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Sun H, Wei S, Gong Y, Ding K, Tang S, Sun W, Yuan C, Huang L, Liu Z, Chen C, Yao L. Neuroprotective effects of cordycepin inhibit glutamate-induced apoptosis in hippocampal neurons. Cell Stress Chaperones 2024; 29:10-20. [PMID: 38219840 PMCID: PMC10939076 DOI: 10.1016/j.cstres.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024] Open
Abstract
Glutamate is a neurotransmitter that can cause excitatory neurotoxicity when its extracellular concentration is too high, leading to disrupted calcium balance and increased production of reactive oxygen species (ROS). Cordycepin, a nucleoside adenosine derivative, has been shown to protect against excitatory neurotoxicity induced by glutamate. To investigate its potential neuroprotective effects, the present study employed fluorescence detection and spectrophotometry techniques to analyze primary hippocampal-cultured neurons. The results showed that glutamate toxicity reduced hippocampal neuron viability, increased ROS production, and increased intracellular calcium levels. Additionally, glutamate-induced cytotoxicity activated acetylcholinesterase and decreased glutathione levels. However, cordycepin inhibited glutamate-induced cell death, improved cell viability, reduced ROS production, and lowered Ca2+ levels. It also inhibited acetylcholinesterase activation and increased glutathione levels. This study suggests that cordycepin can protect against glutamate-induced neuronal injury in cell models, and this effect was inhibited by adenosine A1 receptor blockers, indicating that its neuroprotective effect is achieved through activation of the adenosine A1 receptor.
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Affiliation(s)
- Huizhen Sun
- School of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China; Shan County Renmin Road Primary School, Heze, Shandong,PR China
| | - Shanshan Wei
- School of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China
| | - Yanchun Gong
- School of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China; School of Physical Education and Health, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China
| | - Kaizhi Ding
- School of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China
| | - Shan Tang
- School of Physical Education and Health, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China
| | - Wei Sun
- School of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China
| | - Chunhua Yuan
- School of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China
| | - Liping Huang
- School of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, PR China
| | - Zhibing Liu
- School of Physical Education and Health, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China
| | - Chong Chen
- School of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China; School of Physical Education and Health, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China; NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China.
| | - Lihua Yao
- School of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China; School of Physical Education and Health, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, PR China.
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2
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Bedard GT, Gilaj N, Peregrina K, Brew I, Tosti E, Shaffer K, Tyler PC, Edelmann W, Augenlicht LH, Schramm VL. Combined inhibition of MTAP and MAT2a mimics synthetic lethality in tumor models via PRMT5 inhibition. J Biol Chem 2024; 300:105492. [PMID: 38000655 PMCID: PMC10770533 DOI: 10.1016/j.jbc.2023.105492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Homozygous 5'-methylthioadenosine phosphorylase (MTAP) deletions occur in approximately 15% of human cancers. Co-deletion of MTAP and methionine adenosyltransferase 2 alpha (MAT2a) induces a synthetic lethal phenotype involving protein arginine methyltransferase 5 (PRMT5) inhibition. MAT2a inhibitors are now in clinical trials for genotypic MTAP-/- cancers, however the MTAP-/- genotype represents fewer than 2% of human colorectal cancers (CRCs), limiting the utility of MAT2a inhibitors in these and other MTAP+/+ cancers. Methylthio-DADMe-immucillin-A (MTDIA) is a picomolar transition state analog inhibitor of MTAP that renders cells enzymatically MTAP-deficient to induce the MTAP-/- phenotype. Here, we demonstrate that MTDIA and MAT2a inhibitor AG-270 combination therapy mimics synthetic lethality in MTAP+/+ CRC cell lines with similar effects in mouse xenografts and without adverse histology on normal tissues. Combination treatment is synergistic with a 104-fold increase in drug potency for inhibition of CRC cell growth in culture. Combined MTDIA and AG-270 decreases S-adenosyl-L-methionine and increases 5'-methylthioadenosine in cells. The increased intracellular methylthioadenosine:S-adenosyl-L-methionine ratio inhibits PRMT5 activity, leading to cellular arrest and apoptotic cell death by causing MDM4 alternative splicing and p53 activation. Combination MTDIA and AG-270 treatment differs from direct inhibition of PRMT5 by GSK3326595 by avoiding toxicity caused by cell death in the normal gut epithelium induced by the PRMT5 inhibitor. The combination of MTAP and MAT2a inhibitors expands this synthetic lethal approach to include MTAP+/+ cancers, especially the remaining 98% of CRCs without the MTAP-/- genotype.
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Affiliation(s)
- Gabriel T Bedard
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Nord Gilaj
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Chemistry, Lehman College, Bronx, New York, USA
| | - Karina Peregrina
- Department of Oncology, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Isabella Brew
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Elena Tosti
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Karl Shaffer
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Peter C Tyler
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Leonard H Augenlicht
- Department of Oncology, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
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Jeennor S, Anantayanon J, Panchanawaporn S, Chutrakul C, Vongsangnak W, Laoteng K. Efficient de novo production of bioactive cordycepin by Aspergillus oryzae using a food-grade expression platform. Microb Cell Fact 2023; 22:253. [PMID: 38071331 PMCID: PMC10710699 DOI: 10.1186/s12934-023-02261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Cordycepin (3'-deoxyadenosine) is an important bioactive compound in medical and healthcare markets. The drawbacks of commercial cordycepin production using Cordyceps spp. include long cultivation periods and low cordycepin yields. To overcome these limitations and meet the increasing market demand, the efficient production of cordycepin by the GRAS-status Aspergillus oryzae strain using a synthetic biology approach was developed in this study. RESULTS An engineered strain of A. oryzae capable of cordycepin production was successfully constructed by overexpressing two metabolic genes (cns1 and cns2) involved in cordycepin biosynthesis under the control of constitutive promoters. Investigation of the flexibility of carbon utilization for cordycepin production by the engineered A. oryzae strain revealed that it was able to utilize C6-, C5-, and C12-sugars as carbon sources, with glucose being the best carbon source for cordycepin production. High cordycepin productivity (564.64 ± 9.59 mg/L/d) was acquired by optimizing the submerged fermentation conditions. CONCLUSIONS This study demonstrates a powerful production platform for bioactive cordycepin production by A. oryzae using a synthetic biology approach. An efficient and cost-effective fermentation process for cordycepin production using an engineered strain was established, offering a powerful alternative source for further upscaling.
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Affiliation(s)
- Sukanya Jeennor
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
| | - Jutamas Anantayanon
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Sarocha Panchanawaporn
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chanikul Chutrakul
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
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Zhao B, Zhang Y, Zhang S, Hu T, Guo Y. Multifactorial interaction of selenium, iron, xylose, and glycine on cordycepin metabolism in Cordyceps militaris. Appl Microbiol Biotechnol 2023; 107:7403-7416. [PMID: 37773218 DOI: 10.1007/s00253-023-12792-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/01/2023]
Abstract
Cordycepin, a nucleoside analog, is the main antioxidative and antimicrobial substance in Cordyceps militaris. To improve the metabolism of cordycepin, carbon sources, nitrogen sources, trace elements, and precursors were studied by single factor, Plackett-Burman, and central composite designs in C. militaris mycelial fermentation. Under the regulation of the multifactorial interactions of selenite, ferrous chloride, xylose, and glycine, cordycepin production was increased by 5.2-fold compared with the control. The gene expression of hexokinase, ATP phosphoribosyltransferase, adenylosuccinate synthetase, and cns1-3 in the glycolysis, pentose phosphate, and adenosine synthesis pathways were increased by 3.2-7.5 times due to multifactorial interactions, while the gene expression of histidine biosynthesis trifunctional protein and histidinol-phosphate aminotransferase in histidine synthesis pathway were decreased by 23.4%-56.2%. Increasing with cordycepin production, glucose uptake was accelerated, mycelia growth was inhibited, and the cell wall was damaged. Selenomethionine (SeMet), selenocysteine (SeCys), and selenium nanoparticles (SeNPs) were the major Se species in C. militaris mycelia. This study provides a new insight for promoting cordycepin production by regulating glycolysis, pentose phosphate, and histidine metabolism. KEY POINTS: • Cordycepin production in the CCDmax group was 5.2-fold than that of the control. • Glucose uptake of the CCDmax group was accelerated and cell wall was damaged. • The metabolic flux was concentrated to the cordycepin synthesis pathway.
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Affiliation(s)
- Bingjie Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Yong Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Sasa Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Ting Hu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yanbin Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China.
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5
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Chen HY, Zhao SW. Progress on Z genome biosynthetic pathway of bacteriophage. Yi Chuan 2023; 45:887-903. [PMID: 37872112 DOI: 10.16288/j.yczz.23-059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
There are abundant base modifications in bacteriophages' genomes, mainly for avoiding the digestion of host endonucleases. More than 40 years ago, researchers discovered that 2-amino-adenine (Z) completely replaced adenine (A) and forms a complementary pairing with three hydrogen bonds with thymine (T) in the DNA of cyanophage S-2L, forming a distinct "Z-genome". In recent years, researchers have discovered and validated the biosynthetic pathway of Z-genome in various bacteriophages, constituting a multi-enzyme system. This system includes the phage-encoded enzymes deoxy-2'-aminoadenylosuccinate synthetase (PurZ), deoxyadenosine triphosphate hydrolase (dATPase/DatZ), deoxyadenosine/deoxyguanosine triphosphate pyrophosphatase (DUF550/MazZ) and DNA polymerase (DpoZ). In this review, we provide a concise overview of the historical discovery on diversely modified nucleosides in bacteriophages, then we comprehensively summarize the research progress on multiple enzymes involved in the Z-genome biosynthetic pathway. Finally, the potential applications of the Z-genome and the enzymes in its biosynthetic pathway are discussed in order to provide reference for research in this field.
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Affiliation(s)
- Hui-Yu Chen
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Su-Wen Zhao
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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6
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Ma YC, Huang P, Wang XL, Liu GQ. Multi-omics analysis unravels positive effect of rotenone on the cordycepin biosynthesis in submerged fermentation of Cordyceps militaris. Bioresour Technol 2023; 373:128705. [PMID: 36746212 DOI: 10.1016/j.biortech.2023.128705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Cordycepin is the key pharmacologically active compound of Cordyceps militaris, and various fermentation strategies have been developed to increase cordycepin production. This study aimed to investigate the effect of rotenone on cordycepin biosynthesis in submerged fermentation of C. militaris, and also to explore its possible induction mechanisms via multi-omics analysis. Adding 5 mg/L rotenone significantly increased the cordycepin production by 316.09 %, along with mycelial growth inhibition and cell wall destruction. Moreover, transcriptomic analysis and metabolomic analysis revealed the accumulation of cordycepin was promoted by alterations in energy metabolism and amino acid metabolism pathways. Finally, the integration analysis of the two omics confirmed rotenone altered the nucleotide metabolism pathway toward adenosine and up-regulated the cordycepin synthesis genes (cns1-3) to convert adenosine to cordycepin. This work reports, for the first time, rotenone could act as an effective inducer of cordycepin synthesis.
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Affiliation(s)
- You-Chu Ma
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004, China; Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004, China; Microbial Variety Creation Center, Hunan Provincial Laboratory of Yuelushan Seed Industry, Changsha 410004, China
| | - Ping Huang
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004, China; Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004, China
| | - Xiao-Ling Wang
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004, China; Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004, China; Microbial Variety Creation Center, Hunan Provincial Laboratory of Yuelushan Seed Industry, Changsha 410004, China
| | - Gao-Qiang Liu
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004, China; Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004, China; Microbial Variety Creation Center, Hunan Provincial Laboratory of Yuelushan Seed Industry, Changsha 410004, China.
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7
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Abstract
Cordycepin, a nucleoside from Cordyceps mushrooms, has many beneficial properties for health, including anticancer activities. In cancer cells, cordycepin targets various signaling molecules. Here, we review the possible anticancer mechanisms of cordycepin involving the targeting of kinases. Abnormal kinase expression is involved in cancer development and progression through different molecular mechanisms, including phosphorylation, amplification, genetic mutations, and epigenetic regulation. Research suggests that kinases, such as the c-Jun N-terminal kinase (JNK), mitogen-activated protein kinase (MAPK), AMP kinase (AMPK), phosphoinositide 3-kinase (PI3K)/Akt, extracellular signal-regulated kinase (ERK), mammalian target of rapamycin (mTOR), glycogen synthase kinase (GSK)-3β, and focal adhesion kinase (FAK) pathways, can be targeted by cordycepin and disrupting their activity. Given that kinase inhibitors can have crucial roles in cancer treatment, targeting kinases might be one of the molecular mechanisms involved in the anticancer potential of cordycepin.
