in A. sieboldiana. This report describes the isolation and characterization of two A. sieboldiana double-bond reductases (AsDBR1 and AsDBR2) that catalyze the NADPH-dependent reduction of bisdemethoxycurcumin and curcumin. The optimum pH for the two enzymes was 5.0. The apparent Km values for bisdemethoxycurcumin and NADPH were 4.24 and 3.53 μM in the case of AsDBR1, and 2.55 and 2.13 μM for AsDBR2. The kcat value was 9.4-fold higher for AsDBR1 vs. AsDBR2 when using the bisdemethoxycurcumin substrate. Interestingly, the two AsDBRs failed to reduce the phenylpropanoid monomer.
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Affiliation(s)
- Konosuke Takemoto
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; The United Graduate School of Agricultural Science, Gifu University, 1-1, Yanagido, Gifu-shi, 501-1193, Japan
| | - Akiho Tsurugi-Sakurada
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Ryota Moriuchi
- Functional Genomics Section, Shizuoka Instrumental Analysis Center, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yuko Yoneda
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Shingo Kawai
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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Yu M, Hu S, Tang B, Yang H, Sun D. Engineering Escherichia coli Nissle 1917 as a microbial chassis for therapeutic and industrial applications. Biotechnol Adv 2023; 67:108202. [PMID: 37343690 DOI: 10.1016/j.biotechadv.2023.108202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/19/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
Genetically engineered microbes, especially Escherichia coli, have been widely used in the biosynthesis of proteins and metabolites for medical and industrial applications. As a traditional probiotic with a well-established safety record, E. coli Nissle 1917 (EcN) has recently emerged as a microbial chassis for generating living therapeutics, drug delivery vehicles, and microbial platforms for industrial production. Despite the availability of genetic tools for engineering laboratory E. coli K-12 and B strains, new genetic engineering systems are still greatly needed to expand the application range of EcN. In this review, we have summarized the latest progress in the development of genetic engineering systems in EcN, as well as their applications in the biosynthesis and delivery of valuable small molecules and biomacromolecules of medical and/or industrial interest, followed by a glimpse of how this rapidly growing field will evolve in the future.
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Affiliation(s)
- Mingjing Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Shilong Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Biao Tang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Hua Yang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
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4
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Lee E, McLeod MJ, Redzic JS, Marcolin B, Thorne RE, Agarwal P, Eisenmesser EZ. Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle. Front Mol Biosci 2023; 10:1244587. [PMID: 37645217 PMCID: PMC10461185 DOI: 10.3389/fmolb.2023.1244587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics changes occur between different intermediates of the catalytic cycle and whether these were relegated to just the active site or the entirety of the enzyme. Through X-ray crystallography, we determined the apo BLVRB structure for the first time, revealing subtle global changes compared to the holo structure and identifying the loss of a critical hydrogen bond that "clamps" the R78-loop over the coenzyme. Amide and Cα chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, with more distant global changes observed upon coenzyme binding compared to substrate interactions. NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB during the catalytic cycle. Specifically, the inherently dynamic R78-loop that becomes ordered upon coenzyme binding persists through the catalytic cycle while similar regions experience dynamic exchange. However, the dynamic exchange processes were found to differ through the catalytic cycle with several groups of residues exhibiting similar dynamic responses. Finally, both local and distal structural and dynamic changes occur within BLVRB that are dependent solely on the oxidative state of the coenzyme. Thus, through a comprehensive analysis here, this study revealed structural and dynamic alterations in BLVRB through its catalytic cycle that are not simply relegated to the active site, but instead, are allosterically coupled throughout the enzyme.
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Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Matthew J. McLeod
- Laboratory of Atomic and Solid-State Physics, Cornell University, Ithaca, NY, United States
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Barbara Marcolin
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Robert E. Thorne
- Laboratory of Atomic and Solid-State Physics, Cornell University, Ithaca, NY, United States
| | - Pratul Agarwal
- Department of Physiological Sciences and High Performance Computing Center, Oklahoma State University, Stillwater, OK, United States
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
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5
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Lee E, Redzic JS, Zohar Eisenmesser E. Relaxation and single site multiple mutations to identify and control allosteric networks. Methods 2023; 216:51-57. [PMID: 37302521 PMCID: PMC11066977 DOI: 10.1016/j.ymeth.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023] Open
Abstract
Advances in Nuclear Magnetic Resonance (NMR) spectroscopy have allowed for the identification and characterization of movements in enzymes over the last 20 years that has also revealed the complexities of allosteric coupling. For example, many of the inherent movements of enzymes, and proteins in general, have been shown to be highly localized but nonetheless still coupled over long distances. Such partial couplings provide challenges to both identifying allosteric networks of dynamic communication and determining their roles in catalytic function. We have developed an approach to help identify and engineer enzyme function, called Relaxation And Single Site Multiple Mutations (RASSMM). This approach is a powerful extension of mutagenesis and NMR that is based on the observation that multiple mutations to a single site distal to the active site allosterically induces different effects to networks. Such an approach generates a panel of mutations that can also be subjected to functional studies in order to match catalytic effects with changes to coupled networks. In this review, the RASSMM approach is briefly outlined together with two applications that include cyclophilin-A and Biliverdin Reductase B.
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Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA.
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6
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Chemaly M, Marlevi D, Iglesias MJ, Lengquist M, Kronqvist M, Bos D, van Dam-Nolen DHK, van der Kolk A, Hendrikse J, Kassem M, Matic L, Odeberg J, de Vries MR, Kooi ME, Hedin U. Biliverdin Reductase B Is a Plasma Biomarker for Intraplaque Hemorrhage and a Predictor of Ischemic Stroke in Patients with Symptomatic Carotid Atherosclerosis. Biomolecules 2023; 13:882. [PMID: 37371462 DOI: 10.3390/biom13060882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Intraplaque hemorrhage (IPH) is a hallmark of atherosclerotic plaque instability. Biliverdin reductase B (BLVRB) is enriched in plasma and plaques from patients with symptomatic carotid atherosclerosis and functionally associated with IPH. OBJECTIVE We explored the biomarker potential of plasma BLVRB through (1) its correlation with IPH in carotid plaques assessed by magnetic resonance imaging (MRI), and with recurrent ischemic stroke, and (2) its use for monitoring pharmacotherapy targeting IPH in a preclinical setting. METHODS Plasma BLVRB levels were measured in patients with symptomatic carotid atherosclerosis from the PARISK study (n = 177, 5 year follow-up) with and without IPH as indicated by MRI. Plasma BLVRB levels were also measured in a mouse vein graft model of IPH at baseline and following antiangiogenic therapy targeting vascular endothelial growth factor receptor 2 (VEGFR-2). RESULTS Plasma BLVRB levels were significantly higher in patients with IPH (737.32 ± 693.21 vs. 520.94 ± 499.43 mean fluorescent intensity (MFI), p = 0.033), but had no association with baseline clinical and biological parameters. Plasma BLVRB levels were also significantly higher in patients who developed recurrent ischemic stroke (1099.34 ± 928.49 vs. 582.07 ± 545.34 MFI, HR = 1.600, CI [1.092-2.344]; p = 0.016). Plasma BLVRB levels were significantly reduced following prevention of IPH by anti-VEGFR-2 therapy in mouse vein grafts (1189 ± 258.73 vs. 1752 ± 366.84 MFI; p = 0.004). CONCLUSIONS Plasma BLVRB was associated with IPH and increased risk of recurrent ischemic stroke in patients with symptomatic low- to moderate-grade carotid stenosis, indicating the capacity to monitor the efficacy of IPH-preventive pharmacotherapy in an animal model. Together, these results suggest the utility of plasma BLVRB as a biomarker for atherosclerotic plaque instability.
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Affiliation(s)
- Melody Chemaly
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
| | - David Marlevi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maria-Jesus Iglesias
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry/Biotechnology and Health, KTH Royal Institute of Technology, 11428 Stockholm, Sweden
| | - Mariette Lengquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Malin Kronqvist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Daniel Bos
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Dianne H K van Dam-Nolen
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - Anja van der Kolk
- Department of Medical Imaging, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Department of Radiology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Jeroen Hendrikse
- Department of Radiology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Mohamed Kassem
- Department of Radiology and Nuclear Medicine, CARIM School for Cardiovascular Diseases, Maastricht University Medical Center, 6229 ER Maastricht, The Netherlands
| | - Ljubica Matic
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry/Biotechnology and Health, KTH Royal Institute of Technology, 11428 Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital, Huddinge, 14152 Stockholm, Sweden
- Department of Clinical Medicine, UiT-The Arctic University of Norway, 9019 Tromsø, Norway
| | - Margreet R de Vries
- Einthoven Laboratory, Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - M Eline Kooi
- Department of Radiology and Nuclear Medicine, CARIM School for Cardiovascular Diseases, Maastricht University Medical Center, 6229 ER Maastricht, The Netherlands
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
- Department of Vascular Surgery, Karolinska University Hospital, 17176 Stockholm, Sweden
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7
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Bahou WF, Marchenko N, Nesbitt NM. Metabolic Functions of Biliverdin IXβ Reductase in Redox-Regulated Hematopoietic Cell Fate. Antioxidants (Basel) 2023; 12:antiox12051058. [PMID: 37237924 DOI: 10.3390/antiox12051058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Cytoprotective heme oxygenases derivatize heme to generate carbon monoxide, ferrous iron, and isomeric biliverdins, followed by rapid NAD(P)H-dependent biliverdin reduction to the antioxidant bilirubin. Recent studies have implicated biliverdin IXβ reductase (BLVRB) in a redox-regulated mechanism of hematopoietic lineage fate restricted to megakaryocyte and erythroid development, a function distinct and non-overlapping from the BLVRA (biliverdin IXα reductase) homologue. In this review, we focus on recent progress in BLVRB biochemistry and genetics, highlighting human, murine, and cell-based studies that position BLVRB-regulated redox function (or ROS accumulation) as a developmentally tuned trigger that governs megakaryocyte/erythroid lineage fate arising from hematopoietic stem cells. BLVRB crystallographic and thermodynamic studies have elucidated critical determinants of substrate utilization, redox coupling and cytoprotection, and have established that inhibitors and substrates bind within the single-Rossmann fold. These advances provide unique opportunities for the development of BLVRB-selective redox inhibitors as novel cellular targets that retain potential for therapeutic applicability in hematopoietic (and other) disorders.
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Affiliation(s)
- Wadie F Bahou
- Department of Medicine, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Natalia Marchenko
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Natasha M Nesbitt
- Blood Cell Technologies, 25 Health Sciences Drive, Stony Brook, NY 11790, USA
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8
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Huang C, Cui H, Ren H, Zhao H. Investigation of the Biosynthetic Mechanism of Bipentaromycin Featuring an Unprecedented Cyclic Head-to-Tail Dimeric Scaffold. JACS Au 2023; 3:195-203. [PMID: 36711095 PMCID: PMC9875255 DOI: 10.1021/jacsau.2c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Bipentaromycins are heterodimeric aromatic polyketides featuring two distinctive 5/6/6/6/5 pentacyclic ring systems and exhibit antibacterial activities. However, their overall biosynthetic mechanism, particularly the mechanism for early-stage modifications, such as hydrogenation and methylation, and late-stage dimerization, remains unknown. Herein, by integrating heterologous expression, isotope labeling, gene knockout and complementation, and computational modeling, we determined the biosynthetic origin of the skeleton, identified the enzymes involved in stereo-/regioselective hydrogenation and methylation, and provided new mechanistic insights into the dimerization. This work not only deciphers the biosynthetic mechanism of bipentaromycins but also provides new strategies for creating biologically active dimeric pharmacophores for drug discovery and development.
