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Tehlan A, Bhowmick K, Kumar A, Subbarao N, Dhar SK. The tetrameric structure of Plasmodium falciparum phosphoglycerate mutase is critical for optimal enzymatic activity. J Biol Chem 2022; 298:101713. [PMID: 35150741 PMCID: PMC8913309 DOI: 10.1016/j.jbc.2022.101713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022] Open
Abstract
The glycolytic enzyme phosphoglycerate mutase (PGM) is of utmost importance for overall cellular metabolism and has emerged as a novel therapeutic target in cancer cells. This enzyme is also conserved in the rapidly proliferating malarial parasite Plasmodium falciparum, which have a similar metabolic framework as cancer cells and rely on glycolysis as the sole energy-yielding process during intraerythrocytic development. There is no redundancy among the annotated PGM enzymes in Plasmodium, and PfPGM1 is absolutely required for the parasite survival as evidenced by conditional knockdown in our study. A detailed comparison of PfPGM1 with its counterparts followed by in-depth structure-function analysis revealed unique attributes of this parasitic protein. Here, we report for the first time the importance of oligomerization for the optimal functioning of the enzyme in vivo, as earlier studies in eukaryotes only focused on the effects in vitro. We show that single point mutation of the amino acid residue W68 led to complete loss of tetramerization and diminished catalytic activity in vitro. Additionally, ectopic expression of the WT PfPGM1 protein enhanced parasite growth, whereas the monomeric form of PfPGM1 failed to provide growth advantage. Furthermore, mutation of the evolutionarily conserved residue K100 led to a drastic reduction in enzymatic activity. The indispensable nature of this parasite enzyme highlights the potential of PfPGM1 as a therapeutic target against malaria, and targeting the interfacial residues critical for oligomerization can serve as a focal point for promising drug development strategies that may not be restricted to malaria only.
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Affiliation(s)
- Ankita Tehlan
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Krishanu Bhowmick
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Amarjeet Kumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Suman Kumar Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067.
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Mikawa T, Shibata E, Shimada M, Ito K, Ito T, Kanda H, Takubo K, Shimada A, Lleonart ME, Inagaki N, Yokode M, Kondoh H. Characterization of genetically modified mice for phosphoglycerate mutase, a vitally-essential enzyme in glycolysis. PLoS One 2021; 16:e0250856. [PMID: 33914812 PMCID: PMC8084212 DOI: 10.1371/journal.pone.0250856] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/15/2021] [Indexed: 01/14/2023] Open
Abstract
Glycolytic metabolism is closely involved in physiological homeostasis and pathophysiological states. Among glycolytic enzymes, phosphoglycerate mutase (PGAM) has been reported to exert certain physiological role in vitro, whereas its impact on glucose metabolism in vivo remains unclear. Here, we report the characterization of Pgam1 knockout mice. We observed that homozygous knockout mice of Pgam1 were embryonic lethal. Although we previously reported that both PGAM-1 and -2 affect global glycolytic profile of cancers in vitro, in vivo glucose parameters were less affected both in the heterozygous knockout of Pgam1 and in Pgam2 transgenic mice. Thus, the impact of PGAM on in vivo glucose metabolism is rather complex than expected before.
