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Park J, Lee N, Kim H, Kim D, Shin S, Choi S, Choi GJ, Son H. A mitochondrial NAD/NADH kinase governs fungal virulence through an oxidative stress response and arginine biosynthesis in Fusarium graminearum. Microbiol Res 2024; 283:127692. [PMID: 38508088 DOI: 10.1016/j.micres.2024.127692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
NADP/NADPH plays an indispensable role in cellular metabolism, serving as a pivotal cofactor in numerous enzymatic processes involved in anabolic pathways, antioxidant defense, and the biosynthesis of essential cellular components. NAD/NADH kinases (NADKs) phosphorylate NAD/NADH, constituting the sole de novo synthetic pathway for NADP/NADPH generation. Despite the pivotal role of NADP/NADPH in cellular functions, the physiological role of NADK remains largely unexplored in filamentous fungi. In this study, we identified three putative NADKs in Fusarium graminearum-FgNadk1, FgNadk2, and FgNadk3-responsible for NAD/NADH phosphorylation. NADK-mediated formation of intracellular NADPH proved crucial for vegetative growth, sexual reproduction, and virulence. Specifically, FgNadk2, the mitochondrial NADK, played a role in oxidative stress resistance and the maintenance of mitochondrial reactive oxygen species levels. Moreover, the deletion of FgNADK2 resulted in arginine auxotrophy, contributing to the reduced fungal virulence. These findings underscore the necessity of mitochondrial NADK in fungal virulence in F. graminearum, revealing its involvement in mitochondrial redox homeostasis and the arginine biosynthetic pathway. This study provides critical insights into the interconnectedness of metabolic pathways essential for fungal growth, stress response, and pathogenicity.
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Affiliation(s)
- Jiyeun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Nahyun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Hun Kim
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Dohun Kim
- Childern's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Soobin Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Soyoung Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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Wang Y, Liu C, Qin Y, Du Y, Song C, Kang Z, Guo J, Guo J. Stripe rust effector Pst03724 modulates host immunity by inhibiting NAD kinase activation by a calmodulin. PLANT PHYSIOLOGY 2024; 195:1624-1641. [PMID: 38441329 DOI: 10.1093/plphys/kiae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/19/2024] [Indexed: 06/02/2024]
Abstract
Puccinia striiformis f. sp. tritici (Pst) secretes effector proteins that enter plant cells to manipulate host immune processes. In this report, we present an important Pst effector, Pst03724, whose mRNA expression level increases during Pst infection of wheat (Triticum aestivum). Silencing of Pst03724 reduced the growth and development of Pst. Pst03724 targeted the wheat calmodulin TaCaM3-2B, a positive regulator of wheat immunity. Subsequent investigations revealed that Pst03724 interferes with the TaCaM3-2B-NAD kinase (NADK) TaNADK2 association and thus inhibits the enzyme activity of TaNADK2 activated by TaCaM3-2B. Knocking down TaNADK2 expression by virus-mediated gene silencing significantly increased fungal growth and development, suggesting a decrease in resistance against Pst infection. In conclusion, our findings indicate that Pst effector Pst03724 inhibits the activity of NADK by interfering with the TaCaM3-2B-TaNADK2 association, thereby facilitating Pst infection.
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Affiliation(s)
- Yanfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, P. R. China
| | - Cong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, P. R. China
| | - Yuanyang Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, P. R. China
| | - Yuanyuan Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, P. R. China
| | - Chao Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, P. R. China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, P. R. China
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, P. R. China
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, P. R. China
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3
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Cao K, Cui Y, Sun F, Zhang H, Fan J, Ge B, Cao Y, Wang X, Zhu X, Wei Z, Yao Q, Ma J, Wang Y, Meng C, Gao Z. Metabolic engineering and synthetic biology strategies for producing high-value natural pigments in Microalgae. Biotechnol Adv 2023; 68:108236. [PMID: 37586543 DOI: 10.1016/j.biotechadv.2023.108236] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/16/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Microalgae are microorganisms capable of producing bioactive compounds using photosynthesis. Microalgae contain a variety of high value-added natural pigments such as carotenoids, phycobilins, and chlorophylls. These pigments play an important role in many areas such as food, pharmaceuticals, and cosmetics. Natural pigments have a health value that is unmatched by synthetic pigments. However, the current commercial production of natural pigments from microalgae is not able to meet the growing market demand. The use of metabolic engineering and synthetic biological strategies to improve the production performance of microalgal cell factories is essential to promote the large-scale production of high-value pigments from microalgae. This paper reviews the health and economic values, the applications, and the synthesis pathways of microalgal pigments. Overall, this review aims to highlight the latest research progress in metabolic engineering and synthetic biology in constructing engineered strains of microalgae with high-value pigments and the application of CRISPR technology and multi-omics in this context. Finally, we conclude with a discussion on the bottlenecks and challenges of microalgal pigment production and their future development prospects.
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Affiliation(s)
- Kai Cao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China; School of Life Sciences and medicine, Shandong University of Technology, Zibo 255049, China
| | - Yulin Cui
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Fengjie Sun
- Department of Biological Sciences, School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Hao Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Jianhua Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Yujiao Cao
- School of Foreign Languages, Shandong University of Technology, Zibo 255090, China
| | - Xiaodong Wang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Xiangyu Zhu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China; School of Life Sciences and medicine, Shandong University of Technology, Zibo 255049, China
| | - Zuoxi Wei
- School of Life Sciences and medicine, Shandong University of Technology, Zibo 255049, China
| | - Qingshou Yao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Jinju Ma
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Yu Wang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Chunxiao Meng
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
| | - Zhengquan Gao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
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Azouaoui D, Choinière MR, Khan M, Sayfi S, Jaffer S, Yousef S, Patten DA, Green AE, Menzies KJ. Meta-analysis of NAD(P)(H) quantification results exhibits variability across mammalian tissues. Sci Rep 2023; 13:2464. [PMID: 36774401 PMCID: PMC9922293 DOI: 10.1038/s41598-023-29607-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 02/07/2023] [Indexed: 02/13/2023] Open
Abstract
Nicotinamide Adenine Dinucleotide (NAD+) plays an important role in energy metabolism and signaling pathways controlling crucial cellular functions. The increased interest in NAD+ metabolism and NAD+-boosting therapies has reinforced the necessity for accurate NAD+ quantification. To examine the published NAD(P)(H) measures across mammalian tissues, we performed a meta-analysis of the existing data. An Ovid MEDLINE database search identified articles with NAD(P)(H) quantification results obtained from mammalian tissues published between 1961 and 2021. We screened 4890 records and extracted quantitative data, as well as the quantification methods, pre-analytical conditions, and subject characteristics. The extracted physiological NAD(P)(H) concentrations in various tissues from mice, rats, and humans, revealed an important inter- and intra-method variability that extended to recent publications. This highlights the relatively poor potential for cross-experimental analyses for NAD(P)(H) quantitative data and the importance of standardization for NAD(P)(H) quantification methods and pre-analytical procedures for future preclinical and clinical studies.
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Affiliation(s)
- Dassine Azouaoui
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Michael René Choinière
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Momtafin Khan
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Shahab Sayfi
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Simran Jaffer
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Selvia Yousef
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - David A Patten
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Alexander E Green
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Keir J Menzies
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada.
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5
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Clément DA, Gelin M, Leseigneur C, Huteau V, Mondange L, Pons JL, Dussurget O, Lionne C, Labesse G, Pochet S. Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria. Eur J Med Chem 2023; 246:114941. [PMID: 36455355 DOI: 10.1016/j.ejmech.2022.114941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Nicotinamide adenine dinucleotide kinases (NAD kinases) are essential and ubiquitous enzymes involved in the production of NADP(H) which is an essential cofactor in many metabolic pathways. Targeting NAD kinase (NADK), a rate limiting enzyme of NADP biosynthesis pathway, represents a new promising approach to treat bacterial infections. Previously, we have produced the first NADK inhibitor active against staphylococcal infection. From this linear di-adenosine derivative, namely NKI1, we designed macrocyclic analogues. Here, we describe the synthesis and evaluation of an original series of cyclic diadenosine derivatives as NADK inhibitors of two pathogenic bacteria, Listeria monocytogenes and Staphylococcus aureus. The nature and length of the link between the two adenosine units were examined leading to sub-micromolar inhibitors of NADK1 from L. monocytogenes, including its most potent in vitro inhibitor reported so far (with a 300-fold improvement compared to NKI1).
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Affiliation(s)
- David A Clément
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie et Biocatalyse, F-75015, Paris, France
| | - Muriel Gelin
- Centre de Biologie Structurale (CBS), CNRS UMR5048, INSERM U1054, Université de Montpellier, 34090, Montpellier, France
| | - Clarisse Leseigneur
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, F-75015, Paris, France
| | - Valérie Huteau
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie et Biocatalyse, F-75015, Paris, France
| | - Lou Mondange
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, F-75015, Paris, France
| | - Jean-Luc Pons
- Centre de Biologie Structurale (CBS), CNRS UMR5048, INSERM U1054, Université de Montpellier, 34090, Montpellier, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, F-75015, Paris, France
| | - Corinne Lionne
- Centre de Biologie Structurale (CBS), CNRS UMR5048, INSERM U1054, Université de Montpellier, 34090, Montpellier, France
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS), CNRS UMR5048, INSERM U1054, Université de Montpellier, 34090, Montpellier, France.
| | - Sylvie Pochet
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie et Biocatalyse, F-75015, Paris, France.
