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Gardner PR. Ordered Motions in the Nitric-Oxide Dioxygenase Mechanism of Flavohemoglobin and Assorted Globins with Tightly Coupled Reductases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1414:45-96. [PMID: 36520413 DOI: 10.1007/5584_2022_751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nitric-oxide dioxygenases (NODs) activate and combine O2 with NO to form nitrate. A variety of oxygen-binding hemoglobins with associated partner reductases or electron donors function as enzymatic NODs. Kinetic and structural investigations of the archetypal two-domain microbial flavohemoglobin-NOD have illuminated an allosteric mechanism that employs selective tunnels for O2 and NO, gates for NO and nitrate, transient O2 association with ferric heme, and an O2 and NO-triggered, ferric heme spin crossover-driven, motion-controlled, and dipole-regulated electron-transfer switch. The proposed mechanism facilitates radical-radical coupling of ferric-superoxide with NO to form nitrate while preventing suicidal ferrous-NO formation. Diverse globins display the structural and functional motifs necessary for a similar allosteric NOD mechanism. In silico docking simulations reveal monomeric erythrocyte hemoglobin alpha-chain and beta-chain intrinsically matched and tightly coupled with NADH-cytochrome b5 oxidoreductase and NADPH-cytochrome P450 oxidoreductase, respectively, forming membrane-bound flavohemoglobin-like mammalian NODs. The neuroprotective neuroglobin manifests a potential NOD role in a close-fitting ternary complex with membrane-bound NADH-cytochrome b5 oxidoreductase and cytochrome b5. Cytoglobin interfaces weakly with cytochrome b5 for O2 and NO-regulated electron-transfer and coupled NOD activity. The mechanistic model also provides insight into the evolution of O2 binding cooperativity in hemoglobin and a basis for the discovery of allosteric NOD inhibitors.
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Lessons from the post-genomic era: Globin diversity beyond oxygen binding and transport. Redox Biol 2020; 37:101687. [PMID: 32863222 PMCID: PMC7475203 DOI: 10.1016/j.redox.2020.101687] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Vertebrate hemoglobin (Hb) and myoglobin (Mb) were among the first proteins whose structures and sequences were determined over 50 years ago. In the subsequent pregenomic period, numerous related proteins came to light in plants, invertebrates and bacteria, that shared the myoglobin fold, a signature sequence motif characteristic of a 3-on-3 α-helical sandwich. Concomitantly, eukaryote and bacterial globins with a truncated 2-on-2 α-helical fold were discovered. Genomic information over the last 20 years has dramatically expanded the list of known globins, demonstrating their existence in a limited number of archaeal genomes, a majority of bacterial genomes and an overwhelming majority of eukaryote genomes. In vertebrates, 6 additional globin types were identified, namely neuroglobin (Ngb), cytoglobin (Cygb), globin E (GbE), globin X (GbX), globin Y (GbY) and androglobin (Adgb). Furthermore, functions beyond the familiar oxygen transport and storage have been discovered within the vertebrate globin family, including NO metabolism, peroxidase activity, scavenging of free radicals, and signaling functions. The extension of the knowledge on globin functions suggests that the original roles of bacterial globins must have been enzymatic, involved in defense against NO toxicity, and perhaps also as sensors of O2, regulating taxis away or towards high O2 concentrations. In this review, we aimed to discuss the evolution and remarkable functional diversity of vertebrate globins with particular focus on the variety of non-canonical expression sites of mammalian globins and their according impressive variability of atypical functions.
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Leite GGF, Scicluna BP, van der Poll T, Salomão R. Genetic signature related to heme-hemoglobin metabolism pathway in sepsis secondary to pneumonia. NPJ Syst Biol Appl 2019; 5:26. [PMID: 31396396 PMCID: PMC6672010 DOI: 10.1038/s41540-019-0105-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated inflammatory response to pathogens. Bioinformatics and transcriptomics studies contribute to get a better understanding of the pathogenesis of sepsis. These studies revealed differentially expressed genes (DEGs) in sepsis involved in several pathways. Here we investigated the gene expression profiles of blood leukocytes using three microarray datasets of sepsis secondary to pneumonia, focusing on the heme/hemoglobin metabolism pathway. We demonstrate that the heme/hemoglobin metabolism pathway was found to be enriched in these three cohorts with four common genes (ALAS2, AHSP, HBD, and CA1). Several studies show that these four genes are involved in the cytoprotection of non-erythrocyte cells in response to different stress conditions. The upregulation of heme/hemoglobin metabolism in sepsis might be a protective response of white cells to the hostile environment present in septic patients (follow-up samples).