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Affiliation(s)
- Md Asaduzzaman Khan
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China; Nature Study Society of Bangladesh, Dhaka, Bangladesh.
| | - Mousumi Tania
- Nature Study Society of Bangladesh, Dhaka, Bangladesh; Division of Molecular Cancer Biology, The Red-Green Research Center, Dhaka, Bangladesh.
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8
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Jędrejko K, Kała K, Sułkowska-Ziaja K, Pytko-Polończyk J, Muszyńska B. Effect of Cordyceps spp. and Cordycepin on Functions of Bones and Teeth and Related Processes: A Review. Molecules 2022; 27:molecules27238170. [PMID: 36500262 PMCID: PMC9737375 DOI: 10.3390/molecules27238170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
Cordyceps spp. (belonging to the Ascomycota group) are entomopathogenic mushrooms that have traditionally been used in ethnomedicine in Asian countries such as China, Japan, Korea, and India. They are unique parasites of larvae of selected species of moths. Cordyceps militaris is one of the best sources of cordycepin. Worldwide, osteoporosis is one of the most common bone diseases, whose pharmacotherapy includes various medical interventions; however, the research and development of new molecules and new drugs is required. The impact of adenosine receptors (ARs) on the purinergic signaling pathway may regulate proliferation, differentiate dental pulp stem cells and bone marrow, and modulate osteogenesis and bone repair. The aim of the review was to collect and analyze the available data on the effects of Cordyceps spp. or cordycepin on bone function and related processes. To the best of our knowledge, this is the first systematic review in this perspective, not necessarily using mushroom raw material or even the isolated parent compound cordycepin, but new molecules that are analogs of nucleosides, such as those from C. militaris. This review found that Cordyceps spp. or isolated cordycepin interacts via the AR, 5' adenosine monophosphate-activated protein kinase (AMPK), and adenosine-5'-triphosphate (ATP) signaling pathway and evaluated their impact on bones, teeth, and dental pulp. Cordyceps spp. was found to have the potential to develop regenerative medicines, thus providing an opportunity to expand the treatment or intervention methods in the recovery after traumatic injuries, convalescence, and terminal-stage or devastating diseases.
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Affiliation(s)
- Karol Jędrejko
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Kraków, Poland
- Correspondence: (K.J.); (B.M.)
| | - Katarzyna Kała
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Kraków, Poland
| | - Katarzyna Sułkowska-Ziaja
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Kraków, Poland
| | - Jolanta Pytko-Polończyk
- Chair and Department of Integrated Dentistry, Faculty of Medicine, Jagiellonian University Medical College, 4 Montelupich Street, 31-155 Kraków, Poland
| | - Bożena Muszyńska
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Kraków, Poland
- Correspondence: (K.J.); (B.M.)
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9
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Ward AS, Hsiung CH, Kesterson DG, Kamath VG, McKee EE. Entecavir competitively inhibits deoxyguanosine and deoxyadenosine phosphorylation in isolated mitochondria and the perfused rat heart. J Biol Chem 2022; 298:101876. [PMID: 35358513 PMCID: PMC9097457 DOI: 10.1016/j.jbc.2022.101876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 10/26/2022] Open
Abstract
Deoxyguanosine kinase (dGK) is reported responsible for the phosphorylation of deoxyadenosine (dA) and deoxyguanosine (dG) in the mitochondrial purine salvage pathway. Antiviral nucleoside analogs known as nucleoside reverse transcriptase inhibitors (NRTIs) must be phosphorylated by host enzymes for the analog to become active. We address the possibility that NRTI purine analogs may be competitive inhibitors of dGK. From a group of such analogs, we demonstrate that entecavir (ETV) competitively inhibited the phosphorylation of dG and dA in rat mitochondria. Mitochondria from the brain, heart, kidney, and liver showed a marked preference for phosphorylation of dG over dA (10-30-fold) and ETV over dA (2.5-4-fold). We found that ETV inhibited the phosphorylation of dG with an IC50 of 15.3 ± 2.2 μM and that ETV and dG were both potent inhibitors of dA phosphorylation with IC50s of 0.034 ± 0.007 and 0.028 ± 0.006 μM, respectively. In addition, the phosphorylation of dG and ETV followed Michaelis-Menten kinetics and each competitively inhibited the phosphorylation of the other. We observed that the kinetics of dA phosphorylation were strikingly different from those of dG phosphorylation, with an exponentially lower affinity for dGK and no effect of dA on dG or ETV phosphorylation. Finally, in an isolated heart perfusion model, we demonstrated that dG, dA, and ETV were phosphorylated and dG phosphorylation was inhibited by ETV. Taken together, these data demonstrate that dGK is inhibited by ETV and that the primary role of dGK is in the phosphorylation of dG rather than dA.
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Affiliation(s)
- Avery S Ward
- Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, Michigan, USA
| | - Chia-Heng Hsiung
- Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, Michigan, USA; School of Science, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang Province, China
| | - Daniel G Kesterson
- Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, Michigan, USA; Department of Health Management and Policy, University of Michigan School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Vasudeva G Kamath
- Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, Michigan, USA; Department of Basic Medical Sciences, Touro College of Osteopathic Medicine, Middletown, New York, USA
| | - Edward E McKee
- Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, Michigan, USA.
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Smith CR, Aranda R, Bobinski TP, Briere DM, Burns AC, Christensen JG, Clarine J, Engstrom LD, Gunn RJ, Ivetac A, Jean-Baptiste R, Ketcham JM, Kobayashi M, Kuehler J, Kulyk S, Lawson JD, Moya K, Olson P, Rahbaek L, Thomas NC, Wang X, Waters LM, Marx MA. Fragment-Based Discovery of MRTX1719, a Synthetic Lethal Inhibitor of the PRMT5•MTA Complex for the Treatment of MTAP-Deleted Cancers. J Med Chem 2022; 65:1749-1766. [PMID: 35041419 DOI: 10.1021/acs.jmedchem.1c01900] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The PRMT5•MTA complex has recently emerged as a new synthetically lethal drug target for the treatment of MTAP-deleted cancers. Here, we report the discovery of development candidate MRTX1719. MRTX1719 is a potent and selective binder to the PRMT5•MTA complex and selectively inhibits PRMT5 activity in MTAP-deleted cells compared to MTAP-wild-type cells. Daily oral administration of MRTX1719 to tumor xenograft-bearing mice demonstrated dose-dependent inhibition of PRMT5-dependent symmetric dimethylarginine protein modification in MTAP-deleted tumors that correlated with antitumor activity. A 4-(aminomethyl)phthalazin-1(2H)-one hit was identified through a fragment-based screen, followed by X-ray crystallography, to confirm binding to the PRMT5•MTA complex. Fragment growth supported by structural insights from X-ray crystallography coupled with optimization of pharmacokinetic properties aided the discovery of development candidate MRTX1719.
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Affiliation(s)
| | - Ruth Aranda
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - David M Briere
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Aaron C Burns
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Jeffery Clarine
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Lars D Engstrom
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Robin J Gunn
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Anthony Ivetac
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - John M Ketcham
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Jon Kuehler
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Svitlana Kulyk
- Mirati Therapeutics, San Diego, California 92121, United States
| | - J David Lawson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Krystal Moya
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Peter Olson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Lisa Rahbaek
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Nicole C Thomas
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Xiaolun Wang
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Laura M Waters
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Matthew A Marx
- Mirati Therapeutics, San Diego, California 92121, United States
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11
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Bleasby K, Houle R, Hafey M, Lin M, Guo J, Lu B, Sanchez RI, Fillgrove KL. Islatravir Is Not Expected to Be a Victim or Perpetrator of Drug-Drug Interactions via Major Drug-Metabolizing Enzymes or Transporters. Viruses 2021; 13:1566. [PMID: 34452431 PMCID: PMC8402619 DOI: 10.3390/v13081566] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Islatravir (MK-8591) is a nucleoside reverse transcriptase translocation inhibitor in development for the treatment and prevention of HIV-1. The potential for islatravir to interact with commonly co-prescribed medications was studied in vitro. Elimination of islatravir is expected to be balanced between adenosine deaminase-mediated metabolism and renal excretion. Islatravir did not inhibit uridine diphosphate glucuronosyltransferase 1A1 or cytochrome p450 (CYP) enzymes CYP1A2, 2B6, 2C8, 2C9, 2C19, 2D6, or 3A4, nor did it induce CYP1A2, 2B6, or 3A4. Islatravir did not inhibit hepatic transporters organic anion transporting polypeptide (OATP) 1B1, OATP1B3, organic cation transporter (OCT) 1, bile salt export pump (BSEP), multidrug resistance-associated protein (MRP) 2, MRP3, or MRP4. Islatravir was neither a substrate nor a significant inhibitor of renal transporters organic anion transporter (OAT) 1, OAT3, OCT2, multidrug and toxin extrusion protein (MATE) 1, or MATE2K. Islatravir did not significantly inhibit P-glycoprotein and breast cancer resistance protein (BCRP); however, it was a substrate of BCRP, which is not expected to be of clinical significance. These findings suggest islatravir is unlikely to be the victim or perpetrator of drug-drug interactions with commonly co-prescribed medications, including statins, diuretics, anti-diabetic drugs, proton pump inhibitors, anticoagulants, benzodiazepines, and selective serotonin reuptake inhibitors.
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Affiliation(s)
| | | | | | | | | | | | | | - Kerry L. Fillgrove
- Merck & Co., Inc., Kenilworth, NJ 07033, USA; (K.B.); (R.H.); (M.H.); (M.L.); (J.G.); (B.L.); (R.I.S.)
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12
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Czernecki D, Bonhomme F, Kaminski PA, Delarue M. Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA. Nat Commun 2021; 12:4710. [PMID: 34354070 PMCID: PMC8342488 DOI: 10.1038/s41467-021-25064-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022] Open
Abstract
Cyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes - datZ, mazZ and purZ - was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Frédéric Bonhomme
- Unit of Epigenetic Chemical Biology, CNRS UMR 3523, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Pierre-Alexandre Kaminski
- Unit of Biology of Pathogenic Gram-Positive Bacteria, CNRS UMR 2001, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France.
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13
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Szewczuk M, Boguszewska K, Kaźmierczak-Barańska J, Karwowski BT. The Influence of 5' R and 5' S cdA and cdG on the Activity of BsmAI and SspI Restriction Enzymes. Molecules 2021; 26:molecules26123750. [PMID: 34205449 PMCID: PMC8234751 DOI: 10.3390/molecules26123750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 01/03/2023] Open
Abstract
Restriction endonucleases (REs) are intra-bacterial scissors that are considered tools in the fight against foreign genetic material. SspI and BsmAI, examined in this study, cleave dsDNA at their site of recognition or within a short distance of it. Both enzymes are representatives of type II REs, which have played an extremely important role in research on the genetics of organisms and molecular biology. Therefore, the study of agents affecting their activity has become highly important. Ionizing radiation may damage basic cellular mechanisms by inducing lesions in the genome, with 5',8-cyclo-2'-deoxypurines (cdPus) as a model example. Since cdPus may become components of clustered DNA lesions (CDLs), which are unfavorable for DNA repair pathways, their impact on other cellular mechanisms is worthy of attention. This study investigated the influence of cdPus on the elements of the bacterial restriction-modification system. In this study, it was shown that cdPus present in DNA affect the activity of REs. SspI was blocked by any cdPu lesion present at the enzyme's recognition site. When lesions were placed near the recognition sequence, the SspI was inhibited up to 46%. Moreover, (5'S)-5',8-cyclo-2'-deoxyadenosine (ScdA) present in the oligonucleotide sequence lowered BsmAI activity more than (5'R)-5',8-cyclo-2'-deoxyadenosine (RcdA). Interestingly, in the case of 5',8-cyclo-2'-deoxyguanosine (cdG), both 5'S and 5'R diastereomers inhibited BsmAI activity (up to 55% more than cdA). The inhibition was weaker when cdG was present at the recognition site rather than the cleavage site.