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6
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Inhibition of NAD kinase elevates the hepatic NAD+ pool and alleviates acetaminophen-induced acute liver injury in mice. Biochem Biophys Res Commun 2022; 612:70-76. [DOI: 10.1016/j.bbrc.2022.04.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 11/22/2022]
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7
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Leseigneur C, Boucontet L, Duchateau M, Pizarro-Cerda J, Matondo M, Colucci-Guyon E, Dussurget O. NAD kinase promotes Staphylococcus aureus pathogenesis by supporting production of virulence factors and protective enzymes. eLife 2022; 11:79941. [PMID: 35723663 PMCID: PMC9208755 DOI: 10.7554/elife.79941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Nicotinamide adenine dinucleotide phosphate (NADPH) is the primary electron donor for reductive reactions that are essential for the biosynthesis of major cell components in all organisms. Nicotinamide adenine dinucleotide kinase (NADK) is the only enzyme that catalyzes the synthesis of NADP(H) from NAD(H). While the enzymatic properties and physiological functions of NADK have been thoroughly studied, the role of NADK in bacterial pathogenesis remains unknown. Here, we used CRISPR interference to knock down NADK gene expression to address the role of this enzyme in Staphylococcus aureus pathogenic potential. We find that NADK inhibition drastically decreases mortality of zebrafish infected with S. aureus. Furthermore, we show that NADK promotes S. aureus survival in infected macrophages by protecting bacteria from antimicrobial defense mechanisms. Proteome-wide data analysis revealed that production of major virulence-associated factors is sustained by NADK. We demonstrate that NADK is required for expression of the quorum-sensing response regulator AgrA, which controls critical S. aureus virulence determinants. These findings support a key role for NADK in bacteria survival within innate immune cells and the host during infection.
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Affiliation(s)
- Clarisse Leseigneur
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, Paris, France
| | - Laurent Boucontet
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Unité Macrophages et Développement de l'Immunité, Paris, France
| | - Magalie Duchateau
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Unité de Spectrométrie de Masse pour la Biologie, Plateforme de protéomique, Paris, France
| | - Javier Pizarro-Cerda
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Unité de Spectrométrie de Masse pour la Biologie, Plateforme de protéomique, Paris, France
| | - Emma Colucci-Guyon
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Unité Macrophages et Développement de l'Immunité, Paris, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, Paris, France
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Treatment of SARS-CoV-2-induced pneumonia with NAD + and NMN in two mouse models. Cell Discov 2022; 8:38. [PMID: 35487885 PMCID: PMC9053567 DOI: 10.1038/s41421-022-00409-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/02/2022] [Indexed: 12/14/2022] Open
Abstract
The global COVID-19 epidemic has spread rapidly around the world and caused the death of more than 5 million people. It is urgent to develop effective strategies to treat COVID-19 patients. Here, we revealed that SARS-CoV-2 infection resulted in the dysregulation of genes associated with NAD+ metabolism, immune response, and cell death in mice, similar to that in COVID-19 patients. We therefore investigated the effect of treatment with NAD+ and its intermediate (NMN) and found that the pneumonia phenotypes, including excessive inflammatory cell infiltration, hemolysis, and embolization in SARS-CoV-2-infected lungs were significantly rescued. Cell death was suppressed substantially by NAD+ and NMN supplementation. More strikingly, NMN supplementation can protect 30% of aged mice infected with the lethal mouse-adapted SARS-CoV-2 from death. Mechanically, we found that NAD+ or NMN supplementation partially rescued the disturbed gene expression and metabolism caused by SARS-CoV-2 infection. Thus, our in vivo mouse study supports trials for treating COVID-19 patients by targeting the NAD+ pathway.
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Rather GM, Pramono AA, Szekely Z, Bertino JR, Tedeschi PM. In cancer, all roads lead to NADPH. Pharmacol Ther 2021; 226:107864. [PMID: 33894275 DOI: 10.1016/j.pharmthera.2021.107864] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023]
Abstract
Cancer cells require increased levels of NADPH for increased nucleotide synthesis and for protection from ROS. Recent studies show that increased NADPH is generated in several ways. Activated AKT phosphorylates NAD kinase (NADK), increasing its activity. NADP formed, is rapidly converted to NADPH by glucose 6-phosphate dehydrogenase and malic enzymes, overexpressed in tumor cells with mutant p53. Calmodulin, overexpressed in some cancers, also increases NADK activity. Also, in IDH1/2 mutant cancer, NADPH serves as the cofactor to generate D-2 hydroxyglutarate, an oncometabolite. The requirement of cancer cells for elevated levels of NADPH provides an opportunity to target its synthesis for cancer treatment.
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Affiliation(s)
- Gulam Mohmad Rather
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Alvinsyah Adhityo Pramono
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA; Research Center of Medical Genetics, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Zoltan Szekely
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA; Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Joseph R Bertino
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA; Department of Medicine and Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
| | - Philip Michael Tedeschi
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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Fu W, Wang R, Yu J, Hu D, Cai Y, Shao J, Jiang Y. GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions. J Genet Genomics 2021; 48:248-256. [PMID: 33965348 DOI: 10.1016/j.jgg.2021.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/20/2022]
Abstract
Understanding the evolutionary history and adaptive process depends on the knowledge that we can acquire from both ancient and modern genomic data. With the availability of a deluge of whole-genome sequencing data from ancient and modern goat samples, a user-friendly database making efficient reuse of these important resources is needed. Here, we use the genomes of 208 modern domestic goats, 24 bezoars, 46 wild ibexes, and 82 ancient goats to present a comprehensive goat genome variation database (GGVD). GGVD hosts a total of ∼41.44 million SNPs, ∼5.14 million indels, 6,193 selected loci, and 112 introgression regions. Users can freely visualize the frequency of genomic variations in geographical maps, selective sweeps in interactive tables, Manhattan plots, or line charts, as well as the heatmap patterns of the SNP genotype. Ancient data can be shown in haplotypes to track the state of genetic variants of selection and introgression events in the early, middle, and late stages. For facilitating access to sequence features, the UCSC Genome Browser, BLAT, BLAST, LiftOver, and pcadapt are also integrated into GGVD. GGVD will be a convenient tool for population genetic studies and molecular marker designing in goat breeding programs, and it is publicly available at http://animal.nwsuaf.edu.cn/GoatVar.
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Affiliation(s)
- Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rui Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiantao Yu
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dexiang Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junjie Shao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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MURATA K. Polyphosphate-dependent nicotinamide adenine dinucleotide (NAD) kinase: A novel missing link in human mitochondria. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:479-498. [PMID: 34629356 PMCID: PMC8553519 DOI: 10.2183/pjab.97.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Polyphosphate [poly(P)] is described as a homopolymer of inorganic phosphates. Nicotinamide adenine dinucleotide kinase (NAD kinase) catalyzes the phosphorylation of NAD+ to NADP+ in the presence of ATP (ATP-NAD kinase). Novel NAD kinase that explicitly phosphorylates NAD+ to NADP+ using poly(P), besides ATP [ATP/poly(P)-NAD kinase], was found in bacteria, in particular, Gram-positive bacteria, and the gene encoding ATP/poly(P)-NAD kinase was also newly identified in Mycobacterium tuberculosis H37Rv. Both NAD kinases required multi-homopolymeric structures for activity expression. The enzymatic and genetic results, combined with their primary and tertiary structures, have led to the discovery of a long-awaited human mitochondrial NAD kinase. This discovery showed that the NAD kinase is a bacterial type of ATP/poly(P)-NAD kinase. These pioneering findings, i.e., ATP/poly(P)-NAD kinase, NAD kinase gene, and human mitochondrial NAD kinase, have significantly enhanced research on the biochemistry, molecular biology, and evolutionary biology of NAD kinase, mitochondria, and poly(P), including some biotechnological knowledge applicable to NADP+ production.
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12
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New Chemical Probe Targeting Bacterial NAD Kinase. Molecules 2020; 25:molecules25214893. [PMID: 33105870 PMCID: PMC7660225 DOI: 10.3390/molecules25214893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 12/02/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) kinases are essential and ubiquitous enzymes involved in the tight regulation of NAD/nicotinamide adenine dinucleotide phosphate (NADP) levels in many metabolic pathways. Consequently, they represent promising therapeutic targets in cancer and antibacterial treatments. We previously reported diadenosine derivatives as NAD kinase inhibitors with bactericidal activities on Staphylococcus aureus. Among them, one compound (namely NKI1) was found effective in vivo in a mouse infection model. With the aim to gain detailed knowledge about the selectivity and mechanism of action of this lead compound, we planned to develop a chemical probe that could be used in affinity-based chemoproteomic approaches. Here, we describe the first functionalized chemical probe targeting a bacterial NAD kinase. Aminoalkyl functional groups were introduced on NKI1 for further covalent coupling to an activated SepharoseTM matrix. Inhibitory properties of functionalized NKI1 derivatives together with X-ray characterization of their complexes with the NAD kinase led to identify candidate compounds that are amenable to covalent coupling to a matrix.
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Gelin M, Paoletti J, Nahori MA, Huteau V, Leseigneur C, Jouvion G, Dugué L, Clément D, Pons JL, Assairi L, Pochet S, Labesse G, Dussurget O. From Substrate to Fragments to Inhibitor Active In Vivo against Staphylococcus aureus. ACS Infect Dis 2020; 6:422-435. [PMID: 32017533 DOI: 10.1021/acsinfecdis.9b00368] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibiotic resistance is a worldwide threat due to the decreasing supply of new antimicrobials. Novel targets and innovative strategies are urgently needed to generate pathbreaking drug compounds. NAD kinase (NADK) is essential for growth in most bacteria, as it supports critical metabolic pathways. Here, we report the discovery of a new class of antibacterials that targets bacterial NADK. We generated a series of small synthetic adenine derivatives to screen those harboring promising substituents in order to guide efficient fragment linking. This led to NKI1, a new lead compound inhibiting NADK that showed in vitro bactericidal activity against Staphylococcus aureus. In a murine model of infection, NKI1 restricted survival of the bacteria, including methicillin-resistant S. aureus. Collectively, these findings identify bacterial NADK as a potential drug target and NKI1 as a lead compound in the treatment of staphylococcal infections.
