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Zhang X, Geng L, Tang Y, Wang Y, Zhang Y, Zhu C, Lei H, Xu H, Zhu Q, Wu Y, Gu W. Ubiquitin-specific protease 14 targets PFKL-mediated glycolysis to promote the proliferation and migration of oral squamous cell carcinoma. J Transl Med 2024; 22:193. [PMID: 38388430 PMCID: PMC10885370 DOI: 10.1186/s12967-024-04943-z] [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: 05/30/2023] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
Aberrant upregulation of the ubiquitin-specific protease 14 (USP14) has been found in some malignant tumors, including oral squamous cell carcinoma (OSCC). In this study, we further demonstrated that aberrantly overexpressed USP14 was also closely related to adverse clinicopathological features and poor prognosis in patients with OSCC, so we hypothesized that USP14 might act as a tumor-promoting factor during the progression of OSCC. Notably, we originally proved that USP14 is a deubiquitinating enzyme for phosphofructokinase-1 liver type (PFKL), a key rate-limiting enzyme involved in the glycolytic pathway. USP14 interacts with PFKL and enhances its stability through deubiquitination in OSCC cells, which in turn enhances PFKL-mediated glycolytic metabolism and ultimately promote cellular proliferation, migration, and tumorigenesis. In this work, we have also demonstrated for the first time that USP14 is a critical regulator of glycolysis in OSCC and verified a novel mechanism whereby it is involved in tumor metastasis and growth. Collectively, our findings provide novel insights into the tumor-promoting role of USP14 and establish mechanistic foundations for USP14-targeting therapies.
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Affiliation(s)
- Xingming Zhang
- Department of Clinical Laboratory, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Lou Geng
- Department of Clinical Laboratory, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yi Tang
- Department of Clinical Laboratory, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yingying Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Youping Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chujiao Zhu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hu Lei
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hanzhang Xu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qi Zhu
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yingli Wu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Research Units of Stress and Tumor (2019RU043), Chinese Academy of Medical Sciences, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Wenli Gu
- Department of Clinical Laboratory, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
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2
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Bracken AK, Gekko CE, Suss NO, Lueders EE, Cui Q, Fu Q, Lui ACW, Anderson ET, Zhang S, Abbasov ME. Biomimetic Synthesis and Chemical Proteomics Reveal the Mechanism of Action and Functional Targets of Phloroglucinol Meroterpenoids. J Am Chem Soc 2024; 146:2524-2548. [PMID: 38230968 PMCID: PMC11000255 DOI: 10.1021/jacs.3c10741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Natural products perennially serve as prolific sources of drug leads and chemical probes, fueling the development of numerous therapeutics. Despite their scarcity, natural products that modulate protein function through covalent interactions with lysine residues hold immense potential to unlock new therapeutic interventions and advance our understanding of the biological processes governed by these modifications. Phloroglucinol meroterpenoids constitute one of the most expansive classes of natural products, displaying a plethora of biological activities. However, their mechanism of action and cellular targets have, until now, remained elusive. In this study, we detail the concise biomimetic synthesis, computational mechanistic insights, physicochemical attributes, kinetic parameters, molecular mechanism of action, and functional cellular targets of several phloroglucinol meroterpenoids. We harness synthetic clickable analogues of natural products to probe their disparate proteome-wide reactivity and subcellular localization through in-gel fluorescence scanning and cell imaging. By implementing sample multiplexing and a redesigned lysine-targeting probe, we streamline a quantitative activity-based protein profiling, enabling the direct mapping of global reactivity and ligandability of proteinaceous lysines in human cells. Leveraging this framework, we identify numerous lysine-meroterpenoid interactions in breast cancer cells at tractable protein sites across diverse structural and functional classes, including those historically deemed undruggable. We validate that phloroglucinol meroterpenoids perturb biochemical functions through stereoselective and site-specific modification of lysines in proteins vital for breast cancer metabolism, including lipid signaling, mitochondrial respiration, and glycolysis. These findings underscore the broad potential of phloroglucinol meroterpenoids for targeting functional lysines in the human proteome.
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Affiliation(s)
- Amy K Bracken
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Colby E Gekko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Nina O Suss
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Emma E Lueders
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Qi Cui
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Qin Fu
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Andy C W Lui
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Elizabeth T Anderson
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
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3
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Campos M, Albrecht LV. Hitting the Sweet Spot: How Glucose Metabolism Is Orchestrated in Space and Time by Phosphofructokinase-1. Cancers (Basel) 2023; 16:16. [PMID: 38201444 PMCID: PMC10778546 DOI: 10.3390/cancers16010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Glycolysis is the central metabolic pathway across all kingdoms of life. Intensive research efforts have been devoted to understanding the tightly orchestrated processes of converting glucose into energy in health and disease. Our review highlights the advances in knowledge of how metabolic and gene networks are integrated through the precise spatiotemporal compartmentalization of rate-limiting enzymes. We provide an overview of technically innovative approaches that have been applied to study phosphofructokinase-1 (PFK1), which represents the fate-determining step of oxidative glucose metabolism. Specifically, we discuss fast-acting chemical biology and optogenetic tools that have delineated new links between metabolite fluxes and transcriptional reprogramming, which operate together to enact tissue-specific processes. Finally, we discuss how recent paradigm-shifting insights into the fundamental basis of glycolytic regulatory control have shed light on the mechanisms of tumorigenesis and could provide insight into new therapeutic vulnerabilities in cancer.
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Affiliation(s)
- Melissa Campos
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92697, USA;
| | - Lauren V. Albrecht
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92697, USA;
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
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4
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Voronkova MA, Hansen HL, Cooper MP, Miller J, Sukumar N, Geldenhuys WJ, Robart AR, Webb BA. Cancer-associated somatic mutations in human phosphofructokinase-1 reveal a critical electrostatic interaction for allosteric regulation of enzyme activity. Biochem J 2023; 480:1411-1427. [PMID: 37622331 PMCID: PMC10586780 DOI: 10.1042/bcj20230207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 08/26/2023]
Abstract
Metabolic reprogramming, including increased glucose uptake and lactic acid excretion, is a hallmark of cancer. The glycolytic 'gatekeeper' enzyme phosphofructokinase-1 (PFK1), which catalyzes the step committing glucose to breakdown, is dysregulated in cancers. While altered PFK1 activity and expression in tumors have been demonstrated, little is known about the effects of cancer-associated somatic mutations. Somatic mutations in PFK1 inform our understanding of allosteric regulation by identifying key amino acid residues involved in the regulation of enzyme activity. Here, we characterized mutations disrupting an evolutionarily conserved salt bridge between aspartic acid and arginine in human platelet (PFKP) and liver (PFKL) isoforms. Using purified recombinant proteins, we showed that disruption of the Asp-Arg pair in two PFK1 isoforms decreased enzyme activity and altered allosteric regulation. We determined the crystal structure of PFK1 to 3.6 Å resolution and used molecular dynamic simulations to understand molecular mechanisms of altered allosteric regulation. We showed that PFKP-D564N had a decreased total system energy and changes in the electrostatic surface potential of the effector site. Cells expressing PFKP-D564N demonstrated a decreased rate of glycolysis, while their ability to induce glycolytic flux under conditions of low cellular energy was enhanced compared with cells expressing wild-type PFKP. Taken together, these results suggest that mutations in Arg-Asp pair at the interface of the catalytic-regulatory domains stabilizes the t-state and presents novel mechanistic insight for therapeutic development in cancer.
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Affiliation(s)
- Maria A. Voronkova
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV 26506, U.S.A
| | - Heather L. Hansen
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV 26506, U.S.A
| | - Madison P. Cooper
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV 26506, U.S.A
| | - Jacob Miller
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV 26506, U.S.A
| | - Narayanasami Sukumar
- Northeastern Collaborative Access Team Center for Advanced Macromolecular Crystallography, Argonne National Laboratory, Lemont, IL 60439, U.S.A
| | - Werner J. Geldenhuys
- Department of Pharmaceutical Sciences, West Virginia University School of Pharmacy, Morgantown, WV 26506, U.S.A
| | - Aaron R. Robart
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV 26506, U.S.A
| | - Bradley A. Webb
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV 26506, U.S.A
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5
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Jiang S, Li S, Luo J, Wang X, Shi C. QTL mapping and transcriptome analysis of sugar content during fruit ripening of Pyrus pyrifolia. FRONTIERS IN PLANT SCIENCE 2023; 14:1137104. [PMID: 36950356 PMCID: PMC10025493 DOI: 10.3389/fpls.2023.1137104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Sugar content is an important trait of fruits. The genetic background of fruits can affect their sugar content in different cultivars. The quantitative trait loci and genes related to sugar content during fruit ripening remain unclear. In this study, we performed quantitative trait locus (QTL) mapping of sugar content. Two QTLs (qSugar-LG6-Chr7 and qSugar-LG12-Chr3) were identified based on their total sugar contents. A total of 577 and 519 genes were annotated around these two QTL loci. The contents of fructose, sorbitol, glucose, and sucrose were measured at six time points in four cultivars before fruit maturation, including two sweet cultivars ("Zaoshengxinshui" and "ZQ65") and two general cultivars ("Qiushui" and "ZQ82"). In sweet cultivars, sucrose and fructose accumulate substantially, and sorbitol content decreases significantly during fruit ripening. A transcriptome analysis identified 125 upregulated and 222 downregulated differentially expressed genes (DEGs) in sweet cultivars. Two sucrose transport genes (PpSUT, LOC103964096, and LOC103940043) were negatively correlated with sugar content. A weighted gene co-expression network analysis showed that two genes, sorbitol dehydrogenase (PpSDH, LOC103960512 and LOC103960513), around the locus of qSugar-LG6-Chr7 were negatively co-expressed with the total sugar content, which was downregulated in the sweet cultivars. PpSDH and PpSUT may play important roles in regulating sugar content during pear ripening. Transcriptome analysis also revealed that some DEGs were related to sugars (PpS6PDH and ATP-PpPFK), hormones (PpARG7), and transcription factors (PpEMB1444, PpCYP734A1, and PpWRKY50). In conclusion, this study provides new insights into the molecular mechanisms associated with sugar content in the fruit ripening of Pyrus pyrifolia.