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14
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Karwowski BT. (5' S) 5',8-Cyclo-2'-Deoxyadenosine Cannot Stop BER. Clustered DNA Lesion Studies. Int J Mol Sci 2021; 22:ijms22115934. [PMID: 34072994 PMCID: PMC8199134 DOI: 10.3390/ijms22115934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022] Open
Abstract
As a result of external and endocellular physical-chemical factors, every day approximately ~105 DNA lesions might be formed in each human cell. During evolution, living organisms have developed numerous repair systems, of which Base Excision Repair (BER) is the most common. 5′,8-cyclo-2′-deoxyadenosine (cdA) is a tandem lesion that is removed by the Nucleotide Excision Repair (NER) mechanism. Previously, it was assumed that BER machinery was not able to remove (5′S)cdA from the genome. In this study; however, it has been demonstrated that, if (5′S)cdA is a part of a single-stranded clustered DNA lesion, it can be removed from ds-DNA by BER. The above is theoretically possible in two cases: (A) When, during repair, clustered lesions form Okazaki-like fragments; or (B) when the (5′S)cdA moiety is located in the oligonucleotide strand on the 3′-end side of the adjacent DNA damage site, but not when it appears at the opposite 5′-end side. To explain this phenomenon, pure enzymes involved in BER were used (polymerase β (Polβ), a Proliferating Cell Nuclear Antigen (PCNA), and the X-Ray Repair Cross-Complementing Protein 1 (XRCC1)), as well as the Nuclear Extract (NE) from xrs5 cells. It has been found that Polβ can effectively elongate the primer strand in the presence of XRCC1 or PCNA. Moreover, supplementation of the NE from xrs5 cells with Polβ (artificial Polβ overexpression) forced oligonucleotide repair via BER in all the discussed cases.
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Affiliation(s)
- Boleslaw T Karwowski
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland
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15
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Acosta J, Pérez E, Sánchez-Murcia PA, Fillat C, Fernández-Lucas J. Molecular Basis of NDT-Mediated Activation of Nucleoside-Based Prodrugs and Application in Suicide Gene Therapy. Biomolecules 2021; 11:biom11010120. [PMID: 33477716 PMCID: PMC7831932 DOI: 10.3390/biom11010120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 11/16/2022] Open
Abstract
Herein we report the first proof for the application of type II 2′-deoxyribosyltransferase from Lactobacillus delbrueckii (LdNDT) in suicide gene therapy for cancer treatment. To this end, we first confirm the hydrolytic ability of LdNDT over the nucleoside-based prodrugs 2′-deoxy-5-fluorouridine (dFUrd), 2′-deoxy-2-fluoroadenosine (dFAdo), and 2′-deoxy-6-methylpurine riboside (d6MetPRib). Such activity was significantly increased (up to 30-fold) in the presence of an acceptor nucleobase. To shed light on the strong nucleobase dependence for enzymatic activity, different molecular dynamics simulations were carried out. Finally, as a proof of concept, we tested the LdNDT/dFAdo system in human cervical cancer (HeLa) cells. Interestingly, LdNDT/dFAdo showed a pronounced reduction in cellular viability with inhibitory concentrations in the low micromolar range. These results open up future opportunities for the clinical implementation of nucleoside 2′-deoxyribosyltransferases (NDTs) in cancer treatment.
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Affiliation(s)
- Javier Acosta
- Applied Biotechnology Group, European University of Madrid, c/ Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain; (J.A.); (E.P.)
| | - Elena Pérez
- Applied Biotechnology Group, European University of Madrid, c/ Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain; (J.A.); (E.P.)
| | - Pedro A. Sánchez-Murcia
- Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria;
| | - Cristina Fillat
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08036 Barcelona, Spain
| | - Jesús Fernández-Lucas
- Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria;
- Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66 Barranquilla, Colombia
- Correspondence:
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16
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Ghodke PP, Gonzalez-Vasquez G, Wang H, Johnson KM, Sedgeman CA, Guengerich FP. Enzymatic bypass of an N 6-deoxyadenosine DNA-ethylene dibromide-peptide cross-link by translesion DNA polymerases. J Biol Chem 2021; 296:100444. [PMID: 33617883 PMCID: PMC8024977 DOI: 10.1016/j.jbc.2021.100444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/25/2022] Open
Abstract
Unrepaired DNA-protein cross-links, due to their bulky nature, can stall replication forks and result in genome instability. Large DNA-protein cross-links can be cleaved into DNA-peptide cross-links, but the extent to which these smaller fragments disrupt normal replication is not clear. Ethylene dibromide (1,2-dibromoethane) is a known carcinogen that can cross-link the repair protein O6-alkylguanine-DNA alkyltransferase (AGT) to the N6 position of deoxyadenosine (dA) in DNA, as well as four other positions in DNA. We investigated the effect of a 15-mer peptide from the active site of AGT, cross-linked to the N6 position of dA, on DNA replication by human translesion synthesis DNA polymerases (Pols) η, ⍳, and κ. The peptide-DNA cross-link was bypassed by the three polymerases at different rates. In steady-state kinetics, the specificity constant (kcat/Km) for incorporation of the correct nucleotide opposite to the adduct decreased by 220-fold with Pol κ, tenfold with pol η, and not at all with Pol ⍳. Pol η incorporated all four nucleotides across from the lesion, with the preference dT > dC > dA > dG, while Pol ⍳ and κ only incorporated the correct nucleotide. However, LC-MS/MS analysis of the primer-template extension product revealed error-free bypass of the cross-linked 15-mer peptide by Pol η. We conclude that a bulky 15-mer peptide cross-linked to the N6 position of dA can retard polymerization and cause miscoding but that overall fidelity is not compromised because only correct pairs are extended.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Hui Wang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kevin M Johnson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Carl A Sedgeman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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17
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Rapp J, Rath P, Kilian J, Brilisauer K, Grond S, Forchhammer K. A bioactive molecule made by unusual salvage of radical SAM enzyme byproduct 5-deoxyadenosine blurs the boundary of primary and secondary metabolism. J Biol Chem 2021; 296:100621. [PMID: 33811856 PMCID: PMC8102628 DOI: 10.1016/j.jbc.2021.100621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
5-Deoxyadenosine (5dAdo) is the byproduct of many radical S-adenosyl-l-methionine enzyme reactions in all domains of life. 5dAdo is also an inhibitor of the radical S-adenosyl-l-methionine enzymes themselves, making it necessary for cells to construct pathways to recycle or dispose of this toxic metabolite. However, the specific pathways involved have long remained unexplored. Recent research demonstrated a growth advantage in certain organisms by using 5dAdo or intermediates as a sole carbon source and elucidated the corresponding salvage pathway. We now provide evidence using supernatant analysis by GC-MS for another 5dAdo recycling route. Specifically, in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus), the activity of promiscuous enzymes leads to the synthesis and excretion first of 5-deoxyribose and subsequently of 7-deoxysedoheptulose. 7-Deoxysedoheptulose is an unusual deoxy-sugar, which acts as an antimetabolite of the shikimate pathway, thereby exhibiting antimicrobial and herbicidal activity. This strategy enables organisms with small genomes and lacking canonical gene clusters for the synthesis of secondary metabolites, like S. elongatus, to produce antimicrobial compounds from primary metabolism and enzymatic promiscuity. Our findings challenge the view of bioactive molecules as sole products of secondary metabolite gene clusters and expand the range of compounds that microorganisms can deploy to compete for their ecological niche.
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Affiliation(s)
- Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Pascal Rath
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Joachim Kilian
- Center for Plant Molecular Biology, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Klaus Brilisauer
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany.
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18
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Hao Z, Wu T, Cui X, Zhu P, Tan C, Dou X, Hsu KW, Lin YT, Peng PH, Zhang LS, Gao Y, Hu L, Sun HL, Zhu A, Liu J, Wu KJ, He C. N 6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA. Mol Cell 2020; 78:382-395.e8. [PMID: 32183942 DOI: 10.1016/j.molcel.2020.02.018] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 02/03/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
N6-Methyldeoxyadenosine (6mA) has recently been shown to exist and play regulatory roles in eukaryotic genomic DNA (gDNA). However, the biological functions of 6mA in mammals have yet to be adequately explored, largely due to its low abundance in most mammalian genomes. Here, we report that mammalian mitochondrial DNA (mtDNA) is enriched for 6mA. The level of 6mA in HepG2 mtDNA is at least 1,300-fold higher than that in gDNA under normal growth conditions, corresponding to approximately four 6mA modifications on each mtDNA molecule. METTL4, a putative mammalian methyltransferase, can mediate mtDNA 6mA methylation, which contributes to attenuated mtDNA transcription and a reduced mtDNA copy number. Mechanistically, the presence of 6mA could repress DNA binding and bending by mitochondrial transcription factor (TFAM). Under hypoxia, the 6mA level in mtDNA could be further elevated, suggesting regulatory roles for 6mA in mitochondrial stress response. Our study reveals DNA 6mA as a regulatory mark in mammalian mtDNA.
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Affiliation(s)
- Ziyang Hao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Tong Wu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Xiaolong Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Pingping Zhu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; School of Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Caiping Tan
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiaoyang Dou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Kai-Wen Hsu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Yueh-Te Lin
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Pei-Hua Peng
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Yawei Gao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lulu Hu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Hui-Lung Sun
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Allen Zhu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Jianzhao Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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19
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Guan H, Qi S, Liu W, Ma C, Wang C. A rapid assay to screen adenosine deaminase inhibitors from Ligustri Lucidi Fructus against metabolism of cordycepin utilizing ultra-high-performance liquid chromatography-tandem mass spectrometry. Biomed Chromatogr 2020; 34:e4779. [PMID: 31845520 DOI: 10.1002/bmc.4779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/04/2019] [Accepted: 12/07/2019] [Indexed: 01/25/2023]
Abstract
Cordycepin has recently received increased attention owing to its extensive pharmacological activity. Adenosine deaminase (ADA) is widely distributed in mammalian blood and tissues; as a result, cordycepin is quickly metabolized upon entering into the body and converted into the inactive metabolite 3'-deoxyinosine, thus limiting its activity when administered alone. We herein present a novel ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method for screening ADA inhibitors against the metabolism of cordycepin. Cordycepin and 3'-deoxyinosine were chosen as substrate and product, respectively. A proper separation was achieved for all analytes within 3 min. 3'-Deoxyinosine was quantified in the presence or absence of potential ADA inhibitors to evaluate ADA activity. The assay can simultaneously determine substrate and product, with the endogenous substance and ADA inhibitors added not interfering in its activity. After optimizing the enzymatic incubation and UHPLC-MS/MS conditions, Km and Vmax values for ADA deamination of cordycepin were 95.18 ± 7.85 μm and 363.90 ± 12.16 μmol/min/unit, respectively. Oleanolic acid and ursolic acid from Ligustri Lucidi Fructus were chosen as ADA inhibitors with half maximal inhibitory concentration values of 21.82 ± 0.39 and 18.41 ± 0.14 μm, respectively. A non-competitive inhibition model was constructed and this assay can be used to screen other potential ADA inhibitors quickly and accurately.
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Affiliation(s)
- Huida Guan
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Shanghai, China
| | - Shenglan Qi
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Shanghai, China
| | - Wei Liu
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Shanghai, China
| | - Chao Ma
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Shanghai, China
| | - Changhong Wang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Shanghai, China
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20
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Tsuchiya K, Sano T, Tomioka N, Kohzu A, Komatsu K, Shinohara R, Shimode S, Toda T, Imai A. Incorporation characteristics of exogenous 15N-labeled thymidine, deoxyadenosine, deoxyguanosine and deoxycytidine into bacterial DNA. PLoS One 2020; 15:e0229740. [PMID: 32106263 PMCID: PMC7046229 DOI: 10.1371/journal.pone.0229740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/13/2020] [Indexed: 11/18/2022] Open
Abstract
Bacterial production has been often estimated from DNA synthesis rates by using tritium-labeled thymidine. Some bacteria species cannot incorporate extracellular thymidine into their DNA, suggesting their biomass production might be overlooked when using the conventional method. In the present study, to evaluate appropriateness of deoxyribonucleosides for evaluating bacterial production of natural bacterial communities from the viewpoint of DNA synthesis, incorporation rates of four deoxyribonucleosides (thymidine, deoxyadenosine, deoxyguanosine and deoxycytidine) labeled by nitrogen stable isotope (15N) into bacterial DNA were examined in both ocean (Sagami Bay) and freshwater (Lake Kasumigaura) ecosystems in July 2015 and January 2016. In most stations in Sagami Bay and Lake Kasumigaura, we found that incorporation rates of deoxyguanosine were the highest among those of the four deoxyribonucleosides, and the incorporation rate of deoxyguanosine was approximately 2.5 times higher than that of thymidine. Whereas, incorporation rates of deoxyadenosine and deoxycytidine were 0.9 and 0.2 times higher than that of thymidine. These results clearly suggest that the numbers of bacterial species which can incorporate exogenous deoxyguanosine into their DNA are relatively greater as compared to the other deoxyribonucleosides, and measurement of bacterial production using deoxyguanosine more likely reflects larger numbers of bacterial species productions.
