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Badminton MN, Anderson KE, Deybach JC, Harper P, Sandberg S, Elder GH. From chemistry to genomics: A concise history of the porphyrias. Liver Int 2024; 44:2144-2155. [PMID: 38767598 DOI: 10.1111/liv.15960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
We describe developments in understanding of the porphyrias associated with each step in the haem biosynthesis pathway and the role of individuals whose contributions led to major advances over the past 150 years. The first case of erythropoietic porphyria was reported in 1870, and the first with acute porphyria in 1889. Photosensitisation by porphyrin was confirmed by Meyer-Betz, who self-injected haematoporphyrin. Günther classified porphyrias into haematoporphyria acuta, acuta toxica, congenita and chronica. This was revised by Waldenström into porphyria congenita, acuta and cutanea tarda, with the latter describing those with late-onset skin lesions. Waldenström was the first to recognise porphobilinogen's association with acute porphyria, although its structure was not solved until 1953. Hans Fischer was awarded the Nobel prize in 1930 for solving the structure of porphyrins and the synthesis of haemin. After 1945, research by several groups elucidated the pathway of haem biosynthesis and its negative feedback regulation by haem. By 1961, following the work of Watson, Schmid, Rimington, Goldberg, Dean, Magnus and others, aided by the availability of modern techniques of porphyrin separation, six of the porphyrias were identified and classified as erythropoietic or hepatic. The seventh, 5-aminolaevulinate dehydratase deficiency porphyria, was described by Doss in 1979. The discovery of increased hepatic 5-aminolaevulinate synthase activity in acute porphyria led to development of haematin as a treatment for acute attacks. By 2000, all the haem biosynthesis genes were cloned, sequenced and assigned to chromosomes and disease-specific mutations identified in all inherited porphyrias. These advances have allowed definitive family studies and development of new treatments.
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Affiliation(s)
| | - Karl E Anderson
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jean-Charles Deybach
- French Porphyria Reference Center (CRMR Porphyries France), University Paris, Paris, France
| | - Pauline Harper
- Department of Medical Biochemistry and Biophysics, Centre for inherited Metabolic Diseases, Porphyria Centre Sweden, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sverre Sandberg
- Department of Medical Biochemistry and Biophysics, Centre for inherited Metabolic Diseases, Porphyria Centre Sweden, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Biochemistry and Pharmacology, Norwegian Porphyria Centre, Haukeland University Hospital, Bergen, Norway
- Norwegian Organization for Quality Improvement of Laboratory Examinations (Noklus), Haraldsplass Deaconess Hospital, Bergen, Norway
- Institute of Public Health and Primary Health Care, University of Bergen, Bergen, Norway
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Zhao Y, Zhu L, Shi D, Gao J, Fan M. Key Genes FECH and ALAS2 under Acute High-Altitude Exposure: A Gene Expression and Network Analysis Based on Expression Profile Data. Genes (Basel) 2024; 15:1075. [PMID: 39202434 PMCID: PMC11353374 DOI: 10.3390/genes15081075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/08/2024] [Accepted: 08/11/2024] [Indexed: 09/03/2024] Open
Abstract
High-altitude acclimatization refers to the physiological adjustments and adaptation processes by which the human body gradually adapts to the hypoxic conditions of high altitudes after entering such environments. This study analyzed three mRNA expression profile datasets from the GEO database, focusing on 93 healthy residents from low altitudes (≤1400 m). Peripheral blood samples were collected for analysis on the third day after these individuals rapidly ascended to higher altitudes (3000-5300 m). The analysis identified significant differential expression in 382 genes, with 361 genes upregulated and 21 downregulated. Further, gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the top-ranked enriched pathways are upregulated, involving blood gas transport, erythrocyte development and differentiation, and heme biosynthetic process. Network analysis highlighted ten key genes, namely, SLC4A1, FECH, EPB42, SNCA, GATA1, KLF1, GYPB, ALAS2, DMTN, and GYPA. Analysis revealed that two of these key genes, FECH and ALAS2, play a critical role in the heme biosynthetic process, which is pivotal in the development and maturation of red blood cells. These findings provide new insights into the key gene mechanisms of high-altitude acclimatization and identify potential biomarkers and targets for personalized acclimatization strategies.