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Affiliation(s)
- Chunshuai Huang
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Haiyang Cui
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hengqian Ren
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Biochemistry, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Zhang Y, Martin JE, Edmonds KA, Winkler ME, Giedroc DP. SifR is an Rrf2-family quinone sensor associated with catechol iron uptake in Streptococcus pneumoniae D39. J Biol Chem 2022; 298:102046. [PMID: 35597283 PMCID: PMC9218516 DOI: 10.1016/j.jbc.2022.102046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/15/2023] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is a Gram-positive commensal and human respiratory pathogen. How this bacterium satisfies its nutritional iron (Fe) requirement in the context of endogenously produced hydrogen peroxide is not well understood. Here, we characterize a novel virulence-associated Rrf2-family transcriptional repressor that we term SifR (streptococcal IscR-like family transcriptional repressor) encoded by spd_1448 and conserved in Streptococci. Global transcriptomic analysis of a ΔsifR strain defines the SifR regulon as genes encoding a candidate catechol dioxygenase CatE, an uncharacterized oxidoreductase YwnB, a candidate flavin-dependent ferric reductase YhdA, a candidate heme-based ferric reductase domain-containing protein and the Piu (pneumococcus iron uptake) Fe transporter (piuBCDA). Previous work established that membrane-anchored PiuA binds FeIII-bis-catechol or monocatechol complexes with high affinity, including the human catecholamine stress hormone, norepinephrine. We demonstrate that SifR senses quinone via a single conserved cysteine that represses its regulon when in the reduced form. Upon reaction with catechol-derived quinones, we show that SifR dissociates from the DNA leading to regulon derepression, allowing the pneumococcus to access a catechol-derived source of Fe while minimizing reactive electrophile stress induced by quinones. Consistent with this model, we show that CatE is an FeII-dependent 2,3-catechol dioxygenase with broad substrate specificity, YwnB is an NAD(P)H-dependent quinone reductase capable of reducing the oxidized and cyclized norepinephrine, adrenochrome, and YhdA is capable of reducing a number of FeIII complexes, including PiuA-binding transport substrates. These findings are consistent with a model where FeIII-catechol complexes serve as significant nutritional Fe sources in the host.
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Affiliation(s)
- Yifan Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
| | - Julia E Martin
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA; Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | | | - Malcolm E Winkler
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA; Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA.
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10
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Kim M, Ha JH, Choi J, Kim BR, Gapsys V, Lee KO, Jee JG, Chakrabarti KS, de Groot BL, Griesinger C, Ryu KS, Lee D. Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IXβ Reductase B as a Novel Thrombocytopenia Therapeutic Target. J Med Chem 2021; 65:2548-2557. [PMID: 34957824 DOI: 10.1021/acs.jmedchem.1c01664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biliverdin IXβ reductase B (BLVRB) has recently been proposed as a novel therapeutic target for thrombocytopenia through its reactive oxygen species (ROS)-associated mechanism. Thus, we aim at repurposing drugs as new inhibitors of BLVRB. Based on IC50 (<5 μM), we have identified 20 compounds out of 1496 compounds from the Food and Drug Administration (FDA)-approved library and have clearly mapped their binding sites to the active site. Furthermore, we show the detailed BLVRB-binding modes and thermodynamic properties (ΔH, ΔS, and KD) with nuclear magnetic resonance (NMR) and isothermal titration calorimetry together with complex structures of eight water-soluble compounds. We anticipate that the results will serve as a novel platform for further in-depth studies on BLVRB effects for related functions such as ROS accumulation and megakaryocyte differentiation, and ultimately treatments of platelet disorders.
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Affiliation(s)
- Myeongkyu Kim
- Protein Structure Research Team, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea.,Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jung-Hye Ha
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation(DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 41061, South Korea
| | - Joonhyeok Choi
- Protein Structure Research Team, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea
| | - Bo-Ram Kim
- Protein Structure Research Team, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea
| | - Vytautas Gapsys
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ko On Lee
- Protein Structure Research Team, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea
| | - Jun-Goo Jee
- Research Institute of Pharmaceutical Sciences College of Pharmacy, Kyungpook National University, 80 Daehak-Ro, Buk-Gu, Daegu 41566, South Korea
| | | | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kyoung-Seok Ryu
- Protein Structure Research Team, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock Street, Louisville, Kentucky 40202, United States
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11
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Bortolussi G, Shi X, ten Bloemendaal L, Banerjee B, De Waart DR, Baj G, Chen W, Oude Elferink RP, Beuers U, Paulusma CC, Stocker R, Muro AF, Bosma PJ. Long-Term Effects of Biliverdin Reductase a Deficiency in Ugt1-/- Mice: Impact on Redox Status and Metabolism. Antioxidants (Basel) 2021; 10:antiox10122029. [PMID: 34943131 PMCID: PMC8698966 DOI: 10.3390/antiox10122029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Accumulation of neurotoxic bilirubin due to a transient neonatal or persistent inherited deficiency of bilirubin glucuronidation activity can cause irreversible brain damage and death. Strategies to inhibit bilirubin production and prevent neurotoxicity in neonatal and adult settings seem promising. We evaluated the impact of Bvra deficiency in neonatal and aged mice, in a background of unconjugated hyperbilirubinemia, by abolishing bilirubin production. We also investigated the disposal of biliverdin during fetal development. In Ugt1−/− mice, Bvra deficiency appeared sufficient to prevent lethality and to normalize bilirubin level in adults. Although biliverdin accumulated in Bvra-deficient fetuses, both Bvra−/− and Bvra−/−Ugt1−/− pups were healthy and reached adulthood having normal liver, brain, and spleen histology, albeit with increased iron levels in the latter. During aging, both Bvra−/− and Bvra−/−Ugt1−/− mice presented normal levels of relevant hematological and metabolic parameters. Interestingly, the oxidative status in erythrocytes from 9-months-old Bvra−/− and Bvra−/−Ugt1−/− mice was significantly reduced. In addition, triglycerides levels in these 9-months-old Bvra−/− mice were significantly higher than WT controls, while Bvra−/−Ugt1−/− tested normal. The normal parameters observed in Bvra−/−Ugt1−/− mice fed chow diet indicate that Bvra inhibition to treat unconjugated hyperbilirubinemia seems safe and effective.
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Affiliation(s)
- Giulia Bortolussi
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (G.B.); (B.B.)
| | - Xiaoxia Shi
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.S.); (L.t.B.); (D.R.D.W.); (R.P.O.E.); (U.B.); (C.C.P.)
- Key Laboratory of Protein Modification and Disease, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Lysbeth ten Bloemendaal
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.S.); (L.t.B.); (D.R.D.W.); (R.P.O.E.); (U.B.); (C.C.P.)
| | - Bhaswati Banerjee
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (G.B.); (B.B.)
| | - Dirk R. De Waart
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.S.); (L.t.B.); (D.R.D.W.); (R.P.O.E.); (U.B.); (C.C.P.)
| | - Gabriele Baj
- Light Microscopy Imaging Center, Department of Life Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Weiyu Chen
- Heart Research Institute, Sydney, NSW 2042, Australia; (W.C.); (R.S.)
| | - Ronald P. Oude Elferink
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.S.); (L.t.B.); (D.R.D.W.); (R.P.O.E.); (U.B.); (C.C.P.)
| | - Ulrich Beuers
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.S.); (L.t.B.); (D.R.D.W.); (R.P.O.E.); (U.B.); (C.C.P.)
| | - Coen C. Paulusma
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.S.); (L.t.B.); (D.R.D.W.); (R.P.O.E.); (U.B.); (C.C.P.)
| | - Roland Stocker
- Heart Research Institute, Sydney, NSW 2042, Australia; (W.C.); (R.S.)
| | - Andrés F. Muro
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (G.B.); (B.B.)
- Correspondence: (A.F.M.); (P.J.B.); Tel.: +39-040-3757369 (A.F.M.); +31-20-566-8850 (P.J.B.)
| | - Piter J. Bosma
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (X.S.); (L.t.B.); (D.R.D.W.); (R.P.O.E.); (U.B.); (C.C.P.)
- Correspondence: (A.F.M.); (P.J.B.); Tel.: +39-040-3757369 (A.F.M.); +31-20-566-8850 (P.J.B.)
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12
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Robinson EA, Frankenberg-Dinkel N, Xue F, Wilks A. Recombinant Production of Biliverdin IXβ and δ Isomers in the T7 Promoter Compatible Escherichia coli Nissle. Front Microbiol 2021; 12:787609. [PMID: 34956154 PMCID: PMC8692735 DOI: 10.3389/fmicb.2021.787609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/11/2021] [Indexed: 11/23/2022] Open
Abstract
The ability to obtain purified biliverdin IX (BVIX) isomers other than the commercially available BVIXα is limited due to the low yields obtained by the chemical coupled oxidation of heme. Chemical oxidation requires toxic chemicals, has very poor BVIX yields (<0.05%), and is not conducive to scalable production. Alternative approaches utilizing recombinant E. coli BL21 expressing a cyanobacterial heme oxygenase have been employed for the production BVIXα, but yields are limited by the rate of endogenous heme biosynthesis. Furthermore, the emerging roles of BVIXβ and BVIXδ in biology and their lack of commercial availability has led to a need for an efficient and scalable method with the flexibility to produce all three physiologically relevant BVIX isomers. Herein, we have taken advantage of an optimized non-pathogenic E. coli Nissle (EcN(T7)) strain that encodes an endogenous heme transporter and an integrated T7 polymerase gene. Protein production of the Pseudomonas aeruginosa BVIXβ and BVIXδ selective heme oxygenase (HemO) or its BVIXα producing mutant (HemOα) in the EcN(T7) strain provides a scalable method to obtain all three isomers, that is not limited by the rate of endogenous heme biosynthesis, due to the natural ability of EcN(T7) to transport extracellular heme. Additionally, we have optimized our previous LC-MS/MS protocol for semi-preparative separation and validation of the BVIX isomers. Utilizing this new methodology for scalable production and separation we have increased the yields of the BVIXβ and -δ isomers >300-fold when compared to the chemical oxidation of heme.
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Affiliation(s)
- Elizabeth A. Robinson
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Nicole Frankenberg-Dinkel
- Fachbereich Biologie, Abt. Mikrobiologie, Technische Universität Kaiserlautern, Kaiserslautern, Germany
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Angela Wilks
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
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13
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Machado JH, Ting R, Lin JY, Rodriguez EA. A self-labeling protein based on the small ultra-red fluorescent protein, smURFP. RSC Chem Biol 2021; 2:1221-1226. [PMID: 34458834 PMCID: PMC8341759 DOI: 10.1039/d1cb00127b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/24/2021] [Indexed: 12/25/2022] Open
Abstract
Self-labeling proteins have revolutionized super-resolution and sensor imaging. Tags recognize a bioorthogonal substrate for covalent attachment. We show the small Ultra-Red Fluorescent Protein (smURFP) is a self-labeling protein. The substrate is fluorogenic, fluoresces when attached, and quenches fluorescent cargo. The smURFP-tag has novel properties for tool development.