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Affiliation(s)
- Muriel Gelin
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université Montpellier, 29 route de Navacelles, 34090 Montpellier, France
| | - Julie Paoletti
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS UMR3523, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - Marie-Anne Nahori
- Unité des Toxines Bactériennes, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - Valérie Huteau
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS UMR3523, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - Clarisse Leseigneur
- Unité de Recherche Yersinia, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Grégory Jouvion
- Unité de Neuropathologie Expérimentale, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France
- Sorbonne Université, INSERM UMR S933, Unité de Génétique Médicale, Hôpital Armand Trousseau, APHP, 26 Avenue du Dr Arnold Netter, 75012 Paris, France
| | - Laurence Dugué
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS UMR3523, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - David Clément
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS UMR3523, 25-28 rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Jean-Luc Pons
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université Montpellier, 29 route de Navacelles, 34090 Montpellier, France
| | - Liliane Assairi
- INSERM U759, Institut Curie, Centre Universitaire Paris Sud, 91405 Orsay, France
| | - Sylvie Pochet
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS UMR3523, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - Gilles Labesse
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université Montpellier, 29 route de Navacelles, 34090 Montpellier, France
| | - Olivier Dussurget
- Unité de Recherche Yersinia, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
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Pramono AA, Rather GM, Herman H, Lestari K, Bertino JR. NAD- and NADPH-Contributing Enzymes as Therapeutic Targets in Cancer: An Overview. Biomolecules 2020; 10:biom10030358. [PMID: 32111066 PMCID: PMC7175141 DOI: 10.3390/biom10030358] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/14/2022] Open
Abstract
Actively proliferating cancer cells require sufficient amount of NADH and NADPH for biogenesis and to protect cells from the detrimental effect of reactive oxygen species. As both normal and cancer cells share the same NAD biosynthetic and metabolic pathways, selectively lowering levels of NAD(H) and NADPH would be a promising strategy for cancer treatment. Targeting nicotinamide phosphoribosyltransferase (NAMPT), a rate limiting enzyme of the NAD salvage pathway, affects the NAD and NADPH pool. Similarly, lowering NADPH by mutant isocitrate dehydrogenase 1/2 (IDH1/2) which produces D-2-hydroxyglutarate (D-2HG), an oncometabolite that downregulates nicotinate phosphoribosyltransferase (NAPRT) via hypermethylation on the promoter region, results in epigenetic regulation. NADPH is used to generate D-2HG, and is also needed to protect dihydrofolate reductase, the target for methotrexate, from degradation. NAD and NADPH pools in various cancer types are regulated by several metabolic enzymes, including methylenetetrahydrofolate dehydrogenase, serine hydroxymethyltransferase, and aldehyde dehydrogenase. Thus, targeting NAD and NADPH synthesis under special circumstances is a novel approach to treat some cancers. This article provides the rationale for targeting the key enzymes that maintain the NAD/NADPH pool, and reviews preclinical studies of targeting these enzymes in cancers.
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Affiliation(s)
- Alvinsyah Adhityo Pramono
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; (A.A.P.); (G.M.R.)
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia;
- Center of Excellence in Higher Education for Pharmaceutical Care Innovation, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Gulam M. Rather
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; (A.A.P.); (G.M.R.)
| | - Herry Herman
- Division of Oncology, Department of Orthopaedic Surgery, Faculty of Medicine, Universitas Padjadjaran, Bandung 40161, Indonesia;
| | - Keri Lestari
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia;
- Center of Excellence in Higher Education for Pharmaceutical Care Innovation, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Joseph R. Bertino
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; (A.A.P.); (G.M.R.)
- Department of Pharmacology and Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Correspondence: ; Tel.: +1-(732)-235-8510
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Niacin Protects against Butyrate-Induced Apoptosis in Rumen Epithelial Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:2179738. [PMID: 31737165 PMCID: PMC6815573 DOI: 10.1155/2019/2179738] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/04/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023]
Abstract
The effects and underlying mechanisms of butyrate and butyrate+niacin on apoptosis in sheep rumen epithelial cells were investigated. Cells were exposed to butyrate (0-140 mM) for 6 h. A low concentration (20 mM) of butyrate increased cell viability and promoted growth whereas high concentrations (40-140 mM) inhibited proliferation. Cells were then cocultured with 120 mM butyrate and niacin (0-100 mM) for 6 h. Niacin addition attenuated butyrate-induced cellular damage and promoted proliferation at 20-80 mM; 40 mM presented the optimal effect. Higher concentrations (100 mM) of niacin resulted in low cell viability. Subsequent experiments confirmed that 120 mM butyrate increased intracellular reactive oxygen species (ROS) production and reduced the intracellular total antioxidant capacity (T-AOC) versus the untreated control. Compared with 120 mM butyrate, cotreatment with 40 mM niacin significantly reduced the intracellular ROS content and increased the intracellular T-AOC. Flow cytometry analysis revealed that 120 mM butyrate increased the proportion of apoptotic cells by 17.8% versus the untreated control, and 120 mM butyrate+40 mM niacin treatment reduced the proportion of apoptotic cells by 28.6% and 39.4% versus the untreated control and butyrate treatment, respectively. Treatment with 120 mM butyrate increased caspase-9 and p53 mRNA levels and decreased the expression of Bcl-2 and Bax, and the Bcl-2/Bax ratio versus the untreated control. Treatment with 120 mM butyrate+40 mM niacin downregulated the expression of caspase-3 and p53 and increased the expression of Bcl-2 and Bax versus butyrate treatment alone but had no effect on the Bcl-2/Bax ratio. Thus, high concentrations of butyrate may induce rumen epithelial cell apoptosis by increasing oxidative stress and inducing caspase-9 and p53 expression. Cotreatment with niacin regulates apoptosis-related gene expression by reducing intracellular ROS production and DNA damage and downregulating caspase-3 and p53 expressions to protect rumen epithelial cells against butyrate-induced apoptosis.
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Vickman O, Erives A. Episodic evolution of a eukaryotic NADK repertoire of ancient provenance. PLoS One 2019; 14:e0220447. [PMID: 31369599 PMCID: PMC6675116 DOI: 10.1371/journal.pone.0220447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/16/2019] [Indexed: 12/02/2022] Open
Abstract
NAD kinase (NADK) is the sole enzyme that phosphorylates nicotinamide adenine dinucleotide (NAD+/NADH) into NADP+/NADPH, which provides the chemical reducing power in anabolic (biosynthetic) pathways. While prokaryotes typically encode a single NADK, eukaryotes encode multiple NADKs. How these different NADK genes are all related to each other and those of prokaryotes is not known. Here we conduct phylogenetic analysis of NADK genes and identify major clade-defining patterns of NADK evolution. First, almost all eukaryotic NADK genes belong to one of two ancient eukaryotic sister clades corresponding to cytosolic (“cyto”) and mitochondrial (“mito”) clades. Secondly, we find that the cyto-clade NADK gene is duplicated in connection with loss of the mito-clade NADK gene in several eukaryotic clades or with acquisition of plastids in Archaeplastida. Thirdly, we find that horizontal gene transfers from proteobacteria have replaced mitochondrial NADK genes in only a few rare cases. Last, we find that the eukaryotic cyto and mito paralogs are unrelated to independent duplications that occurred in sporulating bacteria, once in mycelial Actinobacteria and once in aerobic endospore-forming Firmicutes. Altogether these findings show that the eukaryotic NADK gene repertoire is ancient and evolves episodically with major evolutionary transitions.
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Affiliation(s)
- Oliver Vickman
- Department of Biology, University of Iowa, Iowa City, IA, United States of America
| | - Albert Erives
- Department of Biology, University of Iowa, Iowa City, IA, United States of America
- * E-mail:
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Hashida SN, Kawai-Yamada M. Inter-Organelle NAD Metabolism Underpinning Light Responsive NADP Dynamics in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:960. [PMID: 31404160 PMCID: PMC6676473 DOI: 10.3389/fpls.2019.00960] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/09/2019] [Indexed: 05/24/2023]
Abstract
Upon illumination, photosystem I in chloroplasts catalyzes light-driven electron transport from plastocyanin to ferredoxin, followed by the reduction of NADP+ to NADPH by ferredoxin:NADP+ reductase for CO2 fixation. At the beginning of photosynthesis, NADP+ supply control is dominated by de novo NADP+ synthesis rather than being recycled from the Calvin cycle. Importantly, ferredoxin distributes electrons to NADP+ as well as to thioredoxins for light-dependent regulatory mechanisms, to cyclic electron flow for more adenosine triphosphate (ATP) production, and to several metabolites for reductive reactions. We previously demonstrated that the NADP+ synthesis activity and the amount of the NADP pool size, namely the sum of NADP+ and NADPH, varies depending on the light conditions and the ferredoxin-thioredoxin system. In addition, the regulatory mechanism of cytoplasmic NAD+ supply is also involved in the chloroplastic NADP+ supply control because NAD+ is an essential precursor for NADP+ synthesis. In this mini-review, we summarize the most recent advances on our understanding of the regulatory mechanisms of NADP+ production, focusing on the interactions, crosstalk, and co-regulation between chloroplasts and the cytoplasm at the level of NAD+ metabolism and molecular transport.
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Affiliation(s)
- Shin-nosuke Hashida
- Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, Abiko, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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Tai L, Li BB, Nie XM, Zhang PP, Hu CH, Zhang L, Liu WT, Li WQ, Chen KM. Calmodulin Is the Fundamental Regulator of NADK-Mediated NAD Signaling in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:681. [PMID: 31275331 PMCID: PMC6593290 DOI: 10.3389/fpls.2019.00681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/06/2019] [Indexed: 05/02/2023]
Abstract
Calcium (Ca2+) signaling and nicotinamide adenine dinucleotide (NAD) signaling are two basic signal regulation pathways in organisms, playing crucial roles in signal transduction, energy metabolism, stress tolerance, and various developmental processes. Notably, calmodulins (CaMs) and NAD kinases (NADKs) are important hubs for connecting these two types of signaling networks, where CaMs are the unique activators of NADKs. NADK is a key enzyme for NADP (including NADP+ and NADPH) biosynthesis by phosphorylating NAD (including NAD+ and NADH) and therefore, maintains the balance between NAD pool and NADP pool through an allosteric regulation mode. In addition, the two respective derivatives from NAD+ (substrate of NADK) and NADP+ (product of NADK), cyclic ADP-ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate (NAADP), have been considered to be the important messengers for intracellular Ca2+ homeostasis which could finally influence the combination between CaM and NADK, forming a feedback regulation mechanism. In this review article, we briefly summarized the major research advances related to the feedback regulation pathway, which is activated by the interaction of CaM and NADK during plant development and signaling. The theories and fact will lay a solid foundation for further studies related to CaM and NADK and their regulatory mechanisms as well as the NADK-mediated NAD signaling behavior in plant development and response to stress.