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Affiliation(s)
- Giuseppe Gianini Figuerêido Leite
- Division of Infectious Diseases, Department of Medicine, Hospital São Paulo, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Brendon P. Scicluna
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Center of Infection and Immunity Amsterdam, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Center of Infection and Immunity Amsterdam, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Reinaldo Salomão
- Division of Infectious Diseases, Department of Medicine, Hospital São Paulo, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
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Saha D, Koli S, Patgaonkar M, Reddy KVR. Expression of hemoglobin-α and β subunits in human vaginal epithelial cells and their functional significance. PLoS One 2017; 12:e0171084. [PMID: 28178273 PMCID: PMC5298339 DOI: 10.1371/journal.pone.0171084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/16/2017] [Indexed: 11/18/2022] Open
Abstract
Hemoglobin (Hb) is a major protein involved in transport of oxygen (O2). It consists of Hb-α and Hb-β subunits, which are normally expressed by cells of erythroid lineage. However, till recently, it was not known whether non-erythroid cells like vaginal cells synthesize Hb and whether it has any functional significance. Therefore, we designed the following objectives: (1) to establish in-vitro culture system of human primary vaginal epithelial cells (hPVECs), (2) to determine whether Hb-α and Hb-β proteins are truly synthesized by hPVECs, (3) to evaluate the effect of LPS (lipopolysaccharide) on the expression of Hb-α and Hb-β proteins (4) to decipher the significance of the Hb-α and Hb-β expression in hPVECs and (5) to determine the molecular mechanism regulating the expression of Hb-α in hPVECs. To accomplish these studies, we applied a battery of assays such as RT-PCR, qRT-PCR, Flow cytometry, western blot, and immunofluorescence, Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP). The results revealed the expression of Hb-α and Hb-β at both mRNA and protein level in hPVECs. The expression was significantly upregulated following LPS treatment (10μg/ml for 6 hrs) and these results are comparable with the expression induced by LPS in human vaginal epithelial cell line (VK2/E6E7). These cells constitutively produced low levels of pro-inflammatory (IL-6) and anti-inflammatory (IL-10) cytokines. Also, the response of phosphorylated (p65)-NF-κB to LPS was upregulated with increased expression of IL-6, Toll-like receptor-4 (TLR4) and human beta defensin-1 (hBD-1) in hPVECs and VK2/E6E7 cells. However, Bay 11-7082 treatment (5μM for 24 hrs) could neutralize the effect of LPS-induced p65-NF-κB activity and represses the production`of Hb-α and Hb-β. The results of EMSA revealed the presence of putative binding sites of NF-κB in the human Hb-α promoter region (nt-115 to -106). ChIP analysis confirmed the binding of NF-κB to Hb-α promoter. In conclusion, the present findings revealed for the first time that hPVECs synthesized Hb-α and Hb-β and the expression is comparable with the expression of VK2/E6E7 cells. The identification of NF-κB regulatory sequences in Hb-α promoter, whose activation is associated with immune response of hPVECs, indicating Hb-α and Hb-β may act as an endogenous antimicrobial defense protein against vaginal inflammation/infections.
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Affiliation(s)
- Debarchana Saha
- Division of Molecular Immunology and Microbiology (MIM), National Institute for Research in Reproductive Health (NIRRH), Parel, Mumbai, India
| | - Swanand Koli
- Division of Molecular Immunology and Microbiology (MIM), National Institute for Research in Reproductive Health (NIRRH), Parel, Mumbai, India
| | - Mandar Patgaonkar
- Division of Molecular Immunology and Microbiology (MIM), National Institute for Research in Reproductive Health (NIRRH), Parel, Mumbai, India
| | - Kudumula Venkata Rami Reddy
- Division of Molecular Immunology and Microbiology (MIM), National Institute for Research in Reproductive Health (NIRRH), Parel, Mumbai, India
- * E-mail:
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Nishiki-Muranishi N, Harada Y, Minamikawa T, Yamaoka Y, Dai P, Yaku H, Takamatsu T. Label-free evaluation of myocardial infarction and its repair by spontaneous Raman spectroscopy. Anal Chem 2014; 86:6903-10. [PMID: 24914734 DOI: 10.1021/ac500592y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Raman spectroscopy, which provides information about molecular species and structures of biomolecules via intrinsic molecular vibrations, can analyze physiological and pathological states of tissues on the basis of molecular constituents without staining. In this study, we analyzed Raman spectra of myocardial infarction and its repair in rats using the hypothesis that the myocardium in the course of myocardial infarction and its repair could be recognized by spontaneous Raman spectroscopy on the basis of chemical changes in myocardial tissues. Raman spectra were acquired from unfixed frozen cross sections of normal and infarcted heart tissues upon excitation at 532 nm. Raman spectra of the infarcted tissues were successfully obtained at characteristic time points: days 2, 5, and 21 after coronary ligation, at which the main components of the infarcted region were coagulation necrosis, granulation tissue, and fibrotic tissue, respectively. The latent variable weights calculated by a multivariate classification method, partial least-squares-discriminant analysis (PLS-DA), revealed fundamental information about the spectral differences among the types of tissues on the basis of molecular constituents. A prediction model for the evaluation of these tissue types was established via PLS-DA. Cross-validated sensitivities of 99.3, 95.3, 96.4, and 91.3% and specificities of 99.4, 99.5, 96.5, and 98.3% were attained for the discrimination of normal, necrotic, granulation, and fibrotic tissue, respectively. A two-dimensional image of a marginal area of infarction was successfully visualized via PLS-DA. Our results demonstrated that spontaneous Raman spectroscopy combined with PLS-DA is a novel label-free method of evaluating myocardial infarction and its repair.
