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Huang X, Zhao Y, Wei M, Zhuge R, Zheng X. hCINAP alleviates senescence by regulating MDM2 via p14ARF and the HDAC1/CoREST complex. J Mol Cell Biol 2023; 15:mjad015. [PMID: 36881716 PMCID: PMC10476552 DOI: 10.1093/jmcb/mjad015] [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: 09/30/2022] [Revised: 12/05/2022] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Cellular senescence is a major process affected by multiple signals and coordinated by a complex signal response network. Identification of novel regulators of cellular senescence and elucidation of their molecular mechanisms will aid in the discovery of new treatment strategies for aging-related diseases. In the present study, we identified human coilin-interacting nuclear ATPase protein (hCINAP) as a negative regulator of aging. Depletion of cCINAP significantly shortened the lifespan of Caenorhabditis elegans and accelerated primary cell aging. Moreover, mCINAP deletion markedly promoted organismal aging and stimulated senescence-associated secretory phenotype in the skeletal muscle and liver from mouse models of radiation-induced senescence. Mechanistically, hCINAP functions through regulating MDM2 status by distinct mechanisms. On the one hand, hCINAP decreases p53 stability by attenuating the interaction between p14ARF and MDM2; on the other hand, hCINAP promotes MDM2 transcription via inhibiting the deacetylation of H3K9ac in the MDM2 promoter by hindering the HDAC1/CoREST complex integrity. Collectively, our data demonstrate that hCINAP is a negative regulator of aging and provide insight into the molecular mechanisms underlying the aging process.
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Affiliation(s)
- Xinping Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yan Zhao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Min Wei
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruipeng Zhuge
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
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Rebane-Klemm E, Reinsalu L, Puurand M, Shevchuk I, Bogovskaja J, Suurmaa K, Valvere V, Moreno-Sanchez R, Kaambre T. Colorectal polyps increase the glycolytic activity. Front Oncol 2023; 13:1171887. [PMID: 37342183 PMCID: PMC10277630 DOI: 10.3389/fonc.2023.1171887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
In colorectal cancer (CRC) energy metabolism research, the precancerous stage of polyp has remained rather unexplored. By now, it has been shown that CRC has not fully obtained the glycolytic phenotype proposed by O. Warburg and rather depends on mitochondrial respiration. However, the pattern of metabolic adaptations during tumorigenesis is still unknown. Understanding the interplay between genetic and metabolic changes that initiate tumor development could provide biomarkers for diagnosing cancer early and targets for new cancer therapeutics. We used human CRC and polyp tissue material and performed high-resolution respirometry and qRT-PCR to detect changes on molecular and functional level with the goal of generally describing metabolic reprogramming during CRC development. Colon polyps were found to have a more glycolytic bioenergetic phenotype than tumors and normal tissues. This was supported by a greater GLUT1, HK, LDHA, and MCT expression. Despite the increased glycolytic activity, cells in polyps were still able to maintain a highly functional OXPHOS system. The mechanisms of OXPHOS regulation and the preferred substrates are currently unclear and would require further investigation. During polyp formation, intracellular energy transfer pathways become rearranged mainly by increasing the expression of mitochondrial adenylate kinase (AK) and creatine kinase (CK) isoforms. Decreased glycolysis and maintenance of OXPHOS activity, together with the downregulation of the CK system and the most common AK isoforms (AK1 and AK2), seem to play a relevant role in CRC development.
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Affiliation(s)
- Egle Rebane-Klemm
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Leenu Reinsalu
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Marju Puurand
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Igor Shevchuk
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Jelena Bogovskaja
- Clinic of Diagnostics, North Estonia Medical Centre, Tallinn, Estonia
| | - Kulliki Suurmaa
- Department of Gastroenterology, West Tallinn Central Hospital, Tallinn, Estonia
| | - Vahur Valvere
- Oncology and Hematology Clinic, North Estonia Medical Centre, Tallinn, Estonia
| | - Rafael Moreno-Sanchez
- Laboratorio de Control Metabólico, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Iztacala, Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, Mexico
| | - Tuuli Kaambre
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
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Liggri PGV, Pérez-Garrido A, Tsitsanou KE, Dileep KV, Michaelakis A, Papachristos DP, Pérez-Sánchez H, Zographos SE. 2D finger-printing and molecular docking studies identified potent mosquito repellents targeting odorant binding protein 1. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023:103961. [PMID: 37217081 DOI: 10.1016/j.ibmb.2023.103961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Personal protection measures against the mosquitoes like the use of repellents constitute valuable tools in the effort to prevent the transmission of vector-borne diseases. Therefore, the discovery of novel repellent molecules which will be effective at lower concentrations and provide a longer duration of protection remains an urgent need. Mosquito Odorant-Binding Proteins (OBPs) involved in the initial steps of the olfactory signal transduction cascade have been recognized not only as passive carriers of odors and pheromones but also as the first molecular filter to discriminate semiochemicals, hence serving as molecular targets for the design of novel pest control agents. Among the three-dimensional structures of mosquito OBPs solved in the last decades, the OBP1 complexes with known repellents have been widely used as reference structures in docking analysis and molecular dynamics simulation studies for the structure-based discovery of new molecules with repellent activity. Herein, ten compounds known to be active against mosquitoes and/or displaying a binding affinity for Anopheles gambiae AgamOBP1 were used as queries in an in silico screening of over 96 million chemical samples in order to detect molecules with structural similarity. Further filtering of the acquired hits on the basis of toxicity, vapor pressure, and commercial availability resulted in 120 unique molecules that were subjected to molecular docking studies against OBP1. For seventeen potential OBP1-binders, the free energy of binding (FEB) and mode of interaction with the protein were further estimated by molecular docking simulations leading to the selection of eight molecules exhibiting the highest similarity with their parental compounds and favorable energy values. The in vitro determination of their binding affinity to AgamOBP1 and the evaluation of their repellent activity against female Aedes albopictus mosquitoes revealed that our combined ligand similarity screening and OBP1 structure-based molecular docking successfully detected three molecules with enhanced repellent properties. A novel DEET-like repellent with lower volatility (8.55 × 10-4 mmHg) but a higher binding affinity for OBP1 than DEET (1.35 × 10-3 mmHg). A highly active repellent molecule that is predicted to bind to the secondary Icaridin (sIC)-binding site of OBP1 with higher affinity than to the DEET-site and, therefore, represents a new scaffold to be exploited for the discovery of binders targeting multiple OBP sites. Finally, a third potent repellent exhibiting a high degree of volatility was found to be a strong DEET-site binder of OBP1 that could be used in slow-release formulations.
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Affiliation(s)
- Panagiota G V Liggri
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece; Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece.
| | - Alfonso Pérez-Garrido
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), 30107, Spain
| | - Katerina E Tsitsanou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece
| | - Kalarickal V Dileep
- Laboratory for Computational and Structural Biology, Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala, 680005, India
| | - Antonios Michaelakis
- Benaki Phytopathological Institute, Department of Entomology and Agricultural Zoology, 8 S Delta Str. 14561, Kifissia, Athens, Greece
| | - Dimitrios P Papachristos
- Benaki Phytopathological Institute, Department of Entomology and Agricultural Zoology, 8 S Delta Str. 14561, Kifissia, Athens, Greece
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), 30107, Spain.
| | - Spyros E Zographos
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece.
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Regulation of Adenine Nucleotide Metabolism by Adenylate Kinase Isozymes: Physiological Roles and Diseases. Int J Mol Sci 2023; 24:ijms24065561. [PMID: 36982634 PMCID: PMC10056885 DOI: 10.3390/ijms24065561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Adenylate kinase (AK) regulates adenine nucleotide metabolism and catalyzes the ATP + AMP ⇌ 2ADP reaction in a wide range of organisms and bacteria. AKs regulate adenine nucleotide ratios in different intracellular compartments and maintain the homeostasis of the intracellular nucleotide metabolism necessary for growth, differentiation, and motility. To date, nine isozymes have been identified and their functions have been analyzed. Moreover, the dynamics of the intracellular energy metabolism, diseases caused by AK mutations, the relationship with carcinogenesis, and circadian rhythms have recently been reported. This article summarizes the current knowledge regarding the physiological roles of AK isozymes in different diseases. In particular, this review focused on the symptoms caused by mutated AK isozymes in humans and phenotypic changes arising from altered gene expression in animal models. The future analysis of intracellular, extracellular, and intercellular energy metabolism with a focus on AK will aid in a wide range of new therapeutic approaches for various diseases, including cancer, lifestyle-related diseases, and aging.
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5
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Zhuge R, Wang C, Wang J, Yu S, Liao L, Zheng X. hCINAP regulates the differentiation of embryonic stem cells by regulating NEDD4 liquid-liquid phase-separation-mediated YAP1 activation. Cell Rep 2023; 42:111935. [PMID: 36640330 DOI: 10.1016/j.celrep.2022.111935] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/15/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022] Open
Abstract
YAP1 functions in lineage differentiation of pluripotent embryonic stem cells (ESCs); however, the detailed mechanisms underlying the regulation of YAP1 activity during ESC differentiation remain elusive. Here, we report that hCINAP serves as a negative regulator of YAP1 during ESC fate decisions. The expression of mCINAP, the murine homolog of hCINAP, is downregulated during the differentiation process of murine ESC (mESC) ectoderm lineage, leading to liquid-liquid phase separation (LLPS) of NEDD4 and activation of YAP1. Mechanistically, hCINAP interacts with and prevents NEDD4 from forming cytoplasmic condensates that compartmentalize YAP1 and its kinase NLK, facilitating YAP1 phosphorylation at Ser128 and promoting YAP1 activation. mCINAP depletion leads to the formation of NEDD4 condensates and YAP1 activation, which impedes endoderm differentiation of mESCs. Our study shows that hCINAP is a vital regulator of YAP1 activity and is essential for stem cell fate decisions, which provides mechanistic insight into early embryogenesis.
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Affiliation(s)
- Ruipeng Zhuge
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chao Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jie Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Shuyu Yu
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Liming Liao
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China.
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Verma A, Åberg-Zingmark E, Sparrman T, Mushtaq AU, Rogne P, Grundström C, Berntsson R, Sauer UH, Backman L, Nam K, Sauer-Eriksson E, Wolf-Watz M. Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases. SCIENCE ADVANCES 2022; 8:eabm4089. [PMID: 36332013 PMCID: PMC9635829 DOI: 10.1126/sciadv.abm4089] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while 19F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.