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Affiliation(s)
- Takumi Mikawa
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eri Shibata
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Midori Shimada
- Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Ken Ito
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomiko Ito
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroaki Kanda
- Department of Pathology, Saitama Cancer Center, Saitama, Japan
| | - Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | | | | | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Yokode
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Kondoh
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- * E-mail:
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Shen J, Wang W, Wu J, Feng B, Chen W, Wang M, Tang J, Wang F, Cheng F, Pu L, Tang Q, Wang X, Li X. Comparative proteomic profiling of human bile reveals SSP411 as a novel biomarker of cholangiocarcinoma. PLoS One 2012; 7:e47476. [PMID: 23118872 PMCID: PMC3485295 DOI: 10.1371/journal.pone.0047476] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 09/17/2012] [Indexed: 02/06/2023] Open
Abstract
Background Cholangiocarcinoma (CC) is an intractable cancer, arising from biliary epithelial cells, which has a poor prognosis and is increasing in incidence. Early diagnosis of CC is essential as surgical resection remains the only effective therapy. The purpose of this study was to identify improved biomarkers to facilitate early diagnosis and prognostication in CC. Methods A comparative expression profile of human bile samples from patients with cholangitis and CC was constructed using a classic 2D/MS/MS strategy and the expression of selected proteins was confirmed by Western blotting. Immunohistochemistry was performed to determine the expression levels of selected candidate biomarkers in CC and matched normal tissues. Finally, spermatogenesis associated 20 (SSP411; also named SPATA20) was quantified in serum samples using an ELISA. Results We identified 97 differentially expressed protein spots, corresponding to 49 different genes, of which 38 were upregulated in bile from CC patients. Western blotting confirmed that phosphoglycerate mutase 1 (brain) (PGAM-1), protein disulfide isomerase family A, member 3 (PDIA3), heat shock 60 kDa protein 1 (chaperonin) (HSPD1) and SSP411 were significantly upregulated in individual bile samples from CC patients. Immunohistochemistry demonstrated these proteins were also overexpressed in CC, relative to normal tissues. SSP411 displayed value as a potential serum diagnostic biomarker for CC, with a sensitivity of 90.0% and specificity of 83.3% at a cutoff value of 0.63. Conclusions We successfully constructed a proteomic profile of CC bile proteins, providing a valuable pool novel of candidate biomarkers. SSP411 has potential as a biomarker for the diagnosis of CC.
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Affiliation(s)
- Jian Shen
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weizhi Wang
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jindao Wu
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- * E-mail: (XCL); (JDW)
| | - Bing Feng
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wen Chen
- Department of Thoracic and Cardiovascular Surgery, Nanjing First Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Meng Wang
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jincao Tang
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fuqiang Wang
- Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Feng Cheng
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liyong Pu
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiyun Tang
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xuehao Wang
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiangcheng Li
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- * E-mail: (XCL); (JDW)
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Chen N, Koumpouras GC, Polizzi KM, Kontoravdi C. Genome-based kinetic modeling of cytosolic glucose metabolism in industrially relevant cell lines: Saccharomyces cerevisiae and Chinese hamster ovary cells. Bioprocess Biosyst Eng 2012; 35:1023-33. [PMID: 22286123 DOI: 10.1007/s00449-012-0687-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 01/13/2012] [Indexed: 01/23/2023]
Abstract
Model-based analysis of cellular metabolism can facilitate our understanding of intracellular kinetics and aid the improvement of cell growth and biological product manufacturing. In this paper, a model-based kinetic study of cytosolic glucose metabolism for two industrially relevant cell lines, Saccharomyces cerevisiae and Chinese hamster ovary (CHO) cells, based on enzyme genetic presence and expression information is described. We have reconstructed the cytosolic glucose metabolism map for S. cerevisiae and CHO cells, containing 18 metabolites and 18 enzymes using information from the Kyoto Encyclopedia of Genes and Genomes (KEGG). Based on this map, we have developed akinetic mathematical model for the pathways involved,considering regulation and/or inhibition by products orco-substrates. The values of the maximum rates of reactions(V(max)) were estimated based on kinetic parameter information and metabolic flux analysis results available in literature, and the resulting simulation results for steady-state metabolite concentrations are in good agreement with published experimental data. Finally, the model was used to analyse how the production of DHAP, an important intermediate in fine chemicals synthesis, could be increased using gene knockout.