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Affiliation(s)
| | | | - Jun Luo
- *Correspondence: Jun Luo, ; Xiaoqing Wang,
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6
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Meyer DJ, Díaz-García CM, Nathwani N, Rahman M, Yellen G. The Na +/K + pump dominates control of glycolysis in hippocampal dentate granule cells. eLife 2022; 11:e81645. [PMID: 36222651 PMCID: PMC9592084 DOI: 10.7554/elife.81645] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
Cellular ATP that is consumed to perform energetically expensive tasks must be replenished by new ATP through the activation of metabolism. Neuronal stimulation, an energetically demanding process, transiently activates aerobic glycolysis, but the precise mechanism underlying this glycolysis activation has not been determined. We previously showed that neuronal glycolysis is correlated with Ca2+ influx, but is not activated by feedforward Ca2+ signaling (Díaz-García et al., 2021a). Since ATP-powered Na+ and Ca2+ pumping activities are increased following stimulation to restore ion gradients and are estimated to consume most neuronal ATP, we aimed to determine if they are coupled to neuronal glycolysis activation. By using two-photon imaging of fluorescent biosensors and dyes in dentate granule cell somas of acute mouse hippocampal slices, we observed that production of cytoplasmic NADH, a byproduct of glycolysis, is strongly coupled to changes in intracellular Na+, while intracellular Ca2+ could only increase NADH production if both forward Na+/Ca2+ exchange and Na+/K+ pump activity were intact. Additionally, antidromic stimulation-induced intracellular [Na+] increases were reduced >50% by blocking Ca2+ entry. These results indicate that neuronal glycolysis activation is predominantly a response to an increase in activity of the Na+/K+ pump, which is strongly potentiated by Na+ influx through the Na+/Ca2+ exchanger during extrusion of Ca2+ following stimulation.
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Affiliation(s)
- Dylan J Meyer
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
| | | | - Nidhi Nathwani
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
| | - Mahia Rahman
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
| | - Gary Yellen
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
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7
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Zhang X, Bai Y, Zhu W, Lv X, Pei W. ApoM regulates PFKL through the transcription factor SREBF1 to inhibit the proliferation, migration and metastasis of liver cancer cells. Oncol Lett 2022; 24:210. [PMID: 35720503 PMCID: PMC9178675 DOI: 10.3892/ol.2022.13331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/25/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Xiao Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, P.R. China
| | - Yaping Bai
- Anhui Province Key Laboratory of Biological Macro‑Molecules Research, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Wenhao Zhu
- Anhui Province Key Laboratory of Biological Macro‑Molecules Research, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Xinyue Lv
- Anhui Province Key Laboratory of Biological Macro‑Molecules Research, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Wenjun Pei
- Anhui Province Key Laboratory of Biological Macro‑Molecules Research, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
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8
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Yang X, Yin X, Liu J, Niu Z, Yang J, Shen B. Essential role of pyrophosphate homeostasis mediated by the pyrophosphate-dependent phosphofructokinase in Toxoplasma gondii. PLoS Pathog 2022; 18:e1010293. [PMID: 35104280 PMCID: PMC8836295 DOI: 10.1371/journal.ppat.1010293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/11/2022] [Accepted: 01/24/2022] [Indexed: 12/27/2022] Open
Abstract
Many biosynthetic pathways produce pyrophosphate (PPi) as a by-product, which is cytotoxic if accumulated at high levels. Pyrophosphatases play pivotal roles in PPi detoxification by converting PPi to inorganic phosphate. A number of apicomplexan parasites, including Toxoplasma gondii and Cryptosporidium parvum, express a PPi-dependent phosphofructokinase (PPi-PFK) that consumes PPi to power the phosphorylation of fructose-6-phosphate. However, the physiological roles of PPi-PFKs in these organisms are not known. Here, we report that Toxoplasma expresses both ATP- and PPi-dependent phosphofructokinases in the cytoplasm. Nonetheless, only PPi-PFK was indispensable for parasite growth, whereas the deletion of ATP-PFK did not affect parasite proliferation or virulence. The conditional depletion of PPi-PFK completely arrested parasite growth, but it did not affect the ATP level and only modestly reduced the flux of central carbon metabolism. However, PPi-PFK depletion caused a significant increase in cellular PPi and decreased the rates of nascent protein synthesis. The expression of a cytosolic pyrophosphatase in the PPi-PFK depletion mutant reduced its PPi level and increased the protein synthesis rate, therefore partially rescuing its growth. These results suggest that PPi-PFK has a major role in maintaining pyrophosphate homeostasis in T. gondii. This role may allow PPi-PFK to fine-tune the balance of catabolism and anabolism and maximize the utilization efficiency for carbon nutrients derived from host cells, increasing the success of parasitism. Moreover, PPi-PFK is essential for parasite propagation and virulence in vivo but it is not present in human hosts, making it a potential drug target to combat toxoplasmosis. Different from classic ATP-dependent phosphofructokinases, PPi-PFKs use pyrophosphate consumption to power the conversion of fructose-6-phosphate to fructose-1,6-bisphosphate, the committed step of glycolysis. PPi-PFK is found in diverse organisms including archaea, bacteria, protists and plants. However, half a century after its first discovery, the physiological functions of PPi-PFK are still not well defined. Using the Toxoplasma gondii parasite as a model, here we show that PPi-PFK has a coordinator function to assure matched activities of anabolism and catabolism. This is achieved by maintaining the homeostasis of PPi, which is a byproduct, as well as an inhibitor of many biosynthetic reactions. PPi-PFK hydrolyzes PPi to promote anabolism, meanwhile being a glycolytic enzyme involved in catabolism. As such, it gauges the anabolic and catabolic activities in parasites to maximize the utilization efficiency of acquired nutrients. This work provides important insights to understand the physiological significance of PPi-PFK in Toxoplasma and other organisms.
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Affiliation(s)
- Xuke Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Xiaoyan Yin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiaojiao Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zhipeng Niu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jichao Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Bang Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- * E-mail:
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9
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Zhang S, Hua Z, Ba G, Xu N, Miao J, Zhao G, Gong W, Liu Z, Thiele CJ, Li Z. Antitumor effects of the small molecule DMAMCL in neuroblastoma via suppressing aerobic glycolysis and targeting PFKL. Cancer Cell Int 2021; 21:619. [PMID: 34819091 PMCID: PMC8613996 DOI: 10.1186/s12935-021-02330-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022] Open
Abstract
Background Neuroblastoma (NB) is a common solid malignancy in children that is associated with a poor prognosis. Although the novel small molecular compound Dimethylaminomicheliolide (DMAMCL) has been shown to induce cell death in some tumors, little is known about its role in NB. Methods We examined the effect of DMAMCL on four NB cell lines (NPG, AS, KCNR, BE2). Cellular confluence, survival, apoptosis, and glycolysis were detected using Incucyte ZOOM, CCK-8 assays, Annexin V-PE/7-AAD flow cytometry, and Seahorse XFe96, respectively. Synergistic effects between agents were evaluated using CompuSyn and the effect of DMAMCL in vivo was evaluated using a xenograft mouse model. Phosphofructokinase-1, liver type (PFKL) expression was up- and down-regulated using overexpression plasmids or siRNA. Results When administered as a single agent, DMAMCL decreased cell proliferation in a time- and dose-dependent manner, increased the percentage of cells in SubG1 phase, and induced apoptosis in vitro, as well as inhibiting tumor growth and prolonging survival in tumor-bearing mice (NGP, BE2) in vivo. In addition, DMAMCL exerted synergistic effects when combined with etoposide or cisplatin in vitro and displayed increased antitumor effects when combined with etoposide in vivo compared to either agent alone. Mechanistically, DMAMCL suppressed aerobic glycolysis by decreasing glucose consumption, lactate excretion, and ATP production, as well as reducing the expression of PFKL, a key glycolysis enzyme, in vitro and in vivo. Furthermore, PFKL overexpression attenuated DMAMCL-induced cell death, whereas PFKL silencing promoted NB cell death. Conclusions The results of this study suggest that DMAMCL exerts antitumor effects on NB both in vitro and in vivo by suppressing aerobic glycolysis and that PFKL could be a potential target of DMAMCL in NB. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02330-y.
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Affiliation(s)
- Simeng Zhang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environment and Metabolic Diseases, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China
| | - Zhongyan Hua
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environment and Metabolic Diseases, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China
| | - Gen Ba
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environment and Metabolic Diseases, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China
| | - Ning Xu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environment and Metabolic Diseases, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China
| | - Jianing Miao
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environment and Metabolic Diseases, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China
| | - Guifeng Zhao
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environment and Metabolic Diseases, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China
| | - Wei Gong
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environment and Metabolic Diseases, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China
| | - Zhihui Liu
- Cellular & Molecular Biology Section, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Carol J Thiele
- Cellular & Molecular Biology Section, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Zhijie Li
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China. .,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environment and Metabolic Diseases, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China.