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Affiliation(s)
- Apoorv Verma
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | | | - Tobias Sparrman
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | | | - Per Rogne
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | | | - Ronnie Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Uwe H. Sauer
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Lars Backman
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX 76019, USA
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Adenylate Kinase Isozyme 3 Regulates Mitochondrial Energy Metabolism and Knockout Alters HeLa Cell Metabolism. Int J Mol Sci 2022; 23:ijms23084316. [PMID: 35457131 PMCID: PMC9032187 DOI: 10.3390/ijms23084316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 02/05/2023] Open
Abstract
The balance between oxidative phosphorylation and glycolysis is important for cancer cell growth and survival, and changes in energy metabolism are an emerging therapeutic target. Adenylate kinase (AK) regulates adenine nucleotide metabolism, maintaining intracellular nucleotide metabolic homeostasis. In this study, we focused on AK3, the isozyme localized in the mitochondrial matrix that reversibly mediates the following reaction: Mg2+ GTP + AMP ⇌ Mg2+ GDP + ADP. Additionally, we analyzed AK3-knockout (KO) HeLa cells, which showed reduced proliferation and were detected at an increased number in the G1 phase. A metabolomic analysis showed decreased ATP; increased glycolytic metabolites such as glucose 6 phosphate (G6P), fructose 6 phosphate (F6P), and phosphoenolpyruvate (PEP); and decreased levels of tricarboxylic acid (TCA) cycle metabolites in AK3KO cells. An intracellular ATP evaluation of AK3KO HeLa cells transfected with ATeam plasmid, an ATP sensor, showed decreased whole cell levels. Levels of mitochondrial DNA (mtDNA), a complementary response to mitochondrial failure, were increased in AK3KO HeLa cells. Oxidative stress levels increased with changes in gene expression, evidenced as an increase in related enzymes such as superoxide dismutase 2 (SOD2) and SOD3. Phosphoenolpyruvate carboxykinase 2 (PCK2) expression and PEP levels increased, whereas PCK2 inhibition affected AK3KO HeLa cells more than wild-type (WT) cells. Therefore, we concluded that increased PCK2 expression may be complementary to increased GDP, which was found to be deficient through AK3KO. This study demonstrated the importance of AK3 in mitochondrial matrix energy metabolism.
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Zhang J, Gao X, Cai G, Wang Y, Li J, Du H, Wang R, Zhang H, Huang J. An Adenylate Kinase OsAK3 Involves Brassinosteroid Signaling and Grain Length in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2021; 14:105. [PMID: 34962599 PMCID: PMC8714616 DOI: 10.1186/s12284-021-00546-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/17/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Grain size is one of the major determinants of cereal crop yield. As a class of plant polyhydroxysteroids, brassinosteroids (BRs) play essential roles in the regulation of grain size and plant architecture in rice. In a previous research, we cloned qGL3/OsPPKL1 encoding a protein phosphatase with Kelch-like repeat domains, which negatively regulates BR signaling and grain length in rice. RESULTS Here, we screened qGL3-interacting proteins (GIPs) via yeast two-hybrid assay and analyzed the phenotypes of the T-DNA insertion mutants of GIPs. Among these mutants, mutant osak3 presents shorter grain length and dwarfing phenotype. OsAK3 encodes an adenylate kinase, which regulates grain size by controlling cell expansion of rice spikelet glume. Overexpression of OsAK3 resulted in longer grain length. OsAK3 interacts with qGL3 in vivo and in vitro. Lamina inclination, coleoptile elongation and root inhibition experiments showed that the osak3 mutant was less sensitive to exogenous brassinolide (BL) treatment. The transcriptional level of OsAK3 was up-regulated under BL induction. In addition, RNA-Seq data indicate that OsAK3 is involved in a variety of biological processes that regulate BR signaling and grain development in rice. CONCLUSIONS Our study reveals a novel BR signaling component OsAK3 in the regulation of grain length, and provides novel clues for uncovering the potential functions of OsAK3 in rice growth and development.
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Affiliation(s)
- Jiaqi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Xiuying Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Guang Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Yuji Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Jianbo Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Huaying Du
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Ruqin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China.
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9
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Xu R, Yang Y, Zheng X. Unique structural features of the adenylate kinase hCINAP/AK6 and its multifaceted functions in carcinogenesis and tumor progression. FEBS Lett 2021; 595:2071-2084. [PMID: 34245011 DOI: 10.1002/1873-3468.14158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/30/2022]
Abstract
Human coilin-interacting nuclear ATPase protein (hCINAP), also known as adenylate kinase 6 (AK6), is an atypical adenylate kinase with critical roles in many biological processes, including gene transcription, ribosome synthesis, cell metabolism, cell proliferation and apoptosis, DNA damage responses, and genome stability. Furthermore, hCINAP/AK6 dysfunction is associated with cancer and various inflammatory diseases. In this review, we summarize the structural features and biological roles of hCINAP in several important signaling pathways, as well as its connection with tumor onset and progression.
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Affiliation(s)
- Ruidan Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Yongfeng Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
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10
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Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. Genes (Basel) 2021; 12:genes12070963. [PMID: 34202810 PMCID: PMC8305020 DOI: 10.3390/genes12070963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.
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11
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Zhang Y, Jiang L, Qin N, Cao M, Liang X, Wang R. hCINAP is potentially a direct target gene of HIF-1 and is required for hypoxia-induced EMT and apoptosis in cervical cancer cells. Biochem Cell Biol 2021; 99:203-213. [PMID: 32830518 DOI: 10.1139/bcb-2020-0090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The early metastasis of cervical cancer is a multistep process requiring the cancer cells to adapt to the signal input from different tissue environments, including hypoxia. Hypoxia-induced epithelial-to-mesenchymal transition (EMT) plays a critical role in the ability to invade surrounding tissues. However, the molecular mechanisms underlying EMT in cervical cancer remain to be elucidated. Herein, we show that hypoxia-inducible factor-1alpha (HIF-1α) and aryl hydrocarbon receptor nuclear translocator (ARNT) are recruited to the human coilin-interacting nuclear ATPase protein (hCINAP) promoter and initiate hCINAP expression in hypoxia. Ablation of hCINAP decreased the migratory capacity and EMT of cervical cancer cells under hypoxic conditions. Furthermore, hCINAP regulated EMT through the Akt–mTOR signaling pathway, and inhibits hypoxia-induced p53-dependent apoptosis. Our data collectively show that hCINAP may have essential roles in the metastasis of cervical cancer and could be a potential target for curing cervical cancer.
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Affiliation(s)
- Yong Zhang
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Li Jiang
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Nianqun Qin
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Mi Cao
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Xiujuan Liang
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Rensheng Wang
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
- Department of Radiation Oncology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
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12
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Li L, Zhu XM, Shi HB, Feng XX, Liu XH, Lin FC. MoFap7, a ribosome assembly factor, is required for fungal development and plant colonization of Magnaporthe oryzae. Virulence 2020; 10:1047-1063. [PMID: 31814506 PMCID: PMC6930019 DOI: 10.1080/21505594.2019.1697123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Fap7, an important ribosome assembly factor, plays a vital role in pre-40S small ribosomal subunit synthesis in Saccharomyces cerevisiae via its ATPase activity. Currently, the biological functions of its homologs in filamentous fungi remain elusive. Here, MoFap7, a homologous protein of ScFap7, was identified in the rice blast fungus Magnaporthe oryzae, which is a devastating fungal pathogen in rice and threatens food security worldwide. ΔMofap7 mutants exhibited defects in growth and development, conidial morphology, appressorium formation and infection, and were sensitive to oxidative stress. In addition, site-directed mutagenesis analysis confirmed that the conserved Walker A motif and Walker B motif in MoFap7 are essential for the biological functions of M. oryzae. We further analyzed the regulation mechanism of MoFap7 in pathogenicity. MoFap7 was found to interact with MoMst50, a regulator functioning in the MAPK Pmk1 signaling pathway, that participates in modulating plant penetration and cell-to-cell invasion by regulating the phosphorylation of MoPmk1. Moreover, MoFap7 interacted with the GTPases MoCdc42 and MoRac1 to control growth and conidiogenesis. Taken together, the results of this study provide novel insights into MoFap7-mediated orchestration of the development and pathogenesis of filamentous fungi.
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Affiliation(s)
- Lin Li
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
| | - Xue-Ming Zhu
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
| | - Huan-Bin Shi
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiao-Xiao Feng
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
| | - Xiao-Hong Liu
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
| | - Fu-Cheng Lin
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou, China
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13
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Yan Y, Yuan X, Xue C, He Y. Human coilin interacting nuclear ATPase protein in cancer: uncovering new insights into pathogenesis and therapy. Am J Transl Res 2020; 12:4051-4058. [PMID: 32774758 PMCID: PMC7407739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
A deeper understanding of tumor pathogenesis has revolutionized cancer treatment strategies. The discovery of human coilin interacting nuclear ATPase protein (hCINAP) and increasing experimental research over the past 15 years have provided us with new insights into the diagnoses, prognoses, and therapeutic approaches of cancer. In the current review, hCINAP's effect on tumor growth, cell viability, invasion, metastasis, and drug resistance is summarized. In addition, an overview is given of the underlying mechanisms involved, including regulation of signaling pathways, ribosome biogenesis, metabolism, as well as DNA damage repair. Finally, hCINAP-based therapeutic approaches are examined, with the goal of improving efficacy of cancer treatments. This review can, therefore, serve as a reference for further hCINAP-related research and clinical trials, and we advocate those approaches to be initiated without delay.
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Affiliation(s)
- Yuheng Yan
- Department of Hepatobiliary and Pancreatic SurgeryHenan, P. R. China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan ProvinceHenan, P. R. China
| | - Xin Yuan
- Department of Infectious Diseases, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Chen Xue
- Department of Infectious Diseases, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic SurgeryHenan, P. R. China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan ProvinceHenan, P. R. China
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14
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Abstract
Adenylate kinase is a small, usually monomeric, enzyme found in every living thing due to its crucial role in energetic metabolism. This paper outlines the most relevant data about adenylate kinases isoforms, and the connection between dysregulation or mutation of human adenylate kinase and medical conditions. The following datadases were consulted: National Centre for Biotechnology Information, Protein Data Bank, and Mouse Genomic Informatics. The SmartBLAST tool, EMBOSS Needle Program, and Clustal Omega Program were used to analyze the best protein match, and to perform pairwise sequence alignment and multiple sequence alignment. Human adenylate kinase genes are located on different chromosomes, six of them being on the chromosomes 1 and 9. The adenylate kinases' intracellular localization and organ distribution explain their dysregulation in many diseases. The cytosolic isoenzyme 1 and the mitochondrial isoenzyme 2 are the main adenylate kinases that are integrated in the vast network of inflammatory modulators. The cytosolic isoenzyme 5 is correlated with limbic encephalitis and Leu673Pro mutation of the isoenzyme 7 leads to primary male infertility due to impairment of the ciliary function. The impairment of the mitochondrial isoenzymes 2 and 4 is demonstrated in neuroblastoma or glioma. The adenylate kinases are disease modifier that can assess the risk of diseases where oxidative stress plays a crucial role in pathogenesis like metabolic syndrome or neurodegenerative diseases. Because adenylate kinases has ATP as substrate, they are integrated in the global network of energetic process of any organism therefore are valid target for new pharmaceutical compounds.