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Affiliation(s)
- Li Tai
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Bin-Bin Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiu-Min Nie
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Peng-Peng Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Chun-Hong Hu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
- Department of General Biology, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
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Wang C, Xin F, Kong X, Zhao J, Dong W, Zhang W, Ma J, Wu H, Jiang M. Enhanced isopropanol-butanol-ethanol mixture production through manipulation of intracellular NAD(P)H level in the recombinant Clostridium acetobutylicum XY16. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:12. [PMID: 29410706 PMCID: PMC5782381 DOI: 10.1186/s13068-018-1024-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/13/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND The formation of by-products, mainly acetone in acetone-butanol-ethanol (ABE) fermentation, significantly affects the solvent yield and downstream separation process. In this study, we genetically engineered Clostridium acetobutylicum XY16 isolated by our lab to eliminate acetone production and altered ABE to isopropanol-butanol-ethanol (IBE). Meanwhile, process optimization under pH control strategies and supplementation of calcium carbonate were adopted to investigate the interaction between the reducing force of the metabolic networks and IBE production. RESULTS After successful introduction of secondary alcohol dehydrogenase into C. acetobutylicum XY16, the recombinant XY16 harboring pSADH could completely eliminate acetone production and convert it into isopropanol, indicating great potential for large-scale production of IBE mixtures. Especially, pH could significantly improve final solvent titer through regulation of NADH and NADPH levels in vivo. Under the optimal pH level of 4.8, the total IBE production was significantly increased from 3.88 to 16.09 g/L with final 9.97, 4.98 and 1.14 g/L of butanol, isopropanol, and ethanol. Meanwhile, NADH and NADPH levels were maintained at optimal levels for IBE formation compared to the control one without pH adjustment. Furthermore, calcium carbonate could play dual roles as both buffering agency and activator for NAD kinase (NADK), and supplementation of 10 g/L calcium carbonate could finally improve the IBE production to 17.77 g/L with 10.51, 6.02, and 1.24 g/L of butanol, isopropanol, and ethanol. CONCLUSION The complete conversion of acetone into isopropanol in the recombinant C. acetobutylicum XY16 harboring pSADH could alter ABE to IBE. pH control strategies and supplementation of calcium carbonate were effective in obtaining high IBE titer with high isopropanol production. The analysis of redox cofactor perturbation indicates that the availability of NAD(P)H is the main driving force for the improvement of IBE production.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211816 People’s Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Xiangping Kong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211816 People’s Republic of China
| | - Jie Zhao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211816 People’s Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Hao Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211816 People’s Republic of China
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Enhanced production of poly-3-hydroxybutyrate by recombinant Escherichia coli containing NAD kinase and phbCAB operon. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0194-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Spaans SK, Weusthuis RA, van der Oost J, Kengen SWM. NADPH-generating systems in bacteria and archaea. Front Microbiol 2015; 6:742. [PMID: 26284036 PMCID: PMC4518329 DOI: 10.3389/fmicb.2015.00742] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022] Open
Abstract
Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components and many products in biotechnology. The efficient synthesis of many of these products, however, is limited by the rate of NADPH regeneration. Hence, a thorough understanding of the reactions involved in the generation of NADPH is required to increase its turnover through rational strain improvement. Traditionally, the main engineering targets for increasing NADPH availability have included the dehydrogenase reactions of the oxidative pentose phosphate pathway and the isocitrate dehydrogenase step of the tricarboxylic acid (TCA) cycle. However, the importance of alternative NADPH-generating reactions has recently become evident. In the current review, the major canonical and non-canonical reactions involved in the production and regeneration of NADPH in prokaryotes are described, and their key enzymes are discussed. In addition, an overview of how different enzymes have been applied to increase NADPH availability and thereby enhance productivity is provided.
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Affiliation(s)
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen UniversityWageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
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Navarrete C, Nielsen J, Siewers V. Enhanced ethanol production and reduced glycerol formation in fps1∆ mutants of Saccharomyces cerevisiae engineered for improved redox balancing. AMB Express 2014; 4:86. [PMID: 26267115 PMCID: PMC4883998 DOI: 10.1186/s13568-014-0086-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 11/27/2014] [Indexed: 11/30/2022] Open
Abstract
Ethanol is by volume the largest fermentation product. During ethanol production by Saccharomyces cerevisiae about 4-5% of the carbon source is lost to glycerol production. Different approaches have been proposed for improving the ethanol yield while reducing glycerol production. Here we studied the effect of reducing glycerol export/formation through deletion of the aquaglyceroporin gene FPS1 together with expressing gapN encoding NADP+-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans and overexpressing the ATP-NADH kinase gene UTR1 from S. cerevisiae. This strategy will allow reducing the redox balance problem observed when the glycerol pathway is blocked, and hereby improve ethanol production. We found that our strategy enabled increasing the ethanol yield by 4.6% in the case of the best producing strain, compared to the reference strain, without any major effect on the specific growth rate.
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Onda Y, Miyagi A, Takahara K, Uchimiya H, Kawai-Yamada M. Effects of NAD kinase 2 overexpression on primary metabolite profiles in rice leaves under elevated carbon dioxide. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:819-24. [PMID: 24397549 DOI: 10.1111/plb.12131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/16/2013] [Indexed: 05/20/2023]
Abstract
The concentration of carbon dioxide (CO2) in the atmosphere is projected to double by the end of the 21st century. In C3 plants, elevated CO2 concentrations promote photosynthesis but inhibit the assimilation of nitrate into organic nitrogen compounds. Several steps of nitrate assimilation depend on the availability of ATP and sources of reducing power, such as nicotinamide adenine dinucleotide phosphate (NADPH). Plastid-localised NAD kinase 2 (NADK2) plays key roles in increasing the ATP/ADP and NADP(H)/NAD(H) ratios. Here we examined the effects of NADK2 overexpression on primary metabolism in rice (Oryza sativa) leaves in response to elevated CO2. By using capillary electrophoresis mass spectrometry, we showed that the primary metabolite profile of NADK2-overexpressing plants clearly differed from that of wild-type plants under ambient and elevated CO2. In NADK2-overexpressing leaves, expression of the genes encoding glutamine synthetase and glutamate synthase was up-regulated, and the levels of Asn, Gln, Arg, and Lys increased in response to elevated CO2. The present study suggests that overexpression of NADK2 promotes the biosynthesis of nitrogen-rich amino acids under elevated CO2.
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Affiliation(s)
- Y Onda
- Institute for Environmental Science and Technology, Saitama University, Sakura-ku, Saitama, Japan; Department of Food and Applied Life Sciences, Yamagata University, Tsuruoka, Yamagata, Japan
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Gray JP, Alavian KN, Jonas EA, Heart EA. NAD kinase regulates the size of the NADPH pool and insulin secretion in pancreatic β-cells. Am J Physiol Endocrinol Metab 2012; 303:E191-9. [PMID: 22550069 PMCID: PMC3431206 DOI: 10.1152/ajpendo.00465.2011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
NADPH is an important component of the antioxidant defense system and a proposed mediator in glucose-stimulated insulin secretion (GSIS) from pancreatic β-cells. An increase in the NADPH/NADP(+) ratio has been reported to occur within minutes following the rise in glucose concentration in β-cells. However, 30 min following the increase in glucose, the total NADPH pool also increases through a mechanism not yet characterized. NAD kinase (NADK) catalyzes the de novo formation of NADP(+) by phosphorylation of NAD(+). NAD kinases have been shown to be essential for redox regulation, oxidative stress defense, and survival in bacteria and yeast. However, studies on NADK in eukaryotic cells are scarce, and the function of this enzyme has not been described in β-cells. We employed INS-1 832/13 cells, an insulin-secreting rat β-cell line, and isolated rodent islets to investigate the role of NADK in β-cell metabolic pathways. Adenoviral-mediated overexpression of NADK resulted in a two- to threefold increase in the total NADPH pool and NADPH/NADP(+) ratio, suggesting that NADP(+) formed by the NADK-catalyzed reaction is rapidly reduced to NADPH via cytosolic reductases. This increase in the NADPH pool was accompanied by an increase in GSIS in NADK-overexpressing cells. Furthermore, NADK overexpression protected β-cells against oxidative damage by the redox cycling agent menadione and reversed menadione-mediated inhibition of GSIS. Knockdown of NADK via shRNA exerted the opposite effect on all these parameters. These data suggest that NADK kinase regulates intracellular redox and affects insulin secretion and oxidative defense in the β-cell.
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Affiliation(s)
- Joshua P Gray
- United States Coast Guard Academy, New London, CT, USA
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25
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Metabolic networks to combat oxidative stress in Pseudomonas fluorescens. Antonie van Leeuwenhoek 2010; 99:433-42. [PMID: 21153706 DOI: 10.1007/s10482-010-9538-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 11/26/2010] [Indexed: 12/21/2022]
Abstract
Oxidative stress is an unavoidable peril that aerobic organisms have to confront. Thus, it is not surprising that intricate strategies are deployed in an effort to fend the dangers associated with living in an O(2) environment. In the classical models of anti-oxidative defense mechanisms, a variety of stratagems including the reactive oxygen species (ROS) scavenging systems, the NADPH-generating enzymes and the DNA repair machineries are highlighted. However, it is becoming increasingly clear that metabolism may be intimately involved in anti-oxidative defence. Recent data show that metabolic reprogramming plays a pivotal role in the survival of organisms exposed to oxidative stress. Here, we describe how Pseudomonas fluorescens, the metabolically-versatile soil microbe, manipulates its metabolic networks in an effort to counter oxidative stress. An intricate link between metabolism and anti-oxidative defense is presented. P. fluorescens reconfigures its metabolic processes in an effort to satisfy its need for NADPH during oxidative insult. Seemingly, disparate metabolic modules appear to partner together to concomitantly fine-tune the levels of the anti-oxidant NADPH and the pro-oxidant NADH. Central to this shift in the metabolic production of the pyridine nucleotides is the increase in NAD kinase with the concomitant decrease in NADP phosphatase. The tricarboxylic acid cycle is tweaked in an effort to limit the formation of NADH. This metabolic redox-balancing act appears to afford a potent tool against oxidative challenge and may be a more widespread ROS-combating tactic than hitherto recognized.
