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Nowrouzi B, Torres-Montero P, Kerkhoven EJ, Martínez JL, Rios-Solis L. Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production. Metab Eng Commun 2024; 18:e00229. [PMID: 38098801 PMCID: PMC10716015 DOI: 10.1016/j.mec.2023.e00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Saccharomyces cerevisiae has been conveniently used to produce Taxol® anticancer drug early precursors. However, the harmful impact of oxidative stress by the first cytochrome P450-reductase enzymes (CYP725A4-POR) of Taxol® pathway has hampered sufficient progress in yeast. Here, we evolved an oxidative stress-resistant yeast strain with three-fold higher titre of their substrate, taxadiene. The performance of the evolved and parent strains were then evaluated in galactose-limited chemostats before and under the oxidative stress by an oxidising agent. The interaction of evolution and oxidative stress was comprehensively evaluated through transcriptomics and metabolite profiles integration in yeast enzyme-constrained genome scale model. Overall, the evolved strain showed improved respiration, reduced overflow metabolites production and oxidative stress re-induction tolerance. The cross-protection mechanism also potentially contributed to better heme, flavin and NADPH availability, essential for CYP725A4 and POR optimal activity in yeast. The results imply that the evolved strain is a robust cell factory for future efforts towards Taxol© production.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Pablo Torres-Montero
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Eduard J. Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - José L. Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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2
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Martorelli Di Genova B. mSphere of Influence: Deciphering purine auxotrophy in protozoan parasites. mSphere 2024; 9:e0000724. [PMID: 38567972 PMCID: PMC11036795 DOI: 10.1128/msphere.00007-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2024] Open
Abstract
Bruno Martorelli Di Genova works in parasitology, focusing on Toxoplasma gondii metabolism. In this mSphere of Influence article, he reflects on how the articles "Metabolic Reprogramming during Purine Stress in the Protozoan Pathogen Leishmania donovani" and "Yeast-Based High-Throughput Screen Identifies Plasmodium falciparum Equilibrative Nucleoside Transporter 1 Inhibitors That Kill Malaria Parasites" impacted him, informing his research strategies and understanding of metabolic flexibility in Toxoplasma gondii.
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Affiliation(s)
- Bruno Martorelli Di Genova
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
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3
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Sun M, Dai P, Cao Z, Dong J. Purine metabolism in plant pathogenic fungi. Front Microbiol 2024; 15:1352354. [PMID: 38384269 PMCID: PMC10879430 DOI: 10.3389/fmicb.2024.1352354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
In eukaryotic cells, purine metabolism is the way to the production of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and plays key roles in various biological processes. Purine metabolism mainly consists of de novo, salvage, and catabolic pathways, and some components of these pathways have been characterized in some plant pathogenic fungi, such as the rice blast fungus Magnaporthe oryzae and wheat head blight fungus Fusarium graminearum. The enzymatic steps of the de novo pathway are well-conserved in plant pathogenic fungi and play crucial roles in fungal growth and development. Blocking this pathway inhibits the formation of penetration structures and invasive growth, making it essential for plant infection by pathogenic fungi. The salvage pathway is likely indispensable but requires exogenous purines, implying that purine transporters are functional in these fungi. The catabolic pathway balances purine nucleotides and may have a conserved stage-specific role in pathogenic fungi. The significant difference of the catabolic pathway in planta and in vitro lead us to further explore and identify the key genes specifically regulating pathogenicity in purine metabolic pathway. In this review, we summarized recent advances in the studies of purine metabolism, focusing on the regulation of pathogenesis and growth in plant pathogenic fungi.
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Affiliation(s)
- Manli Sun
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | | | | | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
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4
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Chen Y, Wu X, Li P, Liu Y, Song M, Li F, Ou J, Lai J. Integrated metabolomic and transcriptomic responses to heat stress in a high-altitude fish, Triplophysa siluroides. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109118. [PMID: 37774901 DOI: 10.1016/j.fsi.2023.109118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/07/2023] [Accepted: 09/27/2023] [Indexed: 10/01/2023]
Abstract
Species in Triplophysa display strong adaptability to the extreme environment of the plateau, thus offering an ideal model to study the molecular mechanism of fish adaptation to environmental stress. In the present study, we conducted integrated analysis of the transcriptome and metabolism of liver tissue in Triplophysa siluroides under heat stress (28 °C) and control (10 °C) conditions to identify heat stress-induced genes, metabolites and pathways. RNA-Seq identified 2373 differentially expressed genes, which consisted of 1360 upregulated genes and 1013 downregulated genes, in the heat stress group vs. the control group. Genes in the heat shock protein (Hsp) family, including Hsp40, Hsp70, Hsp90 and other Hsps, were strongly upregulated by heat stress. Pathway enrichment analysis revealed that the PI3K/AKT/mTOR and protein processing in the endoplasmic reticulum (ER) pathways were significantly affected by heat stress. Metabolism sequencing identified a total of 155 differentially abundant metabolites, including 118 significantly upregulated metabolites and 37 downregulated metabolites. Combined analysis of the transcriptome and metabolism results showed that ubiquitin-dependent proteolysis and purine metabolism pathways were enhanced in response to acute heat stress to protect cells from damage under stress conditions. The results of this study may contribute to our understanding of the underlying molecular mechanism of the heat stress response in cold-water fish.