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Affiliation(s)
- Yifan Zhao
- School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China;
| | - Lingling Zhu
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China;
| | - Dawei Shi
- School of Automation, Beijing Institute of Technology, Beijing 100850, China;
| | - Jiayue Gao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China;
| | - Ming Fan
- School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China;
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Guo M, Lin Y, Obi CD, Zhao P, Dailey HA, Medlock AE, Shen Y. Impact of Phosphorylation at Various Sites on the Active Pocket of Human Ferrochelatase: Insights from Molecular Dynamics Simulations. Int J Mol Sci 2024; 25:6360. [PMID: 38928065 PMCID: PMC11203519 DOI: 10.3390/ijms25126360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Ferrochelatase (FECH) is the terminal enzyme in human heme biosynthesis, catalyzing the insertion of ferrous iron into protoporphyrin IX (PPIX) to form protoheme IX (Heme). Phosphorylation increases the activity of FECH, and it has been confirmed that the activity of FECH phosphorylated at T116 increases. However, it remains unclear whether the T116 site and other potential phosphorylation modification sites collaboratively regulate the activity of FECH. In this study, we identified a new phosphorylation site, T218, and explored the allosteric effects of unphosphorylated (UP), PT116, PT218, and PT116 + PT218 states on FECH in the presence and absence of substrates (PPIX and Heme) using molecular dynamics (MD) simulations. Binding free energies were evaluated with the MM/PBSA method. Our findings indicate that the PT116 + PT218 state exhibits the lowest binding free energy with PPIX, suggesting the strongest binding affinity. Additionally, this state showed a higher binding free energy with Heme compared to UP, which facilitates Heme release. Moreover, employing multiple analysis methods, including free energy landscape (FEL), principal component analysis (PCA), dynamic cross-correlation matrix (DCCM), and hydrogen bond interaction analysis, we demonstrated that phosphorylation significantly affects the dynamic behavior and binding patterns of substrates to FECH. Insights from this study provide valuable theoretical guidance for treating conditions related to disrupted heme metabolism, such as various porphyrias and iron-related disorders.
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Affiliation(s)
- Mingshan Guo
- School of Chemistry, IGCME, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuhong Lin
- School of Chemistry, IGCME, Sun Yat-sen University, Guangzhou 510006, China
| | - Chibuike David Obi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (C.D.O.); (H.A.D.); (A.E.M.)
| | - Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA;
| | - Harry A. Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (C.D.O.); (H.A.D.); (A.E.M.)
| | - Amy E. Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (C.D.O.); (H.A.D.); (A.E.M.)
- Augusta University/University of Georgia Medical Partnership, Athens, GA 30602, USA
| | - Yong Shen
- School of Chemistry, IGCME, Sun Yat-sen University, Guangzhou 510006, China
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Ma JK, Su LD, Feng LL, Li JL, Pan L, Danzeng Q, Li Y, Shang T, Zhan XL, Chen SY, Ying S, Hu JR, Chen XQ, Zhang Q, Liang T, Lu XJ. TFPI from erythroblasts drives heme production in central macrophages promoting erythropoiesis in polycythemia. Nat Commun 2024; 15:3976. [PMID: 38729948 PMCID: PMC11087540 DOI: 10.1038/s41467-024-48328-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Bleeding and thrombosis are known as common complications of polycythemia for a long time. However, the role of coagulation system in erythropoiesis is unclear. Here, we discover that an anticoagulant protein tissue factor pathway inhibitor (TFPI) plays an essential role in erythropoiesis via the control of heme biosynthesis in central macrophages. TFPI levels are elevated in erythroblasts of human erythroblastic islands with JAK2V617F mutation and hypoxia condition. Erythroid lineage-specific knockout TFPI results in impaired erythropoiesis through decreasing ferrochelatase expression and heme biosynthesis in central macrophages. Mechanistically, the TFPI interacts with thrombomodulin to promote the downstream ERK1/2-GATA1 signaling pathway to induce heme biosynthesis in central macrophages. Furthermore, TFPI blockade impairs human erythropoiesis in vitro, and normalizes the erythroid compartment in mice with polycythemia. These results show that erythroblast-derived TFPI plays an important role in the regulation of erythropoiesis and reveal an interplay between erythroblasts and central macrophages.