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10
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Abstract
Hypoxia inhibits the tricarboxylic acid (TCA) cycle and leaves glycolysis as the primary metabolic pathway responsible for converting glucose into usable energy. However, the mechanisms that compensate for this loss in energy production due to TCA cycle inactivation remain poorly understood. Glycolysis enzymes are typically diffuse and soluble in the cytoplasm under normoxic conditions. In contrast, recent studies have revealed dynamic compartmentalization of glycolysis enzymes in response to hypoxic stress in yeast, C. elegans and mammalian cells. These messenger ribonucleoprotein (mRNP) structures, termed glycolytic (G) bodies in yeast, lack membrane enclosure and display properties of phase-separated biomolecular condensates. Disruption of condensate formation correlates with defects such as impaired synaptic function in C. elegans neurons and decreased glucose flux in yeast. Concentrating glycolysis enzymes into condensates may lead to their functioning as 'metabolons' that enhance rates of glucose utilization for increased energy production. Besides condensates, glycolysis enzymes functionally associate in other organisms and specific tissues through protein-protein interactions and membrane association. However, as discussed in this Review, the functional consequences of coalescing glycolytic machinery are only just beginning to be revealed. Through ongoing studies, we anticipate the physiological importance of metabolic regulation mediated by the compartmentalization of glycolysis enzymes will continue to emerge.
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Affiliation(s)
- Gregory G Fuller
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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11
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Amara N, Cooper MP, Voronkova MA, Webb BA, Lynch EM, Kollman JM, Ma T, Yu K, Lai Z, Sangaraju D, Kayagaki N, Newton K, Bogyo M, Staben ST, Dixit VM. Selective activation of PFKL suppresses the phagocytic oxidative burst. Cell 2021; 184:4480-4494.e15. [PMID: 34320407 PMCID: PMC8802628 DOI: 10.1016/j.cell.2021.07.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/20/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022]
Abstract
In neutrophils, nicotinamide adenine dinucleotide phosphate (NADPH) generated via the pentose phosphate pathway fuels NADPH oxidase NOX2 to produce reactive oxygen species for killing invading pathogens. However, excessive NOX2 activity can exacerbate inflammation, as in acute respiratory distress syndrome (ARDS). Here, we use two unbiased chemical proteomic strategies to show that small-molecule LDC7559, or a more potent designed analog NA-11, inhibits the NOX2-dependent oxidative burst in neutrophils by activating the glycolytic enzyme phosphofructokinase-1 liver type (PFKL) and dampening flux through the pentose phosphate pathway. Accordingly, neutrophils treated with NA-11 had reduced NOX2-dependent outputs, including neutrophil cell death (NETosis) and tissue damage. A high-resolution structure of PFKL confirmed binding of NA-11 to the AMP/ADP allosteric activation site and explained why NA-11 failed to agonize phosphofructokinase-1 platelet type (PFKP) or muscle type (PFKM). Thus, NA-11 represents a tool for selective activation of PFKL, the main phosphofructokinase-1 isoform expressed in immune cells.
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Affiliation(s)
- Neri Amara
- Physiological Chemistry Department, Genentech, South San Francisco, CA 94080, USA
| | - Madison P Cooper
- Biochemistry Department, West Virginia University, Morgantown, WV 26506, USA
| | - Maria A Voronkova
- Biochemistry Department, West Virginia University, Morgantown, WV 26506, USA
| | - Bradley A Webb
- Biochemistry Department, West Virginia University, Morgantown, WV 26506, USA
| | - Eric M Lynch
- Biochemistry Department, University of Washington, Seattle, WA 98195, USA
| | - Justin M Kollman
- Biochemistry Department, University of Washington, Seattle, WA 98195, USA
| | - Taylur Ma
- Microchemistry, Proteomics, and Lipidomics Department, Genentech, South San Francisco, CA 94080, USA
| | - Kebing Yu
- Microchemistry, Proteomics, and Lipidomics Department, Genentech, South San Francisco, CA 94080, USA
| | - Zijuan Lai
- Drug Metabolism and Pharmacokinetics Department, Genentech, South San Francisco, CA 94080, USA
| | - Dewakar Sangaraju
- Drug Metabolism and Pharmacokinetics Department, Genentech, South San Francisco, CA 94080, USA
| | - Nobuhiko Kayagaki
- Physiological Chemistry Department, Genentech, South San Francisco, CA 94080, USA
| | - Kim Newton
- Physiological Chemistry Department, Genentech, South San Francisco, CA 94080, USA
| | - Matthew Bogyo
- Pathology Department, Stanford University, Stanford, CA 94305, USA
| | - Steven T Staben
- Discovery Chemistry Department, Genentech, South San Francisco, CA 94080, USA
| | - Vishva M Dixit
- Physiological Chemistry Department, Genentech, South San Francisco, CA 94080, USA.
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12
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McNae IW, Kinkead J, Malik D, Yen LH, Walker MK, Swain C, Webster SP, Gray N, Fernandes PM, Myburgh E, Blackburn EA, Ritchie R, Austin C, Wear MA, Highton AJ, Keats AJ, Vong A, Dornan J, Mottram JC, Michels PAM, Pettit S, Walkinshaw MD. Fast acting allosteric phosphofructokinase inhibitors block trypanosome glycolysis and cure acute African trypanosomiasis in mice. Nat Commun 2021; 12:1052. [PMID: 33594070 PMCID: PMC7887271 DOI: 10.1038/s41467-021-21273-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
The parasitic protist Trypanosoma brucei is the causative agent of Human African Trypanosomiasis, also known as sleeping sickness. The parasite enters the blood via the bite of the tsetse fly where it is wholly reliant on glycolysis for the production of ATP. Glycolytic enzymes have been regarded as challenging drug targets because of their highly conserved active sites and phosphorylated substrates. We describe the development of novel small molecule allosteric inhibitors of trypanosome phosphofructokinase (PFK) that block the glycolytic pathway resulting in very fast parasite kill times with no inhibition of human PFKs. The compounds cross the blood brain barrier and single day oral dosing cures parasitaemia in a stage 1 animal model of human African trypanosomiasis. This study demonstrates that it is possible to target glycolysis and additionally shows how differences in allosteric mechanisms may allow the development of species-specific inhibitors to tackle a range of proliferative or infectious diseases.
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Affiliation(s)
- Iain W McNae
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - James Kinkead
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Divya Malik
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Li-Hsuan Yen
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Martin K Walker
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | | | - Scott P Webster
- Centre for Cardiovascular Science, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Nick Gray
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Peter M Fernandes
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Elmarie Myburgh
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Elizabeth A Blackburn
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Ryan Ritchie
- Institute of Infection Immunity and Inflammation, College of Medical Veterinary Life-Sciences, University of Glasgow, Glasgow, UK
| | - Carol Austin
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Martin A Wear
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Adrian J Highton
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Andrew J Keats
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Antonio Vong
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Jacqueline Dornan
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Paul A M Michels
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Simon Pettit
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK.
| | - Malcolm D Walkinshaw
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK.
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13
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Fernandes PM, Kinkead J, McNae I, Michels PA, Walkinshaw MD. Biochemical and transcript level differences between the three human phosphofructokinases show optimisation of each isoform for specific metabolic niches. Biochem J 2020; 477:4425-4441. [PMID: 33141153 PMCID: PMC7702303 DOI: 10.1042/bcj20200656] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 01/14/2023]
Abstract
6-Phosphofructokinase-1-kinase (PFK) tetramers catalyse the phosphorylation of fructose 6-phosphate (F6P) to fructose 1,6-bisphosphate (F16BP). Vertebrates have three PFK isoforms (PFK-M, PFK-L, and PFK-P). This study is the first to compare the kinetics, structures, and transcript levels of recombinant human PFK isoforms. Under the conditions tested PFK-M has the highest affinities for F6P and ATP (K0.5ATP 152 µM; K0.5F6P 147 µM), PFK-P the lowest affinities (K0.5ATP 276 µM; K0.5F6P 1333 µM), and PFK-L demonstrates a mixed picture of high ATP affinity and low F6P affinity (K0.5ATP 160 µM; K0.5F6P 1360 µM). PFK-M is more resistant to ATP inhibition compared with PFK-L and PFK-P (respectively, 23%, 31%, 50% decreases in specificity constants). GTP is an alternate phospho donor. Interface 2, which regulates the inactive dimer to active tetramer equilibrium, differs between isoforms, resulting in varying tetrameric stability. Under the conditions tested PFK-M is less sensitive to fructose 2,6-bisphosphate (F26BP) allosteric modulation than PFK-L or PFK-P (allosteric constants [K0.5ATP+F26BP/K0.5ATP] 1.10, 0.92, 0.54, respectively). Structural analysis of two allosteric sites reveals one may be specialised for AMP/ADP and the other for smaller/flexible regulators (citrate or phosphoenolpyruvate). Correlations between PFK-L and PFK-P transcript levels indicate that simultaneous expression may expand metabolic capacity for F16BP production whilst preserving regulatory capabilities. Analysis of cancer samples reveals intriguing parallels between PFK-P and PKM2 (pyruvate kinase M2), and simultaneous increases in PFK-P and PFKFB3 (responsible for F26BP production) transcript levels, suggesting prioritisation of metabolic flexibility in cancers. Our results describe the kinetic and transcript level differences between the three PFK isoforms, explaining how each isoform may be optimised for distinct roles.
