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Hernández-Prieto JH, Martini VP, Iulek J. Structure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii in complex with an aldonic sugar acid. Biochimie 2024; 218:20-33. [PMID: 37709188 DOI: 10.1016/j.biochi.2023.09.013] [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: 02/19/2023] [Revised: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The pathogen Paracoccidioides lutzii (Pb01) is found in South America countries Colombia, Ecuador, Venezuela and Brazil, especially in the central, west, and north regions of the latter. It belongs to the Ajellomycetaceae family, Onygenales order, and is typically thermodimorphic, presenting yeast cells when it grows in animal tissues, but mycelia when in the environment, where it produces the infectious propagule. This fungus is one of the etiologic agents of Paracoccidioidomycosis (PCM), the most important endemic fungal infection in Latin America. Investigations on its genome have contributed to a better understanding about its metabolism and revealed the complexity of several metabolic glycolytic pathways. Glyceraldehyde-3-Phosphate Dehydrogenase from Paracoccidioides lutzii (PlGAPDH) is considered a moonlighting protein and participates in several biological processes of this pathogen. The enzyme was expressed and purified, as seen in SDS-PAGE gel, crystallized and had its three dimensional structure (3D) determined in complex with NAD+, a sulphate ion and d-galactonic acid, therefore, a type of 'GAA site'. It is the first GAPDH structure to show this chemical type in this site and how this protein can bind an acid derived from oxidation of a linear hexose.
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Affiliation(s)
| | | | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil.
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Liang Q, Dong B, Li A, Wu L, Zhang Y, Han T, Liu X. scRNA-seq analysis reveals toxicity mechanisms in shrimp hemocytes subjected to nitrite stress. CHEMOSPHERE 2023; 316:137853. [PMID: 36640974 DOI: 10.1016/j.chemosphere.2023.137853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
In shrimp, hemocytes play an important role in detoxification and immune defense, and are where nitrite accumulates during exposure to this toxic environmental pollutant. However, the heterogeneity mechanisms of toxicity have not been reported under nitrite expose in shrimp. Here, we used single-cell RNA-seq to resolve 24,000 cells, which the responses of different cell populations of hemocytes under nitrite exposure in Penaeus vannamei. We identified 394 specific nitrite-responsive genes in 9 clusters of hemocytes, and found heterogeneity in the nitrite response of the three subpopulations of hemocytes (hyaline, semi-granular and granular cells). In hyaline, the response appeared modest, whereas nitrite-related dysregulation of metabolic processes in granular and semi-granular was pronounced. Ammonia nitrogen will rapidly accumulate in hemocytes of shrimp under nitrite stress. In semi-granular, excessive ammonia will interfere with oxidative phosphorylation and antioxidant system, thus inducing the production of reactive oxygen species. In granular, the abnormality of urea cycle caused by ammonia accumulation is the main toxic factor, which by inhibits arginase and arginine kinase. Collectively, our data provide a single-cell atlas for the dissection of shrimp hemocyte complexity, and reveal the toxicity mechanisms associated with nitrite exposure.
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Affiliation(s)
- QingJian Liang
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, PR China; College of Life Science, South China Normal University, Guangzhou, 510631, PR China.
| | - BeiBei Dong
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, PR China
| | - Ang Li
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, PR China
| | - LiTing Wu
- College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Yu Zhang
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, PR China
| | - Tao Han
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, PR China
| | - Xing Liu
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, 519000, PR China.
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Jung Y, Noda N, Takaya J, Abo M, Toh K, Tajiri K, Cui C, Zhou L, Sato SI, Uesugi M. Discovery of Non-Cysteine-Targeting Covalent Inhibitors by Activity-Based Proteomic Screening with a Cysteine-Reactive Probe. ACS Chem Biol 2022; 17:340-347. [PMID: 35076225 DOI: 10.1021/acschembio.1c00824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covalent inhibitors of enzymes are increasingly appreciated as pharmaceutical seeds, yet discovering non-cysteine-targeting inhibitors remains challenging. Herein, we report an intriguing experience during our activity-based proteomic screening of 1601 reactive small molecules, in which we monitored the ability of library molecules to compete with a cysteine-reactive iodoacetamide probe. One epoxide molecule, F8, exhibited unexpected enhancement of the probe reactivity for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a rate-limiting glycolysis enzyme. In-depth mechanistic analysis suggests that F8 forms a covalent adduct with an aspartic acid in the active site to displace NAD+, a cofactor of the enzyme, with concomitant enhancement of the probe reaction with the catalytic cysteine. The mechanistic underpinning permitted the identification of an optimized aspartate-reactive GAPDH inhibitor. Our findings exemplify that activity-based proteomic screening with a cysteine-reactive probe can be used for discovering covalent inhibitors that react with non-cysteine residues.