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26
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Pain J, Balamurali MM, Dancis A, Pain D. Mitochondrial NADH kinase, Pos5p, is required for efficient iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. J Biol Chem 2010; 285:39409-24. [PMID: 20889970 PMCID: PMC2998133 DOI: 10.1074/jbc.m110.178947] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 09/30/2010] [Indexed: 11/06/2022] Open
Abstract
In Saccharomyces cerevisiae, the mitochondrial inner membrane readily allows transport of cytosolic NAD(+), but not NADPH, to the matrix. Pos5p is the only known NADH kinase in the mitochondrial matrix. The enzyme phosphorylates NADH to NADPH and is the major source of NADPH in the matrix. The importance of mitochondrial NADPH for cellular physiology is underscored by the phenotypes of the Δpos5 mutant, characterized by oxidative stress sensitivity and iron-sulfur (Fe-S) cluster deficiency. Fe-S clusters are essential cofactors of proteins such as aconitase [4Fe-4S] and ferredoxin [2Fe-2S] in mitochondria. Intact mitochondria isolated from wild-type yeast can synthesize these clusters and insert them into the corresponding apoproteins. Here, we show that this process of Fe-S cluster biogenesis in wild-type mitochondria is greatly stimulated and kinetically favored by the addition of NAD(+) or NADH in a dose-dependent manner, probably via transport into mitochondria and subsequent conversion into NADPH. Unlike wild-type mitochondria, Δpos5 mitochondria cannot efficiently synthesize Fe-S clusters on endogenous aconitase or imported ferredoxin, although cluster biogenesis in isolated Δpos5 mitochondria is restored to a significant extent by a small amount of imported Pos5p. Interestingly, Fe-S cluster biogenesis in wild-type mitochondria is further enhanced by overexpression of Pos5p. The effects of Pos5p on Fe-S cluster generation in mitochondria indicate that one or more steps in the biosynthetic process require NADPH. The role of mitochondrial NADPH in Fe-S cluster biogenesis appears to be distinct from its function in anti-oxidant defense.
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Affiliation(s)
- Jayashree Pain
- From the Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07101 and
| | - M. M. Balamurali
- From the Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07101 and
| | - Andrew Dancis
- the Department of Medicine, Division of Hematology-Oncology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Debkumar Pain
- From the Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07101 and
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Lindner SN, Niederholtmeyer H, Schmitz K, Schoberth SM, Wendisch VF. Polyphosphate/ATP-dependent NAD kinase of Corynebacterium glutamicum: biochemical properties and impact of ppnK overexpression on lysine production. Appl Microbiol Biotechnol 2010; 87:583-93. [PMID: 20180116 DOI: 10.1007/s00253-010-2481-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 11/24/2022]
Abstract
Nicotinamide adenine dinucleotide phosphate (NADP) is synthesized by phosphorylation of either oxidized or reduced nicotinamide adenine dinucleotide (NAD/NADH). Here, the cg1601/ppnK gene product from Corynebacterium glutamicum genome was purified from recombinant Escherichia coli and enzymatic characterization revealed its activity as a polyphosphate (PolyP)/ATP-dependent NAD kinase (PPNK). PPNK from C. glutamicum was shown to be active as homotetramer accepting PolyP, ATP, and even ADP for phosphorylation of NAD. The catalytic efficiency with ATP as phosphate donor for phosphorylation of NAD was higher than with PolyP. With respect to the chain length of PolyP, PPNK was active with short-chain PolyPs. PPNK activity was independent of bivalent cations when using ATP, but was enhanced by manganese and in particular by magnesium ions. When using PolyP, PPNK required bivalent cations, preferably manganese ions, for activity. PPNK was inhibited by NADP and NADH at concentrations below millimolar. Overexpression of ppnK in C. glutamicum wild type slightly reduced growth and ppnK overexpression in the lysine producing strain DM1729 resulted in a lysine product yield on glucose of 0.136 +/- 0.006 mol lysine (mol glucose)(-1), which was 12% higher than that of the empty vector control strain.
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Affiliation(s)
- Steffen N Lindner
- Institute of Molecular Microbiology and Biotechnology, Westfalian Wilhelms University Muenster, 48149, Muenster, Germany
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28
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Deletion of the mitochondrial NADH kinase increases mitochondrial DNA stability and life span in the filamentous fungus Podospora anserina. Exp Gerontol 2010; 45:543-9. [PMID: 20096769 DOI: 10.1016/j.exger.2010.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 12/31/2009] [Accepted: 01/14/2010] [Indexed: 01/19/2023]
Abstract
In the filamentous fungus Podospora anserina, aging is systematically associated with mitochondrial DNA (mtDNA) instability. A causal link between deficiency of the cytochrome respiratory pathway and lifespan extension has been demonstrated. Knock out of the cytochrome respiratory pathway induces the expression of an alternative oxidase and is associated with a reduction in free radical production. The question of the links between mtDNA stability, ROS generation and lifespan is therefore clearly raised in this organism. NADPH lies at the heart of many anti-oxidant defenses of the cell. In Saccharomyces cerevisiae, the mitochondrial NADPH is largely provided by the Pos5 NADH kinase. We show here that disruption of PaNdk1 encoding the potential mitochondrial NADH kinase of P. anserina leads to severe somatic and sexual defects and to hypersensitivity to hydrogen peroxide and paraquat. Surprisingly, it also leads to a spectacular increase of mtDNA stability and lifespan. We propose that an adaptative metabolic change including the induction of the alternative oxidase can account for these results.
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29
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Abstract
Molecular modelling suggests that a group of proteins in plants known as the β-hydroxyacid dehydrogenases, or the hydroxyisobutyrate dehydrogenase superfamily, includes enzymes that reduce succinic semialdehyde and glyoxylate to γ-hydroxybutyrate and glycolate respectively. Recent biochemical and expression studies reveal that NADPH-dependent cytosolic (termed GLYR1) and plastidial (termed GLYR2) isoforms of succinic semialdehyde/glyoxylate reductase exist in Arabidopsis. Succinic semialdehyde and glyoxylate are typically generated in leaves via two distinct metabolic pathways, γ-aminobutyrate and glycolate respectively. In the present review, it is proposed that the GLYRs function in the detoxification of both aldehydes during stress and contribute to redox balance. Outstanding questions are highlighted in a scheme for the subcellular organization of the detoxification mechanism in Arabidopsis.
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Panagiotou G, Papadakis M, Topakas E, Olsson L, Christakopoulos P. Identification of NADH kinase activity in filamentous fungi and structural modelling of the novel enzyme from Fusarium oxysporum. Process Biochem 2008. [DOI: 10.1016/j.procbio.2008.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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31
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Structure and function of NAD kinase and NADP phosphatase: key enzymes that regulate the intracellular balance of NAD(H) and NADP(H). Biosci Biotechnol Biochem 2008; 72:919-30. [PMID: 18391451 DOI: 10.1271/bbb.70738] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The functions of NAD(H) (NAD(+) and NADH) and NADP(H) (NADP(+) and NADPH) are undoubtedly significant and distinct. Hence, regulation of the intracellular balance of NAD(H) and NADP(H) is important. The key enzymes involved in the regulation are NAD kinase and NADP phosphatase. In 2000, we first succeeded in identifying the gene for NAD kinase, thereby facilitating worldwide studies of this enzyme from various organisms, including eubacteria, archaea, yeast, plants, and humans. Molecular biological study has revealed the physiological function of this enzyme, that is to say, the significance of NADP(H), in some model organisms. Structural research has elucidated the tertiary structure of the enzyme, the details of substrate-binding sites, and the catalytic mechanism. Research on NAD kinase also led to the discovery of archaeal NADP phosphatase. In this review, we summarize the physiological functions, applications, and structure of NAD kinase, and the way we discovered archaeal NADP phosphatase.
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32
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Ying W. NAD+/NADH and NADP+/NADPH in cellular functions and cell death: regulation and biological consequences. Antioxid Redox Signal 2008; 10:179-206. [PMID: 18020963 DOI: 10.1089/ars.2007.1672] [Citation(s) in RCA: 1047] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Accumulating evidence has suggested that NAD (including NAD+ and NADH) and NADP (including NADP+ and NADPH) could belong to the fundamental common mediators of various biological processes, including energy metabolism, mitochondrial functions, calcium homeostasis, antioxidation/generation of oxidative stress, gene expression, immunological functions, aging, and cell death: First, it is established that NAD mediates energy metabolism and mitochondrial functions; second, NADPH is a key component in cellular antioxidation systems; and NADH-dependent reactive oxygen species (ROS) generation from mitochondria and NADPH oxidase-dependent ROS generation are two critical mechanisms of ROS generation; third, cyclic ADP-ribose and several other molecules that are generated from NAD and NADP could mediate calcium homeostasis; fourth, NAD and NADP modulate multiple key factors in cell death, such as mitochondrial permeability transition, energy state, poly(ADP-ribose) polymerase-1, and apoptosis-inducing factor; and fifth, NAD and NADP profoundly affect aging-influencing factors such as oxidative stress and mitochondrial activities, and NAD-dependent sirtuins also mediate the aging process. Moreover, many recent studies have suggested novel paradigms of NAD and NADP metabolism. Future investigation into the metabolism and biological functions of NAD and NADP may expose fundamental properties of life, and suggest new strategies for treating diseases and slowing the aging process.