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Affiliation(s)
- Mihaela Ileana Ionescu
- Department of Microbiology, Faculty of Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, 6 Louis Pasteur, Cluj-Napoca, 400349, Romania. .,County Emergency Clinical Hospital, Cluj-Napoca, Romania.
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15
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Kaiser M, Hacker C, Duchardt-Ferner E, Wöhnert J. 1H, 13C, 15N backbone NMR resonance assignments for the rRNA methyltransferase Dim1 from the hyperthermophilic archaeon Pyrococcus horikoshii. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:309-314. [PMID: 31069720 DOI: 10.1007/s12104-019-09897-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
The protein dimethyladenosine transferase 1 (Dim1) is a highly conserved protein occurring in organisms ranging from bacteria such as E. coli where it is named KsgA to humans. Since Dim1 is involved in the biogenesis of the small ribosomal subunit it is an essential protein. During ribosome biogenesis Dim1 acts as an rRNA modification enzyme and dimethylates two adjacent adenosine residues of the small ribosomal subunit rRNA. In eukaryotes it is also required to ensure the proper endonucleolytic processing of the small ribosomal subunit rRNA precursor. Recently, a third function was proposed for eukaryotic Dim1. Karbstein and coworkers suggested that Dim1 interacts with the essential ribosome assembly factor Fap7 and that Fap7 is responsible for the dissociation of Dim1 from the nascent small ribosomal subunit. Here, we report the backbone 1H, 13C and 15N NMR resonance assignments for the 30.9 kDa Dim1 homologue from the hyperthermophilic archaeon Pyrococcus horikoshii (PhDim1) as a prerequisite for a detailed structural investigation of the PhDim1/PhFap7 interaction.
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Affiliation(s)
- Marco Kaiser
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
| | - Carolin Hacker
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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16
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Xu R, Yu S, Zhu D, Huang X, Xu Y, Lao Y, Tian Y, Zhang J, Tang Z, Zhang Z, Yi J, Zhu HH, Zheng X. hCINAP regulates the DNA-damage response and mediates the resistance of acute myelocytic leukemia cells to therapy. Nat Commun 2019; 10:3812. [PMID: 31444354 PMCID: PMC6707248 DOI: 10.1038/s41467-019-11795-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 08/01/2019] [Indexed: 01/08/2023] Open
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous malignant disorder of the hematopoietic system, characterized by the accumulation of DNA-damaged immature myeloid precursors. Here, we find that hCINAP is involved in the repair of double-stranded DNA breaks (DSB) and that its expression correlates with AML prognosis. Following DSB, hCINAP is recruited to damage sites where it promotes SENP3-dependent deSUMOylation of NPM1. This in turn results in the dissociation of RAP80 from the damage site and CTIP-dependent DNA resection and homologous recombination. NPM1 SUMOylation is required for recruitment of DNA repair proteins at the early stage of DNA-damage response (DDR), and SUMOylated NPM1 impacts the assembly of the BRCA1 complex. Knockdown of hCINAP also sensitizes a patient-derived xenograft (PDX) mouse model to chemotherapy. In clinical AML samples, low hCINAP expression is associated with a higher overall survival rate in patients. These results provide mechanistic insight into the function of hCINAP during the DNA-damage response and its role in AML resistance to therapy. Acute myeloid leukemia cells are often resistant to radiotherapy and chemotherapy. Here, the authors suggest that hCINAP contributes to the resistance of acute myeloid leukemia cells by regulating SUMOylation of Nucleophosmin during the DNA-damage response.
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Affiliation(s)
- Ruidan Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shuyu Yu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Dan Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xinping Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yuqi Xu
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yimin Lao
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yonglu Tian
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.,State Key Laboratory of Membrane Biology, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jinfang Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zefang Tang
- School of Life Sciences and BIOPIC, Peking University, Beijing, 100871, China
| | - Zemin Zhang
- School of Life Sciences and BIOPIC, Peking University, Beijing, 100871, China
| | - Jing Yi
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hong-Hu Zhu
- Peking University People's Hospital, Peking University, Beijing, 100014, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China. .,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China.
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17
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Dongerdiye R, Kamat P, Jain P, Warang P, Devendra R, Wasekar N, Sharma R, Mhaskar K, Madkaikar MR, Manglani MV, Kedar PS. Red cell adenylate kinase deficiency in India: identification of two novel missense mutations (c.71A>G and c.413G>A). J Clin Pathol 2019; 72:393-398. [PMID: 30918013 DOI: 10.1136/jclinpath-2019-205718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 02/03/2023]
Abstract
Adenylate kinase (AK) deficiency is a rare erythroenzymopathy associated with hereditary nonspherocytic haemolytic anaemia along with mental/psychomotor retardation in few cases. Diagnosis of AK deficiency depends on the decreased level of enzyme activity in red cell and identification of a mutation in the AK1 gene. Until, only eight mutations causing AK deficiency have been reported in the literature. We are reporting two novel missense mutation (c.71A > G and c.413G > A) detected in the AK1 gene by next-generation sequencing (NGS) in a 6-year-old male child from India. Red cell AK enzyme activity was found to be 30% normal. We have screened a total of 32 family members of the patient and showed reduced red cell enzyme activity and confirm mutations by Sanger's sequencing. On the basis of Sanger sequencing, we suggest that the proband has inherited a mutation in AK1 gene exon 4 c.71A > G (p.Gln24Arg) from paternal family and exon 6 c.413G > A (p.Arg138His) from maternal family. Bioinformatics tools, such as SIFT, Polymorphism Phenotyping v.2, Mutation Taster, MutPred, also confirmed the deleterious effect of both the mutations. Molecular modelling suggests that the structural changes induced by p.Gln24Arg and p.Arg138His are pathogenic variants having a direct impact on the structural arrangement of the region close to the active site of the enzyme. In conclusion, NGS will be the best solution for diagnosis of very rare disorders leading to better management of the disease. This is the first report of the red cell AK deficiency from the Indian population.
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Affiliation(s)
- Rashmi Dongerdiye
- Department of Haematogenetics, National Institute of Immunohaematology, Mumbai, India
| | - Pranoti Kamat
- MCGM Comprehensive Thalassemia Care Pediatric Hematology-Oncology and Bone Marrow Transplantation Centre, Mumbai, India
| | - Punit Jain
- MCGM Comprehensive Thalassemia Care Pediatric Hematology-Oncology and Bone Marrow Transplantation Centre, Mumbai, India
| | - Prashant Warang
- Department of Haematogenetics, National Institute of Immunohaematology, Mumbai, India
| | - Rati Devendra
- Department of Haematogenetics, National Institute of Immunohaematology, Mumbai, India
| | - Nilesh Wasekar
- MCGM Comprehensive Thalassemia Care Pediatric Hematology-Oncology and Bone Marrow Transplantation Centre, Mumbai, India
| | - Ratna Sharma
- MCGM Comprehensive Thalassemia Care Pediatric Hematology-Oncology and Bone Marrow Transplantation Centre, Mumbai, India
| | - Ketaki Mhaskar
- MCGM Comprehensive Thalassemia Care Pediatric Hematology-Oncology and Bone Marrow Transplantation Centre, Mumbai, India
| | | | - Mamta V Manglani
- MCGM Comprehensive Thalassemia Care Pediatric Hematology-Oncology and Bone Marrow Transplantation Centre, Mumbai, India
| | - Prabhakar S Kedar
- Department of Haematogenetics, National Institute of Immunohaematology, Mumbai, India
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18
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Dong Y, Lagarde J, Xicota L, Corne H, Chantran Y, Chaigneau T, Crestani B, Bottlaender M, Potier MC, Aucouturier P, Dorothée G, Sarazin M, Elbim C. Neutrophil hyperactivation correlates with Alzheimer's disease progression. Ann Neurol 2019; 83:387-405. [PMID: 29369398 DOI: 10.1002/ana.25159] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Recent studies have underlined the effect of systemic inflammation on the pathophysiology of Alzheimer's disease (AD). Neutrophils are key components of early innate immunity and contribute to uncontrolled systemic inflammation if not tightly regulated. The aim of our study was to fully characterize human circulating neutrophils at different disease stages in AD. METHODS We analyzed neutrophil phenotypes and functions in 42 patients with AD (16 with mild cognitive impairment and 26 with dementia), and compared them to 22 age-matched healthy subjects. This study was performed directly in whole blood to avoid issues with data interpretation related to cell isolation procedures. RESULTS Blood samples from AD patients with dementia revealed neutrophil hyperactivation associated with increased reactive oxygen species production and increased levels of intravascular neutrophil extravascular traps. The homeostasis of circulating neutrophils in these patients also changed: The ratio between the harmful hyperreactive CXCR4high /CD62Llow senescent and the CD16bright /CD62Ldim immunosuppressive neutrophil subsets rose in the later stage of the disease. These abnormalities were greater in fast-decliner than in slow-decliner patients. INTERPRETATION Our results indicate that the inflammatory properties of circulating neutrophils shift as the percentage of aged neutrophils expands in patients with AD-changes that may play an instrumental role in establishing systemic chronic inflammation. Most important, our data strongly suggest that the neutrophil phenotype may be associated with the rate of cognitive decline and may thus constitute an innovative and prognostic blood biomarker in patients with AD. Ann Neurol 2018;83:387-405.