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Affiliation(s)
- Peter M. Fernandes
- School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - James Kinkead
- School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - Iain McNae
- School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - Paul A.M. Michels
- School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - Malcolm D. Walkinshaw
- School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, U.K
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14
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Park DI, Novak B, Yan Y, Kaya ME, Turck CW. Paroxetine binding and activation of phosphofructokinase implicates energy metabolism in antidepressant mode of action. J Psychiatr Res 2020; 129:8-14. [PMID: 32540574 DOI: 10.1016/j.jpsychires.2020.05.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/16/2022]
Abstract
Selective serotonin reuptake inhibitors (SSRIs) are the predominant drugs prescribed for Major Depressive Disorder. The immediate pharmacological target of SSRIs is the serotonin transporter. However, the delayed therapeutic effect and high rate of patient non-response make it highly likely that SSRIs also have other molecular targets that are yet to be identified. Cellular thermal shift assay (CETSA) is a method based on thermal stabilization of target proteins upon drug binding. In the present study, we show that the SSRI paroxetine binds to phosphofructokinase (PFK) protein using CETSA. We found that mouse brain PFK and recombinant human PFK proteins are stabilized by paroxetine incubation. Chronic paroxetine treatment also significantly increased mouse brain PFK thermal stability. Paroxetine significantly elevated in vitro and in vivo PFK activity. Levels of several metabolites in glutamate- and energy metabolism-related pathways are significantly correlated with PFK activity in mouse hippocampus. Our data show that paroxetine can bind to PFK and affect its activity. Implications of these results for the antidepressant mode of action of paroxetine are discussed.
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Affiliation(s)
- Dong Ik Park
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany; Danish Research Institute of Translational Neuroscience (DANDRITE), Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Danish National Research Foundation Center, PROMEMO, Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Božidar Novak
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany
| | - Yu Yan
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany
| | - Melahat Ezgi Kaya
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany
| | - Christoph W Turck
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, 80804, Munich, Germany
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15
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Ohno S, Quek LE, Krycer JR, Yugi K, Hirayama A, Ikeda S, Shoji F, Suzuki K, Soga T, James DE, Kuroda S. Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes. iScience 2020; 23:101479. [PMID: 32891058 PMCID: PMC7479629 DOI: 10.1016/j.isci.2020.101479] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/17/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022] Open
Abstract
Insulin regulates glucose metabolism through thousands of regulatory mechanisms; however, which regulatory mechanisms are keys to control glucose metabolism remains unknown. Here, we performed kinetic trans-omic analysis by integrating isotope-tracing glucose flux and phosphoproteomic data from insulin-stimulated adipocytes and built a kinetic mathematical model to identify key allosteric regulatory and phosphorylation events for enzymes. We identified nine reactions regulated by allosteric effectors and one by enzyme phosphorylation and determined the regulatory mechanisms for three of these reactions. Insulin stimulated glycolysis by promoting Glut4 activity by enhancing phosphorylation of AS160 at S595, stimulated fatty acid synthesis by promoting Acly activity through allosteric activation by glucose 6-phosphate or fructose 6-phosphate, and stimulated glutamate synthesis by alleviating allosteric inhibition of Gls by glutamate. Most of glycolytic reactions were regulated by amounts of substrates and products. Thus, phosphorylation or allosteric modulator-based regulation of only a few key enzymes was sufficient to change insulin-induced metabolism.
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Affiliation(s)
- Satoshi Ohno
- Molecular Genetics Research Laboratory, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Lake-Ee Quek
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - James R. Krycer
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- PRESTO, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
- AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda-Ku, Tokyo 100-0004, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Futaba Shoji
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Kumi Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
- AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda-Ku, Tokyo 100-0004, Japan
| | - David E. James
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Shinya Kuroda
- Molecular Genetics Research Laboratory, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Bunkyo-ku, Tokyo 113-0033, Japan
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16
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Ren C, Deng K, Wang Z, Deng M, Fan Y, Zhang Y, Ma J, Wang S, Liu Z, Wang F. Reinterpreting sheep muscle strand-specific RNA sequencing data showing extensive 3'UTR extensions. Anim Genet 2020; 51:788-798. [PMID: 32696483 DOI: 10.1111/age.12987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 05/16/2020] [Accepted: 06/23/2020] [Indexed: 12/01/2022]
Abstract
The more complex 3' UTR in higher organisms may have the function of increasing post-transcriptional gene regulation. Recent RNA sequencing technologies have provided us with the possibility to capture the complete 3' UTR landscape of different species and cells. However, no systematic analysis of sheep-related 3' UTR has been performed. Here, we conducted a detailed analysis of the 3' UTR with the primary goal of identifying intact 3' UTR landscapes in the sheep muscles of the three developmental stages. Based on strand-specific RNA sequencing (ssRNA-seq) data, we found that thousands of genes in sheep muscle are continuously transcribed after the UTR of the reference genome (Oar_v4.0). More than 66% of the 3' UTR extensions exhibit similar expression trends to their upstream gene exons. These 3' UTR extensions strongly enrich thousands of conserved microRNA binding sites. The 3' UTR extension-associated RNA of PFKM (PuaRNA) was predicted to be derived from the 3' UTR of PFKM. In sheep myocytes, myotubes and various tissues, the expression pattern of PuaRNA is positively correlated with that of PFKM. Taken together, these new 3' UTR annotations greatly extend the range of mammalian post-transcriptional regulatory networks, which have a particular impact on the regulation of sheep muscle development.
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Affiliation(s)
- Caifang Ren
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China.,School of Medicine, Jiangsu University, Zhengjiang, Jiangsu, 212013, China
| | - Kaiping Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Zhibo Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Mingtian Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Yixuan Fan
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Yanli Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Jianyu Ma
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Shuting Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Zifei Liu
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Weigang Street, Xuanwu District, Nanjing, Jiangsu, 210095, China
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17
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Yang Y, Wang P, Jin B, Dong Z, Chen G, Liu D. Screening of Potential Key Transcripts Involved in Planarian Regeneration and Analysis of Its Regeneration Patterns by PacBio Long-Read Sequencing. Front Genet 2020; 11:580. [PMID: 32612637 PMCID: PMC7308552 DOI: 10.3389/fgene.2020.00580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/11/2020] [Indexed: 12/30/2022] Open
Abstract
Dugesia japonica is an excellent animal model for studying the regeneration mechanism due to its characteristics of rapid regeneration and easy breeding. PacBio sequencing was performed on the intact planarians (In) and regenerating planarians of 1 day (1d), 3 days (3d), and 5 days (5d) after amputation. The aim of this study is to deeply profile the transcriptome of D. japonica and to evaluate its regenerate changes. Using robust statistical analysis, we identified 5931, 5115, and 4669 transcripts differentially expressed between 1d and In, 3d and In, 5d and In, respectively. A total of 63 key transcripts were screened from these DETs. These key transcripts enhance the expression in different regenerate stages respectively to regulate specific processes including signal transduction, mitosis, protein synthesis, transport and degradation, apoptosis, neural development, and energy cycling. Finally, according to the biological processes involved in these potential key transcripts, we propose a hypothesis of head regeneration model about D. japonica. In addition, the weighted gene co-expression network analysis provides a new way to screen key transcripts from large amounts of data. Together, these analyses identify a number of potential key regulators controlling proliferation, differentiation, apoptosis, and signal transduction. What's more, this study provides a powerful data foundation for further research on planarians regeneration.
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Affiliation(s)
- Yibo Yang
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Peizheng Wang
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Baijie Jin
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Zimei Dong
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Guangwen Chen
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Dezeng Liu
- College of Life Science, Henan Normal University, Xinxiang, China
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18
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Fernandes PM, Kinkead J, McNae IW, Vásquez-Valdivieso M, Wear MA, Michels PAM, Walkinshaw MD. Kinetic and structural studies of Trypanosoma and Leishmania phosphofructokinases show evolutionary divergence and identify AMP as a switch regulating glycolysis versus gluconeogenesis. FEBS J 2020; 287:2847-2861. [PMID: 31838765 PMCID: PMC7383607 DOI: 10.1111/febs.15177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/13/2019] [Accepted: 12/12/2019] [Indexed: 11/30/2022]
Abstract
Trypanosomatids possess glycosome organelles that contain much of the glycolytic machinery, including phosphofructokinase (PFK). We present kinetic and structural data for PFK from three human pathogenic trypanosomatids, illustrating intriguing differences that may reflect evolutionary adaptations to differing ecological niches. The activity of Leishmania PFK – to a much larger extent than Trypanosoma PFK – is reliant on AMP for activity regulation, with 1 mm AMP increasing the L. infantum PFK (LiPFK) kcat/K0.5F6P value by 10‐fold, compared to only a 1.3‐ and 1.4‐fold increase for T. cruzi and T. brucei PFK, respectively. We also show that Leishmania PFK melts at a significantly lower (> 15 °C) temperature than Trypanosoma PFKs and that addition of either AMP or ATP results in a marked stabilization of the protein. Sequence comparisons of Trypanosoma spp. and Leishmania spp. show that divergence of the two genera involved amino acid substitutions that occur in the enzyme’s ‘reaching arms’ and ‘embracing arms’ that determine tetramer stability. The dramatic effects of AMP on Leishmania activity compared with the Trypanosoma PFKs may be explained by differences between the T‐to‐R equilibria for the two families, with the low‐melting Leishmania PFK favouring the flexible inactive T‐state in the absence of AMP. Sequence comparisons along with the enzymatic and structural data presented here also suggest there was a loss of AMP‐dependent regulation in Trypanosoma species rather than gain of this characteristic in Leishmania species and that AMP acts as a key regulator in Leishmania governing the balance between glycolysis and gluconeogenesis.
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Affiliation(s)
- Peter M Fernandes
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - James Kinkead
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Iain W McNae
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Monserrat Vásquez-Valdivieso
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Martin A Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Paul A M Michels
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
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19
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Park CK, Horton NC. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation. Biophys Rev 2019; 11:927-994. [PMID: 31734826 PMCID: PMC6874960 DOI: 10.1007/s12551-019-00602-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI endonuclease system are also highlighted.