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Affiliation(s)
- Ning Chen
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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Westermann CM, Dorland L, van Diggelen OP, Schoonderwoerd K, Bierau J, Waterham HR, van der Kolk JH. Decreased oxidative phosphorylation and PGAM deficiency in horses suffering from atypical myopathy associated with acquired MADD. Mol Genet Metab 2011; 104:273-8. [PMID: 21843962 DOI: 10.1016/j.ymgme.2011.07.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 07/21/2011] [Indexed: 11/27/2022]
Abstract
Earlier research on ten horses suffering from the frequently fatal disorder atypical myopathy showed that MADD (multiple acyl-CoA dehydrogenase deficiency) is the biochemical derangement behind atypical myopathy. From five horses that died as a result of this disease and seven healthy control horses, urine and plasma were collected ante mortem and muscle biopsies were obtained immediately post-mortem (2 patients and 7 control horses), to analyse creatine, purine and carbohydrate metabolism as well as oxidative phosphorylation. In patients, the mean creatine concentration in urine was increased 17-fold and the concentration of uric acid approximately 4-fold, compared to controls. The highest degree of depletion of glycogen was observed in the patient with the most severe myopathy clinically. In this patient, glycolysis was more active than in the other patients and controls, which may explain this depletion. One patient demonstrated very low phosphoglycerate mutase (PGAM) activity, less than 10% of reference values. Most respiratory chain complex activity in patients was 20-30% lower than in control horses, complex II activity was 42% lower than normal, and one patient had severely decrease ATP-synthase activity, more than 60% lower than in control horses. General markers for myopathic damage are creatine kinase (CK) and lactic acid in plasma, and creatine and uric acid in urine. To obtain more information about the cause of the myopathy analysis of carbohydrate, lipid and protein metabolism as well as oxidative phosphorylation is advised. This study expands the diagnostic possibilities of equine myopathies.
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Affiliation(s)
- C M Westermann
- Department of Equine Sciences, Medicine Section, Faculty of Veterinary Medicine, Yalelaan 114, 3584 CM, Utrecht University, Utrecht, The Netherlands.
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Ren F, Wu H, Lei Y, Zhang H, Liu R, Zhao Y, Chen X, Zeng D, Tong A, Chen L, Wei Y, Huang C. Quantitative proteomics identification of phosphoglycerate mutase 1 as a novel therapeutic target in hepatocellular carcinoma. Mol Cancer 2010; 9:81. [PMID: 20403181 PMCID: PMC2873438 DOI: 10.1186/1476-4598-9-81] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 04/19/2010] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide with poor prognosis due to resistance to conventional chemotherapy and limited efficacy of radiotherapy. There is an urgent need to develop novel biomarkers for early diagnosis, as well as to identify new drug targets for therapeutic interventions. PATIENTS AND METHODS 54 paired HCC samples and 21 normal liver tissues were obtained from West China Hospital of Sichuan University. Informed consent was obtained from all the patients or their relatives prior to analysis, and the project was approved by the Institutional Ethics Committee of Sichuan University. Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)-based proteomics was employed to profile the differentially expressed proteins between a HepG2 human hepatoma cell line and an immortal hepatic cell line L02. Validation of PGAM1 expression was performed by semi-quantitative RT-PCR, immunoblot and immunohistochemistry using clinical samples. shRNA expressing plasmids specifically targeting PGAM1 were designed and constructed by GenePharma Corporation (Shanghai, China), and were utilized to silence expression of PGAM1 in vitro and in vivo. Cell proliferation was measured by a combination of colony formation assay and Ki67 staining. Apoptosis was examined by flow cytometry and TUNEL assay. RESULTS A total of 63 dysregulated proteins were identified, including 51 up-regulated proteins, and 12 down-regulated proteins (over 2-fold, p < 0.01). Phosphoglycerate mutase 1 (PGAM1) was found markedly upregulated. Clinico-pathological analysis indicated that overexpression of PGAM1 was associated with 66.7% HCC, and strongly correlated with poor differentiation and decreased survival rates (p < 0.01). shRNAs-mediated repression of PGAM1 expression resulted in significant inhibition in liver cancer cell growth both in vitro and in vivo. CONCLUSION Our studies suggested that PGAM1 plays an important role in hepatocarcinogenesis, and should be a potential diagnostic biomarker, as well as an attractive therapeutic target for hepatocellular carcinoma.