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Affiliation(s)
- Yuan Dong
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine, team "Immune System, Neuroinflammation and Neurodegenerative Diseases", Hôpital Saint-Antoine, Paris, France
| | - Julien Lagarde
- Unit of Neurology of Memory and Language, Centre Hospitalier Sainte Anne, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Laboratoire Imagerie Moléculaire In Vivo (IMIV), UMR 1023 Inserm/CEA/Université Paris Sud-ERL 9218 CNRS; CEA/I2BM/Service Hospitalier Frédéric Joliot, Orsay, France
| | - Laura Xicota
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1127, CNRS UMR 7225, UMRS 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Hélène Corne
- Unit of Neurology of Memory and Language, Centre Hospitalier Sainte Anne, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Yannick Chantran
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine, team "Immune System, Neuroinflammation and Neurodegenerative Diseases", Hôpital Saint-Antoine, Paris, France
| | - Thomas Chaigneau
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine, team "Immune System, Neuroinflammation and Neurodegenerative Diseases", Hôpital Saint-Antoine, Paris, France
| | - Bruno Crestani
- APHP, Hôpital Bichat, Service de Pneumologie A, Centre de référence des maladies pulmonaires rares, Paris, France
| | - Michel Bottlaender
- Laboratoire Imagerie Moléculaire In Vivo (IMIV), UMR 1023 Inserm/CEA/Université Paris Sud-ERL 9218 CNRS; CEA/I2BM/Service Hospitalier Frédéric Joliot, Orsay, France.,UNIACT, NeuroSpin, Institut d'Imagerie Biomédicale, Direction des sciences du vivant, Commissariat à I'Energie Atomique, Gif-sur-Yvette, France
| | - Marie-Claude Potier
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1127, CNRS UMR 7225, UMRS 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Pierre Aucouturier
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine, team "Immune System, Neuroinflammation and Neurodegenerative Diseases", Hôpital Saint-Antoine, Paris, France
| | - Guillaume Dorothée
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine, team "Immune System, Neuroinflammation and Neurodegenerative Diseases", Hôpital Saint-Antoine, Paris, France
| | - Marie Sarazin
- Unit of Neurology of Memory and Language, Centre Hospitalier Sainte Anne, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Laboratoire Imagerie Moléculaire In Vivo (IMIV), UMR 1023 Inserm/CEA/Université Paris Sud-ERL 9218 CNRS; CEA/I2BM/Service Hospitalier Frédéric Joliot, Orsay, France
| | - Carole Elbim
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine, team "Immune System, Neuroinflammation and Neurodegenerative Diseases", Hôpital Saint-Antoine, Paris, France
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19
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Simultaneous Detection of Activity and Relative Molecular Mass of Adenylate Kinases After SDS-PAGE and Blotting. Methods Mol Biol 2018; 1626:169-178. [PMID: 28608209 DOI: 10.1007/978-1-4939-7111-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Adenylate kinases (AKs) are ubiquitous monomeric phosphotransferases, which play a pivotal role in the energetic metabolism. At the present, nine isoforms are known. AKs catalyze the following reversible reaction: ATP + AMP ↔ 2 ADP, even though isoform 3 uses GTP instead ATP. For many years, the activity of AKs has been detected only after native polyacrylamide gel separations, i.e. in the absence of sodium dodecyl sulfate or methanol. In this work, we report the possibility to detect the activity of the isoforms able to use ATP as substrate, directly onto gel or nitrocellulose sheets, after denaturing SDS-PAGE and electroblotting. This method is innovative because it allows to determine simultaneously the activity and the molecular weight of AKs, especially onto nitrocellulose where bands are sharper, thanks to absence of protein diffusion.
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20
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Adenylate kinase hCINAP determines self-renewal of colorectal cancer stem cells by facilitating LDHA phosphorylation. Nat Commun 2017; 8:15308. [PMID: 28516914 PMCID: PMC5454382 DOI: 10.1038/ncomms15308] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/17/2017] [Indexed: 12/18/2022] Open
Abstract
Targeting the specific metabolic phenotypes of colorectal cancer stem cells (CRCSCs) is an innovative therapeutic strategy for colorectal cancer (CRC) patients with poor prognosis and relapse. However, the context-dependent metabolic traits of CRCSCs remain poorly elucidated. Here we report that adenylate kinase hCINAP is overexpressed in CRC tissues. Depletion of hCINAP inhibits invasion, self-renewal, tumorigenesis and chemoresistance of CRCSCs with a loss of mesenchymal signature. Mechanistically, hCINAP binds to the C-terminal domain of LDHA, the key regulator of glycolysis, and depends on its adenylate kinase activity to promote LDHA phosphorylation at tyrosine 10, resulting in the hyperactive Warburg effect and the lower cellular ROS level and conferring metabolic advantage to CRCSC invasion. Moreover, hCINAP expression is positively correlated with the level of Y10-phosphorylated LDHA in CRC patients. This study identifies hCINAP as a potent modulator of metabolic reprogramming in CRCSCs and a promising drug target for CRC invasion and metastasis.
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21
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Bai D, Zhang J, Li T, Hang R, Liu Y, Tian Y, Huang D, Qu L, Cao X, Ji J, Zheng X. The ATPase hCINAP regulates 18S rRNA processing and is essential for embryogenesis and tumour growth. Nat Commun 2016; 7:12310. [PMID: 27477389 PMCID: PMC4974663 DOI: 10.1038/ncomms12310] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/20/2016] [Indexed: 12/29/2022] Open
Abstract
Dysfunctions in ribosome biogenesis cause developmental defects and increased cancer susceptibility; however, the connection between ribosome assembly and tumorigenesis remains unestablished. Here we show that hCINAP (also named AK6) is required for human 18S rRNA processing and 40S subunit assembly. Homozygous CINAP−/− mice show embryonic lethality. The heterozygotes are viable and show defects in 18S rRNA processing, whereas no delayed cell growth is observed. However, during rapid growth, CINAP haploinsufficiency impairs protein synthesis. Consistently, hCINAP depletion in fast-growing cancer cells inhibits ribosome assembly and abolishes tumorigenesis. These data demonstrate that hCINAP reduction is a specific rate-limiting controller during rapid growth. Notably, hCINAP is highly expressed in cancers and correlated with a worse prognosis. Genome-wide polysome profiling shows that hCINAP selectively modulates cancer-associated translatome to promote malignancy. Our results connect the role of hCINAP in ribosome assembly with tumorigenesis. Modulation of hCINAP expression may be a promising target for cancer therapy. Perturbations in ribosome biogenesis affect development and increase cancer susceptibility. Here, the authors show that hCINAP is required for 18S rRNA processing, is highly expressed in cancers, and promotes cancer cell growth by upregulating the translation of cancer-associated genes.
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Affiliation(s)
- Dongmei Bai
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Jinfang Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Tingting Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Runlai Hang
- State key Laboratory of Plant Genetics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Yonglu Tian
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Dadu Huang
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Linglong Qu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Xiaofeng Cao
- State key Laboratory of Plant Genetics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Surgery, Peking University Caner Hospital and Institute, Beijing 100142, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
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Down-regulation of adenylate kinase 5 in temporal lobe epilepsy patients and rat model. J Neurol Sci 2016; 366:20-26. [DOI: 10.1016/j.jns.2016.04.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/01/2016] [Accepted: 04/19/2016] [Indexed: 11/19/2022]
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Ng ASL, Kramer J, Centurion A, Dalmau J, Huang E, Cotter JA, Geschwind MD. Clinico-pathological correlation in adenylate kinase 5 autoimmune limbic encephalitis. J Neuroimmunol 2015; 287:31-5. [PMID: 26439959 DOI: 10.1016/j.jneuroim.2015.08.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 02/01/2023]
Abstract
Autoantibodies associated with autoimmune limbic encephalitis (ALE) have been well-characterized, with intracellular neuronal antibodies being less responsive to immunotherapy than antibodies to cell surface antigens. Adenylate kinase 5 (AK5) is a nucleoside monophosphate kinase vital for neuronal-specific metabolism and is located intracellularly in the cytosol and expressed exclusively in the brain. Antibodies to AK5 had been previously identified but were not known to be associated with human disease prior to the report of two patients with AK5-related ALE (Tuzun et al., 2007). We present the complete clinical picture for one of these patients and the first reported neuropathology for AK5 ALE.
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Affiliation(s)
- Adeline S L Ng
- Memory and Aging Center, University of California, San Francisco, Sandler Neurosciences Centre, 675 Nelson Rising Lane, Suite 190, San Francisco, CA 94158, USA
| | - Joel Kramer
- Memory and Aging Center, University of California, San Francisco, Sandler Neurosciences Centre, 675 Nelson Rising Lane, Suite 190, San Francisco, CA 94158, USA
| | - Alejandro Centurion
- Community Hospital of the Monterrey Peninsula, 100 Clock Tower Pl, Ste 225, Carmel, CA 93921, USA
| | - Josep Dalmau
- Division of Neuro-oncology, Department of Neurology, Hospital of the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Eric Huang
- Department of Pathology, University of California, San Francisco, 505 Parnassus Avenue, Suite M590, Box 0511, San Francisco, CA 94143, USA
| | - Jennifer A Cotter
- Department of Pathology, University of California, San Francisco, 505 Parnassus Avenue, Suite M590, Box 0511, San Francisco, CA 94143, USA
| | - Michael D Geschwind
- Memory and Aging Center, University of California, San Francisco, Sandler Neurosciences Centre, 675 Nelson Rising Lane, Suite 190, San Francisco, CA 94158, USA.
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Qu L, Ji Y, Zhu X, Zheng X. hCINAP negatively regulates NF-κB signaling by recruiting the phosphatase PP1 to deactivate IKK complex. J Mol Cell Biol 2015; 7:529-42. [PMID: 26089539 DOI: 10.1093/jmcb/mjv041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/27/2015] [Indexed: 01/26/2023] Open
Abstract
Tight regulation of nuclear factor-κB (NF-κB) signaling is essential to maintain homeostasis in immune system in response to various stimuli, which has been studied extensively and deeply. However, the molecular mechanisms responsible for its negative regulation are not completely understood. Here we demonstrate that human coilin-interacting nuclear ATPase protein (hCINAP) is a novel negative regulator in NF-κB signaling by deactivating IκB kinase (IKK) complex. In response to TNF stimulation, hCINAP dynamically associates with IKKα and IKKβ and inhibits IKK phosphorylation. Notably, hCINAP directly interacts with the catalytic subunits of protein phosphatase 1 (PP1) and mediates the formation of IKK-hCINAP-PP1 complex, serving as an adaptor protein that recruits PP1 to dephosphorylate IKK. Furthermore, decreased levels of hCINAP are observed in several inflammatory diseases with NF-κB hyperactivity. Our study suggests a novel mechanism underlying deactivation of IKK and provides new insight into the negative regulation of NF-κB signaling.
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Affiliation(s)
- Linglong Qu
- State Key Lab of Protein and Plant Gene Research, Beijing 100871, China Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yapeng Ji
- State Key Lab of Protein and Plant Gene Research, Beijing 100871, China Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xi Zhu
- Department of Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Xiaofeng Zheng
- State Key Lab of Protein and Plant Gene Research, Beijing 100871, China Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
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25
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Dong Q, Ernst SE, Ostedgaard LS, Shah VS, Ver Heul AR, Welsh MJ, Randak CO. Mutating the Conserved Q-loop Glutamine 1291 Selectively Disrupts Adenylate Kinase-dependent Channel Gating of the ATP-binding Cassette (ABC) Adenylate Kinase Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and Reduces Channel Function in Primary Human Airway Epithelia. J Biol Chem 2015; 290:14140-53. [PMID: 25887396 PMCID: PMC4447984 DOI: 10.1074/jbc.m114.611616] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 11/06/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter cystic fibrosis transmembrane conductance regulator (CFTR) and two other non-membrane-bound ABC proteins, Rad50 and a structural maintenance of chromosome (SMC) protein, exhibit adenylate kinase activity in the presence of physiologic concentrations of ATP and AMP or ADP (ATP + AMP ⇆ 2 ADP). The crystal structure of the nucleotide-binding domain of an SMC protein in complex with the adenylate kinase bisubstrate inhibitor P(1),P(5)-di(adenosine-5') pentaphosphate (Ap5A) suggests that AMP binds to the conserved Q-loop glutamine during the adenylate kinase reaction. Therefore, we hypothesized that mutating the corresponding residue in CFTR, Gln-1291, selectively disrupts adenylate kinase-dependent channel gating at physiologic nucleotide concentrations. We found that substituting Gln-1291 with bulky side-chain amino acids abolished the effects of Ap5A, AMP, and adenosine 5'-monophosphoramidate on CFTR channel function. 8-Azidoadenosine 5'-monophosphate photolabeling of the AMP-binding site and adenylate kinase activity were disrupted in Q1291F CFTR. The Gln-1291 mutations did not alter the potency of ATP at stimulating current or ATP-dependent gating when ATP was the only nucleotide present. However, when physiologic concentrations of ADP and AMP were added, adenylate kinase-deficient Q1291F channels opened significantly less than wild type. Consistent with this result, we found that Q1291F CFTR displayed significantly reduced Cl(-) channel function in well differentiated primary human airway epithelia. These results indicate that a highly conserved residue of an ABC transporter plays an important role in adenylate kinase-dependent CFTR gating. Furthermore, the results suggest that adenylate kinase activity is important for normal CFTR channel function in airway epithelia.