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Affiliation(s)
- Yejin Jung
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naotaka Noda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Junichiro Takaya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiro Abo
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kohei Toh
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ken Tajiri
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Changyi Cui
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Lu Zhou
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shin-ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- School of Pharmacy, Fudan University, Shanghai 201203, China
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
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Sod1 integrates oxygen availability to redox regulate NADPH production and the thiol redoxome. Proc Natl Acad Sci U S A 2022; 119:2023328119. [PMID: 34969852 PMCID: PMC8740578 DOI: 10.1073/pnas.2023328119] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2021] [Indexed: 12/12/2022] Open
Abstract
Cu/Zn superoxide dismutase (Sod1) is a key antioxidant enzyme, and its importance is underscored by the fact that its ablation in cell and animal models results in oxidative stress; metabolic defects; and reductions in cell proliferation, viability, and lifespan. Curiously, Sod1 detoxifies superoxide radicals (O2•−) in a manner that produces an oxidant as byproduct, hydrogen peroxide (H2O2). While much is known about the necessity of scavenging O2•−, it is less clear what the physiological roles of Sod1-derived H2O2 are. We discovered that Sod1-derived H2O2 plays an important role in antioxidant defense by stimulating the production of NADPH, a vital cellular reductant required for reactive oxygen species scavenging enzymes, as well as redox regulating a large network of enzymes. Cu/Zn superoxide dismutase (Sod1) is a highly conserved and abundant antioxidant enzyme that detoxifies superoxide (O2•−) by catalyzing its conversion to dioxygen (O2) and hydrogen peroxide (H2O2). Using Saccharomyces cerevisiae and mammalian cells, we discovered that a major aspect of the antioxidant function of Sod1 is to integrate O2 availability to promote NADPH production. The mechanism involves Sod1-derived H2O2 oxidatively inactivating the glycolytic enzyme, GAPDH, which in turn reroutes carbohydrate flux to the oxidative phase of the pentose phosphate pathway (oxPPP) to generate NADPH. The aerobic oxidation of GAPDH is dependent on and rate-limited by Sod1. Thus, Sod1 senses O2 via O2•− to balance glycolytic and oxPPP flux, through control of GAPDH activity, for adaptation to life in air. Importantly, this mechanism for Sod1 antioxidant activity requires the bulk of cellular Sod1, unlike for its role in protection against O2•− toxicity, which only requires <1% of total Sod1. Using mass spectrometry, we identified proteome-wide targets of Sod1-dependent redox signaling, including numerous metabolic enzymes. Altogether, Sod1-derived H2O2 is important for antioxidant defense and a master regulator of metabolism and the thiol redoxome.
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Noh MAA, Fazalul Rahiman SS, A Wahab H, Mohd Gazzali A. Discovery of new targeting agents against GAPDH receptor for antituberculosis drug delivery. J Basic Clin Physiol Pharmacol 2021; 32:715-722. [PMID: 34214294 DOI: 10.1515/jbcpp-2020-0435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Tuberculosis (TB) remains a public health concern due to the emergence and evolution of multidrug-resistant strains. To overcome this issue, reinforcing the effectiveness of first line antituberculosis agents using targeted drug delivery approach is an option. Glyceraldehyde-3-Phosphate Dehydrogenase (GADPH), a common virulence factor found in the pathogenic microorganisms has recently been discovered on the cell-surface of Mycobacterium tuberculosis, allowing it to be used as a drug target for TB. This study aims to discover active small molecule(s) that target GAPDH and eventually enhance the delivery of antituberculosis drugs. METHODS Ten ligands with reported in vitro and/or in vivo activities against GAPDH were evaluated for their binding interactions through molecular docking studies using AutoDock 4.2 program. The ligand with the best binding energy was then modified to produce 10 derivatives, which were redocked against GAPDH using previous protocols. BIOVIA Discovery Studio Visualizer 2019 was used to explore the ligand-receptor interactions between the derivatives and GAPDH. RESULTS Among the 10 ligands, curcumin, koningic acid and folic acid showed the best binding energies. Further analysis on the docking of two folic acid derivatives, F7 (γ-{[tert-butyl-N-(6-aminohexyl)]carbamate}folic acid) and F8 (folic acid N-hydroxysuccinimide ester) showed that the addition of a bulky substituent at the carboxyl group of the glutamic acid subcomponent resulted in improved binding energy. CONCLUSIONS Folic acid and the two derivatives F7 and F8 have huge potentials to be developed as targeting agents against the GAPDH receptor. Further study is currently on-going to evaluate the effectiveness of these molecules in vitro.