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Affiliation(s)
- Chad K. Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
| | - Nancy C. Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
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20
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Ma Y, Yu H, Liu W, Qin Y, Xing R, Li P. Integrated proteomics and metabolomics analysis reveals the antifungal mechanism of the C-coordinated O-carboxymethyl chitosan Cu(II) complex. Int J Biol Macromol 2019; 155:1491-1509. [PMID: 31751736 DOI: 10.1016/j.ijbiomac.2019.11.127] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/06/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022]
Abstract
With wide application in agriculture, copper fungicides have undergone three stages of development: inorganic copper, synthetic organic copper, and natural organic copper. Using chitin/chitosan (CS) as a substrate, the natural organic copper fungicide C-coordinated O-carboxymethyl chitosan Cu(II) complex (O-CSLn-Cu) was developed in the laboratory. Taking Phytophthora capsici Leonian as an example, we explored the antifungal mechanism of O-CSLn-Cu by combining tandem mass tag (TMT)-based proteomics with non-targeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics. A total of 1172 differentially expressed proteins were identified by proteomics analysis. According to the metabolomics analysis, 93 differentially metabolites were identified. Acetyl-CoA-related and membrane localized proteins showed significant differences in the proteomics analysis. Most of the differential expressed metabolites were distributed in the cytoplasm, followed by mitochondria. The integrated analysis revealed that O-CSLn-Cu could induce the "Warburg effect", with increased glycolysis in the cytoplasm and decreased metabolism in the mitochondria. Therefore, P. capsici Leonian had to compensate for ATP loss in the TCA cycle by increasing the glycolysis rate. However, this metabolic shift could not prevent the death of P. capsici Leonian. To verify this hypothesis, a series of biological experiments, such as scanning electron microscopy (SEM), transmission electron microscopy (TEM), and enzyme activity measurements were carried out. The results suggest that O-CSLn-Cu causes mitochondrial injury, which consequently leads to excessive ROS levels and insufficient ATP levels, thereby killing P. capsici Leonian.
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Affiliation(s)
- Yuzhen Ma
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huahua Yu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China.
| | - Weixiang Liu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Yukun Qin
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Ronge Xing
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Pengcheng Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China.
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21
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Singh J, Suh EH, Sharma G, Khemtong C, Sherry AD, Kovacs Z. Probing carbohydrate metabolism using hyperpolarized 13 C-labeled molecules. NMR IN BIOMEDICINE 2019; 32:e4018. [PMID: 30474153 PMCID: PMC6579721 DOI: 10.1002/nbm.4018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 08/03/2018] [Accepted: 08/11/2018] [Indexed: 05/05/2023]
Abstract
Glycolysis is a fundamental metabolic process in all organisms. Anomalies in glucose metabolism are linked to various pathological conditions. In particular, elevated aerobic glycolysis is a characteristic feature of rapidly growing cells. Glycolysis and the closely related pentose phosphate pathway can be monitored in real time by hyperpolarized 13 C-labeled metabolic substrates such as 13 C-enriched, deuterated D-glucose derivatives, [2-13 C]-D-fructose, [2-13 C] dihydroxyacetone, [1-13 C]-D-glycerate, [1-13 C]-D-glucono-δ-lactone and [1-13 C] pyruvate in healthy and diseased tissues. Elevated glycolysis in tumors (the Warburg effect) was also successfully imaged using hyperpolarized [U-13 C6 , U-2 H7 ]-D-glucose, while the size of the preexisting lactate pool can be measured by 13 C MRS and/or MRI with hyperpolarized [1-13 C]pyruvate. This review summarizes the application of various hyperpolarized 13 C-labeled metabolites to the real-time monitoring of glycolysis and related metabolic processes in normal and diseased tissues.
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Affiliation(s)
- Jaspal Singh
- Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eul Hyun Suh
- Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gaurav Sharma
- Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chalermchai Khemtong
- Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - A. Dean Sherry
- Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Zoltan Kovacs
- Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
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22
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Hu M, Zhang Y, Egecioglu E, Li X, Shao LR, Billig H. Uterine glycolytic enzyme expression is affected by knockout of different estrogen receptor subtypes. Biomed Rep 2019; 11:135-144. [PMID: 31565219 PMCID: PMC6759582 DOI: 10.3892/br.2019.1234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022] Open
Abstract
The estrogen signaling pathway via nuclear estrogen receptors (ER) α and β is considered to be the master regulator of the cellular glucose metabolism in the uterus. While in vivo animal studies have demonstrated that 17β-estradiol (E2) treatment increases the expression levels and activities of several glycolytic enzymes in the uterus, the specific ER subtype-dependent regulation of key glycolytic enzymes in the uterus has not been experimentally verified. In this study, the localization of ERα and ERβ in human and mouse endometria were evaluated using immunohistology. Given that ERα and ERβ are not functionally equivalent, ERα, ERβ and ERαβ knockout (ERα-/-, ERβ-/- and ERαβ-/-) mice were utilized to determine the expression pattern of glycolytic enzymes in the uterus. It was found that the level of ERα was higher than that of ERβ in the human and mouse endometrial epithelial and stromal cells, and both receptors were downregulated by E2 treatment in the mouse uterus. The expression of the hexokinase 1 and GAPDH was increased in ERα-/- and ERβ-/- mice compared with wild-type controls. Increased phosphofructokinase expression was observed in ERα-/- and ERαβ-/- mice, whereas increased pyruvate kinase isozyme M2 and pyruvate dehydrogenase expression was observed in ERβ-/- and ERαβ-/- mice. The findings indicated for the first time that while estrogen regulates ERα and ERβ expression in the uterus, ERα and ERβ selectively regulate uterine glycolytic enzyme expression during glycolysis. Additionally, the link between endometrial ER subtypes and glycolysis in women with polycystic ovary syndrome (PCOS) is discussed. The findings suggested that the E2-dependent ER-mediated regulation of glycolysis may be involved in the disturbance of the glucose metabolism in patients with PCOS with endometrial dysfunction.
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Affiliation(s)
- Min Hu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, P.R. China.,Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Yuehui Zhang
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden.,Department of Obstetrics and Gynecology, Key Laboratory and Unit of Infertility in Chinese Medicine, First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, P.R. China
| | - Emil Egecioglu
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Xin Li
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden.,Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, P.R. China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Fudan University, Shanghai 200011, P.R. China
| | - Linus R Shao
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Håkan Billig
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
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23
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Cortassa S, Aon MA, Sollott SJ. Control and Regulation of Substrate Selection in Cytoplasmic and Mitochondrial Catabolic Networks. A Systems Biology Analysis. Front Physiol 2019; 10:201. [PMID: 30906265 PMCID: PMC6418011 DOI: 10.3389/fphys.2019.00201] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/15/2019] [Indexed: 12/21/2022] Open
Abstract
Appropriate substrate selection between fats and glucose is associated with the success of interventions that maintain health such as exercise or caloric restriction, or with the severity of diseases such as diabetes or other metabolic disorders. Although the interaction and mutual inhibition between glucose and fatty-acids (FAs) catabolism has been studied for decades, a quantitative and integrated understanding of the control and regulation of substrate selection through central catabolic pathways is lacking. We addressed this gap here using a computational model representing cardiomyocyte catabolism encompassing glucose (Glc) utilization, pyruvate transport into mitochondria and oxidation in the tricarboxylic acid (TCA) cycle, β-oxidation of palmitate (Palm), oxidative phosphorylation, ion transport, pH regulation, and ROS generation and scavenging in cytoplasmic and mitochondrial compartments. The model is described by 82 differential equations and 119 enzymatic, electron transport and substrate transport reactions accounting for regulatory mechanisms and key players, namely pyruvate dehydrogenase (PDH) and its modulation by multiple effectors. We applied metabolic control analysis to the network operating with various Glc to Palm ratios. The flux and metabolites’ concentration control were visualized through heat maps providing major insights into main control and regulatory nodes throughout the catabolic network. Metabolic pathways located in different compartments were found to reciprocally control each other. For example, glucose uptake and the ATP demand exert control on most processes in catabolism while TCA cycle activities and membrane-associated energy transduction reactions exerted control on mitochondrial processes namely β-oxidation. PFK and PDH, two highly regulated enzymes, exhibit opposite behavior from a control perspective. While PFK activity was a main rate-controlling step affecting the whole network, PDH played the role of a major regulator showing high sensitivity (elasticity) to substrate availability and key activators/inhibitors, a trait expected from a flexible substrate selector strategically located in the metabolic network. PDH regulated the rate of Glc and Palm consumption, consistent with its high sensitivity toward AcCoA, CoA, and NADH. Overall, these results indicate that the control of catabolism is highly distributed across the metabolic network suggesting that fuel selection between FAs and Glc goes well beyond the mechanisms traditionally postulated to explain the glucose-fatty-acid cycle.
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Affiliation(s)
- Sonia Cortassa
- Laboratory of Cardiovascular Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Miguel A Aon
- Laboratory of Cardiovascular Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Steven J Sollott
- Laboratory of Cardiovascular Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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24
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The kinetic characteristics of human and trypanosomatid phosphofructokinases for the reverse reaction. Biochem J 2019; 476:179-191. [PMID: 30404924 PMCID: PMC6340114 DOI: 10.1042/bcj20180635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023]
Abstract
Eukaryotic ATP-dependent phosphofructokinases (PFKs) are often considered unidirectional enzymes catalysing the transfer of a phospho moiety from ATP to fructose 6-phosphate to produce ADP and fructose 1,6-bisphosphate. The reverse reaction is not generally considered to occur under normal conditions and has never been demonstrated for any eukaryotic ATP-dependent PFKs, though it does occur in inorganic pyrophosphate-dependent PFKs and has been experimentally shown for bacterial ATP-dependent PFKs. The evidence is provided via two orthogonal assays that all three human PFK isoforms can catalyse the reverse reaction in vitro, allowing determination of kinetic properties. Additionally, the reverse reaction was shown possible for PFKs from three clinically important trypanosomatids; these enzymes are contained within glycosomes in vivo. This compartmentalisation may facilitate reversal, given the potential for trypanosomatids to have an altered ATP/ADP ratio in glycosomes compared with the cytosol. The kinetic properties of each trypanosomatid PFK were determined, including the response to natural and artificial modulators of enzyme activity. The possible physiological relevance of the reverse reaction in trypanosomatid and human PFKs is discussed.