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Affiliation(s)
- Qian Dong
- From the Stead Family Department of Pediatrics
| | - Sarah E Ernst
- the Department of Internal Medicine, the Howard Hughes Medical Institute, Iowa City, Iowa 52242
| | | | - Viral S Shah
- the Department of Molecular Physiology and Biophysics, and the Medical Scientist Training Program, University of Iowa, Iowa City, Iowa 52242 and
| | | | - Michael J Welsh
- the Department of Internal Medicine, the Howard Hughes Medical Institute, Iowa City, Iowa 52242 the Department of Molecular Physiology and Biophysics, and
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Su XD, Zhang H, Terwilliger TC, Liljas A, Xiao J, Dong Y. Protein Crystallography from the Perspective of Technology Developments. CRYSTALLOGR REV 2014; 21:122-153. [PMID: 25983389 DOI: 10.1080/0889311x.2014.973868] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Early on, crystallography was a domain of mineralogy and mathematics and dealt mostly with symmetry properties and imaginary crystal lattices. This changed when Wilhelm Conrad Röntgen discovered X-rays in 1895, and in 1912 Max von Laue and his associates discovered X-ray irradiated salt crystals would produce diffraction patterns that could reveal the internal atomic periodicity of the crystals. In the same year the father-and-son team, Henry and Lawrence Bragg successfully solved the first crystal structure of sodium chloride and the era of modern crystallography began. Protein crystallography (PX) started some 20 years later with the pioneering work of British crystallographers. In the past 50-60 years, the achievements of modern crystallography and particularly those in protein crystallography have been due to breakthroughs in theoretical and technical advancements such as phasing and direct methods; to more powerful X-ray sources such as synchrotron radiation (SR); to more sensitive and efficient X-ray detectors; to ever faster computers and to improvements in software. The exponential development of protein crystallography has been accelerated by the invention and applications of recombinant DNA technology that can yield nearly any protein of interest in large amounts and with relative ease. Novel methods, informatics platforms, and technologies for automation and high-throughput have allowed the development of large-scale, high efficiency macromolecular crystallography efforts in the field of structural genomics (SG). Very recently, the X-ray free-electron laser (XFEL) sources and its applications in protein crystallography have shown great potential for revolutionizing the whole field again in the near future.
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Affiliation(s)
- Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Heng Zhang
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Thomas C Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545, USA
| | - Anders Liljas
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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27
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Armenta-Medina D, Segovia L, Perez-Rueda E. Comparative genomics of nucleotide metabolism: a tour to the past of the three cellular domains of life. BMC Genomics 2014; 15:800. [PMID: 25230797 PMCID: PMC4177761 DOI: 10.1186/1471-2164-15-800] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 09/15/2014] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Nucleotide metabolism is central to all biological systems, due to their essential role in genetic information and energy transfer, which in turn suggests its possible presence in the last common ancestor (LCA) of Bacteria, Archaea and Eukarya. In this context, elucidation of the contribution of the origin and diversification of de novo and salvage pathways of nucleotide metabolism will allow us to understand the links between the enzymatic steps associated with the LCA and the emergence of the first metabolic pathways. RESULTS In this work, the taxonomical distribution of the enzymes associated with nucleotide metabolism was evaluated in 1,606 complete genomes. 151 sequence profiles associated with 120 enzymatic reactions were used. The evaluation was based on profile comparisons, using RPS-Blast. Organisms were clustered based on their taxonomical classifications, in order to obtain a normalized measure of the taxonomical distribution of enzymes according to the average of presence/absence of enzymes per genus, which in turn was used for the second step, to calculate the average presence/absence of enzymes per Clade. CONCLUSION From these analyses, it was suggested that divergence at the enzymatic level correlates with environmental changes and related modifications of the cell wall and membranes that took place during cell evolution. Specifically, the divergence of the 5-(carboxyamino) imidazole ribonucleotide mutase to phosphoribosylaminoimidazole carboxylase could be related to the emergence of multicellularity in eukaryotic cells. In addition, segments of salvage and de novo pathways were probably complementary in the LCA to the synthesis of purines and pyrimidines. We also suggest that a large portion of the pathway to inosine 5'-monophosphate (IMP) in purines could have been involved in thiamine synthesis or its derivatives in early stages of cellular evolution, correlating with the fact that these molecules may have played an active role in the protein-RNA world. The analysis presented here provides general observations concerning the adaptation of the enzymatic steps in the early stages of the emergence of life and the LCA.
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Affiliation(s)
- Dagoberto Armenta-Medina
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM Av, Universidad 2001, Cuernavaca, Morelos CP 62210, México.
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RNA mimicry by the fap7 adenylate kinase in ribosome biogenesis. PLoS Biol 2014; 12:e1001860. [PMID: 24823650 PMCID: PMC4019466 DOI: 10.1371/journal.pbio.1001860] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 04/04/2014] [Indexed: 11/22/2022] Open
Abstract
The structure of a ribosome assembly factor in complex bound to a ribosomal protein uncovers a chaperoning function that uses RNA mimicry and is regulated by ATP hydrolysis. During biogenesis of the 40S and 60S ribosomal subunits, the pre-40S particles are exported to the cytoplasm prior to final cleavage of the 20S pre-rRNA to mature 18S rRNA. Amongst the factors involved in this maturation step, Fap7 is unusual, as it both interacts with ribosomal protein Rps14 and harbors adenylate kinase activity, a function not usually associated with ribonucleoprotein assembly. Human hFap7 also regulates Cajal body assembly and cell cycle progression via the p53–MDM2 pathway. This work presents the functional and structural characterization of the Fap7–Rps14 complex. We report that Fap7 association blocks the RNA binding surface of Rps14 and, conversely, Rps14 binding inhibits adenylate kinase activity of Fap7. In addition, the affinity of Fap7 for Rps14 is higher with bound ADP, whereas ATP hydrolysis dissociates the complex. These results suggest that Fap7 chaperones Rps14 assembly into pre-40S particles via RNA mimicry in an ATP-dependent manner. Incorporation of Rps14 by Fap7 leads to a structural rearrangement of the platform domain necessary for the pre-rRNA to acquire a cleavage competent conformation. Ribosomes are the cellular machines responsible for all protein synthesis. In eukaryotes, the assembly of ribosomes from their protein and RNA components is extremely complicated and involves more than 200 nonribosomal factors—three times the number of proteins in the mature complex. Among these factors, the Fap7 protein is particularly intriguing because it interacts with the small subunit ribosomal protein Rps14 and it exhibits adenylate kinase activity—a molecular function more commonly associated with regulating ATP/ADP levels than assembling protein–RNA complexes. Combining structural and biochemical analysis of the Rps14–Fap7 complex, we show that Fap7 uses protein side chains to mimic RNA contacts, rendering the interaction of Rps14 with ribosomal RNA or with Fap7 competitive and mutually exclusive. Once bound, Rps14 blocks the substrate-binding cavity of Fap7, and ATP hydrolysis will then break the Fap7–Rps14 complex apart. At the same time, the ribosome structure at the location where Rps14 binds is disrupted when the Fap7/Rps14 complex is formed, and this process is regulated by ATP binding and hydrolysis. Our model is thus that Fap7 temporarily removes Rps14 from the ribosome to enable a conformational change of the ribosomal RNA that is needed for the final maturation step of the small ribosomal subunit.
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29
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The many isoforms of human adenylate kinases. Int J Biochem Cell Biol 2014; 49:75-83. [PMID: 24495878 DOI: 10.1016/j.biocel.2014.01.014] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 02/05/2023]
Abstract
Adenine nucleotides are involved in a variety of cellular metabolic processes, including nucleic acid synthesis and repair, formation of coenzymes, energy transfer, cell and ciliary motility, hormone secretion, gene expression regulation and ion-channel control. Adenylate kinases are abundant phosphotransferases that catalyze the interconversion of adenine nucleotides and thus regulate the adenine nucleotide ratios in different intracellular compartments. Nine different adenylate kinase isoenzymes have been identified and characterized so far in human tissues, named AK1 to AK9 according to their order of discovery. Adenylate kinases differ in molecular weight, tissue distribution, subcellular localization, substrate and phosphate donor specificity and kinetic properties. The preferred substrate and phosphate donor of all adenylate kinases are AMP and ATP respectively, but some members of the family can phosphorylate other substrates and use other phosphate donors. In addition to their nucleoside monophosphate kinase activity, adenylate kinases were found to possess nucleoside diphosphate kinase activity as they are able to phosphorylate both ribonucleoside and deoxyribonucleoside diphosphates to their corresponding triphosphates. Nucleoside analogues are structural analogues of natural nucleosides, used in the treatment of cancer and viral infections. They are inactive prodrugs that are dependent on intracellular phosphorylation to their pharmacologically active triphosphate form. Novel data presented in this review confirm the role of adenylate kinases in the activation of deoxyadenosine and deoxycytidine nucleoside analogues.
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Adenylate Kinase Isoform Network: A Major Hub in Cell Energetics and Metabolic Signaling. SYSTEMS BIOLOGY OF METABOLIC AND SIGNALING NETWORKS 2014. [DOI: 10.1007/978-3-642-38505-6_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Essential ribosome assembly factor Fap7 regulates a hierarchy of RNA-protein interactions during small ribosomal subunit biogenesis. Proc Natl Acad Sci U S A 2013; 110:15253-8. [PMID: 24003121 DOI: 10.1073/pnas.1306389110] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Factor activating Pos9 (Fap7) is an essential ribosome biogenesis factor important for the assembly of the small ribosomal subunit with an uncommon dual ATPase and adenylate kinase activity. Depletion of Fap7 or mutations in its ATPase motifs lead to defects in small ribosomal subunit rRNA maturation, the absence of ribosomal protein Rps14 from the assembled subunit, and retention of the nascent small subunit in a quality control complex with the large ribosomal subunit. The molecular basis for the role of Fap7 in ribosome biogenesis is, however, not yet understood. Here we show that Fap7 regulates multiple interactions between the precursor rRNA, ribosomal proteins, and ribosome assembly factors in a hierarchical manner. Fap7 binds to Rps14 with a very high affinity. Fap7 binding blocks both rRNA-binding elements of Rps14, suggesting that Fap7 inhibits premature interactions of Rps14 with RNA. The Fap7/Rps14 interaction is modulated by nucleotide binding to Fap7. Rps14 strongly activates the ATPase activity but not the adenylate kinase activity of Fap7, identifying Rps14 as an example of a ribosomal protein functioning as an ATPase-activating factor. In addition, Fap7 inhibits the RNA cleavage activity of Nob1, the endonuclease responsible for the final maturation step of the small subunit rRNA, in a nucleotide independent manner. Thus, Fap7 may regulate small subunit biogenesis at multiple stages.