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Affiliation(s)
- John-Hanson Machado
- Department of Chemistry, The George Washington University Washington DC 20052 USA
| | - Richard Ting
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine New York NY 10065 USA
- Antelope Surgical, Biolabs@NYULangone New York NY 10014 USA
| | - John Y Lin
- Tasmanian School of Medicine, University of Tasmania Hobart Tasmania 7000 Australia
| | - Erik A Rodriguez
- Department of Chemistry, The George Washington University Washington DC 20052 USA
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14
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Nesbitt NM, Malone LE, Liu Z, Jares A, Gnatenko DV, Ma Y, Zhu W, Bahou WF. Divergent erythroid megakaryocyte fates in Blvrb-deficient mice establish non-overlapping cytoprotective functions during stress hematopoiesis. Free Radic Biol Med 2021; 164:164-174. [PMID: 33359909 PMCID: PMC8311568 DOI: 10.1016/j.freeradbiomed.2020.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/17/2020] [Accepted: 12/13/2020] [Indexed: 12/27/2022]
Abstract
Cytoprotective mechanisms of heme oxygenases function by derivatizing heme to generate carbon monoxide, ferrous iron, and isomeric biliverdins, followed by rapid NAD(P)H-dependent biliverdin reduction to the antioxidant bilirubin using two non-overlapping biliverdin reductases that display biliverdin isomer-restricted redox activity. Although cytoprotective functions of heme oxygenases are widely recognized, concomitant effects of downstream biliverdin reductases remain incomplete. A computational model predicated on murine hematopoietic single-cell transcriptomic data identified Blvrb as a biological driver linked to the tumor necrosis factor stress pathway as a predominant source of variation defining hematopoietic cell heterogeneity. In vivo studies using Blvrb-deficient mice established the dispensable role of Blvrb in steady-state hematopoiesis, although model validation using aged Blvrb-deficient mice established an important cytoprotective function in stress hematopoiesis with dichotomous megakaryocyte-biased hematopoietic recovery. Defective stress erythropoiesis was evident in Blvrb-/- spleens and in bone marrow erythroid development, occurring in conjunction with defective lipid peroxidation as a marker of oxidant mishandling. Cell autonomous effects on megakaryocyte lineage bias were documented using multipotential progenitor assays. These data provide the first physiological function of murine Blvrb in a non-redundant pathway of stress cytoprotection. Divergent effects on erythroid/megakaryocyte lineage speciation impute a novel redox-regulated mechanism for lineage partitioning.
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Affiliation(s)
- Natasha M Nesbitt
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Lisa E Malone
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Zhaoyan Liu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, 11727, USA
| | - Alexander Jares
- Department of Pathology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Dmitri V Gnatenko
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Yupo Ma
- Department of Pathology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Wei Zhu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, 11727, USA
| | - Wadie F Bahou
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA.
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15
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Duff MR, Redzic JS, Ryan LP, Paukovich N, Zhao R, Nix JC, Pitts TM, Agarwal P, Eisenmesser EZ. Structure, dynamics and function of the evolutionarily changing biliverdin reductase B family. J Biochem 2021; 168:191-202. [PMID: 32246827 DOI: 10.1093/jb/mvaa039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/19/2020] [Indexed: 11/14/2022] Open
Abstract
Biliverdin reductase B (BLVRB) family members are general flavin reductases critical in maintaining cellular redox with recent findings revealing that BLVRB alone can dictate cellular fate. However, as opposed to most enzymes, the BLVRB family remains enigmatic with an evolutionarily changing active site and unknown structural and functional consequences. Here, we applied a multi-faceted approach that combines X-ray crystallography, NMR and kinetics methods to elucidate the structural and functional basis of the evolutionarily changing BLVRB active site. Using a panel of three BLVRB isoforms (human, lemur and hyrax) and multiple human BLVRB mutants, our studies reveal a novel evolutionary mechanism where coenzyme 'clamps' formed by arginine side chains at two co-evolving positions within the active site serve to slow coenzyme release (Positions 14 and 78). We find that coenzyme release is further slowed by the weaker binding substrate, resulting in relatively slow turnover numbers. However, different BLVRB active sites imposed by either evolution or mutagenesis exhibit a surprising inverse relationship between coenzyme release and substrate turnover that is independent of the faster chemical step of hydride transfer also measured here. Collectively, our studies have elucidated the role of the evolutionarily changing BLVRB active site that serves to modulate coenzyme release and has revealed that coenzyme release is coupled to substrate turnover.
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Affiliation(s)
- Michael R Duff
- Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, 1311 Cumberland Ave., Knoxville, TN 37996, USA
| | - Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Lucas P Ryan
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Natasia Paukovich
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Todd M Pitts
- Division of Medical Oncology, School of Medicine, University of Colorado, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Pratul Agarwal
- Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, 1311 Cumberland Ave., Knoxville, TN 37996, USA
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
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16
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Redzic JS, Duff MR, Blue A, Pitts TM, Agarwal P, Eisenmesser EZ. Modulating Enzyme Function via Dynamic Allostery within Biliverdin Reductase B. Front Mol Biosci 2021; 8:691208. [PMID: 34095235 PMCID: PMC8173106 DOI: 10.3389/fmolb.2021.691208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/30/2021] [Indexed: 11/17/2022] Open
Abstract
The biliverdin reductase B (BLVRB) class of enzymes catalyze the NADPH-dependent reduction of multiple flavin substrates and are emerging as critical players in cellular redox regulation. However, the role of dynamics and allostery have not been addressed, prompting studies here that have revealed a position 15 Å away from the active site within human BLVRB (T164) that is inherently dynamic and can be mutated to control global micro-millisecond motions and function. By comparing the inherent dynamics through nuclear magnetic resonance (NMR) relaxation approaches of evolutionarily distinct BLVRB homologues and by applying our previously developed Relaxation And Single Site Multiple Mutations (RASSMM) approach that monitors both the functional and dynamic effects of multiple mutations to the single T164 site, we have discovered that the most dramatic mutagenic effects coincide with evolutionary changes and these modulate coenzyme binding. Thus, evolutionarily changing sites distal to the active site serve as dynamic "dials" to globally modulate motions and function. Despite the distal dynamic and functional coupling modulated by this site, micro-millisecond motions span an order of magnitude in their apparent kinetic rates of motions. Thus, global dynamics within BLVRB are a collection of partially coupled motions tied to catalytic function.
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Affiliation(s)
- Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Denver, CO, United States
| | - Michael R Duff
- Biochemistry and Cellular and Molecular Biology Department, University of Tennessee, Knoxville, TN, United States
| | - Ashley Blue
- National High Magnetic Field Laboratory, Tallahassee, FL, United States
| | - Todd M Pitts
- Division of Medical Oncology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Pratul Agarwal
- Department of Physiological Sciences and High Performance Computing Center, Oklahoma State University, Stillwater, OK, United States
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Denver, CO, United States
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17
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Haines DD, Tosaki A. Heme Degradation in Pathophysiology of and Countermeasures to Inflammation-Associated Disease. Int J Mol Sci 2020; 21:ijms21249698. [PMID: 33353225 PMCID: PMC7766613 DOI: 10.3390/ijms21249698] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
The class of tetrapyrrol "coordination complexes" called hemes are prosthetic group components of metalloproteins including hemoglobin, which provide functionality to these physiologically essential macromolecules by reversibly binding diatomic gasses, notably O2, which complexes to ferrous (reduced/Fe(II)) iron within the heme porphyrin ring of hemoglobin in a pH- and PCO2-dependent manner-thus allowing their transport and delivery to anatomic sites of their function. Here, pathologies associated with aberrant heme degradation are explored in the context of their underlying mechanisms and emerging medical countermeasures developed using heme oxygenase (HO), its major degradative enzyme and bioactive metabolites produced by HO activity. Tissue deposits of heme accumulate as a result of the removal of senescent or damaged erythrocytes from circulation by splenic macrophages, which destroy the cells and internal proteins, including hemoglobin, leaving free heme to accumulate, posing a significant toxicogenic challenge. In humans, HO uses NADPH as a reducing agent, along with molecular oxygen, to degrade heme into carbon monoxide (CO), free ferrous iron (FeII), which is sequestered by ferritin protein, and biliverdin, subsequently metabolized to bilirubin, a potent inhibitor of oxidative stress-mediated tissue damage. CO acts as a cellular messenger and augments vasodilation. Nevertheless, disease- or trauma-associated oxidative stressors sufficiently intense to overwhelm HO may trigger or exacerbate a wide range of diseases, including cardiovascular and neurologic syndromes. Here, strategies are described for counteracting the effects of aberrant heme degradation, with a particular focus on "bioflavonoids" as HO inducers, shown to cause amelioration of severe inflammatory diseases.
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Affiliation(s)
- Donald David Haines
- Advanced Biotherapeutics, London W2 1EB, UK;
- Department of Pharmacology, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary
| | - Arpad Tosaki
- Department of Pharmacology, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: ; Tel./Fax: +36-52-255586
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18
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Hansen TWR, Wong RJ, Stevenson DK. Molecular Physiology and Pathophysiology of Bilirubin Handling by the Blood, Liver, Intestine, and Brain in the Newborn. Physiol Rev 2020; 100:1291-1346. [PMID: 32401177 DOI: 10.1152/physrev.00004.2019] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Bilirubin is the end product of heme catabolism formed during a process that involves oxidation-reduction reactions and conserves iron body stores. Unconjugated hyperbilirubinemia is common in newborn infants, but rare later in life. The basic physiology of bilirubin metabolism, such as production, transport, and excretion, has been well described. However, in the neonate, numerous variables related to nutrition, ethnicity, and genetic variants at several metabolic steps may be superimposed on the normal physiological hyperbilirubinemia that occurs in the first week of life and results in bilirubin levels that may be toxic to the brain. Bilirubin exists in several isomeric forms that differ in their polarities and is considered a physiologically important antioxidant. Here we review the chemistry of the bilirubin molecule and its metabolism in the body with a particular focus on the processes that impact the newborn infant, and how differences relative to older children and adults contribute to the risk of developing both acute and long-term neurological sequelae in the newborn infant. The final section deals with the interplay between the brain and bilirubin and its entry, clearance, and accumulation. We conclude with a discussion of the current state of knowledge regarding the mechanism(s) of bilirubin neurotoxicity.
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Affiliation(s)
- Thor W R Hansen
- Division of Paediatric and Adolescent Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; and Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Ronald J Wong
- Division of Paediatric and Adolescent Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; and Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - David K Stevenson
- Division of Paediatric and Adolescent Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; and Department of Pediatrics, Stanford University School of Medicine, Stanford, California
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19
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Zhang B, Nesbitt NM, Pereira PJB, Bahou WF. Biochemical characterization of biliverdins IXβ/δ generated by a selective heme oxygenase. Biochem J 2020; 477:601-14. [PMID: 31913441 DOI: 10.1042/BCJ20190810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/26/2022]
Abstract
The pro-oxidant effect of free heme (Fe2+-protoporphyrin IX) is neutralized by phylogenetically-conserved heme oxygenases (HMOX) that generate carbon monoxide, free ferrous iron, and biliverdin (BV) tetrapyrrole(s), with downstream BV reduction by non-redundant NADPH-dependent BV reductases (BLVRA and BLVRB) that retain isomer-restricted functional activity for bilirubin (BR) generation. Regioselectivity for the heme α-meso carbon resulting in predominant BV IXα generation is a defining characteristic of canonical HMOXs, thereby limiting generation and availability of BVs IXβ, IXδ, and IXγ as BLVRB substrates. We have now exploited the unique capacity of the Pseudomonas aeruginosa (P. aeruginosa) hemO/pigA gene for focused generation of isomeric BVs (IXβ and IXδ). A scalable system followed by isomeric separation yielded highly pure samples with predicted hydrogen-bonded structure(s) as documented by 1H NMR spectroscopy. Detailed kinetic studies established near-identical activity of BV IXβ and BV IXδ as BLVRB-selective substrates, with confirmation of an ordered sequential mechanism of BR/NADP+ dissociation. Halogenated xanthene-based compounds previously identified as BLVRB-targeted flavin reductase inhibitors displayed comparable inhibition parameters using BV IXβ as substrate, documenting common structural features of the cofactor/substrate-binding pocket. These data provide further insights into structure/activity mechanisms of isomeric BVs as BLVRB substrates, with potential applicability to further dissect redox-regulated functions in cytoprotection and hematopoiesis.