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25
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Abstract
Carbohydrate kinases activate a wide variety of monosaccharides by adding a phosphate group, usually from ATP. This modification is fundamental to saccharide utilization, and it is likely a very ancient reaction. Modern organisms contain carbohydrate kinases from at least five main protein families. These range from the highly specialized inositol kinases, to the ribokinases and galactokinases, which belong to families that phosphorylate a wide range of substrates. The carbohydrate kinases utilize a common strategy to drive the reaction between the sugar hydroxyl and the donor phosphate. Each sugar is held in position by a network of hydrogen bonds to the non-reactive hydroxyls (and other functional groups). The reactive hydroxyl is deprotonated, usually by an aspartic acid side chain acting as a catalytic base. The deprotonated hydroxyl then attacks the donor phosphate. The resulting pentacoordinate transition state is stabilized by an adjacent divalent cation, and sometimes by a positively charged protein side chain or the presence of an anion hole. Many carbohydrate kinases are allosterically regulated using a wide variety of strategies, due to their roles at critical control points in carbohydrate metabolism. The evolution of a similar mechanism in several folds highlights the elegance and simplicity of the catalytic scheme.
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26
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Synthesis of amide and sulfonamide substituted N-aryl 6-aminoquinoxalines as PFKFB3 inhibitors with improved physicochemical properties. Bioorg Med Chem Lett 2018; 29:646-653. [PMID: 30626557 DOI: 10.1016/j.bmcl.2018.12.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
In oncology, the "Warburg effect" describes the elevated production of energy by glycolysis in cancer cells. The ubiquitous and hypoxia-induced 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) plays a noteworthy role in the regulation of glycolysis by producing fructose-2,6-biphosphate (F-2,6-BP), a potent activator of the glycolysis rate-limiting phosphofructokinase PFK-1. Series of amides and sulfonamides derivatives based on a N-aryl 6-aminoquinoxaline scaffold were synthesized and tested for their inhibition of PFKFB3 in vitro in a biochemical assay as well as in HCT116 cells. The carboxamide series displayed satisfactory kinetic solubility and metabolic stability, and within this class, potent lead compounds with low nanomolar activity have been identified with a suitable profile for further in vivo evaluation.
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27
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Li L, Li L, Li W, Chen T, Bin Zou, Zhao L, Wang H, Wang X, Xu L, Liu X, Wang D, Li B, Mak TW, Du W, Yang X, Jiang P. TAp73-induced phosphofructokinase-1 transcription promotes the Warburg effect and enhances cell proliferation. Nat Commun 2018; 9:4683. [PMID: 30409970 PMCID: PMC6224601 DOI: 10.1038/s41467-018-07127-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/16/2018] [Indexed: 01/09/2023] Open
Abstract
The Warburg effect is a prominent metabolic feature associated with neoplastic diseases; however, the underlying mechanism remains incompletely understood. TAp73, a structural homolog of the tumor suppressor p53, is frequently overexpressed in human tumors, indicating a proliferative advantage that it can confer to tumor cells. Here we show that TAp73 stimulates the expression of phosphofructokinase-1, liver type (PFKL), which catalyzes the committed step in glycolysis. Through this regulation, TAp73 enhances glucose consumption and lactate excretion, promoting the Warburg effect. By activating PFKL, TAp73 also increases ATP production and bolsters anti-oxidant defense. TAp73 deficiency results in a pronounced reduction in tumorigenic potential, which can be rescued by forced PFKL expression. These findings establish TAp73 as a critical regulator of glycolysis and reveal a mechanism by which tumor cells achieve the Warburg effect to enable oncogenic growth. TAp73 is a structural homolog of the tumor suppressor p53. Here they show that TAp73 is critical for promoting glycolysis as it stimulates the transcriptional expression of liver type of phosphofructokinase-1 (PFKL), which catalyzes the committed step in glycolysis.
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Affiliation(s)
- Le Li
- School of Life Sciences, Tsinghua University; Collaborative Innovation Center for Cancer Medicine, 100084, Beijing, China
| | - Lijia Li
- School of Life Sciences, Tsinghua University; Collaborative Innovation Center for Cancer Medicine, 100084, Beijing, China
| | - Wei Li
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 100005, Beijing, China
| | - Taiqi Chen
- School of Life Sciences, Tsinghua University; Collaborative Innovation Center for Cancer Medicine, 100084, Beijing, China
| | - Bin Zou
- School of Life Sciences, Tsinghua University; Collaborative Innovation Center for Cancer Medicine, 100084, Beijing, China
| | - Lina Zhao
- School of Life Sciences, Tsinghua University; Collaborative Innovation Center for Cancer Medicine, 100084, Beijing, China
| | - Huili Wang
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Xueying Wang
- School of Life Sciences, Tsinghua University; Collaborative Innovation Center for Cancer Medicine, 100084, Beijing, China
| | - Lina Xu
- School of Life Sciences, Tsinghua University; Collaborative Innovation Center for Cancer Medicine, 100084, Beijing, China
| | - Xiaohui Liu
- School of Life Sciences, Tsinghua University; Collaborative Innovation Center for Cancer Medicine, 100084, Beijing, China
| | - Dong Wang
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Bo Li
- Zhongshan School of Medicine, Sun Yat-sen University, 510630, Guangzhou, Guangdong, China
| | - Tak W Mak
- The Campbell Family Institute for Breast Cancer Research, Princess Margaret Hospital, Toronto, ON, M5G 2C1, Canada
| | - Wenjing Du
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 100005, Beijing, China.
| | - Xiaolu Yang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Peng Jiang
- School of Life Sciences, Tsinghua University; Collaborative Innovation Center for Cancer Medicine, 100084, Beijing, China.
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28
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Yurkovich JT, Alcantar MA, Haiman ZB, Palsson BO. Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. PLoS Comput Biol 2018; 14:e1006356. [PMID: 30086174 PMCID: PMC6097697 DOI: 10.1371/journal.pcbi.1006356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 08/17/2018] [Accepted: 07/09/2018] [Indexed: 01/08/2023] Open
Abstract
Allosteric regulation has traditionally been described by mathematically-complex allosteric rate laws in the form of ratios of polynomials derived from the application of simplifying kinetic assumptions. Alternatively, an approach that explicitly describes all known ligand-binding events requires no simplifying assumptions while allowing for the computation of enzymatic states. Here, we employ such a modeling approach to examine the "catalytic potential" of an enzyme-an enzyme's capacity to catalyze a biochemical reaction. The catalytic potential is the fundamental result of multiple ligand-binding events that represents a "tug of war" among the various regulators and substrates within the network. This formalism allows for the assessment of interacting allosteric enzymes and development of a network-level understanding of regulation. We first define the catalytic potential and use it to characterize the response of three key kinases (hexokinase, phosphofructokinase, and pyruvate kinase) in human red blood cell glycolysis to perturbations in ATP utilization. Next, we examine the sensitivity of the catalytic potential by using existing personalized models, finding that the catalytic potential allows for the identification of subtle but important differences in how individuals respond to such perturbations. Finally, we explore how the catalytic potential can help to elucidate how enzymes work in tandem to maintain a homeostatic state. Taken together, this work provides an interpretation and visualization of the dynamic interactions and network-level effects of interacting allosteric enzymes.
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Affiliation(s)
- James T. Yurkovich
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Miguel A. Alcantar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Zachary B. Haiman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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29
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Buchsteiner M, Quek LE, Gray P, Nielsen LK. Improving culture performance and antibody production in CHO cell culture processes by reducing the Warburg effect. Biotechnol Bioeng 2018; 115:2315-2327. [PMID: 29704441 DOI: 10.1002/bit.26724] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/08/2018] [Accepted: 04/25/2018] [Indexed: 12/14/2022]
Abstract
Lactate is one of the key waste metabolites of mammalian cell culture. High lactate levels are caused by high aerobic glycolysis, also known as the Warburg effect, and are usually associated with adverse culture performance. Therefore, reducing lactate accumulation has been an ongoing challenge in the cell culture development to improve growth, productivity, and process robustness. The pyruvate dehydrogenase complex (PDC) plays a crucial role for the fate of pyruvate, as it converts pyruvate to acetyl coenzyme A (acetyl-CoA). The PDC activity can be indirectly increased by inhibiting the PDC inhibitor, pyruvate dehydrogenase kinase, using dichloroacetate (DCA), resulting in less pyruvate being available for lactate formation. Here, Chinese hamster ovary cells were cultivated either with 5 mM DCA or without DCA in various batch and fed-batch bioreactor processes. In all cultures, DCA increased peak viable cell density (VCD), culture length and final antibody titer. The strongest effect was observed in a fed batch with media and glucose feeding in which peak VCD was increased by more than 50%, culture length was extended by more than 3 days, and the final antibody titer increased by more than twofold. In cultures with DCA, lactate production and glucose consumption during exponential growth were on average reduced by approximately 40% and 35%, respectively. Metabolic flux analysis showed reduced glycolytic fluxes, whereas fluxes in the tricarboxylic acid (TCA) cycle were not affected, suggesting that cultures with DCA use glucose more efficiently. In a proteomics analysis, only few proteins were identified as being differentially expressed, indicating that DCA acts on a posttranslational level. Antibody quality in terms of aggregation, charge variant, and glycosylation pattern was unaffected. Subsequent bioreactor experiments with sodium lactate and sodium chloride feeding indicated that lower osmolality, rather than lower lactate concentration itself, improved culture performance in DCA cultures. In conclusion, the addition of DCA to the cell culture improved culture performance and increased antibody titers without any disadvantages for cell-specific productivity or antibody quality.