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Simone PD, Pavlov YI, Borgstahl GEO. ITPA (inosine triphosphate pyrophosphatase): from surveillance of nucleotide pools to human disease and pharmacogenetics. Mutat Res 2013; 753:131-146. [PMID: 23969025 DOI: 10.1016/j.mrrev.2013.08.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/31/2013] [Accepted: 08/02/2013] [Indexed: 01/08/2023]
Abstract
Cellular nucleotide pools are often contaminated by base analog nucleotides which interfere with a plethora of biological reactions, from DNA and RNA synthesis to cellular signaling. An evolutionarily conserved inosine triphosphate pyrophosphatase (ITPA) removes the non-canonical purine (d)NTPs inosine triphosphate and xanthosine triphosphate by hydrolyzing them into their monophosphate form and pyrophosphate. Mutations in the ITPA orthologs in model organisms lead to genetic instability and, in mice, to severe developmental anomalies. In humans there is genetic polymorphism in ITPA. One allele leads to a proline to threonine substitution at amino acid 32 and causes varying degrees of ITPA deficiency in tissues and plays a role in patients' response to drugs. Structural analysis of this mutant protein reveals that the protein is destabilized by the formation of a cavity in its hydrophobic core. The Pro32Thr allele is thought to cause the observed dominant negative effect because the resulting active enzyme monomer targets both homo- and heterodimers to degradation.
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Affiliation(s)
- Peter D Simone
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Youri I Pavlov
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, USA; Department of Genetics, St-Petersburg University, St-Petersburg, 199034, Russia
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, USA; Department of Pharmaceutical Sciences, University of Nebraska Medical Center, USA.
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Kong F, Binas B, Moon JH, Kang SS, Kim HJ. Differential expression of adenylate kinase 4 in the context of disparate stress response strategies of HEK293 and HepG2 cells. Arch Biochem Biophys 2013; 533:11-7. [DOI: 10.1016/j.abb.2013.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/05/2013] [Accepted: 02/22/2013] [Indexed: 10/27/2022]
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Cámara MDLM, Bouvier LA, Canepa GE, Miranda MR, Pereira CA. Molecular and functional characterization of a Trypanosoma cruzi nuclear adenylate kinase isoform. PLoS Negl Trop Dis 2013; 7:e2044. [PMID: 23409202 PMCID: PMC3567042 DOI: 10.1371/journal.pntd.0002044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 12/17/2012] [Indexed: 01/30/2023] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas' disease, is an early divergent eukaryote in which control of gene expression relies mainly in post-transcriptional mechanisms. Transcription levels are globally up and down regulated during the transition between proliferating and non-proliferating life-cycle stages. In this work we characterized a nuclear adenylate kinase isoform (TcADKn) that is involved in ribosome biogenesis. Nuclear adenylate kinases have been recently described in a few organisms, being all related to RNA metabolism. Depending on active transcription and translation, TcADKn localizes in the nucleolus or the cytoplasm. A non-canonical nuclear localization signal was mapped towards the N-terminal of the protein, being the phosphate-binding loop essential for its localization. In addition, TcADKn nuclear exportation depends on the nuclear exportation adapter CRM1. TcADKn nuclear shuttling is governed by nutrient availability, oxidative stress and by the equivalent in T. cruzi of the mammalian TOR (Target of Rapamycin) pathway. One of the biological functions of TcADKn is ribosomal 18S RNA processing by direct interaction with ribosomal protein TcRps14. Finally, TcADKn expression is regulated by its 3′ UTR mRNA. Depending on extracellular conditions, cells modulate protein translation rates regulating ribosome biogenesis and nuclear adenylate kinases are probably key components in these processes. Infection with Trypanosoma cruzi produces a condition known as Chagas disease which affects at least 17 million people. Adenylate kinases, so called myokinases, are involved in a wide variety of processes, mainly related to their role in nucleotide interconversion and energy management. Recently, nuclear isoforms have been described in several organisms. This “atypical” isoform in terms of primary structure was associated to ribosomes biogenesis in yeast and to Cajal body organization in humans. Moreover nuclear adenylate kinases are essential for maintaining cellular homeostasis. In this manuscript we characterized T. cruzi nuclear adenylate kinase (TcADKn). TcADKn localizes in the nucleolus or cell cytoplasm. Nuclear shuttling mechanisms were also studied for the first time, being dependent on nutrient availability, oxidative stress and by the equivalent of the mammalian TOR pathway in T. cruzi. Furthermore we characterized the signals involved in nuclear importation and exportation processes. In addition, TcADKn expression levels are regulated at an mRNA level, being its 3′UTR involved in this process. These findings are the first steps in the understanding of ribosome processing in trypanosomatids.
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Affiliation(s)
| | | | | | | | - Claudio A. Pereira
- Laboratorio de Biología Molecular de Trypanosoma cruzi (LBMTC), Instituto de Investigaciones Médicas “Alfredo Lanari”, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
- * E-mail:
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Feng X, Yang R, Zheng X, Zhang F. Identification of a novel nuclear-localized adenylate kinase 6 from Arabidopsis thaliana as an essential stem growth factor. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 61:180-186. [PMID: 23121860 DOI: 10.1016/j.plaphy.2012.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 10/04/2012] [Indexed: 05/27/2023]
Abstract
Adenylate kinase (AK; EC 2.7.4.3) is highly conserved across a wide range of organisms, including Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, and Homo sapiens. While AK6 orthologs play important roles in the growth of yeast and worms, the physiological function of AK6 in A. thaliana is still unknown. In this study, we first cloned and expressed Arabidopsis adenylate kinase 6 (AAK6). Enzyme assays revealed that AAK6 has characteristic adenylate kinase properties, with ATP as the preferred phosphate donor and AMP as the best phosphate acceptor. A subcellular localization assay demonstrated that AAK6 had a predominant nuclear localization. Through biochemical purification and mass spectrometry analysis, a putative homolog of the S. cerevisiae Rps14 protein was identified as a partner of AAK6. Most importantly, we observed that aak6 T-DNA insertion mutants had decreased stem growth compared with wild-type plants. These data indicate that AAK6 exhibits adenylate kinase activity and is an essential growth factor in Arabidopsis.
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Affiliation(s)
- Xue Feng
- Capital Normal University Affiliated Li Ze Middle School, Beijing 100071, China
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Kenyon CP, Roth RL. The role of the C8 proton of ATP in the catalysis of shikimate kinase and adenylate kinase. BMC BIOCHEMISTRY 2012; 13:15. [PMID: 22876783 PMCID: PMC3537612 DOI: 10.1186/1471-2091-13-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 07/26/2012] [Indexed: 11/10/2022]
Abstract
Background It has been demonstrated that the adenyl moiety of ATP plays a direct role in the regulation of ATP binding and/or phosphoryl transfer within a range of kinase and synthetase enzymes. The role of the C8-H of ATP in the binding and/or phosphoryl transfer on the enzyme activity of a number of kinase and synthetase enzymes has been elucidated. The intrinsic catalysis rate mediated by each kinase enzyme is complex, yielding apparent KM values ranging from less than 0.4 μM to more than 1 mM for ATP in the various kinases. Using a combination of ATP deuterated at the C8 position (C8D-ATP) as a molecular probe with site directed mutagenesis (SDM) of conserved amino acid residues in shikimate kinase and adenylate kinase active sites, we have elucidated a mechanism by which the ATP C8-H is induced to be labile in the broader kinase family. We have demonstrated the direct role of the C8-H in the rate of ATP consumption, and the direct role played by conserved Thr residues interacting with the C8-H. The mechanism by which the vast range in KM might be achieved is also suggested by these findings. Results We have demonstrated the mechanism by which the enzyme activities of Group 2 kinases, shikimate kinase (SK) and adenylate kinase 1 (AK1), are controlled by the C8-H of ATP. Mutations of the conserved threonine residues associated with the labile C8-H cause the enzymes to lose their saturation kinetics over the concentration range tested. The relationship between the role C8-H of ATP in the reaction mechanism and the ATP concentration as they influence the saturation kinetics of the enzyme activity is also shown. The SDM clearly identified the amino acid residues involved in both the catalysis and regulation of phosphoryl transfer in SK and AK1 as mediated by C8H-ATP. Conclusions The data outlined serves to demonstrate the “push” mechanism associated with the control of the saturation kinetics of Group 2 kinases mediated by ATP C8-H. It is therefore conceivable that kinase enzymes achieve the observed 2,500-fold variation in KM through a combination of the various conserved “push” and “pull” mechanisms associated with the release of C8-H, the proton transfer cascades unique to the class of kinase in question and the resultant/concomitant creation of a pentavalent species from the γ-phosphate group of ATP. Also demonstrated is the interplay between the role of the C8-H of ATP and the ATP concentration in the observed enzyme activity. The lability of the C8-H mediated by active site residues co-ordinated to the purine ring of ATP therefore plays a significant role in explaining the broad KM range associated with kinase steady state enzyme activities.
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Affiliation(s)
- Colin P Kenyon
- CSIR, Biosciences, Meiring Naude Road, Pretoria 0001, Gauteng, South Africa.
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Ma J, Rahlfs S, Jortzik E, Schirmer RH, Przyborski JM, Becker K. Subcellular localization of adenylate kinases in Plasmodium falciparum. FEBS Lett 2012; 586:3037-43. [PMID: 22819813 DOI: 10.1016/j.febslet.2012.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/14/2012] [Accepted: 07/02/2012] [Indexed: 11/18/2022]
Abstract
Adenylate kinases (AK) play a key role in nucleotide signaling processes and energy metabolism by catalyzing the reversible conversion of ATP and AMP to 2 ADP. In the malaria parasite Plasmodium falciparum this reaction is mediated by AK1, AK2, and a GTP:AMP phosphotransferase (GAK). Here, we describe two additional adenylate kinase-like proteins: PfAKLP1, which is homologous to human AK6, and PfAKLP2. Using GFP-fusion proteins and life cell imaging, we demonstrate a cytosolic localization for PfAK1, PfAKLP1, and PfAKLP2, whereas PfGAK is located in the mitochondrion. PfAK2 is located at the parasitophorous vacuole membrane, and this localization is driven by N-myristoylation.