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Affiliation(s)
- Kenji Tsuchiya
- Faculty of Science and Engineering, Soka University, Tangi, Hachioji, Tokyo, Japan
- Center for Regional Environmental Research, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Tomoharu Sano
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Noriko Tomioka
- Center for Regional Environmental Research, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Ayato Kohzu
- Center for Regional Environmental Research, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Kazuhiro Komatsu
- Center for Regional Environmental Research, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Ryuichiro Shinohara
- Center for Regional Environmental Research, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Shinji Shimode
- Graduate School of Environment and Information Science, Yokohama National University, Tokiwadai, Hodogaya, Yokohama, Kanagawa, Japan
| | - Tatsuki Toda
- Faculty of Science and Engineering, Soka University, Tangi, Hachioji, Tokyo, Japan
| | - Akio Imai
- Center for Regional Environmental Research, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
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21
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Abstract
A novel DNA modification, N-6 methylated deoxyadenosine (m6dA), has recently been discovered in eukaryotic genomes. Despite its low abundance in eukaryotes, m6dA is implicated in human diseases such as cancer. It is therefore important to precisely identify and characterize m6dA in the human genome. Here, we identify m6dA sites at nucleotide level, in different human cells, genome wide. We compare m6dA features between distinct human cells and identify m6dA characteristics in human genomes. Our data demonstrates for the first time that despite low m6dA abundance, the m6dA mark does often occur consistently at the same genomic location within a given human cell type, demonstrating m6dA homogeneity. We further show, for the first time, higher levels of m6dA homogeneity within one chromosome. Most m6dA are found on a single chromosome from a diploid sample, suggesting inheritance. Our transcriptome analysis not only indicates that human genes with m6dA are associated with higher RNA transcript levels but identifies allele-specific gene transcripts showing haplotype-specific m6dA methylation, which are implicated in different biological functions. Our analyses demonstrate the precision and consistency by which the m6dA mark occurs within the human genome, suggesting that m6dA marks are precisely inherited in humans.
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Affiliation(s)
- Clare E Pacini
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Zoology, University of Cambridge, Cambridge, CB3 3EJ, UK
| | - Charles R Bradshaw
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Nigel J Garrett
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Zoology, University of Cambridge, Cambridge, CB3 3EJ, UK
| | - Magdalena J Koziol
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK.
- Department of Zoology, University of Cambridge, Cambridge, CB3 3EJ, UK.
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Yoon JH, Johnson RE, Prakash L, Prakash S. DNA polymerase θ accomplishes translesion synthesis opposite 1,N 6-ethenodeoxyadenosine with a remarkably high fidelity in human cells. Genes Dev 2019; 33:282-287. [PMID: 30808656 PMCID: PMC6411006 DOI: 10.1101/gad.320531.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/08/2019] [Indexed: 11/24/2022]
Abstract
Here we show that translesion synthesis (TLS) opposite 1,N6-ethenodeoxyadenosine (εdA), which disrupts Watson-Crick base pairing, occurs via Polι/Polζ-, Rev1-, and Polθ-dependent pathways. The requirement of Polι/Polζ is consistent with the ability of Polι to incorporate nucleotide opposite εdA by Hoogsteen base pairing and of Polζ to extend synthesis. Rev1 polymerase and Polθ conduct TLS opposite εdA via alternative error-prone pathways. Strikingly, in contrast to extremely error-prone TLS opposite εdA by purified Polθ, it performs predominantly error-free TLS in human cells. Reconfiguration of the active site opposite εdA would provide Polθ the proficiency for error-free TLS in human cells.
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Affiliation(s)
- Jung-Hoon Yoon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Robert E Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
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Hu T, Liang Y, Zhao G, Wu W, Li H, Guo Y. Selenium Biofortification and Antioxidant Activity in Cordyceps militaris Supplied with Selenate, Selenite, or Selenomethionine. Biol Trace Elem Res 2019; 187:553-561. [PMID: 29855849 DOI: 10.1007/s12011-018-1386-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 05/09/2018] [Indexed: 12/29/2022]
Abstract
Selenium (Se) is an essential trace element with multiple functions that may help mitigate adverse health conditions. Cordyceps militaris is an edible mushroom with medicinal properties. The experiment was conducted under artificial cultivation, with five Se concentrations (0, 5, 10, 20, and 40 μg g-1) and three forms of Se (selenate, selenite, and selenomethionine). C. militaris can absorb inorganic from the substrate and convert it to organic Se compounds (selenocystine, selenomethionine, and an unknown species) in fruiting bodies. Compared with the control treatment, Se applications (40 μg g-1 selenate and selenite) significantly increased the Se concentration in fruiting bodies by 130.9 and 128.1 μg g-1, respectively. The biofortification with selenate and selenite did not affect fruiting body production, in some case, but did enhance the biological efficiency. Moreover, the abundance of cordycepin and adenosine increased, while the amino acid contents remained relatively stable. Meanwhile, Se-biofortified C. militaris showed effective antioxidant activities. These results suggest that Se-biofortified C. militaris fruiting bodies may enhance human and animal health when it was included as part of a healthy diet or used as Se supplements.
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Affiliation(s)
- Ting Hu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Yue Liang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Guishen Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Wenliang Wu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Huafen Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Yanbin Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China.
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24
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Vafaee R, Soori H, Hedayati M, Ainy E, Hatamabadi H. Effects of resveratrol supplementation in male Wistar rats undergoing an endurance exercise and acute exercise training. Hum Antibodies 2019; 27:257-264. [PMID: 31127758 DOI: 10.3233/hab-190380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
OBJECTIVE The present study was aimed to assess the effect of Resveratrol supplementation, endurance exercise and acute exercise training on oxidative stress and tissue damage markers. METHODS Sixty-four male Wistar rats were categorized into four groups including resveratrol group, exercise group, exercise + resveratrol group (n= 16) and control group (n= 16). RES was orally administered to male rats for 28 day at a dose of 10 mg per kg body during exercise. Following the familiarization sessions, rats were acclimated to a calibrated motor driven rodent treadmill for endurance exercise and acute exercise implementation. Changes in oxidative stress and tissue damage markers including 8-hydroxy-2'-deoxyguanosine (8-OhdG), Lactate dehydrogenase (LDH), Creatine Phosphokinase (CPK), protein carbonyl were biochemically measured using commercial ELISA kits based on the manufacturer's instructions. RESULTS The endurance and acute exercise training led to an increase in the levels of CPK and LDH, However, following the endurance and acute exercise training, a reduction in the level of carbonyl and 8-OHdG was observed. RES supplementation did not have any effect on the levels of CPK and LDH; nevertheless, reduced significantly carbonyl, and 8-OHdG levels. Based on this evidence, RES may have protective effects against exercise-induced oxidative stress. CONCLUSION This study provides further evidence of the antioxidant effects of RES after exercise. However, several factors such as type and duration of exercise, the type of model, the amount of RES supplementation and the time-course consideration can affect the quality of the results. For this reason, further studies in this field are required.
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Affiliation(s)
- Reza Vafaee
- Safety Promotion and Injury Prevention Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Proteomics Research Center, Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Soori
- Safety Promotion and Injury Prevention Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elaheh Ainy
- Safety Promotion and Injury Prevention Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Hatamabadi
- Safety Promotion and Injury Prevention Research Center, Department of Emergency Medicine, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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25
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Koh C, Goh YT, Toh J, Neo SP, Ng S, Gunaratne J, Gao YG, Quake SR, Burkholder W, Goh W. Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome. Nucleic Acids Res 2018; 46:11659-11670. [PMID: 30412255 PMCID: PMC6294517 DOI: 10.1093/nar/gky1104] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/15/2018] [Accepted: 10/22/2018] [Indexed: 01/08/2023] Open
Abstract
N6-methyldeoxyadenosine (6mA) is a well-characterized DNA modification in prokaryotes but reports on its presence and function in mammals have been controversial. To address this issue, we established the capacity of 6mA-Crosslinking-Exonuclease-sequencing (6mACE-seq) to detect genome-wide 6mA at single-nucleotide-resolution, demonstrating this by accurately mapping 6mA in synthesized DNA and bacterial genomes. Using 6mACE-seq, we generated a human-genome-wide 6mA map that accurately reproduced known 6mA enrichment at active retrotransposons and revealed mitochondrial chromosome-wide 6mA clusters asymmetrically enriched on the heavy-strand. We identified a novel putative 6mA-binding protein in single-stranded DNA-binding protein 1 (SSBP1), a mitochondrial DNA (mtDNA) replication factor known to coat the heavy-strand, linking 6mA with the regulation of mtDNA replication. Finally, we characterized AlkB homologue 1 (ALKBH1) as a mitochondrial protein with 6mA demethylase activity and showed that its loss decreases mitochondrial oxidative phosphorylation. Our results show that 6mA clusters play a previously unappreciated role in regulating human mitochondrial function, despite 6mA being an uncommon DNA modification in the human genome.
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Affiliation(s)
- Casslynn W Q Koh
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Yeek Teck Goh
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Joel D W Toh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Suat Peng Neo
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Sarah B Ng
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Yong-Gui Gao
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Stephen R Quake
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - William F Burkholder
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Wee Siong S Goh
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
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26
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Luo GZ, Hao Z, Luo L, Shen M, Sparvoli D, Zheng Y, Zhang Z, Weng X, Chen K, Cui Q, Turkewitz AP, He C. N 6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA. Genome Biol 2018; 19:200. [PMID: 30454035 PMCID: PMC6245762 DOI: 10.1186/s13059-018-1573-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 10/22/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND N6-methyldeoxyadenosine (6mA or m6dA) was shown more than 40 years ago in simple eukaryotes. Recent studies revealed the presence of 6mA in more prevalent eukaryotes, even in vertebrates. However, functional characterizations have been limited. RESULTS We use Tetrahymena thermophila as a model organism to examine the effects of 6mA on nucleosome positioning. Independent methods reveal the enrichment of 6mA near and after transcription start sites with a periodic pattern and anti-correlation relationship with the positions of nucleosomes. The distribution pattern can be recapitulated by in vitro nucleosome assembly on native Tetrahymena genomic DNA but not on DNA without 6mA. Model DNA containing artificially installed 6mA resists nucleosome assembling compared to unmodified DNA in vitro. Computational simulation indicates that 6mA increases dsDNA rigidity, which disfavors nucleosome wrapping. Knockout of a potential 6mA methyltransferase leads to a transcriptome-wide change of gene expression. CONCLUSIONS These findings uncover a mechanism by which DNA 6mA assists to shape the nucleosome positioning and potentially affects gene expression.
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Affiliation(s)
- Guan-Zheng Luo
- The State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China.
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
| | - Ziyang Hao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Liangzhi Luo
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Mingren Shen
- Graduate Program in Biophysics, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 Univ. Ave., Madison, WI, 53706, USA
| | - Daniela Sparvoli
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA
| | - Yuqing Zheng
- Graduate Program in Biophysics, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 Univ. Ave., Madison, WI, 53706, USA
| | - Zijie Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Xiaocheng Weng
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Kai Chen
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Qiang Cui
- Graduate Program in Biophysics, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 Univ. Ave., Madison, WI, 53706, USA
| | - Aaron P Turkewitz
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
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North JA, Miller AR, Wildenthal JA, Young SJ, Tabita FR. Microbial pathway for anaerobic 5'-methylthioadenosine metabolism coupled to ethylene formation. Proc Natl Acad Sci U S A 2017; 114:E10455-E10464. [PMID: 29133429 PMCID: PMC5715764 DOI: 10.1073/pnas.1711625114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Numerous cellular processes involving S-adenosyl-l-methionine result in the formation of the toxic by-product, 5'-methylthioadenosine (MTA). To prevent inhibitory MTA accumulation and retain biologically available sulfur, most organisms possess the "universal" methionine salvage pathway (MSP). However, the universal MSP is inherently aerobic due to a requirement of molecular oxygen for one of the key enzymes. Here, we report the presence of an exclusively anaerobic MSP that couples MTA metabolism to ethylene formation in the phototrophic bacteria Rhodospirillum rubrum and Rhodopseudomonas palustris In vivo metabolite analysis of gene deletion strains demonstrated that this anaerobic MSP functions via sequential action of MTA phosphorylase (MtnP), 5-(methylthio)ribose-1-phosphate isomerase (MtnA), and an annotated class II aldolase-like protein (Ald2) to form 2-(methylthio)acetaldehyde as an intermediate. 2-(Methylthio)acetaldehyde is reduced to 2-(methylthio)ethanol, which is further metabolized as a usable organic sulfur source, generating stoichiometric amounts of ethylene in the process. Ethylene induction experiments using 2-(methylthio)ethanol versus sulfate as sulfur sources further indicate anaerobic ethylene production from 2-(methylthio)ethanol requires protein synthesis and that this process is regulated. Finally, phylogenetic analysis reveals that the genes corresponding to these enzymes, and presumably the pathway, are widespread among anaerobic and facultatively anaerobic bacteria from soil and freshwater environments. These results not only establish the existence of a functional, exclusively anaerobic MSP, but they also suggest a possible route by which ethylene is produced by microbes in anoxic environments.