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Affiliation(s)
- Jun-Kai Ma
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Li-Da Su
- Neuroscience Care Unit, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Lin-Lin Feng
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Jing-Lin Li
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Li Pan
- The General Hospital of Tibet Military Area Command, Lhasa, China
| | - Qupei Danzeng
- Department of Tibetan Medicine; University of Tibetan Medicine, Lhasa, 540100, China
| | - Yanwei Li
- Core Facilities, Zhejiang University School of Medicine, Hangzhou, China
| | - Tongyao Shang
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xiao-Lin Zhan
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Si-Ying Chen
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Shibo Ying
- School of Public Health, Hangzhou Medical College, Hangzhou, 310013, China
| | - Jian-Rao Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Xue Qun Chen
- Zhejiang University, School of Brain Science and Brain Medicine, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Xin-Jiang Lu
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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Biswas P, Palazzo J, Schlanger S, Jayaram DT, Islam S, Page RC, Stuehr DJ. Visualizing mitochondrial heme flow through GAPDH in living cells and its regulation by NO. Redox Biol 2024; 71:103120. [PMID: 38507973 PMCID: PMC10966083 DOI: 10.1016/j.redox.2024.103120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Iron protoporphyrin IX (heme) is a redox-active cofactor that is bound in mammalian cells by GAPDH and allocated by a process influenced by physiologic levels of NO. This impacts the activity of many heme proteins including indoleamine dioxygenase-1 (IDO1), a redox enzyme involved in immune response and tumor growth. To gain further understanding we created a tetra-Cys human GAPDH reporter construct (TC-hGAPDH) which after labeling could indicate its heme binding by fluorescence quenching. When purified or expressed in a human cell line, TC-hGAPDH had properties like native GAPDH and heme binding quenched its fluorescence by 45-65%, allowing it to report on GAPDH binding of mitochondrially-generated heme in live cells in real time. In cells with active mitochondrial heme synthesis, low-level NO exposure increased heme allocation to IDO1 while keeping the TC-hGAPDH heme level constant due to replenishment by mitochondria. When mitochondrial heme synthesis was blocked, low NO caused a near complete transfer of the existing heme in TC-hGAPDH to IDO1 in a process that required IDO1 be able to bind the heme and have an active hsp90 present. Higher NO exposure had the opposite effect and caused IDO1 heme to transfer back to TC-hGAPDH. This demonstrated: (i) flow of mitochondrial heme through GAPDH is tightly coupled to target delivery, (ii) NO up- or down-regulates IDO1 activity by promoting a conserved heme exchange with GAPDH that goes in either direction according to the NO exposure level. The ability to drive a concentration-dependent, reversible protein heme exchange is unprecedented and reveals a new role for NO in biology.
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Affiliation(s)
- Pranjal Biswas
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Joseph Palazzo
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Simon Schlanger
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, 44195, USA
| | | | - Sidra Islam
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Dennis J Stuehr
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, 44195, USA.
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Biswas P, Palazzo J, Schlanger S, Jayaram DT, Islam S, Page RC, Stuehr DJ. Visualizing Mitochondrial Heme Flow through GAPDH to Targets in Living Cells and its Regulation by NO. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575067. [PMID: 38260356 PMCID: PMC10802506 DOI: 10.1101/2024.01.10.575067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Iron protoporphyrin IX (heme) is an essential cofactor that is chaperoned in mammalian cells by GAPDH in a process regulated by NO. To gain further understanding we generated a tetra-Cys human GAPDH reporter construct (TC-hGAPDH) which after being expressed and labeled with fluorescent FlAsH reagent could indicate heme binding by fluorescence quenching. When purified or expressed in HEK293T mammalian cells, FlAsH-labeled TC-hGAPDH displayed physical, catalytic, and heme binding properties like native GAPDH and its heme binding (2 mol per tetramer) quenched its fluorescence by 45-65%. In live HEK293T cells we could visualize TC-hGAPDH binding mitochondrially-generated heme and releasing it to the hemeprotein target IDO1 by monitoring cell fluorescence in real time. In cells with active mitochondrial heme synthesis, a low-level NO exposure increased heme allocation into IDO1 while keeping steady the level of heme-bound TC-hGAPDH. When mitochondrial heme synthesis was blocked at the time of NO exposure, low NO caused cells to reallocate existing heme from TC-hGAPDH to IDO1 by a mechanism requiring IDO1 be present and able to bind heme. Higher NO exposure had an opposite effect and caused cells to reallocate existing heme from IDO1 to TC-hGAPDH. Thus, with TC-hGAPDH we could follow mitochondrial heme as it travelled onto and through GAPDH to a downstream target (IDO1) in living cells, and to learn that NO acted at or downstream from the GAPDH heme complex to promote a heme reallocation in either direction depending on the level of NO exposure.
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Ducamp S, Ostuni MA. Physiology of Red Cell Lineage: From Erythroblast Progenitors to Mature Red Blood Cell. Int J Mol Sci 2023; 24:ijms24119715. [PMID: 37298665 DOI: 10.3390/ijms24119715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Red blood cells (RBC) are the most abundant cells in mammals [...].