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Affiliation(s)
- Jipeng Ma
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, 35392 Giessen, Germany
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Ru H, Zhao L, Ding W, Jiao L, Shaw N, Liang W, Zhang L, Hung LW, Matsugaki N, Wakatsuki S, Liu ZJ. S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:521-30. [PMID: 22525750 PMCID: PMC3335285 DOI: 10.1107/s0907444912004490] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 02/02/2012] [Indexed: 12/17/2022]
Abstract
A subset of tumour necrosis factor receptor (TNFR) superfamily members contain death domains in their cytoplasmic tails. Death receptor 6 (DR6) is one such member and can trigger apoptosis upon the binding of a ligand by its cysteine-rich domains (CRDs). The crystal structure of the ectodomain (amino acids 1-348) of human death receptor 6 (DR6) encompassing the CRD region was phased using the anomalous signal from S atoms. In order to explore the feasibility of S-SAD phasing at longer wavelengths (beyond 2.5 Å), a comparative study was performed on data collected at wavelengths of 2.0 and 2.7 Å. In spite of sub-optimal experimental conditions, the 2.7 Å wavelength used for data collection showed potential for S-SAD phasing. The results showed that the R(ano)/R(p.i.m.) ratio is a good indicator for monitoring the anomalous data quality when the anomalous signal is relatively strong, while d''/sig(d'') calculated by SHELXC is a more sensitive and stable indicator applicable for grading a wider range of anomalous data qualities. The use of the `parameter-space screening method' for S-SAD phasing resulted in solutions for data sets that failed during manual attempts. SAXS measurements on the ectodomain suggested that a dimer defines the minimal physical unit of an unliganded DR6 molecule in solution.
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Affiliation(s)
- Heng Ru
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing 100 049, People’s Republic of China
| | - Lixia Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Wei Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Lianying Jiao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Neil Shaw
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, People’s Republic of China
| | - Wenguang Liang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Liguo Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Li-Wei Hung
- Physics Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Naohiro Matsugaki
- Structure Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Soichi Wakatsuki
- Structure Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, People’s Republic of China
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Drakou CE, Malekkou A, Hayes JM, Lederer CW, Leonidas DD, Oikonomakos NG, Lamond AI, Santama N, Zographos SE. hCINAP is an atypical mammalian nuclear adenylate kinase with an ATPase motif: structural and functional studies. Proteins 2011; 80:206-20. [PMID: 22038794 DOI: 10.1002/prot.23186] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 08/01/2011] [Accepted: 08/27/2011] [Indexed: 11/11/2022]
Abstract
Human coilin interacting nuclear ATPase protein (hCINAP) directly interacts with coilin, a marker protein of Cajal Bodies (CBs), nuclear organelles involved in the maturation of small nuclear ribonucleoproteins UsnRNPs and snoRNPs. hCINAP has previously been designated as an adenylate kinase (AK6), but is very atypical as it exhibits unusually broad substrate specificity, structural features characteristic of ATPase/GTPase proteins (Walker motifs A and B) and also intrinsic ATPase activity. Despite its intriguing structure, unique properties and cellular localization, the enzymatic mechanism and biological function of hCINAP have remained poorly characterized. Here, we offer the first high-resolution structure of hCINAP in complex with the substrate ADP (and dADP), the structure of hCINAP with a sulfate ion bound at the AMP binding site, and the structure of the ternary complex hCINAP-Mg(2+) ADP-Pi. Induced fit docking calculations are used to predict the structure of the hCINAP-Mg(2+) ATP-AMP ternary complex. Structural analysis suggested a functional role for His79 in the Walker B motif. Kinetic analysis of mutant hCINAP-H79G indicates that His79 affects both AK and ATPase catalytic efficiency and induces homodimer formation. Finally, we show that in vivo expression of hCINAP-H79G in human cells is toxic and drastically deregulates the number and appearance of CBs in the cell nucleus. Our findings suggest that hCINAP may not simply regulate nucleotide homeostasis, but may have broader functionality, including control of CB assembly and disassembly in the nucleus of human cells.
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Affiliation(s)
- Christina E Drakou
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Athens 11635, Greece
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40
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Su XD, Jin FJ. Davydov-Pang model: an improved Davydov protein soliton theory: comment on "The theory of bio-energy transport in the protein molecules and its properties" by Xiaofeng Pang. Phys Life Rev 2011; 8:300-1; discussion 302-6. [PMID: 21900056 DOI: 10.1016/j.plrev.2011.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 08/18/2011] [Indexed: 12/01/2022]
Affiliation(s)
- Xiao-Dong Su
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, PR China.
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41
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Peterson AW, Pendrak ML, Roberts DD. ATP binding to hemoglobin response gene 1 protein is necessary for regulation of the mating type locus in Candida albicans. J Biol Chem 2011; 286:13914-24. [PMID: 21372131 PMCID: PMC3077592 DOI: 10.1074/jbc.m110.180190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 02/28/2011] [Indexed: 11/06/2022] Open
Abstract
HBR1 (hemoglobin response gene 1) is an essential gene in Candida albicans that positively regulates mating type locus MTLα gene expression and thereby regulates cell type-specific developmental genes. Hbr1p contains a phosphate-binding loop (P-loop), a highly conserved motif characteristic of ATP- and GTP-binding proteins. Recombinant Hbr1p was isolated in an oligomeric state that specifically bound ATP with K(d) ∼2 μM. ATP but not ADP, AMP, GTP, or dATP specifically protected Hbr1p from proteolysis by trypsin. Site-directed mutagenesis of the highly conserved P-loop lysine (K22Q) and the less conserved glycine (G19S) decreased the binding affinity for soluble ATP and ATP immobilized through its γ-phosphate. ATP bound somewhat more avidly than ATPγS to wild type and mutant Hbr1p. Although Hbr1p exhibits sequence motifs characteristic of adenylate kinases, and adenylate kinase and ATPase activities have been reported for the apparent human ortholog of Hbr1p, assays for adenylate kinase activity, autophosphorylation, and ATPase activity proved negative. Overexpression of wild type but not the mutant forms of Hbr1p restored MTlα2 expression in an HBR1/hbr1 mutant, indicating that ATP binding to the P-loop is necessary for this function of Hbr1p.
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Affiliation(s)
- Alexander W. Peterson
- From the Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1500
| | - Michael L. Pendrak
- From the Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1500
| | - David D. Roberts
- From the Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1500
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42
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The characterization of human adenylate kinases 7 and 8 demonstrates differences in kinetic parameters and structural organization among the family of adenylate kinase isoenzymes. Biochem J 2011; 433:527-34. [PMID: 21080915 DOI: 10.1042/bj20101443] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Differences in expression profiles, substrate specificities, kinetic properties and subcellular localization among the AK (adenylate kinase) isoenzymes have been shown to be important for maintaining a proper adenine nucleotide composition for many different cell functions. In the present study, human AK7 was characterized and its substrate specificity, kinetic properties and subcellular localization determined. In addition, a novel member of the human AK family, with two functional domains, was identified and characterized and assigned the name AK8. AK8 is the second known human AK with two complete and active AK domains within its polypeptide chain, a feature that has previously been shown for AK5. The full-length AK8, as well as its two domains AK8p1 and AK8p2, all showed similar AK enzyme activity. AK7, full-length AK8, AK8p1 and AK8p2 phosphorylated AMP, CMP, dAMP and dCMP with ATP as the phosphate donor, and also AMP, CMP and dCMP with GTP as the phosphate donor. Both AK7 and full-length AK8 showed highest affinity for AMP with ATP as the phosphate donor, and proved to be more efficient in AMP phosphorylation as compared with the major cytosolic isoform AK1. Expression of the proteins fused with green fluorescent protein demonstrated a cytosolic localization for both AK7 and AK8.
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43
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Sakumi K, Abolhassani N, Behmanesh M, Iyama T, Tsuchimoto D, Nakabeppu Y. ITPA protein, an enzyme that eliminates deaminated purine nucleoside triphosphates in cells. Mutat Res 2010; 703:43-50. [PMID: 20601097 DOI: 10.1016/j.mrgentox.2010.06.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 06/13/2010] [Indexed: 12/14/2022]
Abstract
Inosine triphosphate pyrophosphatase (ITPA protein) (EC 3.6.1.19) hydrolyzes deaminated purine nucleoside triphosphates, such as ITP and dITP, to their corresponding purine nucleoside monophosphate and pyrophosphate. In mammals, this enzyme is encoded by the Itpa gene. Using the Itpa gene-disrupted mouse as a model, we have elucidated the biological significance of the ITPA protein and its substrates, ITP and dITP. Itpa(-/-) mice exhibited peri- or post-natal lethality dependent on the genetic background. The heart of the Itpa(-/-) mouse was found to be structurally and functionally abnormal. Significantly higher levels of deoxyinosine and inosine were detected in nuclear DNA and RNA prepared from Itpa(-/-) embryos compared to wild type embryos. In addition, an accumulation of ITP was observed in the erythrocytes of Itpa(-/-) mice. We found that Itpa(-/-) primary mouse embryonic fibroblasts (MEFs), which have no detectable ability to generate IMP from ITP in whole cell extracts, exhibited a prolonged population-doubling time, increased chromosome abnormalities and accumulation of single-strand breaks in their nuclear DNA, in comparison to primary MEFs prepared from wild type embryos. These results revealed that (1) ITP and dITP are spontaneously produced in vivo and (2) accumulation of ITP and dITP is responsible for the harmful effects observed in the Itpa(-/-) mouse. In addition to its effect as the precursor nucleotide for RNA transcription, ITP has the potential to influence the activity of ATP/GTP-binding proteins. The biological significance of ITP and dITP in the nucleotide pool remains to be elucidated.
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Affiliation(s)
- Kunihiko Sakumi
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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44
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Malekkou A, Lederer CW, Lamond AI, Santama N. The nuclear ATPase/adenylate kinase hCINAP is recruited to perinucleolar caps generated upon RNA pol.II inhibition. FEBS Lett 2010; 584:4559-64. [PMID: 20974138 PMCID: PMC3839081 DOI: 10.1016/j.febslet.2010.10.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 10/01/2010] [Accepted: 10/19/2010] [Indexed: 11/19/2022]
Abstract
hCINAP is an atypical nucleoplasmic enzyme, combining structural features of adenylate kinases and ATPases, which exhibits dual enzymatic activity. It interacts with the Cajal Body marker coilin and its level of expression and enzymatic activity influence Cajal Body numbers. Here we show that upon specific transcriptional inhibition of RNA pol.II, hCINAP segregates in perinuclear caps identified as Dark Nucleolar Caps (DNCs). These are distinct from perinucleolar caps where coilin and fibrillarin (both Cajal Body components) accumulate. In DNCs, hCINAP co-localizes with Paraspeckle Protein (PSP1) and also co-segregates with PSP1, and not coilin, in nuclear and nucleolar foci upon UV irradiation.