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Affiliation(s)
- Justin A North
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - Anthony R Miller
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - John A Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - Sarah J Young
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - F Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
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28
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Hung YP, Lee CL. Higher Anti-Liver Fibrosis Effect of Cordyceps militaris-Fermented Product Cultured with Deep Ocean Water via Inhibiting Proinflammatory Factors and Fibrosis-Related Factors Expressions. Mar Drugs 2017; 15:md15060168. [PMID: 28594374 PMCID: PMC5484118 DOI: 10.3390/md15060168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/26/2017] [Accepted: 06/01/2017] [Indexed: 12/20/2022] Open
Abstract
Deep ocean water (DOW) has been shown to enhance the functional components of fungi, resulting in increased health benefits. Therefore, using DOW for culturing fungi can enhance the cordycepin and adenosine of Cordyceps militaris (CM) and its protective effects on the liver. In this study, the antiliver fibrosis effects and mechanisms of ultrapure water-cultured CM (UCM), DOW-cultured CM (DCM), synthetic water-cultured CM, DOW, cordycepin, and adenosine were compared in the liver fibrosis mice induced by intraperitoneal injections of thioacetamide (TAA). The results indicated that DCM exhibited superior performance in reducing liver collagen accumulation, mitigating liver injuries, inhibiting proinflammatory factors and fibrosis-related factor (TGF-β1, Smad2/3, α-SMA, COL1A1) expression compared with UCM. DOW, cordycepin, and adenosine also performed antiliver fibrosis effect. Therefore, because DCM is rich in DOW and functional components, it can achieve anti-liver fibrosis effects through multiple pathways. These ameliorative effects are considerably superior to those of UCM.
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Affiliation(s)
- Yu-Ping Hung
- Department of Life Science, National Taitung University, 369, Section 2, University Rd., Taitung 95092, Taiwan.
| | - Chun-Lin Lee
- Department of Life Science, National Taitung University, 369, Section 2, University Rd., Taitung 95092, Taiwan.
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29
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Brooks PJ. The cyclopurine deoxynucleosides: DNA repair, biological effects, mechanistic insights, and unanswered questions. Free Radic Biol Med 2017; 107:90-100. [PMID: 28011151 DOI: 10.1016/j.freeradbiomed.2016.12.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 12/23/2022]
Abstract
Patients with the genetic disease xeroderma pigmentosum (XP) who lack the capacity to carry out nucleotides excision repair (NER) have a dramatically elevated risk of skin cancer on sun exposed areas of the body. NER is the DNA repair mechanism responsible for the removal of DNA lesions resulting from ultraviolet light. In addition, a subset of XP patients develop a progressive neurodegenerative disease, referred to as XP neurologic disease, which is thought to be the result of accumulation of endogenous DNA lesions that are repaired by NER but not other repair pathways. The 8,5-cyclopurine deoxynucleotides (cyPu) have emerged as leading candidates for such lesions, in that they result from the reaction of the hydroxyl radical with DNA, are strong blocks to transcription in human cells, and are repaired by NER but not base excision repair. Here I present a focused perspective on progress into understating the repair and biological effects of these lesions. In doing so, I emphasize the role of Tomas Lindahl and his laboratory in stimulating cyPu research. I also include a critical evaluation of the evidence supporting a role for cyPu lesions in XP neurologic disease, with a focus on outstanding questions, and conceptual and technologic challenges.
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Affiliation(s)
- Philip J Brooks
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, MD 20852, USA
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30
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Akishev Z, Taipakova S, Joldybayeva B, Zutterling C, Smekenov I, Ishchenko AA, Zharkov DO, Bissenbaev AK, Saparbaev M. The major Arabidopsis thaliana apurinic/apyrimidinic endonuclease, ARP is involved in the plant nucleotide incision repair pathway. DNA Repair (Amst) 2016; 48:30-42. [PMID: 27836324 DOI: 10.1016/j.dnarep.2016.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022]
Abstract
Apurinic/apyrimidinic (AP) endonucleases are important DNA repair enzymes involved in two overlapping pathways: DNA glycosylase-initiated base excision (BER) and AP endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, AP endonucleases cleave DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases, whereas in NIR, the same AP endonucleases incise DNA 5' to a wide variety of oxidized bases. The flowering plant Arabidopsis thaliana contains three genes encoding homologues of major human AP endonuclease 1 (APE1): Arp, Ape1L and Ape2. It has been shown that all three proteins contain AP site cleavage and 3'-repair phosphodiesterase activities; however, it was not known whether the plant AP endonucleases contain the NIR activity. Here, we report that ARP proteins from Arabidopsis and common wheat (Triticum aestivum) contain NIR and 3'→5' exonuclease activities in addition to their AP endonuclease and 3'-repair phosphodiesterase functions. The steady-state kinetic parameters of reactions indicate that Arabidopsis ARP cleaves oligonucleotide duplexes containing α-anomeric 2'-deoxyadenosine (αdA) and 5,6-dihydrouridine (DHU) with efficiencies (kcat/KM=134 and 7.3 μM-1·min-1, respectively) comparable to those of the human counterpart. However, the ARP-catalyzed 3'-repair phosphodiesterase and 3'→5' exonuclease activities (kcat/KM=314 and 34 μM-1·min-1, respectively) were about 10-fold less efficient as compared to those of APE1. Interestingly, homozygous A. thaliana arp-/- mutant exhibited high sensitivity to methyl methanesulfonate and tert-butyl hydroperoxide, but not to H2O2, suggesting that ARP is a major plant AP endonuclease that removes abasic sites and specific types of oxidative DNA base damage. Taken together, these data establish the presence of the NIR pathway in plants and suggest its possible role in the repair of DNA damage generated by oxidative stress.
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Affiliation(s)
- Zhiger Akishev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Botagoz Joldybayeva
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Caroline Zutterling
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Izat Smekenov
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Dmitry O Zharkov
- Novosibirsk State University, Novosibirsk 630090, Russia; SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Amangeldy K Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan.
| | - Murat Saparbaev
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France.
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Kamiya H, Ito M, Nishi K, Harashima H. In vivo selection of active deoxyribonucleoside kinase by a mutagenic nucleoside analog. J Biotechnol 2016; 228:52-57. [PMID: 27131895 DOI: 10.1016/j.jbiotec.2016.04.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/20/2016] [Accepted: 04/26/2016] [Indexed: 11/18/2022]
Abstract
A novel in vivo selection method for active deoxyribonucleoside kinase proteins is described here. A pool of randomly mutated genes for deoxyribonucleoside kinase from Drosophila melanogaster (Dm-dNK) was prepared and inserted into an expression vector. Enzymatically active mutants were selected by repeated cycles, including (i) introduction into Escherichia coli, (ii) treatment of the E. coli pool with a mutagenic deoxyribonucleoside (2-hydroxy-dA), and (iii) selection of antibiotic-resistant colonies resulting from mutations by phosphorylated 2-hydroxy-dA and the subsequent isolation of the plasmid DNAs. The ratio of the resistant colonies increased by two orders of magnitude from the first cycle to the fifth cycle, and then reached a plateau. Fifteen Dm-dNK mutants selected after the seventh and eighth evolution cycles were actually active in vivo. Moreover, one of the mutant proteins was as active as the wild-type protein in vitro. These results indicate that this novel in vivo evolution method was useful and that similar strategies would be applicable to other deoxyribonucleoside kinases. In addition, the distribution of mutated amino acids suggests important residues/regions in the Dm-dNK protein.
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Affiliation(s)
- Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan; Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan.
| | - Mana Ito
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kosuke Nishi
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama 790-8566, Japan
| | - Hideyoshi Harashima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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Zierer W, Hajirezaei MR, Eggert K, Sauer N, von Wirén N, Pommerrenig B. Phloem-Specific Methionine Recycling Fuels Polyamine Biosynthesis in a Sulfur-Dependent Manner and Promotes Flower and Seed Development. Plant Physiol 2016; 170:790-806. [PMID: 26662272 PMCID: PMC4734553 DOI: 10.1104/pp.15.00786] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 12/06/2015] [Indexed: 05/17/2023]
Abstract
The Yang or Met Cycle is a series of reactions catalyzing the recycling of the sulfur (S) compound 5'-methylthioadenosine (MTA) to Met. MTA is produced as a by-product in ethylene, nicotianamine, and polyamine biosynthesis. Whether the Met Cycle preferentially fuels one of these pathways in a S-dependent manner remained unclear so far. We analyzed Arabidopsis (Arabidopsis thaliana) mutants with defects in the Met Cycle enzymes 5-METHYLTHIORIBOSE-1-PHOSPHATE-ISOMERASE1 (MTI1) and DEHYDRATASE-ENOLASE-PHOSPHATASE-COMPLEX1 (DEP1) under different S conditions and assayed the contribution of the Met Cycle to the regeneration of S for these pathways. Neither mti1 nor dep1 mutants could recycle MTA but showed S-dependent reproductive failure, which was accompanied by reduced levels of the polyamines putrescine, spermidine, and spermine in mutant inflorescences. Complementation experiments with external application of these three polyamines showed that only the triamine spermine could specifically rescue the S-dependent reproductive defects of the mutant plants. Furthermore, expressing gene-reporter fusions in Arabidopsis showed that MTI1 and DEP1 were mainly expressed in the vasculature of all plant parts. Phloem-specific reconstitution of Met Cycle activity in mti1 and dep1 mutant plants was sufficient to rescue their S-dependent mutant phenotypes. We conclude from these analyses that phloem-specific S recycling during periods of S starvation is essential for the biosynthesis of polyamines required for flowering and seed development.
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Affiliation(s)
- Wolfgang Zierer
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Biology, Molecular Plant Physiology, 91058 Erlangen, Germany (W.Z., N.S.); andMolecular Plant Nutrition (M.R.H., K.E., N.v.W.) and Metalloid Transport (B.P.), Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Mohammad R Hajirezaei
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Biology, Molecular Plant Physiology, 91058 Erlangen, Germany (W.Z., N.S.); andMolecular Plant Nutrition (M.R.H., K.E., N.v.W.) and Metalloid Transport (B.P.), Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Kai Eggert
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Biology, Molecular Plant Physiology, 91058 Erlangen, Germany (W.Z., N.S.); andMolecular Plant Nutrition (M.R.H., K.E., N.v.W.) and Metalloid Transport (B.P.), Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Norbert Sauer
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Biology, Molecular Plant Physiology, 91058 Erlangen, Germany (W.Z., N.S.); andMolecular Plant Nutrition (M.R.H., K.E., N.v.W.) and Metalloid Transport (B.P.), Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Nicolaus von Wirén
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Biology, Molecular Plant Physiology, 91058 Erlangen, Germany (W.Z., N.S.); andMolecular Plant Nutrition (M.R.H., K.E., N.v.W.) and Metalloid Transport (B.P.), Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Benjamin Pommerrenig
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Biology, Molecular Plant Physiology, 91058 Erlangen, Germany (W.Z., N.S.); andMolecular Plant Nutrition (M.R.H., K.E., N.v.W.) and Metalloid Transport (B.P.), Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
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Meng Z, Kang J, Wen T, Lei B, Hyde KD. Cordycepin and N6-(2-hydroxyethyl)-adenosine from Cordyceps pruinosa and their interaction with human serum albumin. PLoS One 2015; 10:e0121669. [PMID: 25811172 PMCID: PMC4374796 DOI: 10.1371/journal.pone.0121669] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 02/03/2015] [Indexed: 12/28/2022] Open
Abstract
Cordyceps pruinosa (CP) is often used as Traditional Chinese Medicine, but the substance basis of its medicinal properties is unclear. In this study, two compounds were isolated from CP cultures by column chromatography, and identified as cordycepin and N6-(2-hydroxyethyl)-adenosine (HEA) by Nuclear Magnetic Resonance. In order to understand the efficacy of these two substances as potential therapeutic agents, it is necessary to explore their binding with proteins. The molecular mechanisms of interaction between cordycepin, HEA and human serum albumin (HSA) were studied using UV and fluorescence spectroscopy. The bingding constants between HSA and cordycepin were 4.227, 3.573 and 3.076 × 10(3)·at 17, 27 and 37°C respectively, and that of HSA and HEA were 27.102, 19.409 and 13.002 × 10(3)·at the three tempretures respectively. Both cordycepin and HEA can quench the intrinsic fluorescence of HSA via static quenching, and they can bind with HSA to form complexes with a single binding site. The interaction forces between cordycepin and HSA were determined as electrostatic and hydrophobic, and those of HEA and HSA were hydrogen bonding and van der Waals forces. Using Foster's equation, the distance between fluorophores of cordycepin and HSA, and HEA and HSA are estimated to be 5.31 nm and 4.98 nm, respectively. In this study, cordycepin was isolated for the first time from CP, and will provide a new source of cordycepin and expand the use of this taxon. The interaction mechanisms between cordycepin and HSA was studied for the first time, which will provide a useful guide for the clinical application of cordycepin. The pharmacological importance of this study is to understand the interaction of HSA with cordycepin and HEA, which will be essential for the future designing of drugs based on the two compounds.