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Affiliation(s)
- Maria Buchsteiner
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Lake-Ee Quek
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter Gray
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.,Novo Nordisk Foundation Center for Biosustainability, The Technical University of Denmark, Kongens Lyngby, Denmark
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30
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Natarajan G, Perriotte-Olson C, Bhinderwala F, Powers R, Desouza CV, Talmon GA, Yuhang J, Zimmerman MC, Kabanov AV, Saraswathi V. Nanoformulated copper/zinc superoxide dismutase exerts differential effects on glucose vs lipid homeostasis depending on the diet composition possibly via altered AMPK signaling. Transl Res 2017; 188:10-26. [PMID: 28867395 PMCID: PMC5819896 DOI: 10.1016/j.trsl.2017.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022]
Abstract
Evidence suggests that superoxide dismutase 1 (SOD1) promotes glucose vs lipid metabolism depending on the diet type. We recently reported that nanoformulated SOD1 (Nano) improved lipid metabolism without altering glucose homeostasis in high-fat (HF) diet-fed mice. Here, we sought to determine the effects and potential mechanisms of Nano in modulating glucose and lipid homeostasis in mice fed a normal chow diet (CD) vs HF diet. Mice were fed a CD or a HF diet (45%) for 10 wk and injected with Nano once every 2 days for 15 days. The fasting glucose level was lower (P < 0.05) in CD + Nano-treated mice compared to control. Conversely, blood glucose was not altered but serum triglycerides were lower in HF + Nano-treated mice. Genes involved in fatty acid synthesis were reduced by Nano in the skeletal muscle of CD but not of HF diet-fed mice. Adenosine monophosphate-activated protein kinase (AMPK), which promotes both glucose and lipid metabolism depending on the fuel availability, is activated by Nano in CD-fed mice. Moreover, Nano increased phosphorylation of ACC, a downstream target of AMPK, in both CD and HF diet-fed mice. Nano increased mitochondrial respiration in C2C12 myocytes in the presence of glucose or fatty acid, and this effect is inhibited by Compound C, an AMPK inhibitor. Our data suggest that Nano promotes glucose and lipid metabolism in CD and HF diet-fed mice, respectively, and this effect is mediated partly via AMPK signaling.
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Affiliation(s)
- Gopalakrishnan Natarajan
- Department of Internal Medicine/Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, Neb
| | - Curtis Perriotte-Olson
- Department of Internal Medicine/Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, Neb
| | - Fatema Bhinderwala
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Neb; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Neb
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Neb; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Neb
| | - Cyrus V Desouza
- VA Nebraska-Western Iowa Health Care System, Omaha, Neb; Department of Internal Medicine/Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, Neb
| | - Geoffrey A Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Neb
| | - Jiang Yuhang
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew C Zimmerman
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Neb
| | - Alexander V Kabanov
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Viswanathan Saraswathi
- Department of Internal Medicine/Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, Neb; VA Nebraska-Western Iowa Health Care System, Omaha, Neb.
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Hacker SM, Backus KM, Lazear MR, Forli S, Correia BE, Cravatt BF. Global profiling of lysine reactivity and ligandability in the human proteome. Nat Chem 2017; 9:1181-1190. [PMID: 29168484 DOI: 10.1038/nchem.2826] [Citation(s) in RCA: 283] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/07/2017] [Indexed: 12/28/2022]
Abstract
Nucleophilic amino acids make important contributions to protein function, including performing key roles in catalysis and serving as sites for post-translational modification. Electrophilic groups that target amino-acid nucleophiles have been used to create covalent ligands and drugs, but have, so far, been mainly limited to cysteine and serine. Here, we report a chemical proteomic platform for the global and quantitative analysis of lysine residues in native biological systems. We have quantified, in total, more than 9,000 lysines in human cell proteomes and have identified several hundred residues with heightened reactivity that are enriched at protein functional sites and can frequently be targeted by electrophilic small molecules. We have also discovered lysine-reactive fragment electrophiles that inhibit enzymes by active site and allosteric mechanisms, as well as disrupt protein-protein interactions in transcriptional regulatory complexes, emphasizing the broad potential and diverse functional consequences of liganding lysine residues throughout the human proteome.
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Affiliation(s)
- Stephan M Hacker
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92307, USA
| | - Keriann M Backus
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92307, USA
| | - Michael R Lazear
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92307, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92307, USA
| | - Bruno E Correia
- Laboratory of Protein Design & Immunoengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Benjamin F Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92307, USA
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32
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Wang H, Nicolay BN, Chick JM, Gao X, Geng Y, Ren H, Gao H, Yang G, Williams JA, Suski JM, Keibler MA, Sicinska E, Gerdemann U, Haining WN, Roberts TM, Polyak K, Gygi SP, Dyson NJ, Sicinski P. The metabolic function of cyclin D3-CDK6 kinase in cancer cell survival. Nature 2017; 546:426-430. [PMID: 28607489 DOI: 10.1038/nature22797] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/28/2017] [Indexed: 01/08/2023]
Abstract
D-type cyclins (D1, D2 and D3) and their associated cyclin-dependent kinases (CDK4 and CDK6) are components of the core cell cycle machinery that drives cell proliferation. Inhibitors of CDK4 and CDK6 are currently being tested in clinical trials for patients with several cancer types, with promising results. Here, using human cancer cells and patient-derived xenografts in mice, we show that the cyclin D3-CDK6 kinase phosphorylates and inhibits the catalytic activity of two key enzymes in the glycolytic pathway, 6-phosphofructokinase and pyruvate kinase M2. This re-directs the glycolytic intermediates into the pentose phosphate (PPP) and serine pathways. Inhibition of cyclin D3-CDK6 in tumour cells reduces flow through the PPP and serine pathways, thereby depleting the antioxidants NADPH and glutathione. This, in turn, increases the levels of reactive oxygen species and causes apoptosis of tumour cells. The pro-survival function of cyclin D-associated kinase operates in tumours expressing high levels of cyclin D3-CDK6 complexes. We propose that measuring the levels of cyclin D3-CDK6 in human cancers might help to identify tumour subsets that undergo cell death and tumour regression upon inhibition of CDK4 and CDK6. Cyclin D3-CDK6, through its ability to link cell cycle and cell metabolism, represents a particularly powerful oncoprotein that affects cancer cells at several levels, and this property can be exploited for anti-cancer therapy.
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Affiliation(s)
- Haizhen Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Brandon N Nicolay
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts 02129, USA
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xueliang Gao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hong Ren
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hui Gao
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Guizhi Yang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Juliet A Williams
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Jan M Suski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mark A Keibler
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Ulrike Gerdemann
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Division of Pediatric Hematology and Oncology, Children's Hospital, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Thomas M Roberts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts 02129, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Rossetti M, Ranallo S, Idili A, Palleschi G, Porchetta A, Ricci F. Allosteric DNA nanoswitches for controlled release of a molecular cargo triggered by biological inputs. Chem Sci 2016; 8:914-920. [PMID: 28572901 PMCID: PMC5452262 DOI: 10.1039/c6sc03404g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/03/2016] [Indexed: 12/14/2022] Open
Abstract
A rationally designed new class of DNA-based nanoswitches allosterically regulated by specific biological targets, antibodies and transcription factors, can load and release a molecular cargo in a controlled fashion.
Here we demonstrate the rational design of a new class of DNA-based nanoswitches which are allosterically regulated by specific biological targets, antibodies and transcription factors, and are able to load and release a molecular cargo (i.e. doxorubicin) in a controlled fashion. In our first model system we rationally designed a stem-loop DNA-nanoswitch that adopts two mutually exclusive conformations: a “Load” conformation containing a doxorubicin-intercalating domain and a “Release” conformation containing a duplex portion recognized by a specific transcription-factor (here Tata Binding Protein). The binding of the transcription factor pushes this conformational equilibrium towards the “Release” state thus leading to doxorubicin release from the nanoswitch. In our second model system we designed a similar stem-loop DNA-nanoswitch for which conformational change and subsequent doxorubicin release can be triggered by a specific antibody. Our approach augments the current tool kit of smart drug release mechanisms regulated by different biological inputs.
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Affiliation(s)
- Marianna Rossetti
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Simona Ranallo
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Andrea Idili
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Giuseppe Palleschi
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Alessandro Porchetta
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Francesco Ricci
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
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34
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A conserved phosphatase destroys toxic glycolytic side products in mammals and yeast. Nat Chem Biol 2016; 12:601-7. [PMID: 27294321 DOI: 10.1038/nchembio.2104] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 03/28/2016] [Indexed: 11/08/2022]
Abstract
Metabolic enzymes are very specific. However, most of them show weak side activities toward compounds that are structurally related to their physiological substrates, thereby producing side products that may be toxic. In some cases, 'metabolite repair enzymes' eliminating side products have been identified. We show that mammalian glyceraldehyde 3-phosphate dehydrogenase and pyruvate kinase, two core glycolytic enzymes, produce 4-phosphoerythronate and 2-phospho-L-lactate, respectively. 4-Phosphoerythronate strongly inhibits an enzyme of the pentose phosphate pathway, whereas 2-phospho-L-lactate inhibits the enzyme producing the glycolytic activator fructose 2,6-bisphosphate. We discovered that a single, widely conserved enzyme, known as phosphoglycolate phosphatase (PGP) in mammals, dephosphorylates both 4-phosphoerythronate and 2-phospho-L-lactate, thereby preventing a block in the pentose phosphate pathway and glycolysis. Its yeast ortholog, Pho13, similarly dephosphorylates 4-phosphoerythronate and 2-phosphoglycolate, a side product of pyruvate kinase. Our work illustrates how metabolite repair enzymes can make up for the limited specificity of metabolic enzymes and permit high flux in central metabolic pathways.