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20
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Canesin G, Hejazi SM, Swanson KD, Wegiel B. Heme-Derived Metabolic Signals Dictate Immune Responses. Front Immunol 2020; 11:66. [PMID: 32082323 PMCID: PMC7005208 DOI: 10.3389/fimmu.2020.00066] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/10/2020] [Indexed: 12/21/2022] Open
Abstract
Heme is one of the most abundant molecules in the body acting as the functional core of hemoglobin/myoglobin involved in the O2/CO2 carrying in the blood and tissues, redox enzymes and cytochromes in mitochondria. However, free heme is toxic and therefore its removal is a significant priority for the host. Heme is a well-established danger-associated molecular pattern (DAMP), which binds to toll-like receptor 4 (TLR4) to induce immune responses. Heme-derived metabolites including the bile pigments, biliverdin (BV) and bilirubin (BR), were first identified as toxic drivers of neonatal jaundice in 1800 but have only recently been appreciated as endogenous drivers of multiple signaling pathways involved in protection from oxidative stress and regulators of immune responses. The tissue concentration of heme, BV and BR is tightly controlled. Heme oxygenase-1 (HO-1, encoded by HMOX1) produces BV by heme degradation, while biliverdin reductase-A (BLVR-A) generates BR by the subsequent conversion of BV. BLVR-A is a fascinating protein that possesses a classical protein kinase domain, which is activated in response to BV binding to its enzymatic site and initiates the downstream mitogen-activated protein kinases (MAPK) and phosphatidylinositol 3-kinase (PI3K) pathways. This links BLVR-A activity to cell growth and survival pathways. BLVR-A also contains a bZip DNA binding domain and a nuclear export sequence (NES) and acts as a transcription factor to regulate the expression of immune modulatory genes. Here we will discuss the role of heme-related immune response and the potential for targeting the heme system for therapies directed toward hepatitis and cancer.
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Affiliation(s)
- Giacomo Canesin
- Department of Surgery, Cancer Research Institute and Transplant Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
| | - Seyed M Hejazi
- Department of Surgery, Cancer Research Institute and Transplant Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
| | - Kenneth D Swanson
- Brain Tumor Center and Neuro-Oncology Unit, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Barbara Wegiel
- Department of Surgery, Cancer Research Institute and Transplant Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
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21
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Sugishima M, Wada K, Unno M, Fukuyama K. Bilin-metabolizing enzymes: site-specific reductions catalyzed by two different type of enzymes. Curr Opin Struct Biol 2019; 59:73-80. [PMID: 30954759 DOI: 10.1016/j.sbi.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 01/09/2019] [Accepted: 03/04/2019] [Indexed: 02/05/2023]
Abstract
In mammals, the green heme metabolite biliverdin is converted to a yellow anti-oxidant by NAD(P)H-dependent biliverdin reductase (BVR), whereas in O2-dependent photosynthetic organisms it is converted to photosynthetic or light-sensing pigments by ferredoxin-dependent bilin reductases (FDBRs). In NADP+-bound and biliverdin-bound BVR-A, two biliverdins are stacked at the binding cleft; one is positioned to accept hydride from NADPH, and the other appears to donate a proton to the first biliverdin through a neighboring arginine residue. During the FDBR-catalyzed reaction, electrons and protons are supplied to bilins from ferredoxin and from FDBRs and waters bound within FDBRs, respectively. Thus, the protonation sites of bilin and catalytic residues are important for the analysis of site-specific reduction. The neutron structure of FDBR sheds light on this issue.
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Affiliation(s)
- Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka 830-0011, Japan.
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, Ibaraki 316-8511, Japan
| | - Keiichi Fukuyama
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
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22
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Sibbersen C, Schou Oxvig AM, Bisgaard Olesen S, Nielsen CB, Galligan JJ, Jørgensen KA, Palmfeldt J, Johannsen M. Profiling of Methylglyoxal Blood Metabolism and Advanced Glycation End-Product Proteome Using a Chemical Probe. ACS Chem Biol 2018; 13:3294-3305. [PMID: 30508371 DOI: 10.1021/acschembio.8b00732] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Methylglyoxal (MG) is quantitatively the most important precursor to advanced glycation end-products (AGEs), and evidence is accumulating that it is also a causally linked to diabetes and aging related diseases. Living systems primarily reside on the glyoxalase system to detoxify MG into benign d-lactate. The flux to either glycation or detoxification, accordingly, is a key parameter for how well a system handles the ubiquitous glyoxal burden. Furthermore, insight into proteins and in particular their individual modification sites are central to understanding the involvement of MG and AGE in diabetes and aging related diseases. Here, we present a simple method to simultaneously monitor the flux of MG both to d-lactate and to protein AGE formation in a biological sample by employing an alkyne-labeled methylglyoxal probe. We apply the method to blood and plasma to demonstrate the impact of blood cell glyoxalase activity on plasma protein AGE formation. We move on to isolate proteins modified by the MG probe and accordingly can present the first general inventory of more than 100 proteins and 300 binding sites of the methylglyoxal probe on plasma as well as erythrocytic proteins. Some of the data could be validated against a number of in vivo and in vitro targets for advanced glycation previously known from the literature; the majority of proteins and specific sites however were previously unknown and may guide future research into MG and AGE to elucidate how these are functionally linked to diabetic disease and aging.
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Affiliation(s)
- Christian Sibbersen
- Department of Forensic Medicine, Aarhus University, Aarhus 8200, Denmark
- Department of Chemistry, Aarhus University, Aarhus 8000, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus 8000, Denmark
| | - Anne-Mette Schou Oxvig
- Department of Forensic Medicine, Aarhus University, Aarhus 8200, Denmark
- Department of Chemistry, Aarhus University, Aarhus 8000, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus 8000, Denmark
| | - Sarah Bisgaard Olesen
- Department of Forensic Medicine, Aarhus University, Aarhus 8200, Denmark
- Department of Chemistry, Aarhus University, Aarhus 8000, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus 8000, Denmark
| | | | - James J. Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | | | - Johan Palmfeldt
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus 8000, Denmark
| | - Mogens Johannsen
- Department of Forensic Medicine, Aarhus University, Aarhus 8200, Denmark
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23
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Matic LP, Jesus Iglesias M, Vesterlund M, Lengquist M, Hong MG, Saieed S, Sanchez-Rivera L, Berg M, Razuvaev A, Kronqvist M, Lund K, Caidahl K, Gillgren P, Pontén F, Uhlén M, Schwenk JM, Hansson GK, Paulsson-Berne G, Fagman E, Roy J, Hultgren R, Bergström G, Lehtiö J, Odeberg J, Hedin U. Novel Multiomics Profiling of Human Carotid Atherosclerotic Plaques and Plasma Reveals Biliverdin Reductase B as a Marker of Intraplaque Hemorrhage. JACC Basic Transl Sci 2018; 3:464-480. [PMID: 30175270 PMCID: PMC6115646 DOI: 10.1016/j.jacbts.2018.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 12/31/2022]
Abstract
Clinical tools to identify individuals with unstable atherosclerotic lesions are required to improve prevention of myocardial infarction and ischemic stroke. Here, a systems-based analysis of atherosclerotic plaques and plasma from patients undergoing carotid endarterectomy for stroke prevention was used to identify molecular signatures with a causal relationship to disease. Local plasma collected in the lesion proximity following clamping prior to arteriotomy was profiled together with matched peripheral plasma. This translational workflow identified biliverdin reductase B as a novel marker of intraplaque hemorrhage and unstable carotid atherosclerosis, which should be investigated as a potential predictive biomarker for cardiovascular events in larger cohorts.
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Key Words
- BLVR, biliverdin reductase
- BiKE, Biobank of Karolinska Endarterectomies
- CAC, coronary artery calcium
- CEA, carotid endarterectomy
- HMOX, heme oxygenase
- Hb, hemoglobin
- Hp, haptoglobin
- IPH, intraplaque hemorrhage
- LC-MS/MS, liquid chromatography mass spectrometry/mass spectrometry
- TMT, tandem mass tags
- atherosclerosis
- biomarkers
- intraplaque hemorrhage
- mRNA, messenger ribonucleic acid
- omics analyses
- translational studies
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Affiliation(s)
- Ljubica Perisic Matic
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Maria Jesus Iglesias
- Science for Life Laboratory, Department of Proteomics, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Mattias Vesterlund
- Department of Oncology-Pathology, Cancer Proteomics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Mariette Lengquist
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Mun-Gwan Hong
- Science for Life Laboratory, Department of Proteomics, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Shanga Saieed
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Laura Sanchez-Rivera
- Science for Life Laboratory, Department of Proteomics, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Martin Berg
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Anton Razuvaev
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Malin Kronqvist
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Kent Lund
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Kenneth Caidahl
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Peter Gillgren
- Department of Clinical Science and Education, Södersjukhuset, Stockholm, Sweden.,Department of Surgery, Södersjukhuset, Stockholm, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Proteomics, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Proteomics, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Göran K Hansson
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Erika Fagman
- Department of Radiology, Sahlgrenska Academy, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Joy Roy
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Rebecka Hultgren
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Janne Lehtiö
- Department of Oncology-Pathology, Cancer Proteomics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Proteomics, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden.,Department of Medicine, Karolinska Institute, Stockholm, Sweden.,Coagulation Unit, Centre for Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
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24
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Wu YF, Zheng HB, Liu XY, Cheng AX, Lou HX. Molecular Diversity of Alkenal Double Bond Reductases in the Liverwort Marchantia paleacea. Molecules 2018; 23:molecules23071630. [PMID: 29973530 PMCID: PMC6099575 DOI: 10.3390/molecules23071630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022] Open
Abstract
Alkenal double bond reductases (DBRs), capable of catalyzing the NADPH-dependent reduction of the α,β-unsaturated double bond, play key roles in the detoxication of alkenal carbonyls. Here, the isolation and characterization of two DBRs encoded by the liverwort species Marchantia paleacea are described. The two DBRs share a relatively low similarity, and phylogenetic analysis indicated that MpMDBRL is more closely related to microbial DBRs than to other plant DBRs, while MpDBR shares common ancestry with typical plant DBRs. Both DBR proteins exhibited hydrogenation ability towards hydroxycinnamyl aldehydes; however, their temperature optimums were strikingly different. MpMDBRL demonstrated slightly weaker catalytic efficiency compared to MpDBR, and the structural models of their active binding sites to the substrate may provide a parsimonious explanation. Furthermore, both DBRs significantly responded to phytohormone treatment. In conclusion, M. paleacea produces two distinct types of functional DBRs, both of which participate in the protection against environmental stress in liverwort. The presence of a microbial type of DBR in a plant is herein reported for the first time.