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Affiliation(s)
- Zebin Meng
- The Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Huaxi, Guiyang, Guizhou Province, PR China
- Guizhou Bioresource Development and Utilization Key Laboratory, Guizhou Normal College, Guiyang, Guizhou Province, China
| | - Jichuan Kang
- The Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Huaxi, Guiyang, Guizhou Province, PR China
| | - Tingchi Wen
- The Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Huaxi, Guiyang, Guizhou Province, PR China
| | - Bangxing Lei
- The Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Huaxi, Guiyang, Guizhou Province, PR China
| | - Kevin David Hyde
- Institute of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai, Thailand
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Pazmandi K, Agod Z, Kumar BV, Szabo A, Fekete T, Sogor V, Veres A, Boldogh I, Rajnavolgyi E, Lanyi A, Bacsi A. Oxidative modification enhances the immunostimulatory effects of extracellular mitochondrial DNA on plasmacytoid dendritic cells. Free Radic Biol Med 2014; 77:281-90. [PMID: 25301097 DOI: 10.1016/j.freeradbiomed.2014.09.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/03/2014] [Accepted: 09/26/2014] [Indexed: 12/14/2022]
Abstract
Inflammation is associated with oxidative stress and characterized by elevated levels of damage-associated molecular pattern (DAMP) molecules released from injured or even living cells into the surrounding microenvironment. One of these endogenous danger signals is the extracellular mitochondrial DNA (mtDNA) containing evolutionary conserved unmethylated CpG repeats. Increased levels of reactive oxygen species (ROS) generated by recruited inflammatory cells modify mtDNA oxidatively, resulting primarily in accumulation of 8-oxo-7,8-dihydroguanine (8-oxoG) lesions. In this study, we examined the impact of native and oxidatively modified mtDNAs on the phenotypic and functional properties of plasmacytoid dendritic cells (pDCs), which possess a fundamental role in the regulation of inflammation and T cell immunity. Treatment of human primary pDCs with native mtDNA up-regulated the expression of a costimulatory molecule (CD86), a specific maturation marker (CD83), and a main antigen-presenting molecule (HLA-DQ) on the cell surface, as well as increased TNF-α and IL-8 production from the cells. These effects were more apparent when pDCs were exposed to oxidatively modified mtDNA. Neither native nor oxidized mtDNA molecules were able to induce interferon (IFN)-α secretion from pDCs unless they formed a complex with human cathelicidin LL-37, an antimicrobial peptide. Interestingly, simultaneous administration of a Toll-like receptor (TLR)9 antagonist abrogated the effects of both native and oxidized mtDNAs on human pDCs. In a murine model, oxidized mtDNA also proved a more potent activator of pDCs compared to the native form, except for induction of IFN-α production. Collectively, we demonstrate here for the first time that elevated levels of 8-oxoG bases in the extracellular mtDNA induced by oxidative stress increase the immunostimulatory capacity of mtDNA on pDCs.
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Affiliation(s)
- Kitti Pazmandi
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary
| | - Zsofia Agod
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary
| | - Brahma V Kumar
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary
| | - Attila Szabo
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary
| | - Tunde Fekete
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary
| | - Viktoria Sogor
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary
| | - Agota Veres
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Blvd., Galveston, TX 77555, USA
| | - Eva Rajnavolgyi
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary
| | - Arpad Lanyi
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Blvd., Debrecen H-4012, Hungary.
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Limm K, Wallner S, Milenkovic VM, Wetzel CH, Bosserhoff AK. The metabolite 5'-methylthioadenosine signals through the adenosine receptor A2B in melanoma. Eur J Cancer 2014; 50:2714-24. [PMID: 25087184 DOI: 10.1016/j.ejca.2014.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 06/06/2014] [Accepted: 07/07/2014] [Indexed: 11/19/2022]
Abstract
Several recent studies have shown evidence supporting the general knowledge that tumour cells exhibit changes in metabolism. It is becoming increasingly important to understand how these metabolic changes in tumour cells promote carcinogenesis and disease progression. We recently discovered a lack of methylthioadenosine phosphorylase (MTAP) expression in melanoma, which resulted in an accumulation of the metabolite 5'-methylthioadenosine (MTA) in melanoma cells and in the extracellular environment. MTA was shown to affect cell proliferation of surrounding stroma cells and cell invasiveness and the activation of the transcription factor activator protein-1 (AP-1) in melanoma cells. In this study, we addressed the regulation of cellular signalling by extracellular MTA accumulation. By focusing on putative receptors that could modulate MTA signalling, we identified the adenosine receptor ADORA2B as an important candidate. Knockdown experiments and the use of specific agonists and antagonists confirmed a link between MTA and AP-1 signalling through the ADORA2B receptor. Interestingly, stimulation of the cells with MTA did not result in activation of the classical cyclic adenosine monophosphate (cAMP) signalling cascades or in Ca(2+)-dependent signalling. We instead showed protein kinase C (PKC) signalling to be involved in MTA-mediated AP-1 activation. In summary, we identified ADORA2B to be the specific receptor and signalling pathway for the metabolite MTA. These findings may influence the use of MTA in a therapeutic manner.
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Affiliation(s)
- Katharina Limm
- Institute of Pathology, University of Regensburg, Germany
| | | | - Vladimir M Milenkovic
- Molecular Neurosciences, Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
| | - Christian H Wetzel
- Molecular Neurosciences, Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
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Abstract
The prokaryotic DNA(cytosine-5)methyltransferase M.SssI shares the specificity of eukaryotic DNA methyltransferases (CG) and is an important model and experimental tool in the study of eukaryotic DNA methylation. Previously, M.SssI was shown to be able to catalyze deamination of the target cytosine to uracil if the methyl donor S-adenosyl-methionine (SAM) was missing from the reaction. To test whether this side-activity of the enzyme can be used to distinguish between unmethylated and C5-methylated cytosines in CG dinucleotides, we re-investigated, using a sensitive genetic reversion assay, the cytosine deaminase activity of M.SssI. Confirming previous results we showed that M.SssI can deaminate cytosine to uracil in a slow reaction in the absence of SAM and that the rate of this reaction can be increased by the SAM analogue 5'-amino-5'-deoxyadenosine. We could not detect M.SssI-catalyzed deamination of C5-methylcytosine ((m5)C). We found conditions where the rate of M.SssI mediated C-to-U deamination was at least 100-fold higher than the rate of (m5)C-to-T conversion. Although this difference in reactivities suggests that the enzyme could be used to identify C5-methylated cytosines in the epigenetically important CG dinucleotides, the rate of M.SssI mediated cytosine deamination is too low to become an enzymatic alternative to the bisulfite reaction. Amino acid replacements in the presumed SAM binding pocket of M.SssI (F17S and G19D) resulted in greatly reduced methyltransferase activity. The G19D variant showed cytosine deaminase activity in E. coli, at physiological SAM concentrations. Interestingly, the C-to-U deaminase activity was also detectable in an E. coli ung (+) host proficient in uracil excision repair.
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Affiliation(s)
- Ildikó Stier
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail:
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Zhang W, Sato K, Hayashi T, Omori N, Nagano I, Kato S, Horiuchi S, Abe K. Extension of ischemic therapeutic time window by a free radical scavenger, Edaravone, reperfused with tPA in rat brain. Neurol Res 2013; 26:342-8. [PMID: 15142331 DOI: 10.1179/016164104225014058] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
3-methyl-1-phenyl-2-pyrazolin-5-one (Edaravone) is a free radical scavenger. We tested the hypothesis that combination treatment of Edaravone and recombinant tissue plasminogen activator (tPA) extends the therapeutic time window. Male Wistar rats were subjected to 1.5-, 3.0- or 4.5-hour middle cerebral artery (MCA) occlusion (MCAO) by a nylon thread. Animals were randomly divided into four groups. The Sham group rats were operated without MCAO and drug injection. In the Vehicle-treated group the same volume of saline was given every 1.5 hours from just after MCAO to just before reperfusion. In the Vehicle + tPA-treated group saline injection was given as above and tPA (5 mg/kg, i.v.) was given once just after reperfusion. Edaravone+tPA-treated group: Edaravone (3 mg/kg, i.v.) was given every 1.5 hours instead of saline and tPA injection as above. Survival rate, infarct size and evidence of apoptosis and hemorrhage were examined in the animals. Combining administration of Edaravone+tPA significantly increased survival rate after 3 hours of transient MCAO, and reduced infarct volume after 1.5 hours of transient MCAO compared with the vehicle or vehicle+tPA groups. In Edaravone+tPA-treated group, the number of terminal deoxynucleotidyl transferase-mediated dUTP-biotin in situ nick end labeling (TUNEL) and 4-hydroxynonenal (4-HNE) positive cells were reduced at 16 hours after 3 hours of transient MCAO, but not in advanced glycation end products (AGEs) and 8-hydroxy-2'-deoxyguanosine (8-OHdG). Hemorrhage rate and the area decreased in the Edaravone+tPA-treated group. The combination therapy of Edaravone+tPA increased survival rate, and reduced the infarct volume and hemorrhage with reduction of lipid peroxidation. Therefore, Edaravone combination is expected to extend the therapeutic time window of tPA in the clinical situation.
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Affiliation(s)
- Wenri Zhang
- Department of Neurology, Graduate School of Medicine and Dentistry, Okayama University, 2-5-1 Shikatacho, Okayama, Japan
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Chen ZG, Zhang DN, Cao L, Han YB. Highly efficient and regioselective acylation of pharmacologically interesting cordycepin catalyzed by lipase in the eco-friendly solvent 2-methyltetrahydrofuran. Bioresour Technol 2013; 133:82-86. [PMID: 23425581 DOI: 10.1016/j.biortech.2013.01.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/21/2013] [Accepted: 01/21/2013] [Indexed: 06/01/2023]
Abstract
A total of nine lipases and three proteases were tested for enzymatic regioselective acylation(s) of cordycepin with vinyl acetate in organic media. The highest conversion with better initial reaction rate was achieved with immobilized Candida antarctica lipase B (Novozym 435). An eco-friendly solvent 2-methyltetrahydrofuran (MeTHF) was thought to be the most suitable reaction medium. Novozym 435 was found to be a useful biocatalyst for the 25-g scale syntheses of cordycepin acetate (96.2% isolated yield), and the biocatalyst displayed excellent regioselectivity and high operational stability during the transformation. The 5'-substituted cordycepin derivative was the sole detectable product from each acylation reaction. Novozym 435 could be recycled for the synthesis of cordycepin derivative on a 25-g scale and 63% of its original activity was maintained after being reused for 7 batches. MeTHF could be considered as an eco-friendly solvent for the large scale use in biotransformation.