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Abstract
Phosphofructokinase-1 (Pfk) acts as the main control point of flux through glycolysis. It is involved in complex allosteric regulation and Pfk mutations have been linked to cancer development. Whereas the 3D structure and structural basis of allosteric regulation of prokaryotic Pfk has been studied in great detail, our knowledge about the molecular basis of the allosteric behaviour of the more complex mammalian Pfk is still very limited. To characterize the structural basis of allosteric regulation, the subunit interfaces and the functional consequences of modifications in Tarui's disease and cancer, we analysed the physiological homotetramer of human platelet Pfk at up to 2.67 Å resolution in two crystal forms. The crystallized enzyme is permanently activated by a deletion of the 22 C-terminal residues. Complex structures with ADP and fructose-6-phosphate (F6P) and with ATP suggest a role of three aspartates in the deprotonation of the OH-nucleophile of F6P and in the co-ordination of the catalytic magnesium ion. Changes at the dimer interface, including an asymmetry observed in both crystal forms, are the primary mechanism of allosteric regulation of Pfk by influencing the F6P-binding site. Whereas the nature of this conformational switch appears to be largely conserved in bacterial, yeast and mammalian Pfk, initiation of these changes differs significantly in eukaryotic Pfk.
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36
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Webb BA, Forouhar F, Szu FE, Seetharaman J, Tong L, Barber DL. Structures of human phosphofructokinase-1 and atomic basis of cancer-associated mutations. Nature 2015; 523:111-4. [PMID: 25985179 PMCID: PMC4510984 DOI: 10.1038/nature14405] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 03/03/2015] [Indexed: 12/22/2022]
Abstract
Phosphofructokinase-1 (PFK1), the “gatekeeper” of glycolysis, catalyses the committed step of the glycolytic pathway by converting fructose 6-phosphate (F6P) to fructose 1,6-bisphosphate. Allosteric activation and inhibition of PFK1 by over 10 metabolites and in response to hormonal signaling fine-tune glycolytic flux to meet energy requirements1. Mutations inhibiting PFK1 activity cause glycogen storage disease type VII, also known as Tarui disease2, and mice deficient in muscle PFK1 have decreased fat stores3. Additionally, PFK1 is suggested to have important roles in metabolic reprograming in cancer4,5. Despite its critical role in glucose flux, the biologically relevant crystal structure of the mammalian PFK1 tetramer has not been determined. We report here the first structures of the mammalian PFK1 tetramer, for the human platelet isoform (PFKP), in complex with ATP-Mg2+ and ADP at 3.1 and 3.4 Å, respectively. The structures reveal substantial conformational changes in the enzyme upon nucleotide hydrolysis as well as a unique tetramer interface. Mutations of residues in this interface can affect tetramer formation, enzyme catalysis and regulation, indicating the functional importance of the tetramer. With altered glycolytic flux being a hallmark of cancers6, these new structures allow a molecular understanding of the functional consequences of somatic PFK1 mutations identified in human cancers. We characterized three of these mutations and show they have distinct effects on allosteric regulation of PFKP activity and lactate production. The PFKP structural blueprint for somatic mutations as well as the catalytic site can guide therapeutic targeting of PFK1 activity to control dysregulated glycolysis in disease.
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Affiliation(s)
- Bradley A Webb
- Department of Cell and Tissue Biology, University of California, San Francisco, California 94143, USA
| | - Farhad Forouhar
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, USA
| | - Fu-En Szu
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, USA
| | - Jayaraman Seetharaman
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, USA
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, California 94143, USA
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The sarcomeric M-region: a molecular command center for diverse cellular processes. BIOMED RESEARCH INTERNATIONAL 2015; 2015:714197. [PMID: 25961035 PMCID: PMC4413555 DOI: 10.1155/2015/714197] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/08/2015] [Indexed: 02/07/2023]
Abstract
The sarcomeric M-region anchors thick filaments and withstands the mechanical stress of contractions by deformation, thus enabling distribution of physiological forces along the length of thick filaments. While the role of the M-region in supporting myofibrillar structure and contractility is well established, its role in mediating additional cellular processes has only recently started to emerge. As such, M-region is the hub of key protein players contributing to cytoskeletal remodeling, signal transduction, mechanosensing, metabolism, and proteasomal degradation. Mutations in genes encoding M-region related proteins lead to development of severe and lethal cardiac and skeletal myopathies affecting mankind. Herein, we describe the main cellular processes taking place at the M-region, other than thick filament assembly, and discuss human myopathies associated with mutant or truncated M-region proteins.
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38
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New potential eukaryotic substrates of the mycobacterial protein tyrosine phosphatase PtpA: hints of a bacterial modulation of macrophage bioenergetics state. Sci Rep 2015; 5:8819. [PMID: 25743628 PMCID: PMC5390082 DOI: 10.1038/srep08819] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/27/2015] [Indexed: 11/16/2022] Open
Abstract
The bacterial protein tyrosine phosphatase PtpA is a key virulence factor released by Mycobacterium tuberculosis in the cytosol of infected macrophages. So far only two unrelated macrophage components (VPS33B, GSK3α) have been identified as PtpA substrates. As tyrosine phosphatases are capable of using multiple substrates, we developed an improved methodology to pull down novel PtpA substrates from an enriched P-Y macrophage extract using the mutant PtpA D126A. This methodology reduced non-specific protein interactions allowing the identification of four novel putative PtpA substrates by MALDI-TOF-MS and nano LC-MS: three mitochondrial proteins - the trifunctional enzyme (TFP), the ATP synthase, and the sulfide quinone oxidoreductase - and the cytosolic 6-phosphofructokinase. All these proteins play a relevant role in cell energy metabolism. Using surface plasmon resonance, PtpA was found to bind immunopurified human TFP through its catalytic site since TFP-PtpA association was inhibited by a specific phosphatase inhibitor. Moreover, PtpA wt was capable of dephosphorylating immunopurified human TFP in vitro supporting that TFP may be a bona fide PtpA susbtrate. Overall, these results suggest a novel scenario where PtpA-mediated dephosphorylation may affect pathways involved in cell energy metabolism, particularly the beta oxidation of fatty acids through modulation of TFP activity and/or cell distribution.
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39
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Yugi K, Kubota H, Toyoshima Y, Noguchi R, Kawata K, Komori Y, Uda S, Kunida K, Tomizawa Y, Funato Y, Miki H, Matsumoto M, Nakayama KI, Kashikura K, Endo K, Ikeda K, Soga T, Kuroda S. Reconstruction of insulin signal flow from phosphoproteome and metabolome data. Cell Rep 2014; 8:1171-83. [PMID: 25131207 DOI: 10.1016/j.celrep.2014.07.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/13/2014] [Accepted: 07/15/2014] [Indexed: 12/20/2022] Open
Abstract
Cellular homeostasis is regulated by signals through multiple molecular networks that include protein phosphorylation and metabolites. However, where and when the signal flows through a network and regulates homeostasis has not been explored. We have developed a reconstruction method for the signal flow based on time-course phosphoproteome and metabolome data, using multiple databases, and have applied it to acute action of insulin, an important hormone for metabolic homeostasis. An insulin signal flows through a network, through signaling pathways that involve 13 protein kinases, 26 phosphorylated metabolic enzymes, and 35 allosteric effectors, resulting in quantitative changes in 44 metabolites. Analysis of the network reveals that insulin induces phosphorylation and activation of liver-type phosphofructokinase 1, thereby controlling a key reaction in glycolysis. We thus provide a versatile method of reconstruction of signal flow through the network using phosphoproteome and metabolome data.
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Affiliation(s)
- Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Kubota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Division of integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan; PRESTO, Japan Science and Technology Corporation, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yu Toyoshima
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rei Noguchi
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kentaro Kawata
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasunori Komori
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinsuke Uda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Division of integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Katsuyuki Kunida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoko Tomizawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Kasumi Kashikura
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Keiko Endo
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Kazutaka Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; CREST, Japan Science and Technology Corporation, Bunkyo-ku, Tokyo 113-0033, Japan.
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40
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Kloos M, Brüser A, Kirchberger J, Schöneberg T, Sträter N. Crystallization and preliminary crystallographic analysis of human muscle phosphofructokinase, the main regulator of glycolysis. Acta Crystallogr F Struct Biol Commun 2014; 70:578-82. [PMID: 24817713 PMCID: PMC4014322 DOI: 10.1107/s2053230x14008723] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 04/17/2014] [Indexed: 11/10/2022] Open
Abstract
Whereas the three-dimensional structure and the structural basis of the allosteric regulation of prokaryotic 6-phosphofructokinases (Pfks) have been studied in great detail, knowledge of the molecular basis of the allosteric behaviour of the far more complex mammalian Pfks is still very limited. The human muscle isozyme was expressed heterologously in yeast cells and purified using a five-step purification protocol. Protein crystals suitable for diffraction experiments were obtained by the vapour-diffusion method. The crystals belonged to space group P6222 and diffracted to 6.0 Å resolution. The 3.2 Å resolution structure of rabbit muscle Pfk (rmPfk) was placed into the asymmetric unit and optimized by rigid-body and group B-factor refinement. Interestingly, the tetrameric enzyme dissociated into a dimer, similar to the situation observed in the structure of rmPfk.
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Affiliation(s)
- Marco Kloos
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Antje Brüser
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Jürgen Kirchberger
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Torsten Schöneberg
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
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