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Affiliation(s)
- Yi-Feng Wu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
| | - Hong-Bo Zheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
| | - Xin-Yan Liu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
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25
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Paukovich N, Xue M, Elder JR, Redzic JS, Blue A, Pike H, Miller BG, Pitts TM, Pollock DD, Hansen K, D'Alessandro A, Eisenmesser EZ. Biliverdin Reductase B Dynamics Are Coupled to Coenzyme Binding. J Mol Biol 2018; 430:3234-3250. [PMID: 29932944 DOI: 10.1016/j.jmb.2018.06.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 12/28/2022]
Abstract
Biliverdin reductase B (BLVRB) is a newly identified cellular redox regulator that catalyzes the NADPH-dependent reduction of multiple substrates. Through mass spectrometry analysis, we identified high levels of BLVRB in mature red blood cells, highlighting the importance of BLVRB in redox regulation. The BLVRB conformational changes that occur during conezyme/substrate binding and the role of dynamics in BLVRB function, however, remain unknown. Through a combination of NMR, kinetics, and isothermal titration calorimetry studies, we determined that BLVRB binds its coenzyme 500-fold more tightly than its substrate. While the active site of apo BLVRB is highly dynamic on multiple timescales, active site dynamics are largely quenched within holo BLVRB, in which dynamics are redistributed to other regions of the enzyme. We show that a single point mutation of Arg78➔Ala leads to both an increase in active site micro-millisecond motions and an increase in the microscopic rate constants of coenzyme binding. This demonstrates that altering BLVRB active site dynamics can directly cause a change in functional characteristics. Our studies thus address the solution behavior of apo and holo BLVRB and identify a role of enzyme dynamics in coenzyme binding.
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Affiliation(s)
- Natasia Paukovich
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Mengjun Xue
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - James R Elder
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Ashley Blue
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Hamish Pike
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Brian G Miller
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32310, USA
| | - Todd M Pitts
- Division of Medical Oncology, School of Medicine, Aurora, CO 80045, USA
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Kirk Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA.
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26
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Abstract
The buildup of fat in the liver (hepatic steatosis) is the first step in a series of incidents that may drive hepatic disease. Obesity is the leading cause of nonalcoholic fatty liver disease (NAFLD), in which hepatic steatosis progresses to liver disease. Chronic alcohol exposure also induces fat accumulation in the liver and shares numerous similarities to obesity-induced NAFLD. Regardless of whether hepatic steatosis is due to obesity or long-term alcohol use, it still may lead to hepatic fibrosis, cirrhosis, or possibly hepatocellular carcinoma. The antioxidant bilirubin and the enzyme that generates it, biliverdin reductase A (BVRA), are components of the heme catabolic pathway that have been shown to reduce hepatic steatosis. This review discusses the roles for bilirubin and BVRA in the prevention of steatosis, their functions in the later stages of liver disease, and their potential therapeutic application.
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Affiliation(s)
- Lauren Weaver
- 1Department of Physiology and Pharmacology, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine, Toledo, Ohio
| | - Abdul-rizaq Hamoud
- 1Department of Physiology and Pharmacology, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine, Toledo, Ohio
| | - David E. Stec
- 2Department of Physiology and Biophysics, Mississippi Center for Obesity Research, University of Mississippi Medical Center, Jackson, Mississippi
| | - Terry D. Hinds
- 1Department of Physiology and Pharmacology, Center for Hypertension and Personalized Medicine, University of Toledo College of Medicine, Toledo, Ohio
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27
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Zhang X, Liao S, Cao F, Zhao L, Pei J, Tang F. Cloning and characterization of enoate reductase with high β-ionone to dihydro-β-ionone bioconversion productivity. BMC Biotechnol 2018; 18:26. [PMID: 29743047 PMCID: PMC5944158 DOI: 10.1186/s12896-018-0438-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/23/2018] [Indexed: 11/28/2022] Open
Abstract
Background Dihydro-β-ionone is a principal aroma compound and has received considerable attention by flavor and fragrance industry. The traditional method of preparing dihydro-β-ionone has many drawbacks, which has restricted its industrial application. Therefore, it is necessary to find a biotechnological method to produce dihydro-β-ionone. Results In this study, the enoate reductase with high conversion efficiency of β-ionone to dihydro-β-ionone, DBR1, was obtained by screening four genetically engineered bacteria. The product, dihydro-β-ionone, was analyzed by GC and GC-MS. The highest dihydro-β-ionone production with 308.3 mg/L was detected in the recombinant strain expressing DBR1 which was later on expressed and purified. Its optimal temperature and pH were 45 °C and 6.5, respectively. The greatest activity of the purified enzyme was 356.39 U/mg using β-ionone as substrate. In the enzymatic conversion system, 1 mM of β-ionone was transformed into 91.08 mg/L of dihydro-β-ionone with 93.80% of molar conversion. Conclusion DBR1 had high selectivity to hydrogenated the 10,11-unsaturated double bond of β-ionone as well as high catalytic efficiency for the conversion of β-ionone to dihydro-β-ionone. It is the first report on the bioconversion of β-ionone to dihydro-β-ionone by using enoate reductase. Electronic supplementary material The online version of this article (10.1186/s12896-018-0438-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuesong Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Long Pan Road, Nanjing, 210037, China.,College of Tea and Food Science and Technology, Jiangsu Polytechnic College of Agriculture and Forestry, Jurong, 212400, China
| | - Shiyong Liao
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing, 210037, China
| | - Fuliang Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Long Pan Road, Nanjing, 210037, China
| | - Linguo Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Long Pan Road, Nanjing, 210037, China. .,College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing, 210037, China.
| | - Jianjun Pei
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing, 210037, China.,Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, 159 Long Pan Road, Nanjing, 210037, China
| | - Feng Tang
- International centre for bamboo and rattan, 8 FuTong East Street, Beijing, 100714, China
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28
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Li Z, Nesbitt NM, Malone LE, Gnatenko DV, Wu S, Wang D, Zhu W, Girnun GD, Bahou WF. Heme degradation enzyme biliverdin IXβ reductase is required for stem cell glutamine metabolism. Biochem J 2018; 475:1211-23. [PMID: 29500232 DOI: 10.1042/BCJ20180016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/16/2018] [Accepted: 02/28/2018] [Indexed: 12/21/2022]
Abstract
Bioenergetic requirements of hematopoietic stem cells and pluripotent stem cells (PSCs) vary with lineage fate, and cellular adaptations rely largely on substrate (glucose/glutamine) availability and mitochondrial function to balance tricarboxylic acid (TCA)-derived anabolic and redox-regulated antioxidant functions. Heme synthesis and degradation converge in a linear pathway that utilizes TCA cycle-derived carbon in cataplerotic reactions of tetrapyrrole biosynthesis, terminated by NAD(P)H-dependent biliverdin reductases (IXα, BLVRA and IXβ, BLVRB) that lead to bilirubin generation and cellular antioxidant functions. We now demonstrate that PSCs with targeted deletion of BLVRB display physiologically defective antioxidant activity and cellular viability, associated with a glutamine-restricted defect in TCA entry that was computationally predicted using gene/metabolite topological network analysis and subsequently validated by bioenergetic and isotopomeric studies. Defective BLVRB-regulated glutamine utilization was accompanied by exaggerated glycolytic accumulation of the rate-limiting hexokinase reaction product glucose-6-phosphate. BLVRB-deficient embryoid body formation (a critical size parameter of early lineage fate potential) demonstrated enhanced sensitivity to the pentose phosphate pathway (PPP) inhibitor 6-aminonicotinamide with no differences in the glycolytic pathway inhibitor 2-deoxyglucose. These collective data place heme catabolism in a crucial pathway of glutamine-regulated bioenergetic metabolism and suggest that early stages of lineage fate potential require glutamine anaplerotic functions and an intact PPP, which are, in part, regulated by BLVRB activity. In principle, BLVRB inhibition represents an alternative strategy for modulating cellular glutamine utilization with consequences for cancer and hematopoietic metabolism.
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29
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Nesbitt NM, Zheng X, Li Z, Manso JA, Yen WY, Malone LE, Ripoll-Rozada J, Pereira PJB, Mantle TJ, Wang J, Bahou WF. In silico and crystallographic studies identify key structural features of biliverdin IXβ reductase inhibitors having nanomolar potency. J Biol Chem 2018; 293:5431-5446. [PMID: 29487133 DOI: 10.1074/jbc.ra118.001803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/23/2018] [Indexed: 12/20/2022] Open
Abstract
Heme cytotoxicity is minimized by a two-step catabolic reaction that generates biliverdin (BV) and bilirubin (BR) tetrapyrroles. The second step is regulated by two non-redundant biliverdin reductases (IXα (BLVRA) and IXβ (BLVRB)), which retain isomeric specificity and NAD(P)H-dependent redox coupling linked to BR's antioxidant function. Defective BLVRB enzymatic activity with antioxidant mishandling has been implicated in metabolic consequences of hematopoietic lineage fate and enhanced platelet counts in humans. We now outline an integrated platform of in silico and crystallographic studies for the identification of an initial class of compounds inhibiting BLVRB with potencies in the nanomolar range. We found that the most potent BLVRB inhibitors contain a tricyclic hydrocarbon core structure similar to the isoalloxazine ring of flavin mononucleotide and that both xanthene- and acridine-based compounds inhibit BLVRB's flavin and dichlorophenolindophenol (DCPIP) reductase functions. Crystallographic studies of ternary complexes with BLVRB-NADP+-xanthene-based compounds confirmed inhibitor binding adjacent to the cofactor nicotinamide and interactions with the Ser-111 side chain. This residue previously has been identified as critical for maintaining the enzymatic active site and cellular reductase functions in hematopoietic cells. Both acridine- and xanthene-based compounds caused selective and concentration-dependent loss of redox coupling in BLVRB-overexpressing promyelocytic HL-60 cells. These results provide promising chemical scaffolds for the development of enhanced BLVRB inhibitors and identify chemical probes to better dissect the role of biliverdins, alternative substrates, and BLVRB function in physiologically relevant cellular contexts.