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Affiliation(s)
- Zhi-Gang Chen
- College of Food Science & Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
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Zhang J, Zhu T, Kipen H, Wang G, Huang W, Rich D, Zhu P, Wang Y, Lu SE, Ohman-Strickland P, Diehl S, Hu M, Tong J, Gong J, Thomas D. Cardiorespiratory biomarker responses in healthy young adults to drastic air quality changes surrounding the 2008 Beijing Olympics. Res Rep Health Eff Inst 2013:5-174. [PMID: 23646463 PMCID: PMC4086245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
Associations between air pollution and cardiorespiratory mortality and morbidity have been well established, but data to support biologic mechanisms underlying these associations are limited. We designed this study to examine several prominently hypothesized mechanisms by assessing Beijing residents' biologic responses, at the biomarker level, to drastic changes in air quality brought about by unprecedented air pollution control measures implemented during the 2008 Beijing Olympics. To test the hypothesis that changes in air pollution levels are associated with changes in biomarker levels reflecting inflammation, hemostasis, oxidative stress, and autonomic tone, we recruited and retained 125 nonsmoking adults (19 to 33 years old) free of cardiorespiratory and other chronic diseases. Using the combination of a quasi-experimental design and a panel-study approach, we measured biomarkers of autonomic dysfunction (heart rate [HR*] and heart rate variability [HRV]), of systemic inflammation and oxidative stress (plasma C-reactive protein [CRP], fibrinogen, blood cell counts and differentials, and urinary 8-hydroxy-2'-deoxyguanosine [8-OHdG]), of pulmonary inflammation and oxidative stress (fractional exhaled nitric oxide [FeNO], exhaled breath condensate [EBC] pH, EBC nitrate, EBC nitrite, EBC nitrite+nitrate [sum of the concentrations of nitrite and nitrate], and EBC 8-isoprostane), of hemostasis (platelet activation [plasma sCD62P and sCD40L], platelet aggregation, and von Willebrand factor [vWF]), and of blood pressure (systolic blood pressure [SBP] and diastolic blood pressure [DBP]). These biomarkers were measured on each subject twice before, twice during, and twice after the Beijing Olympics. For each subject, repeated measurements were separated by at least one week to avoid potential residual effects from a prior measurement. We measured a large suite of air pollutants (PM2.5 [particulate matter < or = 2.5 microm in aerodynamic diameter] and constituents, sulfur dioxide [SO2], carbon monoxide [CO], nitrogen dioxide [NO2], and ozone [O3]) throughout the study at a central Beijing site near the residences and workplaces of the subjects on a daily basis. Total particle number (TPN) was also measured at a separate site. We used a time-series analysis to assess changes in pollutant concentration by period (pre-, during-, and post-Olympics periods). We used mixed-effects models to assess changes in biomarker levels by period and to estimate changes associated with increases in pollutant concentrations, controlling for ambient temperature, relative humidity (RH), sex, and the day of the week of the biomarker measurements. We conducted sensitivity analyses to assess the impact of potential temporal confounding and exposure misclassification. We observed reductions in mean concentrations for all measured pollutants except O3 from the pre-Olympics period to the during-Olympics period. On average, elemental carbon (EC) changed by -36%, TPN by -22%, SO2 by -60%, CO by -48%, and NO2 by -43% (P < 0.05 for all these pollutants). Reductions were observed in mean concentrations of PM2.5 (by -27%), sulfate (SO4(2-)) (by -13%), and organic carbon (OC) (by -23%); however, these values were not statistically significant. Both 24-hour averages and 1-hour maximums of O3 increased (by 20% and 17%, respectively) from the pre-Olympics to the during-Olympics period. In the post-Olympics period after the pollution control measures were relaxed, mean concentrations of most pollutants (with the exception of SO4(2-) and O3) increased to levels similar to or higher than pre-Olympics levels. Concomitantly and consistent with the hypothesis, we observed, from the pre-Olympics to the during-Olympics period, statistically significant (P < or = 0.05) or marginally significant (0.05 < P < 0.1) decreases in HR (-1 bpm or -1.7% [95% CI, -3.4 to -0.1]), SBP (-1.6 mmHg or -1.8% [95% CI, -3.9 to 0.4]), 8-OHdG (-58.3% [95% CI, -72.5 to -36.7]), FeNO (-60.3% [95% CI, -66.0 to -53.6]), EBC nitrite (-30.0% [95% CI, -39.3 to -19.3]), EBC nitrate (-21.5% [95% CI, -35.5 to -4.5]), EBC nitrite+nitrate (-17.6% [95% CI, -28.4 to -5.1]), EBC hydrogen ions (-46% [calculated from EBC pH], or +3.5% in EBC pH [95% CI, 2.2 to 4.9]), sCD62P (-34% [95% CI, -38.4 to -29.2]), sCD40L (-5.7% [95% CI, -10.5 to -0.7]), and vWF (-13.1% [95% CI, -18.6 to -7.5]). Moreover, the percentages of above-detection values out of all observations were significantly lower for plasma CRP and EBC 8-isoprostane in the during-Olympics period compared with the pre-Olympics period. In the post-Olympics period, the levels of the following biomarkers reversed (increased, either with or without statistical significance) from those in the during-Olympics period: SBP (10.7% [95% CI, 2.8 to 18.6]), fibrinogen (4.3% [95% CI, -1.7 to 10.2), neutrophil count (4.7% [95% CI, -7.7 to 17.0]), 8-OHdG (315% [95% CI, 62.0 to 962]), FeNO (130% [95% CI, 62.5 to 225]), EBC nitrite (159% [95% CI, 71.8 to 292]), EBC nitrate (161% [95% CI, 48.0 to 362]), EBC nitrite+nitrate (124% [95% CI, 50.9 to 233]), EBC hydrogen ions (146% [calculated from EBC pH] or -4.8% in EBC pH [95% CI, -9.4 to -0.21), sCD62P (33.7% [95% CI, 17.7 to 51.8]), and sCD40L (9.1% [95% CI, -3.7 to 23.5]). Furthermore, these biomarkers also showed statistically significant associations with multiple pollutants across different lags after adjusting for meteorologic parameters. The associations were in the directions hypothesized and were consistent with the findings from the comparisons between periods, providing further evidence that the period effects were due to changes in air quality, independent of season and meteorologic conditions or other potential confounders. Contrary to our hypothesis, however, we observed increases in platelet aggregation, red blood cells (RBCs) and white blood cells (WBCs) associated with the during-Olympics period, as well as significant negative associations of these biomarkers with pollutant concentrations. We did not observe significant changes in any of the HRV indices and DBP by period. However, we observed associations between a few HRV indices and pollutant concentrations. Changes in air pollution levels during the Beijing Olympics were associated with acute changes in biomarkers of pulmonary and systemic inflammation, oxidative stress, and hemostasis and in measures of cardiovascular physiology (HR and SBP) in healthy, young adults. These changes support the prominently hypothesized mechanistic pathways underlying the cardiorespiratory effects of air pollution.
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Affiliation(s)
- Junfeng Zhang
- University of Medicine and Dentistry of New Jersey-School of Public Health, Piscataway, NJ, USA.
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Pande P, Das RS, Sheppard C, Kow YW, Basu AK. Repair efficiency of (5'S)-8,5'-cyclo-2'-deoxyguanosine and (5'S)-8,5'-cyclo-2'-deoxyadenosine depends on the complementary base. DNA Repair (Amst) 2012; 11:926-31. [PMID: 23063091 DOI: 10.1016/j.dnarep.2012.09.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/30/2012] [Accepted: 09/06/2012] [Indexed: 11/19/2022]
Abstract
5'-R and 5'-S diastereoisomers of 8,5'-cyclo-2'-deoxyadenosine (cdA) and 8,5'-cyclo-2'-deoxyguanosine (cdG) containing a base-sugar covalent bond are formed by hydroxyl radicals. R-cdA and S-cdA are repaired by nucleotide excision repair (NER) in mammalian cellular extracts. Here, we have examined seven purified base excision repair enzymes for their ability to repair S-cdG or S-cdA. We could not detect either excision or binding of these enzymes on duplex oligonucleotide substrates containing these lesions. However, both lesions were repaired by HeLa cell extracts. Dual incisions by human NER on a 136-mer duplex generated 24-32 bp fragments. The time course of dual incisions were measured in comparison to cis-anti-B[a]P-N(2)-dG, an excellent substrate for human NER, which showed that cis-anti-B[a]P-N(2)-dG was repaired more efficiently than S-cdG, which, in turn, was repaired more efficiently than S-cdA. When NER efficiency of S-cdG with different complementary bases was investigated, the wobble pair S-cdG·dT was excised more efficiently than the S-cdG·dC pair that maintains nearly normal Watson-Crick base pairing. But S-cdG·dA mispair with no hydrogen bonds was excised less efficiently than the S-cdG·dC pair. Similar pattern was noted for S-cdA. The S-cdA·dC mispair was excised much more efficiently than the S-cdA·dT pair, whereas the S-cdA·dA pair was excised less efficiently. This result adds to complexity of human NER, which discriminates the damaged base pairs on the basis of multiple criteria.
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Affiliation(s)
- Paritosh Pande
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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Hiscox MJ, Driesener RC, Roach PL. Enzyme catalyzed formation of radicals from S-adenosylmethionine and inhibition of enzyme activity by the cleavage products. Biochim Biophys Acta 2012; 1824:1165-77. [PMID: 22504666 DOI: 10.1016/j.bbapap.2012.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 03/06/2012] [Accepted: 03/27/2012] [Indexed: 01/06/2023]
Abstract
A large superfamily of enzymes have been identified that make use of radical intermediates derived by reductive cleavage of S-adenosylmethionine. The primary nature of the radical intermediates makes them highly reactive and potent oxidants. They are used to initiate biotransformations by hydrogen atom abstraction, a process that allows a particularly diverse range of substrates to be functionalized, including substrates with relatively inert chemical structures. In the first part of this review, we discuss the evidence supporting the mechanism of radical formation from S-adenosylmethionine. In the second part of the review, we examine the potential of reaction products arising from S-adenosylmethionine to cause product inhibition. The effects of this product inhibition on kinetic studies of 'radical S-adenosylmethionine' enzymes are discussed and strategies to overcome these issues are reviewed. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Martyn J Hiscox
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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Waduwara-Jayabahu I, Oppermann Y, Wirtz M, Hull ZT, Schoor S, Plotnikov AN, Hell R, Sauter M, Moffatt BA. Recycling of methylthioadenosine is essential for normal vascular development and reproduction in Arabidopsis. Plant Physiol 2012; 158:1728-44. [PMID: 22345506 PMCID: PMC3320181 DOI: 10.1104/pp.111.191072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
5'-Methylthioadenosine (MTA) is the common by-product of polyamine (PA), nicotianamine (NA), and ethylene biosynthesis in Arabidopsis (Arabidopsis thaliana). The methylthiol moiety of MTA is salvaged by 5'-methylthioadenosine nucleosidase (MTN) in a reaction producing methylthioribose (MTR) and adenine. The MTN double mutant, mtn1-1mtn2-1, retains approximately 14% of the MTN enzyme activity present in the wild type and displays a pleiotropic phenotype that includes altered vasculature and impaired fertility. These abnormal traits were associated with increased MTA levels, altered PA profiles, and reduced NA content. Exogenous feeding of PAs partially recovered fertility, whereas NA supplementation improved fertility and also reversed interveinal chlorosis. The analysis of PA synthase crystal structures containing bound MTA suggests that the corresponding enzyme activities are sensitive to available MTA. Mutant plants that expressed either MTN or human methylthioadenosine phosphorylase (which metabolizes MTA without producing MTR) appeared wild type, proving that the abnormal traits of the mutant are due to MTA accumulation rather than reduced MTR. Based on our results, we propose that the key targets affected by increased MTA content are thermospermine synthase activity and spermidine-dependent posttranslational modification of eukaryotic initiation factor 5A.
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Liu Y, Tang L, Chen B. Effects of antioxidant gene therapy on retinal neurons and oxidative stress in a model of retinal ischemia/reperfusion. Free Radic Biol Med 2012; 52:909-15. [PMID: 22240151 DOI: 10.1016/j.freeradbiomed.2011.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 12/08/2011] [Accepted: 12/14/2011] [Indexed: 11/16/2022]
Abstract
Retinal ischemia/reperfusion (I/R) results in neuronal death and generation of reactive oxygen species. The aim of this study was to investigate the neuroprotective effect of manganese superoxide dismutase (SOD2) on retinal ganglion cells (RGCs) in an I/R-induced retinal injury model. One eye of each Wistar rat was pretreated with recombinant adeno-associated virus containing the SOD2 gene (AAV-SOD2) or recombinant AAV containing the GFP gene (AAV-GFP) by intravitreal injection 21 days before initiation of I/R injury. Retinal I/R injury was induced by elevating intraocular pressure for 1h, and reperfusion was established immediately afterward. The number of RGCs and the inner plexiform layer (IPL) thickness were measured by Fluorogold retrograde labeling and hematoxylin and eosin staining at 6 h, 24 h, 72 h, and 5 days after injury. Superoxide anion, the number of RGCs, IPL thickness, malondialdehyde (MDA) level, 8-hydroxy-2-deoxyguanosine (8-OHdG) level, MnSOD (manganese superoxide dismutase) activity, and nitrotyrosine level were measured by fluorescence staining, immunohistochemistry, and enzyme-linked immunosorbent analysis at 5 days after I/R injury. Severe RGC loss, reduced IPL thickness, reduced MnSOD activity, and increased superoxide ion, MDA, 8-OHdG, and nitrotyrosine production were observed after I/R injury. Administration of AAV-SOD2 significantly reduced the levels of superoxide ion, MDA, 8-OHdG, and nitrotyrosine and prevented the damage to RGCs and IPL. Delivery of the antioxidant gene inhibited I/R-induced RGC and IPL damage by reducing oxidative stress and nitrative stress, suggesting that MnSOD may be relevant for the neuroprotection of the inner retina from I/R-related diseases.