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Affiliation(s)
- Weihai Ying
- Department of Neurology, University of California at San Francisco, San Francisco, California 94121, USA.
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33
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Pollak N, Niere M, Ziegler M. NAD kinase levels control the NADPH concentration in human cells. J Biol Chem 2007; 282:33562-33571. [PMID: 17855339 DOI: 10.1074/jbc.m704442200] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NAD kinases (NADKs) are vital, as they generate the cellular NADP pool. As opposed to three compartment-specific isoforms in plants and yeast, only a single NADK has been identified in mammals whose cytoplasmic localization we established by immunocytochemistry. To understand the physiological roles of the human enzyme, we generated and analyzed cell lines stably deficient in or overexpressing NADK. Short hairpin RNA-mediated down-regulation led to similar (about 70%) decrease of both NADK expression, activity, and the NADPH concentration and was accompanied by increased sensitivity toward H(2)O(2). Overexpression of NADK resulted in a 4-5-fold increase in the NADPH, but not NADP(+), concentration, although the recombinant enzyme phosphorylated preferentially NAD(+). Surprisingly, NADK overexpression and the ensuing increase of the NADPH level only moderately enhanced protection against oxidant treatment. Apparently, to maintain the NADPH level for the regeneration of oxidative defense systems human cells depend primarily on NADP-dependent dehydrogenases (which re-reduce NADP(+)), rather than on a net increase of NADP. The stable shifts of the NADPH level in the generated cell lines were also accompanied by alterations in the expression of peroxiredoxin 5 and Nrf2. Because the basal oxygen radical level in the cell lines was only slightly changed, the redox state of NADP may be a major transmitter of oxidative stress.
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Affiliation(s)
- Nadine Pollak
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Marc Niere
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Mathias Ziegler
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.
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34
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Mailloux RJ, Singh R, Appanna VD. In-gel activity staining of oxidized nicotinamide adenine dinucleotide kinase by blue native polyacrylamide gel electrophoresis. Anal Biochem 2006; 359:210-5. [PMID: 17083911 DOI: 10.1016/j.ab.2006.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2006] [Revised: 09/21/2006] [Accepted: 09/22/2006] [Indexed: 10/24/2022]
Abstract
Oxidized nicotinamide adenine dinucleotide (NAD(+)) kinase (NADK, E.C. 2.7.1.23) plays an instrumental role in cellular metabolism. Here we report on a blue native polyacrylamide gel electrophoretic technique that allows the facile detection of this enzyme. The product, oxidized nicotinamide adenine dinucleotide phosphate (NADP(+)), formed following the reaction of NADK with NAD(+) and adenosine 5'-triphosphate was detected with the aid of glucose-6-phosphate dehydrogenase or NADP(+)-isocitrate dehydrogenase, iodonitrotetrazolium chloride, and phenazine methosulfate. The bands at the respective activity sites were excised and subjected to native and denaturing two-dimensional electrophoresis for the determination of protein levels. Hence this novel electrophoretic method allows the easy detection of NADK, a critical enzyme involved in pyridine homeostasis. Furthermore, this technique allowed the monitoring of the activity and expression of this kinase in various biological systems.
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Affiliation(s)
- Ryan J Mailloux
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada P3E 2C6
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35
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Chai MF, Wei PC, Chen QJ, An R, Chen J, Yang S, Wang XC. NADK3, a novel cytoplasmic source of NADPH, is required under conditions of oxidative stress and modulates abscisic acid responses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 47:665-74. [PMID: 16856986 DOI: 10.1111/j.1365-313x.2006.02816.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In plants, excess reactive oxygen species are toxic molecules induced under environmental stresses, including pathogen invasions and abiotic stresses. Many anti-oxidant defense systems have been reported to require NADPH as an important reducing energy equivalent. However, the sources of NADPH and the molecular mechanisms of maintaining cytoplasmic redox balance are unclear. Here, we report the biological function of a putative cytoplasmic NADH kinase (NADK3) in several abiotic stress responses in Arabidopsis. We found that cytoplasmic NADPH is provided mostly by the product of the NADK3 gene in Arabidopsis. Expression of he NADK3 gene is responsive to abscisic acid (ABA) and abiotic stress conditions, including methyl violgen (MV), high salinity and osmotic shock. An NADK3 null mutant showed hypersensitivity to oxidative stress in both seed germination and seedling growth. Seed germination of the mutant plants also showed increased sensitivity to ABA, salt and mannitol. Furthermore, stress-related target genes were identified as upregulated in the mutant by mannitol and MV. Our study indicates that this cytoplasmic NADH kinase, a key source of the cellular reductant NADPH, is required for various abiotic stress responses.
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Affiliation(s)
- Mao-Feng Chai
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100094, China
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36
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Grose JH, Joss L, Velick SF, Roth JR. Evidence that feedback inhibition of NAD kinase controls responses to oxidative stress. Proc Natl Acad Sci U S A 2006; 103:7601-6. [PMID: 16682646 PMCID: PMC1472491 DOI: 10.1073/pnas.0602494103] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Formation of NADP+ from NAD+ is catalyzed by NAD kinase (NadK; EC 2.7.1.23). Evidence is presented that NadK is the only NAD kinase of Salmonella enterica and is essential for growth. NadK is inhibited allosterically by NADPH and NADH. Without effectors, NadK exists as an equilibrium mixture of dimers and tetramers (KD = 1.0 +/- 0.8 mM) but is converted entirely to tetramers in the presence of the inhibitor NADPH. Comparison of NadK kinetic parameters with pool sizes of NADH and NADPH suggests that NadK is substantially inhibited during normal growth and, thus, can increase its activity greatly in response to temporary drops in the pools of inhibitory NADH and NADPH. The primary inhibitor is NADPH during aerobic growth and NADH during anaerobic growth. A model is proposed in which variation of NadK activity is central to the adjustment of pyridine nucleotide pools in response to changes in aeration, oxidative stress, and UV irradiation. It is suggested that each of these environmental factors causes a decrease in the level of reduced pyridine nucleotides, activates NadK, and increases production of NADP(H) at the expense of NAD(H). Activation of NadK may constitute a defensive response that resists loss of protective NADPH.
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Affiliation(s)
- Julianne H. Grose
- *Department of Biology, University of Utah, Salt Lake City, UT 84112
| | - Lisa Joss
- Department of Biochemistry, University of Utah Medical School, Salt Lake City, UT 84112
| | - Sidney F. Velick
- Department of Biochemistry, University of Utah Medical School, Salt Lake City, UT 84112
| | - John R. Roth
- *Department of Biology, University of Utah, Salt Lake City, UT 84112
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37
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Shianna KV, Marchuk DA, Strand MK. Genomic characterization of POS5, the Saccharomyces cerevisiae mitochondrial NADH kinase. Mitochondrion 2006; 6:94-101. [PMID: 16621727 DOI: 10.1016/j.mito.2006.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Revised: 02/11/2006] [Accepted: 02/16/2006] [Indexed: 11/22/2022]
Abstract
Disruption of the Saccharomyces cerevisiae mitochondrial NADH kinase POS5 increases the mitochondrial mutation rate 50-fold. Whereas most multicellular eukaryotic genomes have one NADH kinase gene, the yeast genome contains three distinct genes encoding NAD/H kinase activity. To determine if all three genes are essential for viability we constructed combinations of gene knockouts. We show that only the pos5Deltautr1Delta combination is synthetically lethal, demonstrating an essential overlapping function, and showing that NAD/H kinase activity is essential for eukaryotic viability. The single human NAD/H kinase gene can rescue the lethality of the double knockout in yeast, demonstrating that the single human gene can fill the various functions provided by the three yeast genes. The human NAD/H kinase gene harbors very common sequence variants, but all of these equally complement the synthetic lethality in yeast, illustrating that each of these are functionally wild-type. To understand the molecular mechanism of the mitochondrial genome instability of pos5 mutation we performed gene expression analysis on the pos5Delta. The pos5Delta resulted in an increase in expression of most of the iron transport genes including key genes involved in iron-sulfur cluster assembly. Decreased expression occurred in many genes involved in the electron transport chain. We show that the pos5Delta expression pattern is similar to the frataxin homolog knockout (yfh1Delta), the yeast model for Friedreich's ataxia. These combined data show that the POS5 NAD/H kinase is an important protein required for a variety of essential cellular pathways and that deficient iron-sulfur cluster assembly may play a critical role in the mitochondrial mutator phenotype observed in the pos5Delta.
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Affiliation(s)
- Kevin V Shianna
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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38
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Shi F, Kawai S, Mori S, Kono E, Murata K. Identification of ATP-NADH kinase isozymes and their contribution to supply of NADP(H) in Saccharomyces cerevisiae. FEBS J 2005; 272:3337-49. [PMID: 15978040 DOI: 10.1111/j.1742-4658.2005.04749.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ATP-NAD kinase phosphorylates NAD to produce NADP by using ATP, whereas ATP-NADH kinase phosphorylates both NAD and NADH. Three NAD kinase homologues, namely, ATP-NAD kinase (Utr1p), ATP-NADH kinase (Pos5p) and function-unknown Yel041wp (Yef1p), are found in the yeast Saccharomyces cerevisiae. In this study, Yef1p was identified as an ATP-NADH kinase. The ATP-NADH kinase activity of Utr1p was also confirmed. Thus, the three NAD kinase homologues were biochemically identified as ATP-NADH kinases. The phenotypic analysis of the single, double and triple mutants, which was unexpectedly found to be viable, for UTR1, YEF1 and POS5 demonstrated the critical contribution of Pos5p to mitochondrial function and survival at 37 degrees C and the critical contribution of Utr1p to growth in low iron medium. The contributions of the other two enzymes were also demonstrated; however, these were observed only in the absence of the critical contributor, which was supported by complementation for some pos5 phenotypes by the overexpression of UTR1 and YEF1. The viability of the triple mutant suggested that a 'novel' enzyme, whose primary structure is different from those of all known NAD and NADH kinases, probably catalyses the formation of cytosolic NADP in S. cerevisiae. Finally, we found that LEU2 of Candida glabrata, encoding beta-isopropylmalate dehydrogenase and being used to construct the triple mutant, complemented some pos5 phenotypes; however, overexpression of LEU2 of S. cerevisiae did not. The complementation was putatively attributed to an ability of Leu2p of C. glabrata to use NADP as a coenzyme and to supply NADPH.