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Affiliation(s)
- Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Xiaoyun Wu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Pengcheng Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Ya Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Mingjiang Song
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Feiyang Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Jun Ou
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Jiansheng Lai
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China.
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Nguyen TP, Meng DR, Chang CH, Su PY, Ou CA, Hou PF, Sung HM, Chou CH, Ohme-Takagi M, Huang HJ. Antifungal mechanism of volatile compounds emitted by Actinomycetota Paenarthrobacter ureafaciens from a disease-suppressive soil on Saccharomyces cerevisiae. mSphere 2023; 8:e0032423. [PMID: 37750721 PMCID: PMC10597458 DOI: 10.1128/msphere.00324-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
Increasing evidence suggests that in disease-suppressive soils, microbial volatile compounds (mVCs) released from bacteria may inhibit the growth of plant-pathogenic fungi. However, the antifungal activities and molecular responses of fungi to different mVCs remain largely undescribed. In this study, we first evaluated the responses of pathogenic fungi to treatment with mVCs from Paenarthrobacter ureafaciens. Then, we utilized the well-characterized fungal model organism Saccharomyces cerevisiae to study the potential mechanistic effects of the mVCs. Our data showed that exposure to P. ureafaciens mVCs leads to reduced growth of several pathogenic fungi, and in yeast cells, mVC exposure prompts the accumulation of reactive oxygen species. Further experiments with S. cerevisiae deletion mutants indicated that Slt2/Mpk1 and Hog1 MAPKs play major roles in the yeast response to P. ureafaciens mVCs. Transcriptomic analysis revealed that exposure to mVCs was associated with 1,030 differentially expressed genes (DEGs) in yeast. According to gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses, many of these DEGs are involved in mitochondrial dysfunction, cell integrity, mitophagy, cellular metabolism, and iron uptake. Genes encoding antimicrobial proteins were also significantly altered in the yeast after exposure to mVCs. These findings suggest that oxidative damage and mitochondrial dysfunction are major contributors to the fungal toxicity of mVCs. Furthermore, our data showed that cell wall, antioxidant, and antimicrobial defenses are induced in yeast exposed to mVCs. Thus, our findings expand upon previous research by delineating the transcriptional responses of the fungal model. IMPORTANCE Since the use of bacteria-emitted volatile compounds in phytopathogen control is of considerable interest, it is important to understand the molecular mechanisms by which fungi may adapt to microbial volatile compounds (mVCs). Paenarthrobacter ureafaciens is an isolated bacterium from disease-suppressive soil that belongs to the Actinomycetota phylum. P. ureafaciens mVCs showed a potent antifungal effect on phytopathogens, which may contribute to disease suppression in soil. However, our knowledge about the antifungal mechanism of mVCs is limited. This study has proven that mVCs are toxic to fungi due to oxidative stress and mitochondrial dysfunction. To deal with mVC toxicity, antioxidants and physical defenses are required. Furthermore, iron uptake and CAP proteins are required for antimicrobial defense, which is necessary for fungi to deal with the thread from mVCs. This study provides essential foundational knowledge regarding the molecular responses of fungi to inhibitory mVCs.