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Affiliation(s)
- Fenglian Ren
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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van Wijk R, van Solinge WW. The energy-less red blood cell is lost: erythrocyte enzyme abnormalities of glycolysis. Blood 2005; 106:4034-42. [PMID: 16051738 DOI: 10.1182/blood-2005-04-1622] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The red blood cell depends solely on the anaerobic conversion of glucose by the Embden-Meyerhof pathway for the generation and storage of high-energy phosphates, which is necessary for the maintenance of a number of vital functions. Many red blood cell enzymopathies have been described that disturb the erythrocyte's integrity, shorten its cellular survival, and result in hemolytic anemia. By far the majority of these enzymopathies are hereditary in nature. In this review, we summarize the current knowledge regarding the genetic, biochemical, and structural features of clinically relevant red blood cell enzymopathies involved in the Embden-Meyerhof pathway and the Rapoport-Luebering shunt.
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Affiliation(s)
- Richard van Wijk
- Department of Laboratory Medicine, Rm G03.550, University Medical Center Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
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Wang Y, Wei Z, Liu L, Cheng Z, Lin Y, Ji F, Gong W. Crystal structure of human B-type phosphoglycerate mutase bound with citrate. Biochem Biophys Res Commun 2005; 331:1207-15. [PMID: 15883004 DOI: 10.1016/j.bbrc.2005.03.243] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Indexed: 11/28/2022]
Abstract
The B-type cofactor-dependent phosphoglycerate mutase (dPGM-B) catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in glycolysis and gluconeogenesis pathways using 2,3-bisphosphoglycerate as the cofactor. The crystal structures of human dPGM-B bound with citrate were determined in two crystal forms. These structures reveal a dimerization mode conserved in both of dPGM and BPGM (bisphosphoglycerate mutase), based on which a dPGM/BPGM heterodimer structure is proposed. Structural comparison supports that the conformational changes of residues 13-21 and 98-117 determine PGM/BPGM activity differences. The citrate-binding mode suggests a substrate-binding model, consistent with the structure of Escherichia coli dPGM/vanadate complex. A chloride ion was found in the center of the dimer, providing explanation for the contribution of chloride ion to dPGM activities. Based on the structural information, the possible reasons for the deficient human dPGM mutations found in some patients are also discussed.
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Affiliation(s)
- Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
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Centeno NB, Planas-Iglesias J, Oliva B. Comparative modelling of protein structure and its impact on microbial cell factories. Microb Cell Fact 2005; 4:20. [PMID: 15989691 PMCID: PMC1183243 DOI: 10.1186/1475-2859-4-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 06/30/2005] [Indexed: 11/22/2022] Open
Abstract
Comparative modeling is becoming an increasingly helpful technique in microbial cell factories as the knowledge of the three-dimensional structure of a protein would be an invaluable aid to solve problems on protein production. For this reason, an introduction to comparative modeling is presented, with special emphasis on the basic concepts, opportunities and challenges of protein structure prediction. This review is intended to serve as a guide for the biologist who has no special expertise and who is not involved in the determination of protein structure. Selected applications of comparative modeling in microbial cell factories are outlined, and the role of microbial cell factories in the structural genomics initiative is discussed.
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Affiliation(s)
- Nuria B Centeno
- Structural Bioinformatics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF. c/ Dr. Aiguader 80. 08003 Barcelona, Spain
| | - Joan Planas-Iglesias
- Structural Bioinformatics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF. c/ Dr. Aiguader 80. 08003 Barcelona, Spain
| | - Baldomero Oliva
- Structural Bioinformatics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF. c/ Dr. Aiguader 80. 08003 Barcelona, Spain
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