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Affiliation(s)
- Feng Shi
- Department of Basic and Applied Molecular Biotechnology, Division of Food and Biological Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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39
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Oganesyan V, Huang C, Adams PD, Jancarik J, Yokota HA, Kim R, Kim SH. Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:640-6. [PMID: 16511117 PMCID: PMC1952466 DOI: 10.1107/s1744309105019780] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Accepted: 06/22/2005] [Indexed: 01/11/2023]
Abstract
NAD kinase is the only known enzyme that catalyzes the formation of NADP, a coenzyme involved in most anabolic reactions and in the antioxidant defense system. Despite its importance, very little is known regarding the mechanism of catalysis and only recently have several NAD kinase structures been deposited in the PDB. Here, an independent investigation of the crystal structure of inorganic polyphosphate/ATP-NAD kinase, PPNK_THEMA, a protein from Thermotoga maritima, is reported at a resolution of 2.3 A. The crystal structure was solved using single-wavelength anomalous diffraction (SAD) data collected at the Se absorption-peak wavelength in a state in which no cofactors or substrates were bound. It revealed that the 258-amino-acid protein is folded into two distinct domains, similar to recently reported NAD kinases. The N-terminal alpha/beta-domain spans the first 100 amino acids and the last 30 amino acids of the polypeptide and has several topological matches in the PDB, whereas the other domain, which spans the middle 130 residues, adopts a unique beta-sandwich architecture and only appreciably matches the recently deposited PDB structures of NAD kinases.
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Affiliation(s)
- Vaheh Oganesyan
- Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Candice Huang
- Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Paul D. Adams
- Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jaru Jancarik
- Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Hisao A. Yokota
- Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Rosalind Kim
- Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sung-Hou Kim
- Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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40
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Mori S, Kawai S, Shi F, Mikami B, Murata K. Molecular conversion of NAD kinase to NADH kinase through single amino acid residue substitution. J Biol Chem 2005; 280:24104-12. [PMID: 15855156 DOI: 10.1074/jbc.m502518200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NAD kinase phosphorylates NAD+ to form NADP+ and is strictly specific to NAD+, whereas NADH kinase phosphorylates both NAD+ and NADH, thereby showing relaxed substrate specificity. Based on their primary and tertiary structures, the difference in the substrate specificities between NAD and NADH kinases was proposed to be caused by one aligned residue: Gly or polar amino acid (Gln or Thr) in five NADH kinases and a charged amino acid (Arg) in two NAD kinases. The substitution of Arg with Gly in the two NAD kinases relaxed the substrate specificity (i.e. converted the NAD kinases to NADH kinases). The substitution of Arg in one NAD kinase with polar amino acids also relaxed the substrate specificity, whereas substitution with charged and hydrophobic amino acids did not show a similar result. In contrast, the substitution of Gly with Arg in one NADH kinase failed to convert it to NAD kinase. These results suggest that a charged or hydrophobic amino acid residue in the position of interest is crucial for strict specificity of NAD kinases to NAD+, whereas Gly or polar amino acid residue is not the sole determinant for the relaxed substrate specificity of NADH kinases. The significance of the conservation of the residue at the position in 207 NAD kinase homologues is also discussed.
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Affiliation(s)
- Shigetarou Mori
- Department of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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41
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Ochiai A, Mori S, Kawai S, Murata K. Overexpression, purification, and characterization of ATP-NAD kinase of Sphingomonas sp. A1. Protein Expr Purif 2005; 36:124-30. [PMID: 15177293 DOI: 10.1016/j.pep.2004.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2004] [Revised: 03/25/2004] [Indexed: 11/15/2022]
Abstract
The NAD kinase gene (nadK) of Sphingomonas sp. A1 was cloned and then overexpressed in Escherichia coli, and the gene product (NadK) was purified from the E. coli cells through five steps with a 25% yield of activity. NadK was a homodimer of 32 kDa subunits, utilized ATP or other nucleoside triphosphates, but not inorganic polyphosphates, as phosphoryl donors for the phosphorylation of NAD, most efficiently at pH 8.0 and 50-55 degrees C, and was designated as ATP-NAD kinase (NadK). NadK showed no NADH kinase activity and was slightly inhibited by NADP(H). Precursors for NAD biosynthesis such as quinolinic acid, nicotinic acid mononucleotide, nicotinic acid adenine dinucleotide, and nicotinic acid had no effect on the NadK activity, as observed in the cases of the NAD kinases of Micrococcus flavus, Mycobacterium tuberculosis, and E. coli. Taken together with the report that the NAD kinase of Bacillus subtilis is activated by quinolinic acid [J. Bacteriol. 185 (2003) 4844], it is indicated that the regulatory patterns of NAD kinases differ even among bacterial NAD kinases.
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Affiliation(s)
- Akihito Ochiai
- Department of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, 611-0011, Japan
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42
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Berrin JG, Pierrugues O, Brutesco C, Alonso B, Montillet JL, Roby D, Kazmaier M. Stress induces the expression of AtNADK-1, a gene encoding a NAD(H) kinase in Arabidopsis thaliana. Mol Genet Genomics 2005; 273:10-9. [PMID: 15711971 DOI: 10.1007/s00438-005-1113-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2004] [Accepted: 12/22/2004] [Indexed: 11/30/2022]
Abstract
A novel Arabidopsis thaliana gene (AtNADK-1) was identified based on its response to radiation and oxidative stress. Levels of AtNADK-1 mRNA increase eight-fold following exposure to ionising radiation and are enhanced three-fold by treatment with hydrogen peroxide. The gene also appears to be differentially regulated during compatible and incompatible plant-pathogen interactions in response to Pseudomonas syringae pv. tomato. The full-length AtNADK-1 cDNA encodes a 58-kDa protein that shows high sequence homology to the recently defined family of NAD(H) kinases. Recombinant AtNADK-1 utilises ATP to phosphorylate both NAD and NADH, showing a two-fold preference for NADH. Using reverse genetics, we demonstrate that AtNADK-1 deficient plants display enhanced sensitivity to gamma irradiation and to paraquat-induced oxidative stress. Our results indicate that this novel NAD(H) kinase may contribute to the maintenance of redox status in Arabidopsis thaliana.
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Affiliation(s)
- Jean-Guy Berrin
- Département d'Ecophysiologie Végétale et de Microbiologie, Laboratoire de Bioénergétique Cellulaire, CEA Cadarache, Bât 156, 13108 Saint-Paul Lez Durance, France
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43
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Turner WL, Waller JC, Vanderbeld B, Snedden WA. Cloning and characterization of two NAD kinases from Arabidopsis. identification of a calmodulin binding isoform. PLANT PHYSIOLOGY 2004; 135:1243-55. [PMID: 15247403 PMCID: PMC519044 DOI: 10.1104/pp.104.040428] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Revised: 04/22/2004] [Accepted: 04/26/2004] [Indexed: 05/17/2023]
Abstract
NAD kinase (NADK; ATP:NAD 2'-phosphotransferase, EC 2.7.1.23), an enzyme found in both prokaryotes and eukaryotes, generates the important pyridine nucleotide NADP from substrates ATP and NAD. The role of NADKs in plants is poorly understood, and cDNAs encoding plant NADKs have not previously been described to our knowledge. We have cloned two cDNAs from Arabidopsis predicted to encode NADK isoforms, designated NADK1 and NADK2, respectively. Expressed as recombinant proteins in bacteria, both NADK1 and NADK2 were catalytically active, thereby confirming their identity as NADKs. Transcripts for both isoforms were detected in all tissues examined and throughout development. Although the predicted catalytic regions for NADK1 and NADK2 show sequence similarity to NADKs from other organisms, NADK2 possesses a large N-terminal extension that appears to be unique to plants. Using recombinant glutathione-S-transferase fusion proteins and calmodulin (CaM)-affinity chromatography, we delineated a Ca2+-dependent CaM-binding domain to a 45-residue region within the N-terminal extension of NADK2. Although recombinant NADK2 was not responsive to CaM in vitro, immunoblot analysis suggests that native NADK2 is a CaM-binding protein. In Arabidopsis crude extracts, CaM-dependent NADK activity was much greater than CaM-independent activity throughout development, particularly in young seedlings. A native CaM-dependent NADK was partially purified from Arabidopsis seedlings (Km NAD=0.20 mM, Km Mg2+ -ATP=0.17 mM). The enzyme was fully activated by conserved CaM (S0.5 = 2.2 nm) in the presence of calcium but displayed differential responsiveness to eight CaM-like Arabidopsis proteins. Possible roles for NADKs in plants are discussed in light of our observations.