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Affiliation(s)
- Tri-Phuong Nguyen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - De-Rui Meng
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Han Chang
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
| | - Pei-Yu Su
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chieh-An Ou
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Fu Hou
- Kaohsiung District Agricultural Research and Extension Station, Pingtung, Taiwan
| | - Huang-Mo Sung
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chang-Hung Chou
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Masaru Ohme-Takagi
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
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6
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Liang ZW, Li SY, Zhang XL, Chen CY, Sun WJ, Gu ZQ, Huang J, He JY, Qi PZ, Guo BY, Liao Z, Yan XJ. Morphological change and differential proteomics analysis of gill in Mytilus coruscus under starvation. Front Physiol 2023; 14:1150521. [PMID: 37064882 PMCID: PMC10097965 DOI: 10.3389/fphys.2023.1150521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/03/2023] [Indexed: 04/01/2023] Open
Abstract
Mytilus coruscus is a dominant shellfish in the Yangtze estuary and its adjacent sea area. Food deprivation often occurs during their growth due to fluctuations in algal abundance caused by seasonal freshwater flushing and high-density aquaculture mode. To investigate the coping strategies of M. coruscus to starvation stress, electron microscopy and differential proteomic analysis were performed on the critical feeding organ gill of the mussels after 9 days of starvation. The electron microscopy results showed that the cilia of the mussel gills were dissolved, and the gaps between gill filaments widened under starvation. Differential proteomic analysis revealed that phagocytosis-related proteins such as ATPeV1E, ATPeV1C, LAMP1_2 and CTSL were significantly upregulated, and the phagocytosis pathway was significantly enriched (p < 0.05). In addition, the corin content in gill and myeloperoxidase level as well as the number of dead cells in blood were both significantly increased (p < 0.05). What’s more, proteomic data suggested that immune maintenance, cellular transport and metabolism related pathways were significantly enriched, which illustrated an immune and metabolism responses under starvation. This study reveals for the first time that phagocytosis functions as an essential strategy for M. coruscus to cope with starvation, which provides new scientific knowledge and a theoretical basis for understanding the adaptation mechanisms of mussel to starvation and for rational optimization of mussel culture patterns.
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Affiliation(s)
- Ze-Wei Liang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Si-Yuan Li
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Xiao-Lin Zhang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- *Correspondence: Xiao-Lin Zhang, ; Xiao-Jun Yan,
| | - Chuan-Yue Chen
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Wen-Jing Sun
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Zhong-Qi Gu
- China Bureau of Science and Technology Shengsi, Zhoushan, Zhejiang, China
| | - Ji Huang
- China Bureau of Science and Technology Shengsi, Zhoushan, Zhejiang, China
| | - Jian-Yu He
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- Donghai Laboratory, Zhoushan, Zhejiang, China
| | - Peng-Zhi Qi
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Bao-Ying Guo
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Zhi Liao
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Xiao-Jun Yan
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- *Correspondence: Xiao-Lin Zhang, ; Xiao-Jun Yan,
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7
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Pavão G, Sfalcin I, Bonatto D. Biocontainment Techniques and Applications for Yeast Biotechnology. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9040341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid patented yeast gene technologies spreading outside the production facility. In this review, the different biocontainment technologies currently available for GMYs were evaluated. Interestingly, uniplex-type biocontainment approaches (UTBAs), which rely on nutrient auxotrophies induced by gene mutation or deletion or the expression of the simple kill switches apparatus, are still the major biocontainment approaches in use with GMY. While bacteria such as Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs.
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8
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Wang C, Yu L, Zhang J, Zhou Y, Sun B, Xiao Q, Zhang M, Liu H, Li J, Li J, Luo Y, Xu J, Lian Z, Lin J, Wang X, Zhang P, Guo L, Ren R, Deng D. Structural basis of the substrate recognition and inhibition mechanism of Plasmodium falciparum nucleoside transporter PfENT1. Nat Commun 2023; 14:1727. [PMID: 36977719 PMCID: PMC10050424 DOI: 10.1038/s41467-023-37411-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
By lacking de novo purine biosynthesis enzymes, Plasmodium falciparum requires purine nucleoside uptake from host cells. The indispensable nucleoside transporter ENT1 of P. falciparum facilitates nucleoside uptake in the asexual blood stage. Specific inhibitors of PfENT1 prevent the proliferation of P. falciparum at submicromolar concentrations. However, the substrate recognition and inhibitory mechanism of PfENT1 are still elusive. Here, we report cryo-EM structures of PfENT1 in apo, inosine-bound, and inhibitor-bound states. Together with in vitro binding and uptake assays, we identify that inosine is the primary substrate of PfENT1 and that the inosine-binding site is located in the central cavity of PfENT1. The endofacial inhibitor GSK4 occupies the orthosteric site of PfENT1 and explores the allosteric site to block the conformational change of PfENT1. Furthermore, we propose a general "rocker switch" alternating access cycle for ENT transporters. Understanding the substrate recognition and inhibitory mechanisms of PfENT1 will greatly facilitate future efforts in the rational design of antimalarial drugs.
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Affiliation(s)
- Chen Wang
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China
| | - Leiye Yu
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China
- Warshal Institute of Computational Biology, School of Life and Health Sciences, the Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Jiying Zhang
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Yanxia Zhou
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Bo Sun
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Qingjie Xiao
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Minhua Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Huayi Liu
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinhong Li
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Jialu Li
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunzi Luo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of MOE, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jie Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhong Lian
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jingwen Lin
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiang Wang
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Li Guo
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China.
| | - Ruobing Ren
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China.