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Affiliation(s)
- Nanae Nishiki-Muranishi
- Department of Pathology and Cell Regulation and ‡Department of Cardiovascular Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , 465 Kajii-cho Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
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Park SK, Ryu AR, Lee MY. Protein expression profiling in the liver of rats exposed to phenanthrene. Mol Cell Toxicol 2013. [DOI: 10.1007/s13273-013-0034-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Toriseva M, Laato M, Carpén O, Ruohonen ST, Savontaus E, Inada M, Krane SM, Kähäri VM. MMP-13 regulates growth of wound granulation tissue and modulates gene expression signatures involved in inflammation, proteolysis, and cell viability. PLoS One 2012; 7:e42596. [PMID: 22880047 PMCID: PMC3413640 DOI: 10.1371/journal.pone.0042596] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 07/09/2012] [Indexed: 01/01/2023] Open
Abstract
Proteinases play a pivotal role in wound healing by regulating cell-matrix interactions and availability of bioactive molecules. The role of matrix metalloproteinase-13 (MMP-13) in granulation tissue growth was studied in subcutaneously implanted viscose cellulose sponge in MMP-13 knockout (Mmp13(-/-)) and wild type (WT) mice. The tissue samples were harvested at time points day 7, 14 and 21 and subjected to histological analysis and gene expression profiling. Granulation tissue growth was significantly reduced (42%) at day 21 in Mmp13(-/-) mice. Granulation tissue in Mmp13(-/-) mice showed delayed organization of myofibroblasts, increased microvascular density at day 14, and virtual absence of large vessels at day 21. Gene expression profiling identified differentially expressed genes in Mmp13(-/-) mouse granulation tissue involved in biological functions including inflammatory response, angiogenesis, cellular movement, cellular growth and proliferation and proteolysis. Among genes linked to angiogenesis, Adamts4 and Npy were significantly upregulated in early granulation tissue in Mmp13(-/-) mice, and a set of genes involved in leukocyte motility including Il6 were systematically downregulated at day 14. The expression of Pdgfd was downregulated in Mmp13(-/-) granulation tissue in all time points. The expression of matrix metalloproteinases Mmp2, Mmp3, Mmp9 was also significantly downregulated in granulation tissue of Mmp13(-/-) mice compared to WT mice. Mmp13(-/-) mouse skin fibroblasts displayed altered cell morphology and impaired ability to contract collagen gel and decreased production of MMP-2. These results provide evidence for an important role for MMP-13 in wound healing by coordinating cellular activities important in the growth and maturation of granulation tissue, including myofibroblast function, inflammation, angiogenesis, and proteolysis.
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Affiliation(s)
- Mervi Toriseva
- Department of Dermatology, University of Turku and Turku University Hospital, Turku, Finland
- MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Matti Laato
- Department of Surgery, Turku University Hospital, Turku, Finland
| | - Olli Carpén
- Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | - Suvi T. Ruohonen
- Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland
| | - Eriika Savontaus
- Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland
| | - Masaki Inada
- Department of Life Science and Biotechnology, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Stephen M. Krane
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Veli-Matti Kähäri
- Department of Dermatology, University of Turku and Turku University Hospital, Turku, Finland
- MediCity Research Laboratory, University of Turku, Turku, Finland
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Proteomic biosignatures for monocyte-macrophage differentiation. Cell Immunol 2011; 271:239-55. [PMID: 21788015 DOI: 10.1016/j.cellimm.2011.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/01/2011] [Indexed: 12/13/2022]
Abstract
We used pulsed stable isotope labeling of amino acids in cell culture (pSILAC) to assess protein dynamics during monocyte-macrophage differentiation. pSILAC allows metabolic labeling of newly synthesized proteins. Such de novo protein production was evaluated from 3 to 7 days in culture. Proteins were identified by liquid chromatography-tandem mass spectrometry then quantified by MaxQuant. Protein-protein linkages were then assessed by Ingenuity Pathway Analysis. Proteins identified were linked to cell homeostasis, free radical scavenging, molecular protein transport, carbohydrate metabolism, small molecule chemistry, and cell morphology. The data demonstrates specific biologic events that are linked to monocyte transformation in a defined biologic system.
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