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Affiliation(s)
- William L Turner
- Department of Biology, Queen's University, Kingston, Ontario, Canada, K7L3N6
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44
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Nulton-Persson AC, Starke DW, Mieyal JJ, Szweda LI. Reversible inactivation of alpha-ketoglutarate dehydrogenase in response to alterations in the mitochondrial glutathione status. Biochemistry 2003; 42:4235-42. [PMID: 12680778 DOI: 10.1021/bi027370f] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a previous study, we found that treatment of rat heart mitochondria with H(2)O(2) resulted in a decline and subsequent recovery in the rate of state 3 NADH-linked respiration. These effects were shown to be mediated by reversible alterations in NAD(P)H utilization and in the activities of specific Krebs cycle enzymes alpha-ketoglutarate dehydrogenase (KGDH) and succinate dehydrogenase. The purpose of the current study was to examine potential mechanism(s) by which H(2)O(2) reversibly alters KGDH activity. We report here that inactivation is not simply due to direct interaction of H(2)O(2) with KGDH. In addition, incubation of mitochondria with deferroxamine, an iron chelator, or 1,3-dimethyl-2-thiourea, an oxygen radical scavenger, prior to addition of H(2)O(2) did not alter the rate or extent of inactivation. Thus, inactivation does not appear to involve a more potent oxygen radical formed upon metal-catalyzed oxidation. Inactive KGDH from H(2)O(2)-treated mitochondria was reactivated with dithiothreitol, implicating oxidation of a protein sulfhydryl(s). However, the thioredoxin system had no effect, indicating that enzyme inactivation is not due to the formation of intra- or intermolecular disulfide(s) or a sulfenic acid. Upon incubation of mitochondria with H(2)O(2), reduced GSH levels fell rapidly prior to enzyme inactivation but recovered at the same time as enzyme activity. Importantly, treatment of inactive KGDH with glutaredoxin facilitated the GSH-dependent recovery of KGDH activity. Glutaredoxin is characterized as a specific and efficient catalyst of protein deglutathionylation. Thus, the results of the current study indicate that KGDH activity appears to be modulated through enzymatic glutathionylation and deglutathionylation. These studies demonstrate a novel mechanism by which KGDH activity and mitochondrial function can be modulated by redox status.
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Affiliation(s)
- Amy C Nulton-Persson
- Department of Physiology and Biophysics and Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Lerner F, Niere M, Ludwig A, Ziegler M. Structural and functional characterization of human NAD kinase. Biochem Biophys Res Commun 2001; 288:69-74. [PMID: 11594753 DOI: 10.1006/bbrc.2001.5735] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
NADP is essential for biosynthetic pathways, energy, and signal transduction. Its synthesis is catalyzed by NAD kinase. Very little is known about the structure, function, and regulation of this enzyme from multicellular organisms. We identified a human NAD kinase cDNA and the corresponding gene using available database information. A cDNA was amplified from a human fibroblast cDNA library and functionally overexpressed in Escherichia coli. The obtained cDNA, slightly different from that deposited in the database, encodes a protein of 49 kDa. The gene is expressed in most human tissues, but not in skeletal muscle. Human NAD kinase differs considerably from that of prokaryotes by subunit molecular mass (49 kDa vs 30-35 kDa). The catalytically active homotetramer is highly selective for its substrates, NAD and ATP. It did not phosphorylate the nicotinic acid derivative of NAD (NAAD) suggesting that the potent calcium-mobilizing pyridine nucleotide NAADP is synthesized by an alternative route.
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Affiliation(s)
- F Lerner
- Freie Universität Berlin, Institut für Biochemie, Thielallee 63, 14195 Berlin, Germany
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46
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Kawai S, Mori S, Mukai T, Hashimoto W, Murata K. Molecular characterization of Escherichia coli NAD kinase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:4359-65. [PMID: 11488932 DOI: 10.1046/j.1432-1327.2001.02358.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
NAD kinase was purified to homogeneity from Escherichia coli MG1655. The enzyme was a hexamer consisting of 30 kDa subunits and utilized ATP or other nucleoside triphosphates as phosphoryl donors for the phosphorylation of NAD, most efficiently at pH 7.5 and 60 degrees C. The enzyme could not use inorganic polyphosphates as phosphoryl donors and was designated as ATP-NAD kinase. The N-terminal amino-acid sequence of the purified enzyme was encoded by yfjB, which had been deposited as a gene of unknown function in the E. coli whole genomic DNA sequence database. yfjB was cloned and expressed in E. coli BL21(DE3)pLysS. The purified product (YfjB) showed NAD kinase activity, and was identical to ATP-NAD kinase purified from E. coli MG1655 in molecular structure and other enzymatic properties. The deduced amino-acid sequence of YfjB exhibited homology with that of Mycobacterium tuberculosis inorganic polyphosphate/ATP-NAD kinase [Kawai, S., Mori, S., Mukai, T., Suzuki, S., Hashimoto, W., Takeshi, Y. & Murata, K. (2000) Biochem. Biophys. Res. Commun. 276, 57-63], and those of many hypothetical proteins for which functions have not yet been revealed. The YfjB homologues were considered to be NAD kinases and alignment of their sequences revealed highly conserved regions, XXX-XGGDG-XL and DGXXX-TPTGSTAY, where X represents a hydrophobic amino-acid residue.
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Affiliation(s)
- S Kawai
- Research Institute for Food Science, Kyoto University, Uji, Japan
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47
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Abstract
The ubiquitous NAD+ kinase (NADK) is the only known enzyme to catalyze formation of NADP+ from NAD+. The capacity to maintain an adequate supply of NADP(H) has important implications for development because of its requirement as a cofactor and electron donor in biosynthesis and detoxication reactions. Modulation of NADK may directly influence NADP(H) concentrations and cell sensitivity to embryotoxicants. Measurable activities of NADK were not detected in gestational day (GD) 10 rat conceptuses. By GD 11, specific activities of 1.8 and 7.0 pmol NADP+/min/microg protein were measured in embryos and visceral yolk sacs (VYSs), respectively. The VYS specific activities decreased thereafter to 0.5 pmol NADP+/min/microg protein by GD 18. Specific activities of NADK in placenta increased from 1.3 pmol NADP+/min/microg protein on GD 11 to 32.7 pmol NADP+/min/microg protein on GD 15. Specific activities in the liver increased from 1.7 pmol NADP+/min/microg protein on GD 15 to 51.1 pmol NADP+/min/microg protein on GD 21. NADK specific activities were also determined in other developmentally relevant tissues such as the heart and the brain. In the heart, NADK activity was at its lowest just before birth while in the brain it peaked at 5.4 pmol NADP+/min/microg protein just prior to birth. In the lung, activity increased from 0.9 pmol NADP+/min/microg protein on GD 17 to 5.9 pmol NADP+/min/microg protein on GD 21. However, activities dropped in the kidney from 2.0 pmol NADP+/min/microg protein on GD 17 to 1.1 pmol NADP+/min/microg protein on GD 21. These results demonstrate dramatic temporal and spatial variations in NADK activity. Tissue variations in NADK activities may reflect alterations in functional needs for cofactors during differentiation and a cooperation between tissues to optimize detoxification capacity. This is particularly important when chemical exposure during pregnancy disrupts pyridine nucleotide redox status and the conceptus must rely on NADK to provide additional NADP(H).
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Affiliation(s)
- S S Akella
- Toxicology Program, The University of Michigan, Ann Arbor, Michigan 48109, USA
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48
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Establishment of a mass-production system for NADP using bacterial inorganic polyphosphate/ATP-NAD kinase. J Biosci Bioeng 2001. [DOI: 10.1016/s1389-1723(01)80294-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Kawai S, Mori S, Mukai T, Suzuki S, Yamada T, Hashimoto W, Murata K. Inorganic Polyphosphate/ATP-NAD kinase of Micrococcus flavus and Mycobacterium tuberculosis H37Rv. Biochem Biophys Res Commun 2000; 276:57-63. [PMID: 11006082 DOI: 10.1006/bbrc.2000.3433] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An enzyme with both inorganic polyphosphate [poly(P)]- and ATP-dependent NAD kinase activities was isolated from Micrococcus flavus. The enzyme was a dimer consisting of 34 kDa subunits, and was named poly(P)/ATP-NAD kinase. Internal amino acid sequences of the enzyme showed homologies with some function-unknown proteins released on the GenBank database. Among such proteins, hypothetical Rv1695 protein (Accession No. Z98268-16), which was encoded by a gene named "Rv1695" on genomic DNA of Mycobacterium tuberculosis H37Rv, was proposed to be poly(P)-dependent NAD kinase. By cloning and expression in Escherichia coli, Rv1695 was shown to encode poly(P)/ATP-NAD kinase and named ppnk. The ppnk product, recombinant-poly(P)/ATP-NAD kinase (Ppnk) was purified and characterized. The enzyme was a tetramaer consisting of 35 kDa subunits when expressed in E. coli. Poly(P)/ATP-NAD kinases of M. flavus and Ppnk of M. tuberculosis H37Rv specifically and completely phosphorylated NAD by utilizing commercially available poly(P)s and nucleoside triphosphates as phosphoryl donors.
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Affiliation(s)
- S Kawai
- Research Institute for Food Science, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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50
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Stephan C, Renard M, Montrichard F. Evidence for the existence of two soluble NAD(+) kinase isoenzymes in Euglena gracilis Z. Int J Biochem Cell Biol 2000; 32:855-63. [PMID: 10940642 DOI: 10.1016/s1357-2725(00)00032-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two soluble NAD(+) kinase isoenzymes (isoenzymes 1 and 2) from Euglena gracilis were separated by preparative electrophoresis and characterized. They display several similar properties: both have an identical apparent molecular weight of 68 kDa and their activities are independent on calmodulin, insensitive to 2-mercaptoethanol but inhibited by p-chloromercurybenzoate, 5, 5'-dithiobis(2-nitrobenzoate) and, surprisingly, by low dithiothreitol concentrations, the inhibition by dithiothreitol being irreversible for isoenzyme 1 but reversible for isoenzyme 2. Nevertheless, the two isoenzymes mainly differ by their specificities towards triphosphate nucleotides and their catalytic mechanisms. Isoenzyme 1 is as active in the presence of ATP as of GTP and acts by a ping-pong mechanism with a k(M) for NAD(+) of 0.26 mM and a k(M) for low MgATP(2-)concentrations of 0.03 mM. Isoenzyme 2 is three-fold more active in the presence of GTP than of ATP and operates by a sequential mechanism with k(M)s for NAD(+) and MgGTP(2-) of 1.03 and 0.20 mM, respectively. This study shows the evidence for the existence of two structurally similar but catalytically different NAD(+) kinase isoenzymes in E. gracilis. One resembles the enzyme previously described in bacteria. The other displays a catalytic mechanism identical to that of NAD(+) kinase from other organisms but remains unique among all the NAD(+) kinases studied to-date regarding its specificity towards GTP.
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Affiliation(s)
- C Stephan
- GBBMV-EA917, UFR Sciences, 2 Boulevard Lavoisier, 49045, Angers, France
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