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Affiliation(s)
| | - Xiliang Zheng
- the State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, ChangChun, Jilin 130022, China
| | | | - José A Manso
- the IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,the i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal, and
| | | | | | - Jorge Ripoll-Rozada
- the IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,the i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal, and
| | - Pedro José Barbosa Pereira
- the IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,the i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal, and
| | - Timothy J Mantle
- the Department of Biochemistry, Trinity College, Dublin 2, Ireland
| | - Jin Wang
- Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York 11794-8151,
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30
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Chu WT, Nesbitt NM, Gnatenko DV, Li Z, Zhang B, Seeliger MA, Browne S, Mantle TJ, Bahou WF, Wang J. Enzymatic Activity and Thermodynamic Stability of Biliverdin IXβ Reductase Are Maintained by an Active Site Serine. Chemistry 2017; 23:1891-1900. [PMID: 27897348 DOI: 10.1002/chem.201604517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 11/10/2022]
Abstract
Biliverdin reductase IXβ (BLVRB) is a crucial enzyme in heme metabolism. Recent studies in humans have identified a loss-of-function mutation (Ser111Leu) that unmasks a fundamentally important role in hematopoiesis. We have undertaken experimental and thermodynamic modeling studies to provide further insight into the role of the cofactor in substrate accessibility and protein folding properties regulating BLVRB catalytic mechanisms. Site-directed mutagenesis with molecular dynamic (MD) simulations establish the critical role of NAD(P)H-dependent conformational changes on substrate accessibility by forming the "hydrophobic pocket", along with identification of a single key residue (Arg35) modulating NADPH/NADH selectivity. Loop80 and Loop120 block the hydrophobic substrate binding pocket in apo BLVRB (open), whereas movement of these structures after cofactor binding results in the "closed" (catalytically active) conformation. Both enzymatic activity and thermodynamic stability are affected by mutation(s) involving Ser111, which is located in the core of the BLVRB active site. This work 1) elucidates the crucial role of Ser111 in enzymatic catalysis and thermodynamic stability by active site hydrogen bond network; 2) defines a dynamic model for apo BLVRB extending beyond the crystal structure of the binary BLVRB/NADP+ complex; 3) provides a structural basis for the "encounter" and "equilibrium" states of the binary complex, which are regulated by NAD(P)H.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Natasha M Nesbitt
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Dmitri V Gnatenko
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Zongdong Li
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Beibei Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Seamus Browne
- Department of Biochemistry, Trinity College, Dublin 2, Ireland
| | | | - Wadie F Bahou
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,Department of Chemistry and Physics, Stony Brook University, Stony Brook, NY, 11794, USA
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31
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Kim H, Chaurasia AK, Kim T, Choi J, Ha SC, Kim D, Kim KK. Structural and functional study of ChuY from Escherichia coli strain CFT073. Biochem Biophys Res Commun 2016; 482:1176-1182. [PMID: 27919686 DOI: 10.1016/j.bbrc.2016.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 12/02/2016] [Indexed: 10/20/2022]
Abstract
The uropathogenic Escherichia coli strain CFT073 contains multiple iron and heme transport systems, which facilitate infection of the host urinary tract. To elucidate the molecular and cellular function of ChuY, a hypothetical gene in the heme degradation/utilization pathway, we solved the crystal structure of ChuY at 2.4 Å resolution. ChuY has high structural homology with human biliverdin and flavin reductase. We confirmed that ChuY has flavin mononucleotide (FMN) reductase activity, using NAD(P)H as a cofactor, and shows porphyrin ring binding affinity. A chuY deletion-insertion strain showed reduced survival potential compared to wild-type and complemented strains in mammalian cells. Current results suggest ChuY acts as a reductase in heme homeostasis to maintain the virulence potential of E. coli CFT073.
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Affiliation(s)
- Hun Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi 16419, South Korea
| | - Akhilesh Kumar Chaurasia
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi 16419, South Korea
| | - Truc Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi 16419, South Korea
| | - Jongkeun Choi
- Department of Cosmetic Science, Chungwoon University, Hongseong, Chungnam 32244, South Korea
| | - Sung Chul Ha
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, South Korea
| | - Doyoun Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi 16419, South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi 16419, South Korea.
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32
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Hinds TD, Burns KA, Hosick PA, McBeth L, Nestor-Kalinoski A, Drummond HA, AlAmodi AA, Hankins MW, Vanden Heuvel JP, Stec DE. Biliverdin Reductase A Attenuates Hepatic Steatosis by Inhibition of Glycogen Synthase Kinase (GSK) 3β Phosphorylation of Serine 73 of Peroxisome Proliferator-activated Receptor (PPAR) α. J Biol Chem 2016; 291:25179-25191. [PMID: 27738106 DOI: 10.1074/jbc.m116.731703] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 09/30/2016] [Indexed: 01/21/2023] Open
Abstract
Non-alcoholic fatty liver disease is the most rapidly growing form of liver disease and if left untreated can result in non-alcoholic steatohepatitis, ultimately resulting in liver cirrhosis and failure. Biliverdin reductase A (BVRA) is a multifunctioning protein primarily responsible for the reduction of biliverdin to bilirubin. Also, BVRA functions as a kinase and transcription factor, regulating several cellular functions. We report here that liver BVRA protects against hepatic steatosis by inhibiting glycogen synthase kinase 3β (GSK3β) by enhancing serine 9 phosphorylation, which inhibits its activity. We show that GSK3β phosphorylates serine 73 (Ser(P)73) of the peroxisome proliferator-activated receptor α (PPARα), which in turn increased ubiquitination and protein turnover, as well as decreased activity. Interestingly, liver-specific BVRA KO mice had increased GSK3β activity and Ser(P)73 of PPARα, which resulted in decreased PPARα protein and activity. Furthermore, the liver-specific BVRA KO mice exhibited increased plasma glucose and insulin levels and decreased glycogen storage, which may be due to the manifestation of hepatic steatosis observed in the mice. These findings reveal a novel BVRA-GSKβ-PPARα axis that regulates hepatic lipid metabolism and may provide unique targets for the treatment of non-alcoholic fatty liver disease.
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Affiliation(s)
- Terry D Hinds
- the Center for Hypertension and Personalized Medicine, Department of Physiology & Pharmacology,
| | - Katherine A Burns
- the Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, and.,the Department of Environmental Health, Division of Environmental Genetics and Molecular Toxicology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - Peter A Hosick
- From the Department of Physiology & Biophysics, Mississippi Center for Obesity Research, University of Mississippi Medical Center, Jackson, Mississippi 39216.,the Department of Exercise Science and Physical Education, Montclair State University, Montclair, New Jersey 07043
| | - Lucien McBeth
- the Center for Hypertension and Personalized Medicine, Department of Physiology & Pharmacology
| | - Andrea Nestor-Kalinoski
- Advanced Microscopy & Imaging Center, Department of Surgery, University of Toledo College of Medicine and Life Sciences, Toledo Ohio 43614
| | - Heather A Drummond
- From the Department of Physiology & Biophysics, Mississippi Center for Obesity Research, University of Mississippi Medical Center, Jackson, Mississippi 39216
| | - Abdulhadi A AlAmodi
- From the Department of Physiology & Biophysics, Mississippi Center for Obesity Research, University of Mississippi Medical Center, Jackson, Mississippi 39216
| | - Michael W Hankins
- From the Department of Physiology & Biophysics, Mississippi Center for Obesity Research, University of Mississippi Medical Center, Jackson, Mississippi 39216
| | - John P Vanden Heuvel
- the Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, and
| | - David E Stec
- From the Department of Physiology & Biophysics, Mississippi Center for Obesity Research, University of Mississippi Medical Center, Jackson, Mississippi 39216,
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33
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Bock T, Müller R, Blankenfeldt W. Crystal structure of AibC, a reductase involved in alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus. Acta Crystallogr F Struct Biol Commun 2016; 72:652-8. [PMID: 27487931 DOI: 10.1107/s2053230x16011146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/08/2016] [Indexed: 11/10/2022]
Abstract
Isovaleryl coenzyme A (IV-CoA) performs a crucial role during development and fruiting-body formation in myxobacteria, which is reflected in the existence of a de novo biosynthetic pathway that is highly upregulated when leucine, the common precursor of IV-CoA, is limited. The final step in de novo IV-CoA biosynthesis is catalyzed by AibC, a medium-chain dehydrogenase/reductase. Here, the crystal structure of AibC from Myxococcus xanthus refined to 2.55 Å resolution is presented. The protein adopts two different conformations in the crystal lattice, which is a consequence of partial interaction with the purification tag. Based on this structure, it is suggested that AibC most probably uses a Zn(2+)-supported catalytic mechanism in which NADPH is preferred over NADH. Taken together, this study reveals structural details of the alternative IV-CoA-producing pathway in myxobacteria, which may serve as a base for further biotechnological research and biofuel production.
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Affiliation(s)
- Tobias Bock
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Saarland University, Universitätscampus E8 1, 66123 Saarbrücken, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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34
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Ahmed FH, Mohamed AE, Carr PD, Lee BM, Condic-Jurkic K, O'Mara ML, Jackson CJ. Rv2074 is a novel F420 H2 -dependent biliverdin reductase in Mycobacterium tuberculosis. Protein Sci 2016; 25:1692-709. [PMID: 27364382 DOI: 10.1002/pro.2975] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/29/2016] [Indexed: 12/12/2022]
Abstract
Bilirubin is a potent antioxidant that is produced from the reduction of the heme degradation product biliverdin. In mammalian cells and Cyanobacteria, NADH/NADPH-dependent biliverdin reductases (BVRs) of the Rossmann-fold have been shown to catalyze this reaction. Here, we describe the characterization of Rv2074 from Mycobacterium tuberculosis, which belongs to a structurally and mechanistically distinct family of F420 H2 -dependent BVRs (F-BVRs) that are exclusively found in Actinobacteria. We have solved the crystal structure of Rv2074 bound to its cofactor, F420 , and used this alongside molecular dynamics simulations, site-directed mutagenesis and NMR spectroscopy to elucidate its catalytic mechanism. The production of bilirubin by Rv2074 could exploit the anti-oxidative properties of bilirubin and contribute to the range of immuno-evasive mechanisms that have evolved in M. tuberculosis to allow persistent infection.
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Affiliation(s)
- F Hafna Ahmed
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - A Elaaf Mohamed
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Paul D Carr
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Brendon M Lee
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Karmen Condic-Jurkic
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
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35
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Wu S, Li Z, Gnatenko DV, Zhang B, Zhao L, Malone LE, Markova N, Mantle TJ, Nesbitt NM, Bahou WF. BLVRB redox mutation defines heme degradation in a metabolic pathway of enhanced thrombopoiesis in humans. Blood 2016; 128:699-709. [PMID: 27207795 DOI: 10.1182/blood-2016-02-696997] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/10/2016] [Indexed: 12/21/2022] Open
Abstract
Human blood cell counts are tightly maintained within narrow physiologic ranges, largely controlled by cytokine-integrated signaling and transcriptional circuits that regulate multilineage hematopoietic specification. Known genetic loci influencing blood cell production account for <10% of platelet and red blood cell variability, and thrombopoietin/cellular myeloproliferative leukemia virus liganding is dispensable for definitive thrombopoiesis, establishing that fundamentally important modifier loci remain unelucidated. In this study, platelet transcriptome sequencing and extended thrombocytosis cohort analyses identified a single loss-of-function mutation (BLVRB(S111L)) causally associated with clonal and nonclonal disorders of enhanced platelet production. BLVRB(S111L) encompassed within the substrate/cofactor [α/β dinucleotide NAD(P)H] binding fold is a functionally defective redox coupler using flavin and biliverdin (BV) IXβ tetrapyrrole(s) and results in exaggerated reactive oxygen species accumulation as a putative metabolic signal leading to differential hematopoietic lineage commitment and enhanced thrombopoiesis. These data define the first physiologically relevant function of BLVRB and implicate its activity and/or heme-regulated BV tetrapyrrole(s) in a unique redox-regulated bioenergetic pathway governing terminal megakaryocytopoiesis; these observations also define a mechanistically restricted drug target retaining potential for enhancing human platelet counts.