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Affiliation(s)
- Anna Malekkou
- Department of Biological Sciences, University of Cyprus and Cyprus Institute of Neurology and Genetics, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Carsten W. Lederer
- Department of Biological Sciences, University of Cyprus and Cyprus Institute of Neurology and Genetics, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Angus I. Lamond
- Division of Gene Regulation and Expression, University of Dundee, MSI/WTB Complex, Dundee DD1 5EH, Scotland, UK
| | - Niovi Santama
- Department of Biological Sciences, University of Cyprus and Cyprus Institute of Neurology and Genetics, P.O. Box 20537, 1678 Nicosia, Cyprus
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Cheng X, Xu Z, Wang J, Zhai Y, Lu Y, Liang C. ATP-dependent pre-replicative complex assembly is facilitated by Adk1p in budding yeast. J Biol Chem 2010; 285:29974-80. [PMID: 20659900 PMCID: PMC2943264 DOI: 10.1074/jbc.m110.161455] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 07/16/2010] [Indexed: 01/30/2023] Open
Abstract
Pre-replicative complex (pre-RC) assembly is a critical part of the mechanism that controls the initiation of DNA replication, and ATP binding and hydrolysis by multiple pre-RC proteins are essential for pre-RC assembly and activation. Here, we demonstrate that Adk1p (adenylate kinase 1 protein) plays an important role in pre-RC assembly in Saccharomyces cerevisiae. Isolated from a genetic screen, adk1(G20S) cells with a mutation within the nucleotide-binding site were defective in replication initiation. adk1Δ cells were viable at 25 °C but not at 37°C. Flow cytometry indicated that both the adk1-td (temperature-inducible degron) and adk1(G20S) mutants were defective in S phase entry. Furthermore, Adk1p bound to chromatin throughout the cell cycle and physically interacted with Orc3p, whereas the Adk1(G20S) protein had a reduced ability to bind chromatin and Orc3p without affecting the cellular ATP level. In addition, Adk1p associated with replication origins by ChIP assay. Finally, Adk1-td protein depletion prevented pre-RC assembly during the M-to-G(1) transition. We suggest that Adk1p regulates ATP metabolism on pre-RC proteins to promote pre-RC assembly and activation.
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Affiliation(s)
- Xue Cheng
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
| | - Zhen Xu
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
| | - Jiafeng Wang
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
- the School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanliang Zhai
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
| | - Yongjun Lu
- the School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chun Liang
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
- the School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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46
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Zhang J, Zhang F, Zheng X. Depletion of hCINAP by RNA interference causes defects in Cajal body formation, histone transcription, and cell viability. Cell Mol Life Sci 2010; 67:1907-18. [PMID: 20186459 PMCID: PMC11115741 DOI: 10.1007/s00018-010-0301-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 01/25/2010] [Accepted: 02/02/2010] [Indexed: 10/19/2022]
Abstract
hCINAP is a highly conserved and ubiquitously expressed protein in eukaryotic organisms and its overexpression decreases the average number of Cajal bodies (CBs) with diverse nuclear functions. Here, we report that hCINAP is associated with important components of CBs. Depletion of hCINAP by RNA interference causes defects in CB formation and disrupts subcellular localizations of its components including coilin, survival motor neurons protein, spliceosomal small nuclear ribonucleoproteins, and nuclear protein ataxia-telangiectasia. Moreover, knockdown of hCINAP expression results in marked reduction of histone transcription, lower levels of U small nuclear RNAs (U1, U2, U4, and U5), and a loss of cell viability. Detection of increased caspase-3 activities in hCINAP-depleted cells indicate that apoptosis is one of the reasons for the loss of viability. Altogether, these data suggest that hCINAP is essential for the formation of canonical CBs, histone transcription, and cell viability.
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Affiliation(s)
- Jinfang Zhang
- National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871 China
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing, 100871 China
| | - Feiyun Zhang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Capital Normal University, Beijing, 100037 China
| | - Xiaofeng Zheng
- National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871 China
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing, 100871 China
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Yin S, Loo JA. Elucidating the site of protein-ATP binding by top-down mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:899-907. [PMID: 20163968 DOI: 10.1016/j.jasms.2010.01.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 01/08/2010] [Accepted: 01/08/2010] [Indexed: 05/11/2023]
Abstract
A Fourier-transform ion cyclotron resonance (FT-ICR) top-down mass spectrometry strategy for determining the adenosine triphosphate (ATP)-binding site on chicken adenylate kinase is described. Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS), but the ability to detect protein-ligand complexes depends on their stability in the gas phase. Previously, we showed that collisionally activated dissociation (CAD) of protein-nucleotide triphosphate complexes yield products from the dissociation of a covalent phosphate bond of the nucleotide with subsequent release of the nucleotide monophosphate (Yin, S. et al., J. Am. Soc. Mass Spectrom. 2008, 19, 1199-1208). The intrinsic stability of electrostatic interactions in the gas phase allows the diphosphate group to remain noncovalently bound to the protein. This feature is exploited to yield positional information on the site of ATP-binding on adenylate kinase. CAD and electron capture dissociation (ECD) of the adenylate kinase-ATP complex generate product ions bearing mono- and diphosphate groups from regions previously suggested as the ATP-binding pocket by NMR and crystallographic techniques. Top-down MS may be a viable tool to determine the ATP-binding sites on protein kinases and identify previously unknown protein kinases in a functional proteomics study.
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Affiliation(s)
- Sheng Yin
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, USA
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Panayiotou C, Solaroli N, Johansson M, Karlsson A. Evidence of an intact N-terminal translocation sequence of human mitochondrial adenylate kinase 4. Int J Biochem Cell Biol 2009; 42:62-9. [PMID: 19766732 DOI: 10.1016/j.biocel.2009.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 09/08/2009] [Accepted: 09/11/2009] [Indexed: 10/20/2022]
Abstract
Adenylate kinases are abundant nucleoside monophosphate kinases, which catalyze the phosphorylation of AMP by using ATP or GTP as phosphate donors. A previously cloned cDNA was named adenylate kinase 4 (AK4) based on its sequence similarity with known AKs but with no confirmed AK enzyme activity. In the present study the AK4 cDNA was expressed in Escherichia coli and the substrate specificity and kinetic properties of the recombinant protein were characterized. The enzyme catalyzed the phosphorylation of AMP, dAMP, CMP and dCMP with ATP or GTP as phosphate donors and AK4 also phosphorylated AMP with UTP as phosphate donor. The kinetic parameters of the enzyme were determined for AMP and dAMP with ATP as phosphate donor and for AMP with GTP as phosphate donor. AK4 showed its highest efficiency when phosphorylating AMP with GTP and a slightly lower efficiency for the phosphorylation of AMP with ATP. Among the three reactions for which kinetics were performed, dAMP was the poorest substrate. The AK4 mitochondrial localization was confirmed by expression of AK4 as a fusion protein with GFP in HeLa cells. The mitochondrial import sequence was shown to be located within the first N-terminal 11 amino acid residues, very close to the ATP-binding region of the enzyme. Import analysis suggested that the mitochondrial import sequence was not cleaved and thus the enzyme retained its activity upon entering the mitochondria. Site directed mutagenesis of amino acids Lys 4 and Arg 7 showed that these two residues were essential for mitochondrial import.
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Affiliation(s)
- Christakis Panayiotou
- Department of Laboratory Medicine, Karolinska Institute, F68, S-141 86 Huddinge, Sweden.
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Kuettel S, Mosimann M, Mäser P, Kaiser M, Brun R, Scapozza L, Perozzo R. Adenosine Kinase of T. b. Rhodesiense identified as the putative target of 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine using chemical proteomics. PLoS Negl Trop Dis 2009; 3:e506. [PMID: 19707572 PMCID: PMC2724708 DOI: 10.1371/journal.pntd.0000506] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 07/23/2009] [Indexed: 11/20/2022] Open
Abstract
Background Human African trypanosomiasis (HAT), a major parasitic disease spread in Africa, urgently needs novel targets and new efficacious chemotherapeutic agents. Recently, we discovered that 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine (compound 1) exhibits specific antitrypanosomal activity with an IC50 of 1.0 µM on Trypanosoma brucei rhodesiense (T. b. rhodesiense), the causative agent of the acute form of HAT. Methodology/Principal Findings In this work we show adenosine kinase of T. b. rhodesiense (TbrAK), a key enzyme of the parasite purine salvage pathway which is vital for parasite survival, to be the putative intracellular target of compound 1 using a chemical proteomics approach. This finding was confirmed by RNA interference experiments showing that down-regulation of adenosine kinase counteracts compound 1 activity. Further chemical validation demonstrated that compound 1 interacts specifically and tightly with TbrAK with nanomolar affinity, and in vitro activity measurements showed that compound 1 is an enhancer of TbrAK activity. The subsequent kinetic analysis provided strong evidence that the observed hyperactivation of TbrAK is due to the abolishment of the intrinsic substrate-inhibition. Conclusions/Significance The results suggest that TbrAK is the putative target of this compound, and that hyperactivation of TbrAK may represent a novel therapeutic strategy for the development of trypanocides. Human African trypanosomiasis (HAT), a devastating and fatal parasitic disease endemic in sub-Saharan Africa, urgently needs novel targets and efficacious chemotherapeutic agents. Recently, we discovered that 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine exhibits specific antitrypanosomal activity toward T. b. rhodesiense, the causative agent of the acute form of HAT. Here we applied a chemical proteomics approach to find the cellular target of this compound. Adenosine kinase, a key enzyme of the parasite purine salvage pathway, was isolated and identified as compound binding partner. Direct binding assays using recombinant protein, and tests on an adenosine kinase knock-down mutant of the parasite produced by RNA interference confirmed TbrAK as the putative target. Kinetic analyses showed that the title compound is an activator of adenosine kinase and that the observed hyperactivation of TbrAK is due to the abolishment of the intrinsic substrate-inhibition. Whereas hyperactivation as a mechanism of action is well known from drugs targeting cell signaling, this is a novel and hitherto unexplored concept for compounds targeting metabolic enzymes, suggesting that hyperactivation of TbrAK may represent a novel therapeutic strategy for the development of trypanocides.
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Affiliation(s)
- Sabine Kuettel
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Marc Mosimann
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Pascal Mäser
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Marcel Kaiser
- Parasite Chemotherapy, Swiss Tropical Institute, Basel, Switzerland
| | - Reto Brun
- Parasite Chemotherapy, Swiss Tropical Institute, Basel, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
- * E-mail: (LS); (RP)
| | - Remo Perozzo
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
- * E-mail: (LS); (RP)
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Solaroli N, Panayiotou C, Johansson M, Karlsson A. Identification of two active functional domains of human adenylate kinase 5. FEBS Lett 2009; 583:2872-6. [DOI: 10.1016/j.febslet.2009.07.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 07/23/2009] [Accepted: 07/27/2009] [Indexed: 11/25/2022]
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