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Affiliation(s)
- Muhammad Amirul Asyraf Noh
- Discipline of Pharmaceutical Technology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Siti Sarah Fazalul Rahiman
- Discipline of Physiology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Habibah A Wahab
- Discipline of Pharmaceutical Technology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Amirah Mohd Gazzali
- Discipline of Pharmaceutical Technology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
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Thapa J, Hashimoto K, Sugawara S, Tsujikawa R, Okubo T, Nakamura S, Yamaguchi H. Hypoxia promotes Chlamydia trachomatis L2/434/Bu growth in immortal human epithelial cells via activation of the PI3K-AKT pathway and maintenance of a balanced NAD +/NADH ratio. Microbes Infect 2020; 22:441-450. [PMID: 32442683 DOI: 10.1016/j.micinf.2020.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 01/09/2023]
Abstract
Chlamydia trachomatis LGV (CtL2) causes systemic infection and proliferates in lymph nodes as well as genital tract or rectum producing a robust inflammatory response, presumably leading to a low oxygen environment. We therefore assessed how CtL2 growth in immortal human epithelial cells adapts to hypoxic conditions. Assessment of inclusion forming units, the quantity of chlamydial 16S rDNA, and inclusion size showed that hypoxia promotes CtL2 growth. Under hypoxia, HIF-1α was stabilized and p53 was degraded in infected cells. Moreover, AKT was strongly phosphorylated at S473 by CtL2 infection. This activation was significantly diminished by LY-294002, a PI3K-AKT inhibitor, which decreased the number of CtL2 progeny. HIF-1α stabilizers (CoCl2, desferrioxamine) had no effect on increasing CtL2 growth, indicating no autocrine impact of growth factors produced by HIF-1α stabilization. Furthermore, in normoxia, CtL2 infection changed the NAD+/NADH ratio of cells with increased gapdh expression; in contrast, under hypoxia, the NAD+/NADH ratio was the same in infected and uninfected cells with high and stable expression of gapdh, suggesting that CtL2-infected cells adapted better to hypoxia. Together, these data indicate that hypoxia promotes CtL2 growth in immortal human epithelial cells by activating the PI3K-AKT pathway and maintaining the NAD+/NADH ratio with stably activated glycolysis.
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Affiliation(s)
- Jeewan Thapa
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan.
| | - Kent Hashimoto
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan.
| | - Saori Sugawara
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan.
| | - Ryoya Tsujikawa
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan.
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan.
| | - Shinji Nakamura
- Division of Biomedical Imaging Research, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan.
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Yang J. Identification of novel biomarkers, MUC5AC, MUC1, KRT7, GAPDH, CD44 for gastric cancer. Med Oncol 2020; 37:34. [PMID: 32219571 DOI: 10.1007/s12032-020-01362-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/10/2020] [Indexed: 01/19/2023]
Abstract
Gastric cancer (GC) is one of the most common malignant tumors in the world, and it is also the third largest cause of cancer-related death in the world. As far as we know, no biomarker has been widely accepted for early diagnosis and prognosis prediction of gastric cancer. The purpose of this study is to find potential biomarkers to predict the prognosis of GC. The gene expression profiles of GSE2685 were downloaded from GEO database. Morpheus was used to calculate the differentially expressed genes (DEGs) between primary advanced gastric cancer tissues and noncancerous gastric tissues. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed, and protein-protein interaction (PPI) network of DEGs was constructed. Kaplan-Meier Plotter was used to determine the overall survival (OS) outcomes of UC5AC, MUC1, KRT7, GAPDH, CD44, and GEPIA was used to determine the Pearson correlation analysis. In total, 710 DEGs were identified in GC, including 396 upregulated genes and 314 downregulated genes. GO enrichment revealed that they were mainly enriched in binding, catalytic activity, cellular process and cell. KEGG pathway revealed that they were mainly enriched in metabolic pathways, pathways in cancer and PI3K-Akt signaling pathway. MUC5AC, MUC1, KRT7, GAPDH, CD44 were identified from the PPI network. MUC5AC, MUC1, KRT7, GAPDH, CD44 were demonstrated to have prognostic value for patients with GC. MUC5AC, MUC1 exhibited low expression levels in GC tissues, KRT7, GAPDH, CD44 presented high expression levels in GC tissues. In particular, KRT7 is hardly expressed in normal gastric tissues. MUC5AC and MUC1 were negatively correlated with GAPDH, CD44, respectively; and GAPDH was positively correlated with CD44 and KRT7, respectively. Moreover. MUC5AC, MUC1, KRT7, GAPDH, and CD44 are not only related to GC but also to apoptosis pathway. Results from the present study suggested that MUC5AC, MUC1, KRT7, GAPDH, CD44 may represent novel prognostic biomarkers for GC.
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Affiliation(s)
- Jie Yang
- Central Laboratory, Danyang People's Hospital of Jiangsu Province, Danyang, Jiangsu, China.
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