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36
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Huan L, Bao C, Chen D, Li Y, Lian J, Ding J, Huang S, Liang L, He X. MicroRNA-127-5p targets the biliverdin reductase B/nuclear factor-κB pathway to suppress cell growth in hepatocellular carcinoma cells. Cancer Sci 2016; 107:258-66. [PMID: 26708147 PMCID: PMC4814244 DOI: 10.1111/cas.12869] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/13/2015] [Accepted: 12/20/2015] [Indexed: 12/23/2022] Open
Abstract
Nuclear factor-κB (NF-κB) activation is one of the major mediators of inflammation-induced cancer cell growth and progression. In previous studies, we screened a series of microRNAs (miRNAs) that targeted the NF-κB signaling pathway. In this study, we showed that miR-127-5p suppressed NF-κB activity through inhibition of p65 nuclear translocation. In addition, miR-127-5p also inhibited the transcription of downstream targets of the NF-κB signaling pathway. While exploring the mechanism of the inhibition of NF-κB activity by miR-127-5p, we found that miR-127-5p decreased the phosphorylation of p65. MicroRNA-127-5p inhibited the growth and colony formation of hepatocellular carcinoma (HCC) cells and decreased biliverdin reductase B (BLVRB) expression by directly binding to its 3'-UTR. RNA interference of BLVRB suppressed HCC cell growth, whereas the overexpression of BLVRB promoted HCC cell growth. Furthermore, BLVRB blockade inhibited the phosphorylation of p65 protein and the expression of downstream targets of the NF-κB signaling pathway, mimicking the function of miR-127-5p. The restoration of BLVRB in HCC cells overexpressing miR-127-5p impaired the suppression of HCC growth by miR-127-5p. Moreover, miR-127-5p was downregulated in 58% of HCC samples. In summary, we found that miR-127-5p suppressed NF-κB activity by directly targeting BLVRB in HCC cells, and this finding improves our understanding of the molecular mechanism of inflammation-induced HCC growth and proliferation and the successful inhibition of NF-κB activity by cancer treatment.
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Affiliation(s)
- Lin Huan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunyang Bao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Di Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Junwei Lian
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Ding
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Linhui Liang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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Abstract
The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are related to the primary target by sequence and fold, many ligands bind to unrelated pairs of proteins, and these are harder to anticipate. If the binding site in the off-target can be related to that of the primary target, this challenge resolves into aligning the two pockets. However, other cases are possible: the ligand might interact with entirely different residues and environments in the off-target, or wholly different ligand atoms may be implicated in the two complexes. To investigate these scenarios at atomic resolution, the structures of 59 ligands in 116 complexes (62 pairs in total), where the protein pairs were unrelated by fold but bound an identical ligand, were examined. In almost half of the pairs, the ligand interacted with unrelated residues in the two proteins (29 pairs), and in 14 of the pairs wholly different ligand moieties were implicated in each complex. Even in those 19 pairs of complexes that presented similar environments to the ligand, ligand superposition rarely resulted in the overlap of related residues. There appears to be no single pattern-matching "code" for identifying binding sites in unrelated proteins that bind identical ligands, though modeling suggests that there might be a limited number of different patterns that suffice to recognize different ligand functional groups.
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Affiliation(s)
- Sarah Barelier
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
| | - Teague Sterling
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
| | - Matthew J. O’Meara
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
| | - Brian K. Shoichet
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
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38
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Di Domenico F, Pupo G, Mancuso C, Barone E, Paolini F, Arena A, Blarzino C, Schmitt FA, Head E, Butterfield DA, Perluigi M. Bach1 overexpression in Down syndrome correlates with the alteration of the HO-1/BVR-a system: insights for transition to Alzheimer's disease. J Alzheimers Dis 2015; 44:1107-20. [PMID: 25391381 DOI: 10.3233/jad-141254] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Bach1, among the genes encoded on chromosome 21, is a transcription repressor, which binds to antioxidant response elements of DNA thus inhibiting the transcription of specific genes involved in the cell stress response including heme oxygenase-1 (HO-1). HO-1 and its partner, biliverdin reductase-A (BVR-A), are upregulated in response to oxidative stress in order to protect cells against further damage. Since oxidative stress is an early event in Down syndrome (DS) and might contribute to the development of multiple deleterious DS phenotypes, including Alzheimer's disease (AD) pathology, we investigated the status of the Bach1/HO-1/BVR-A axis in DS and its possible implications for the development of AD. In the present study, we showed increased total Bach1 protein levels in the brain of all DS cases coupled with reduced induction of brain HO-1. Furthermore, increased oxidative stress could, on one hand, overcome the inhibitory effects of Bach1 and, on the other hand, promote BVR-A impairment. Our data show that the development of AD in DS subjects is characterized by (i) increased Bach1 total and poly-ubiquitination; (ii) increased HO-1 protein levels; and (iii) increased nitration of BVR-A followed by reduced activity. To corroborate our findings, we analyzed Bach1, HO-1, and BVR-A status in the Ts65Dn mouse model at 3 (young) and 15 (old) months of age. The above data support the hypothesis that the dysregulation of HO-1/BVR-A system contributes to the early increase of oxidative stress in DS and provide potential mechanistic paths involved in the neurodegenerative process and AD development.
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Affiliation(s)
- Fabio Di Domenico
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Gilda Pupo
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Cesare Mancuso
- Institute of Pharmacology, Catholic University School of Medicine, Rome, Italy
| | - Eugenio Barone
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Francesca Paolini
- Laboratory of Virology, Regina Elena National Cancer Institute, Rome, Italy
| | - Andrea Arena
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Carla Blarzino
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Frederick A Schmitt
- Sanders-Brown Centre of Aging, University of Kentucky, Lexington, KY, USA Department of Neurology, University of Kentucky, Lexington, KY, USA
| | - Elizabeth Head
- Sanders-Brown Centre of Aging, University of Kentucky, Lexington, KY, USA Department of Pharmacology & Nutritional Sciences, University of Kentucky, Lexington, KY, USA
| | - D Allan Butterfield
- Sanders-Brown Centre of Aging, University of Kentucky, Lexington, KY, USA Department of Chemistry, University of Kentucky, Lexington, KY, USA
| | - Marzia Perluigi
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
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39
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Wong WC, Yap CK, Eisenhaber B, Eisenhaber F. dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity. Biol Direct 2015; 10:39. [PMID: 26228544 PMCID: PMC4521371 DOI: 10.1186/s13062-015-0068-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/20/2015] [Indexed: 11/10/2022] Open
Abstract
Background Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplistic similarity approach in the case of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc.) is not justified and a pertinent source for mistaken homologies. The latter is either due to positional sequence conservation as a result of a very simple, physically induced pattern or integral sequence properties that are critical for function. Furthermore, against the backdrop that the number of well-studied proteins continues to grow at a slow rate, it necessitates for a search methodology to dive deeper into the sequence similarity space to connect the unknown sequences to the well-studied ones, albeit more distant, for biological function postulations. Results Based on our previous work of dissecting the hidden markov model (HMMER) based similarity score into fold-critical and the non-globular contributions to improve homology inference, we propose a framework-dissectHMMER, that identifies more fold-related domain hits from standard HMMER searches. Subsequent statistical stratification of the fold-related hits into cohorts of functionally-related domains allows for the function postulation of the query sequence. Briefly, the technical problems as to how to recognize non-globular parts in the domain model, resolve contradictory HMMER2/HMMER3 results and evaluate fold-related domain hits for homology, are addressed in this work. The framework is benchmarked against a set of SCOP-to-Pfam domain models. Despite being a sequence-to-profile method, dissectHMMER performs favorably against a profile-to-profile based method-HHsuite/HHsearch. Examples of function annotation using dissectHMMER, including the function discovery of an uncharacterized membrane protein Q9K8K1_BACHD (WP_010899149.1) as a lactose/H+ symporter, are presented. Finally, dissectHMMER webserver is made publicly available at http://dissecthmmer.bii.a-star.edu.sg. Conclusions The proposed framework-dissectHMMER, is faithful to the original inception of the sequence homology concept while improving upon the existing HMMER search tool through the rescue of statistically evaluated false-negative yet fold-related domain hits to the query sequence. Overall, this translates into an opportunity for any novel protein sequence to be functionally characterized. Reviewers This article was reviewed by Masanori Arita, Shamil Sunyaev and L. Aravind. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0068-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wing-Cheong Wong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
| | - Choon-Kong Yap
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore. .,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore, 117597, Singapore. .,School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore.
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40
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Han X, Qian L, Zhang L, Liu X. Structural and biochemical insights into nucleotide-rhamnose synthase/epimerase-reductase from Arabidopsis thaliana. Biochim Biophys Acta 2015; 1854:1476-86. [PMID: 26116145 DOI: 10.1016/j.bbapap.2015.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/03/2015] [Accepted: 06/20/2015] [Indexed: 11/26/2022]
Abstract
L-Rhamnose (Rha) is synthesized via a similar enzymatic pathway in bacteria, plants and fungi. In plants, nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER) catalyzes the final step in the conversion of dTDP/UDP-α-D-Glc to dTDP/UDP-β-L-Rha in an NAD(P)H dependent manner. Currently, only biochemical evidence for the function of NRS/ER has been described. In this study, a crystal structure for Arabidopsis thaliana NRS/ER was determined, which is the first report of a eukaryotic rhamnose synthase with both epimerase and reductase activities. NRS/ER functions as a metal ion independent homodimer that forms through hydrophobic interactions via a four-helix bundle. Each monomer exhibits α/β folding that can be divided into two regions, nucleotide cofactor binding domain and sugar substrate binding domain. The affinities of ligands with NRS/ER were measured using isothermal titration calorimetry, which showed that NRS/ER has a preference for dTDP over UDP, while the cofactor binding site has a similar affinity for NADH and NADPH. Structural analysis coupled to site-directed mutagenesis suggested C115 and K183 as the acid/base pair responsible for epimerization, while T113, Y144 and K148 are the conserved residues in reduction. These findings shed light on the molecular mechanism of NRS/ER and were helpful to explore other eukaryotic enzymes involved in L-Rha synthesis.
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Affiliation(s)
- Xiaodong Han
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China; Food and Pharmaceutical Engineering Institute, Shanxi University of Traditional Chinese Medicine, Taiyuan 030024, China.
| | - Lei Qian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China.
| | - Lianwen Zhang
- College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China.
| | - Xinqi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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41
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Abstract
The biliverdin reductase (BVR) isozymes BVRA and BVRB are cell surface membrane receptors with pleiotropic functions. This review compares, for the first time, the structural and functional differences between the isozymes. They reduce biliverdin, a byproduct of heme catabolism, to bilirubin, display kinase activity, and BVRA, but not BVRB, can act as a transcription factor. The binding motifs present in the BVR isozymes allow a wide range of interactions with components of metabolically important signaling pathways such as the insulin receptor kinase cascades, protein kinases (PKs), and inflammatory mediators. In addition, serum bilirubin levels have been negatively associated with abdominal obesity and hypertriglyceridemia. We discuss the roles of the BVR isozymes in metabolism and their potential as therapeutic targets.
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Affiliation(s)
- Luke O'Brien
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Peter A Hosick
- Department of Exercise Science and Physical Education, Montclair State University, Montclair, NJ 07043, USA
| | - Kezia John
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - David E Stec
- Center for Excellence in Cardiovascular-Renal Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
| | - Terry D Hinds
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA.
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Barone E, Butterfield DA. Insulin resistance in Alzheimer disease: Is heme oxygenase-1 an Achille's heel? Neurobiol Dis 2015; 84:69-77. [PMID: 25731746 DOI: 10.1016/j.nbd.2015.02.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/18/2015] [Indexed: 01/10/2023] Open
Abstract
Insulin resistance, clinically defined as the inability of insulin to increase glucose uptake and utilization, has been found to be associated with the progression of Alzheimer disease (AD). Indeed, postmortem AD brain shows all the signs of insulin resistance including: (i) reduced brain insulin receptor (IR) sensitivity, (ii) hypophosphorylation of the insulin receptor and downstream second messengers such as IRS-1, and (iii) attenuated insulin and insulin growth factor (IGF)-1 receptor expression. However, the exact mechanisms driving insulin resistance have not been completely elucidated. Quite recently, the levels of the peripheral inducible isoform of heme oxygenase (HO-1), a well-known protein up-regulated during cell stress response, were proposed to be among the strongest positive predictors of metabolic disease, including insulin resistance. Because our group previously reported on levels, activation state and oxidative stress-induced post-translational modifications of HO-1 in AD brain and our ongoing studies to better elucidate the role of HO-1 in insulin resistance-associated AD pathology, the aim of this review is to provide reader with a critical analysis on new aspects of the interplay between HO-1 and insulin resistance and on how the available lines of evidence could be useful for further comprehension of processes in AD brain.