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Affiliation(s)
- Yu Liu
- Department of Ophthalmology, Second Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
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Alway SE, Cutlip RG. Resistance loading and signaling assays for oxidative stress in rodent skeletal muscle. Methods Mol Biol 2012; 798:185-211. [PMID: 22130838 DOI: 10.1007/978-1-61779-343-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Resistance loading provides an important tool for understanding skeletal muscle responses and adaptations to various perturbations. A model using anesthetized rodents provides the means to control the input parameters carefully, and to measure the output parameters of each muscle contraction. Unilateral models of anesthetized loading also provide the advantage of comparing an unloaded and loaded muscle from the same animal. Voluntary models for resistance loading arguably provide a more "physiological response" but it also introduces more variability in the input parameters, which can be affected by the stimulus used to motivate the animal to exercise. After either acute or chronic periods of muscle loading, the loaded muscles can be removed and various signaling proteins can be determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) or enzyme assays. Several assays are described, which provide an indication of downstream markers for oxidative stress.
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Affiliation(s)
- Stephen E Alway
- Laboratory of Muscle Biology and Sarcopenia, Department of Exercise Physiology and Center for Cardiovascular and Respiratory Sciences, West Virginia University School of Medicine, Morgantown, WV, USA.
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Potenza L, Calcabrini C, Bellis RD, Mancini U, Polidori E, Zeppa S, Alloni R, Cucchiarini L, Dacha M. Effect of surgical stress on nuclear and mitochondrial DNA from healthy sections of colon and rectum of patients with colorectal cancer. J Biosci 2011; 36:243-51. [PMID: 21654079 DOI: 10.1007/s12038-011-9064-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Surgical resection at any location in the body leads to stress response with cellular and subcellular change, leading to tissue damage. The intestine is extremely sensitive to surgical stress with consequent postoperative complications. It has been suggested that the increase of reactive oxygen species as subcellular changes plays an important role in this process. This article focuses on the effect of surgical stress on nuclear and mitochondrial DNA from healthy sections of colon and rectum of patients with colorectal cancer. Mitochondrial DNA copy number, mitochondrial common deletion and nuclear and mitochondrial 8-oxo-2'-deoxyguanosine content were measured. Both the colon and rectal tissue were significantly damaged either at the nuclear or mitochondrial level. In particular, mitochondrial DNA was more damaged in rectum than in colon. The present investigation found an association between surgical stress and nuclear and mitochondrial DNA damage, suggesting that surgery may generate an increase in free radicals, which trigger a cascade of molecular changes, including alterations in DNA.
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Affiliation(s)
- Lucia Potenza
- Dipartimento di Scienze Biomolecolari, Universita degli Studi di Urbino 'Carlo Bo', Urbino, Italy.
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Abstract
Hepatitis C virus (HCV) is capable of disrupting different facets of lipid metabolism and lipids have been shown to play a crucial role in the viral life cycle. The aim of this study was to examine the effect HCV infection has on the hepatocyte metabolome. Huh-7.5 cells were infected using virus produced by the HCV J6/JFH1 cell culture system and cells were harvested 24, 48, and 72-hours following infection. Metabolic profiling was performed using a non-targeted multiple platform methodology combining ultrahigh performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS2) and gas chromatography/mass spectrometry (GC/MS). There was a significant increase in a number of metabolites involved in nucleotide synthesis and RNA replication during early HCV infection. NAD levels were also significantly increased along with several amino acids. A number of lipid metabolic pathways were disrupted by HCV infection, resulting in an increase in cholesterol and sphingolipid levels, altered phospholipid metabolism and a possible disruption in mitochondrial fatty acid transport. Fluctuations in 5′-methylthioadenosine levels were also noted, along with alterations in the glutathione synthesis pathway. These results highlight a number of previously unreported metabolic interactions and give a more in depth insight into the effect HCV has on host cell biochemical processes.
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Affiliation(s)
- Barbara Roe
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland.
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Pommerrenig B, Feussner K, Zierer W, Rabinovych V, Klebl F, Feussner I, Sauer N. Phloem-specific expression of Yang cycle genes and identification of novel Yang cycle enzymes in Plantago and Arabidopsis. Plant Cell 2011; 23:1904-19. [PMID: 21540433 PMCID: PMC3123959 DOI: 10.1105/tpc.110.079657] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 03/14/2011] [Accepted: 04/15/2011] [Indexed: 05/19/2023]
Abstract
The 5-methylthioadenosine (MTA) or Yang cycle is a set of reactions that recycle MTA to Met. In plants, MTA is a byproduct of polyamine, ethylene, and nicotianamine biosynthesis. Vascular transcriptome analyses revealed phloem-specific expression of the Yang cycle gene 5-METHYLTHIORIBOSE KINASE1 (MTK1) in Plantago major and Arabidopsis thaliana. As Arabidopsis has only a single MTK gene, we hypothesized that the expression of other Yang cycle genes might also be vascular specific. Reporter gene studies and quantitative analyses of mRNA levels for all Yang cycle genes confirmed this hypothesis for Arabidopsis and Plantago. This includes the Yang cycle genes 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE1 and DEHYDRATASE-ENOLASE-PHOSPHATASE-COMPLEX1. We show that these two enzymes are sufficient for the conversion of methylthioribose-1-phosphate to 1,2-dihydroxy-3-keto-5-methylthiopentene. In bacteria, fungi, and animals, the same conversion is catalyzed in three to four separate enzymatic steps. Furthermore, comparative analyses of vascular and nonvascular metabolites identified Met, S-adenosyl Met, and MTA preferentially or almost exclusively in the vascular tissue. Our data represent a comprehensive characterization of the Yang cycle in higher plants and demonstrate that the Yang cycle works primarily in the vasculature. Finally, expression analyses of polyamine biosynthetic genes suggest that the Yang cycle in leaves recycles MTA derived primarily from polyamine biosynthesis.
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Affiliation(s)
- Benjamin Pommerrenig
- Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
- Erlangen Center of Plant Science, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
| | - Kirstin Feussner
- Abteilung Biochemie der Pflanze, Albrecht-von-Haller-Institut für Pflanzenwissenschaften, Georg-August-Universität Göttingen, 37077 Gottingen, Germany
| | - Wolfgang Zierer
- Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
| | - Valentyna Rabinovych
- Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
| | - Franz Klebl
- Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
| | - Ivo Feussner
- Abteilung Biochemie der Pflanze, Albrecht-von-Haller-Institut für Pflanzenwissenschaften, Georg-August-Universität Göttingen, 37077 Gottingen, Germany
| | - Norbert Sauer
- Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
- Erlangen Center of Plant Science, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
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Obtułowicz T, Winczura A, Speina E, Swoboda M, Janik J, Janowska B, Cieśla JM, Kowalczyk P, Jawien A, Gackowski D, Banaszkiewicz Z, Krasnodebski I, Chaber A, Olinski R, Nair J, Bartsch H, Douki T, Cadet J, Tudek B. Aberrant repair of etheno-DNA adducts in leukocytes and colon tissue of colon cancer patients. Free Radic Biol Med 2010; 49:1064-71. [PMID: 20600828 DOI: 10.1016/j.freeradbiomed.2010.06.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 06/07/2010] [Accepted: 06/21/2010] [Indexed: 11/18/2022]
Abstract
To assess the role of lipid peroxidation-induced DNA damage and repair in colon carcinogenesis, the excision rates and levels of 1,N(6)-etheno-2'-deoxyadenosine (epsilondA), 3,N(4)-etheno-2'-deoxycytidine (epsilondC), and 1,N(2)-etheno-2'-deoxyguanosine (1,N(2)-epsilondG) were analyzed in polymorphic blood leukocytes (PBL) and resected colon tissues of 54 colorectal carcinoma (CRC) patients and PBL of 56 healthy individuals. In PBL the excision rates of 1,N(6)-ethenoadenine (epsilonAde) and 3,N(4)-ethenocytosine (epsilonCyt), measured by the nicking of oligodeoxynucleotide duplexes with single lesions, and unexpectedly also the levels of epsilondA and 1,N(2)-epsilondG, measured by LC/MS/MS, were lower in CRC patients than in controls. In contrast the mRNA levels of repair enzymes, alkylpurine- and thymine-DNA glycosylases and abasic site endonuclease (APE1), were higher in PBL of CRC patients than in those of controls, as measured by QPCR. In the target colon tissues epsilonAde and epsilonCyt excision rates were higher, whereas the epsilondA and epsilondC levels in DNA, measured by (32)P-postlabeling, were lower in tumor than in adjacent colon tissue, although a higher mRNA level was observed only for APE1. This suggests that during the onset of carcinogenesis, etheno adduct repair in the colon seems to be under a complex transcriptional and posttranscriptional control, whereby deregulation may act as a driving force for malignancy.
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Affiliation(s)
- Tomasz Obtułowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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Dechakhamphu S, Pinlaor S, Sitthithaworn P, Bartsch H, Yongvanit P. Accumulation of miscoding etheno-DNA adducts and highly expressed DNA repair during liver fluke-induced cholangiocarcinogenesis in hamsters. Mutat Res 2010; 691:9-16. [PMID: 20541562 DOI: 10.1016/j.mrfmmm.2010.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 05/26/2010] [Accepted: 06/02/2010] [Indexed: 05/29/2023]
Abstract
Infection by Opisthorchis viverrini, a risk factor for cholangiocarcinoma (CCA) may act through chronic inflammation, oxidative stress and lipid peroxidation (LPO)-related damage and growth stimuli. 1,N6-etheno-2'-deoxyadenosine (epsilondA), and 3,N4-etheno-2'-deoxycytidine (epsilondC), markers for LPO-derived DNA damage were highly increased in white blood cell and urine of O. viverrini-infected Thai patients. In order to investigate tissue specificity etheno adducts were measured in a cholangiocarcinogenesis model, in O. viverrini-infected hamsters that had received N-nitrosodimethylamine (NDMA, 12.5 ppm in dw) for 2 months. epsilondA- and epsilondC-levels were analyzed in paraffin-embedded liver sections by a novel immunohistochemical method, from 21 up to 180 days post-O. viverrini-infection. In inflamed areas of the liver, etheno adducts were localized in the nuclei of inflammatory cells and in the epithelial lining of the bile duct. Semi-quantitative image analysis showed higher adduct levels in the liver of O. viverrini-infected hamsters, treated with or w/o NDMA when compared with untreated controls. Levels were found highest in the liver of O. viverrini-infected plus NDMA-treated hamsters. Adducts increased in an age-dependent manner from O. viverrini-infection until CCA development. Increased adduct formation paralleled histopathological changes in plasma alkaline phosphatase (ALP) activity, bile duct hyperplasia, dysplasia, precancerous lesions, and CCA appearance. Also elevated expression of alkyladenine DNA glycosylase (AAG), which excises 1,N6-ethenoadenine (epsilonA) was linked to higher adduct formation, suggesting imbalanced repair. Our results implicate accumulation of inflammation-related, promutagenic DNA damage in target tissue and possibly imbalanced repair in the onset of cholangiocarcinogenesis.
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Affiliation(s)
- Somkid Dechakhamphu
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
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Gelin A, Redrejo-Rodríguez M, Laval J, Fedorova OS, Saparbaev M, Ishchenko AA. Genetic and biochemical characterization of human AP endonuclease 1 mutants deficient in nucleotide incision repair activity. PLoS One 2010; 5:e12241. [PMID: 20808930 PMCID: PMC2923195 DOI: 10.1371/journal.pone.0012241] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 07/25/2010] [Indexed: 11/19/2022] Open
Abstract
Background Human apurinic/apyrimidinic endonuclease 1 (APE1) is a key DNA repair enzyme involved in both base excision repair (BER) and nucleotide incision repair (NIR) pathways. In the BER pathway, APE1 cleaves DNA at AP sites and 3′-blocking moieties generated by DNA glycosylases. In the NIR pathway, APE1 incises DNA 5′ to a number of oxidatively damaged bases. At present, physiological relevance of the NIR pathway is fairly well established in E. coli, but has yet to be elucidated in human cells. Methodology/Principal Finding We identified amino acid residues in the APE1 protein that affect its function in either the BER or NIR pathway. Biochemical characterization of APE1 carrying single K98A, R185A, D308A and double K98A/R185A amino acid substitutions revealed that all mutants exhibited greatly reduced NIR and 3′→5′ exonuclease activities, but were capable of performing BER functions to some extent. Expression of the APE1 mutants deficient in the NIR and exonuclease activities reduced the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to an alkylating agent, methylmethanesulfonate, suggesting that our APE1 mutants are able to repair AP sites. Finally, the human NIR pathway was fully reconstituted in vitro using the purified APE1, human flap endonuclease 1, DNA polymerase β and DNA ligase I proteins, thus establishing the minimal set of proteins required for a functional NIR pathway in human cells. Conclusion/Significance Taken together, these data further substantiate the role of NIR as a distinct and separable function of APE1 that is essential for processing of potentially lethal oxidative DNA lesions.
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Affiliation(s)
- Aurore Gelin
- CNRS UMR8126, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Modesto Redrejo-Rodríguez
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Jacques Laval
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Murat Saparbaev
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Alexander A. Ishchenko
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
- * E-mail:
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