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Affiliation(s)
- Sarah Ducamp
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mariano A Ostuni
- Université Paris Cité and Université des Antilles, INSERM U1134, BIGR, F-75014 Paris, France
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Llauger M, Arnau J, Albano-Gaglio M, Bover-Cid S, Martín B, Bou R. Utilization of Porcine Livers through the Formation of Zn-Protoporphyrin Pigment Optimized by a Response Surface Methodology. Foods 2023; 12:foods12091903. [PMID: 37174439 PMCID: PMC10178239 DOI: 10.3390/foods12091903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
There is a growing demand for clean-label products. This study aimed to obtain a food-grade coloring ingredient for meat products based on the formation of Zn-protoporphyrin from porcine livers, thus contributing to the development of nitrite-free products. First, the effects of sodium disulfite and acetic, ascorbic, and lactic acids on the formation of Zn-protoporphyrin and the total microbial count were studied. The combination of ascorbic and acetic acids resulted in a higher Zn-protoporphyrin content than acetic acid alone, and microbial levels were maintained (ca. 3 log CFU/mL). Second, a response surface methodology was used to maximize Zn-protoporphyrin while maintaining microbiological food standards. To that end, the effects of pH (4.2-5.4), incubation time (3-30 h), and temperature (25-50 °C) were studied. The selected conditions for Zn-protoporphyrin formation involved anaerobic incubation at pH 4.8 and 45 °C for 24 h. The safety was validated through challenge testing for relevant pathogens (Listeria monocytogenes, Salmonella spp., and Clostridium perfringens). A significant reduction (>6 log units) was observed in the selected conditions for L. monocytogenes and Salmonella, whereas C. perfringens spores remained at the inoculated levels. The optimized procedure is proven to be microbiologically safe, and may improve the color of nitrite-free meat products.
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Affiliation(s)
- Mar Llauger
- Food Safety and Functionality Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Jacint Arnau
- Food Quality and Technology Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Michela Albano-Gaglio
- Food Quality and Technology Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Sara Bover-Cid
- Food Safety and Functionality Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Belén Martín
- Food Safety and Functionality Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Ricard Bou
- Food Quality and Technology Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
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Obi CD, Dailey HA, Jami-Alahmadi Y, Wohlschlegel JA, Medlock AE. Proteomic Analysis of Ferrochelatase Interactome in Erythroid and Non-Erythroid Cells. Life (Basel) 2023; 13:577. [PMID: 36836934 PMCID: PMC9958551 DOI: 10.3390/life13020577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/24/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Heme is an essential cofactor for multiple cellular processes in most organisms. In developing erythroid cells, the demand for heme synthesis is high, but is significantly lower in non-erythroid cells. While the biosynthesis of heme in metazoans is well understood, the tissue-specific regulation of the pathway is less explored. To better understand this, we analyzed the mitochondrial heme metabolon in erythroid and non-erythroid cell lines from the perspective of ferrochelatase (FECH), the terminal enzyme in the heme biosynthetic pathway. Affinity purification of FLAG-tagged-FECH, together with mass spectrometric analysis, was carried out to identify putative protein partners in human and murine cell lines. Proteins involved in the heme biosynthetic process and mitochondrial organization were identified as the core components of the FECH interactome. Interestingly, in non-erythroid cell lines, the FECH interactome is highly enriched with proteins associated with the tricarboxylic acid (TCA) cycle. Overall, our study shows that the mitochondrial heme metabolon in erythroid and non-erythroid cells has similarities and differences, and suggests new roles for the mitochondrial heme metabolon and heme in regulating metabolic flux and key cellular processes.
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Affiliation(s)
- Chibuike David Obi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Harry A. Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Amy E. Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Augusta University/University of Georgia Medical Partnership, Athens, GA 30606, USA
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Lewczuk A, Boratyńska-Jasińska A, Zabłocka B. Validation of the Reference Genes for Expression Analysis in the Hippocampus after Transient Ischemia/Reperfusion Injury in Gerbil Brain. Int J Mol Sci 2023; 24:ijms24032756. [PMID: 36769080 PMCID: PMC9917415 DOI: 10.3390/ijms24032756] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Transient brain ischemia in gerbils is a common model to study the mechanisms of neuronal changes in the hippocampus. In cornu ammonnis 2-3, dentate gyrus (CA2-3,DG) regions of the hippocampus, neurons are resistant to 5-min ischemia/reperfusion (I/R) insult, while cornu ammonnis 1 (CA1) is found to be I/R-vulnerable. The quantitative polymerase chain reaction (qRT-PCR) is widely used to study the expression of genes involved in these phenomena. It requires stable and reliable genes for normalization, which is crucial for comparable and reproducible analyses of expression changes of the genes of interest. The aim of this study was to determine the best housekeeping gene for the I/R gerbil model in two parts of the hippocampus in controls and at 3, 48, and 72 h after recanalization. We selected and tested six reference genes frequently used in central nervous system studies: Gapdh, Actb, 18S rRNA, Hprt1, Hmbs, Ywhaz, and additionally Bud23, using RefFinder, a comprehensive tool based on four commonly used algorithms: delta cycle threshold (Ct), BestKeeper, NormFinder, and geNorm, while Hprt1 and Hmbs were the most stable ones in CA2-3,DG. Hmbs was the most stable in the whole hippocampal formation. This indicates that the general use of Hmbs, especially in combination with Gapdh, a highly expressed reference gene, seems to be suitable for qRT-PCR normalization in all hippocampal regions in this model.
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