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Affiliation(s)
- Eugenio Barone
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - D Allan Butterfield
- Department of Chemistry and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506-0055, USA.
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Tikh IB, Quin MB, Schmidt-Dannert C. A tale of two reductases: extending the bacteriochlorophyll biosynthetic pathway in E. coli. PLoS One 2014; 9:e89734. [PMID: 24586995 PMCID: PMC3931815 DOI: 10.1371/journal.pone.0089734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/23/2014] [Indexed: 12/23/2022] Open
Abstract
The creation of a synthetic microbe that can harvest energy from sunlight to drive its metabolic processes is an attractive approach to the economically viable biosynthetic production of target compounds. Our aim is to design and engineer a genetically tractable non-photosynthetic microbe to produce light-harvesting molecules. Previously we created a modular, multienzyme system for the heterologous production of intermediates of the bacteriochlorophyll (BChl) pathway in E. coli. In this report we extend this pathway to include a substrate promiscuous 8-vinyl reductase that can accept multiple intermediates of BChl biosynthesis. We present an informative comparative analysis of homologues of 8-vinyl reductase from the model photosynthetic organisms Rhodobacter sphaeroides and Chlorobaculum tepidum. The first purification of the enzymes leads to their detailed biochemical and biophysical characterization. The data obtained reveal that the two 8-vinyl reductases are substrate promiscuous, capable of reducing the C8-vinyl group of Mg protoporphyrin IX, Mg protoporphyrin IX methylester, and divinyl protochlorophyllide. However, activity is dependent upon the presence of chelated Mg2+ in the porphyrin ring, with no activity against non-Mg2+ chelated intermediates observed. Additionally, CD analyses reveal that the two 8-vinyl reductases appear to bind the same substrate in a different fashion. Furthermore, we discover that the different rates of reaction of the two 8-vinyl reductases both in vitro, and in vivo as part of our engineered system, results in the suitability of only one of the homologues for our BChl pathway in E. coli. Our results offer the first insights into the different functionalities of homologous 8-vinyl reductases. This study also takes us one step closer to the creation of a nonphotosynthetic microbe that is capable of harvesting energy from sunlight for the biosynthesis of molecules of choice.
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Affiliation(s)
- Ilya B. Tikh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Maureen B. Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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Barone E, Di Domenico F, Butterfield DA. Statins more than cholesterol lowering agents in Alzheimer disease: their pleiotropic functions as potential therapeutic targets. Biochem Pharmacol 2013; 88:605-16. [PMID: 24231510 DOI: 10.1016/j.bcp.2013.10.030] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/22/2013] [Accepted: 10/28/2013] [Indexed: 02/05/2023]
Abstract
Alzheimer disease (AD) is a progressive neurodegenerative disorder characterized by severe cognitive impairment, inability to perform activities of daily living and mood changes. Statins, long known to be beneficial in conditions where dyslipidemia occurs by lowering serum cholesterol levels, also have been proposed for use in neurodegenerative conditions, including AD. However, it is not clear that the purported effectiveness of statins in neurodegenerative disorders is directly related to cholesterol-lowering effects of these agents; rather, the pleiotropic functions of statins likely play critical roles. The aim of this review is to provide an overview on the new discoveries about the effects of statin therapy on the oxidative and nitrosative stress levels as well as on the modulation of the heme oxygenase/biliverdin reductase (HO/BVR) system in the brain. We propose a novel mechanism of action for atorvastatin which, through the activation of HO/BVR-A system, may contribute to the neuroprotective effects thus suggesting a potential therapeutic role in AD and potentially accounting for the observation of decreased AD incidence with persons on statin.
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Affiliation(s)
- Eugenio Barone
- Department of Chemistry, Center of Membrane Sciences, and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506-0055, USA
| | - Fabio Di Domenico
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506-0055, USA.
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Unno M, Ardèvol A, Rovira C, Ikeda-Saito M. Structures of the substrate-free and product-bound forms of HmuO, a heme oxygenase from corynebacterium diphtheriae: x-ray crystallography and molecular dynamics investigation. J Biol Chem 2013; 288:34443-58. [PMID: 24106279 DOI: 10.1074/jbc.m113.486936] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe(3+)-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 Å resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe(3+)-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe(3+)-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe(3+)-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit.
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Affiliation(s)
- Masaki Unno
- From the Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan
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Barone E, Di Domenico F, Mancuso C, Butterfield DA. The Janus face of the heme oxygenase/biliverdin reductase system in Alzheimer disease: it's time for reconciliation. Neurobiol Dis 2014; 62:144-59. [PMID: 24095978 DOI: 10.1016/j.nbd.2013.09.018] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/24/2013] [Indexed: 12/23/2022] Open
Abstract
Alzheimer disease (AD) is the most common form of dementia among the elderly and is characterized by progressive loss of memory and cognition. These clinical features are due in part to the increase of reactive oxygen and nitrogen species that mediate neurotoxic effects. The up-regulation of the heme oxygenase-1/biliverdin reductase-A (HO-1/BVR-A) system is one of the earlier events in the adaptive response to stress. HO-1/BVR-A reduces the intracellular levels of pro-oxidant heme and generates equimolar amounts of the free radical scavengers biliverdin-IX alpha (BV)/bilirubin-IX alpha (BR) as well as the pleiotropic gaseous neuromodulator carbon monoxide (CO) and ferrous iron. Two main and opposite hypotheses for a role of the HO-1/BVR-A system in AD propose that this system mediates neurotoxic and neuroprotective effects, respectively. This apparent controversy was mainly due to the fact that for over about 20years HO-1 was the only player on which all the analyses were focused, excluding the other important and essential component of the entire system, BVR. Following studies from the Butterfield laboratory that reported alterations in BVR activity along with decreased phosphorylation and increased oxidative/nitrosative post-translational modifications in the brain of subjects with AD and amnestic mild cognitive impairment (MCI) subjects, a debate was opened on the real pathophysiological and clinical significance of BVR-A. In this paper we provide a review of the main discoveries about the HO/BVR system in AD and MCI, and propose a mechanism that reconciles these two hypotheses noted above of neurotoxic and the neuroprotective aspects of this important stress responsive system.
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Pallua JD, Schaefer G, Seifarth C, Becker M, Meding S, Rauser S, Walch A, Handler M, Netzer M, Popovscaia M, Osl M, Baumgartner C, Lindner H, Kremser L, Sarg B, Bartsch G, Huck CW, Bonn GK, Klocker H. MALDI-MS tissue imaging identification of biliverdin reductase B overexpression in prostate cancer. J Proteomics 2013; 91:500-14. [DOI: 10.1016/j.jprot.2013.08.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 07/30/2013] [Accepted: 08/03/2013] [Indexed: 01/18/2023]
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Wu Y, Cai Y, Sun Y, Xu R, Yu H, Han X, Lou H, Cheng A. A single amino acid determines the catalytic efficiency of two alkenal double bond reductases produced by the liverwort Plagiochasma appendiculatum. FEBS Lett 2013; 587:3122-8. [PMID: 23954295 DOI: 10.1016/j.febslet.2013.07.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 11/30/2022]
Abstract
Alkenal double bond reductases (DBRs) catalyze the NADPH-dependent reduction of the α,β-unsaturated double bond of many secondary metabolites. Two alkenal double bond reductase genes PaDBR1 and PaDBR2 were isolated from the liverwort species Plagiochasma appendiculatum. Recombinant PaDBR2 protein had a higher catalytic activity than PaDBR1 with respect to the reduction of the double bond present in hydroxycinnamyl aldehydes. The residue at position 56 appeared to be responsible for this difference in enzyme activity. The functionality of a C56 to Y56 mutation in PaDBR1 was similar to that of PaDBR2. Further site-directed mutagenesis and structural modeling suggested that the phenol ring stacking between this residue and the substrate was an important determinant of catalytic efficiency.
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Affiliation(s)
- Yifeng Wu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
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Fu G, Liu H, Doerksen RJ. Molecular modeling to provide insight into the substrate binding and catalytic mechanism of human biliverdin-IXα reductase. J Phys Chem B 2012; 116:9580-94. [PMID: 22823425 DOI: 10.1021/jp301456j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human biliverdin-IXα reductase (hBVR-A) catalyzes the conversion of biliverdin-IXα to bilirubin-IXα in the last step of heme degradation and is a key enzyme in regulating a wide range of cellular responses. Though the X-ray structure of hBVR-A is available including cofactor, a crystal structure with a bound substrate would be even more useful as a starting point for protein-structure-based inhibitor design, but none have been reported. The present study employed induced fit docking (IFD) to study the substrate binding modes to hBVR-A of biliverdin-IXα and four analogues. The proposed substrate binding modes were examined further by performing molecular dynamics (MD) simulations followed by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The predicted binding free energies for the five biliverdin-IXα analogues match well with the relative potency of their reported experimental binding affinities, supporting that the proposed binding modes are reasonable. Furthermore, the ternary complex structure of hBVR-A binding with biliverdin-IXα and the electron donor cofactor NADPH obtained from MD simulations was exploited to investigate the catalytic mechanism, by calculating the reaction energy profile using the quantum mechanics/molecular mechanics (QM/MM) method. On the basis of our calculations, the energetically preferred pathway consists of an initial protonation of the pyrrolic nitrogen on the biliverdin substrate followed by hydride transfer to yield the reduction product. This conclusion is consistent with a previous mechanistic study on human biliverdin IXβ reductase (hBVR-B).
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Affiliation(s)
- Gang Fu
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
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Wegiel B, Gallo D, Csizmadia E, Roger T, Kaczmarek E, Harris C, Zuckerbraun BS, Otterbein LE. Biliverdin inhibits Toll-like receptor-4 (TLR4) expression through nitric oxide-dependent nuclear translocation of biliverdin reductase. Proc Natl Acad Sci U S A 2011; 108:18849-54. [PMID: 22042868 DOI: 10.1073/pnas.1108571108] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The cellular response to an inflammatory stressor requires a proinflammatory cellular activation followed by a controlled resolution of the response to restore homeostasis. We hypothesized that biliverdin reductase (BVR) by binding biliverdin (BV) quells the cellular response to endotoxin-induced inflammation through phosphorylation of endothelial nitric oxide synthase (eNOS). The generated NO, in turn, nitrosylates BVR, leading to nuclear translocation where BVR binds to the Toll-like receptor-4 (TLR4) promoter at the Ap-1 sites to block transcription. We show in macrophages that BV-induced eNOS phosphorylation (Ser-1177) and NO production are mediated in part by Ca(2+)/calmodulin-dependent kinase kinase. Furthermore, we show that BVR is S-nitrosylated on one of three cysteines and that this posttranslational modification is required for BVR-mediated signaling. BV-induced nuclear translocation of BVR and inhibition of TLR4 expression is lost in macrophages derived from Enos(-/-) mice. In vivo in mice, BV provides protection from acute liver damage and is dependent on the availability of NO. Collectively, we elucidate a mechanism for BVR in regulating the inflammatory response to endotoxin that requires eNOS-derived NO and TLR4 signaling in macrophages.
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