- Shanghai Qi Zhi Institute, Shanghai, 200030, China.
| | - Dong Deng
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China.
- NHC key Laboratory of Chronobiology, Sichuan University, Chengdu, 610041, China.
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, 610041, China.
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9
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Desiatkina O, Mösching M, Anghel N, Boubaker G, Amdouni Y, Hemphill A, Furrer J, Păunescu E. New Nucleic Base-Tethered Trithiolato-Bridged Dinuclear Ruthenium(II)-Arene Compounds: Synthesis and Antiparasitic Activity. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238173. [PMID: 36500266 PMCID: PMC9738179 DOI: 10.3390/molecules27238173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
Aiming toward compounds with improved anti-Toxoplasma activity by exploiting the parasite auxotrophies, a library of nucleobase-tethered trithiolato-bridged dinuclear ruthenium(II)-arene conjugates was synthesized and evaluated. Structural features such as the type of nucleobase and linking unit were progressively modified. For comparison, diruthenium hybrids with other type of molecules were also synthesized and assessed. A total of 37 compounds (diruthenium conjugates and intermediates) were evaluated in a primary screening for in vitro activity against transgenic Toxoplasma gondii tachyzoites constitutively expressing β-galactosidase (T. gondii β-gal) at 0.1 and 1 µM. In parallel, the cytotoxicity in non-infected host cells (human foreskin fibroblasts, HFF) was determined by alamarBlue assay. Twenty compounds strongly impairing parasite proliferation with little effect on HFF viability were subjected to T. gondii β-gal half maximal inhibitory concentration determination (IC50) and their toxicity for HFF was assessed at 2.5 µM. Two promising compounds were identified: 14, ester conjugate with 9-(2-oxyethyl)adenine, and 36, a click conjugate bearing a 2-(4-(hydroxymethyl)-1H-1,2,3-triazol-1-yl)methyl substituent, with IC50 values of 0.059 and 0.111 µM respectively, significantly lower compared to pyrimethamine standard (IC50 = 0.326 µM). Both 14 and 36 exhibited low toxicity against HFF when applied at 2.5 µM and are candidates for potential treatment options in a suitable in vivo model.
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Affiliation(s)
- Oksana Desiatkina
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Martin Mösching
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Nicoleta Anghel
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Ghalia Boubaker
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Yosra Amdouni
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
- Laboratoire de Parasitologie, Institution de la Recherche et de l'Enseignement Supérieur Agricoles, Université de la Manouba, École Nationale de Médecine Vétérinaire de Sidi Thabet, Sidi Thabet 2020, Tunisia
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Julien Furrer
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Emilia Păunescu
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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10
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Luo K, Chen L, Du L, Zhao Y, Chen Q. Response of the aerobic denitrifying phosphorus accumulating bacteria Pseudomonas psychrophila HA-2 to low temperature and zinc oxide nanoparticles stress. BIORESOURCE TECHNOLOGY 2022; 354:127162. [PMID: 35429594 DOI: 10.1016/j.biortech.2022.127162] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Performance and molecular changes of an aerobic denitrifying phosphorus accumulating bacteria Pseudomonas psychrophila HA-2 have been investigated under different temperatures and ZnO nanoparticles (NPs) exposures. Strain HA-2 removed 95.7% of total nitrogen (TN) and 24.6% of phosphorus at 10 °C, which was attributed to the joint up-regulation of intracellular energy metabolism and ribosome. Moreover, with the increase of ZnO NPs from 0 to 100 mg/L, TN and phosphurs removal efficiencies decreased from 95.7% to 44.5% and 24.6% to 6.8% at 10 °C, respectively, whereas phosphorus removal rate increased from 10.5% to 24.5% at 20 °C. Further transcriptomics and proteomics revealed that significant down-regulation of purine and amino acid metabolisms was the main reason for the inhibitory effect at 10 °C, while the up-regulation of antioxidant pathways and functional genes expressions was responsible for the promoted phosphorus accumulation at 20 °C. This study provides a potential solution for improving biological nutrients removal processes in winter months.
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Affiliation(s)
- Kongyan Luo
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Long Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Lei Du
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yuanyi Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China.
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Anghel N, Müller J, Serricchio M, Jelk J, Bütikofer P, Boubaker G, Imhof D, Ramseier J, Desiatkina O, Păunescu E, Braga-Lagache S, Heller M, Furrer J, Hemphill A. Cellular and Molecular Targets of Nucleotide-Tagged Trithiolato-Bridged Arene Ruthenium Complexes in the Protozoan Parasites Toxoplasma gondii and Trypanosoma brucei. Int J Mol Sci 2021; 22:ijms221910787. [PMID: 34639127 PMCID: PMC8509533 DOI: 10.3390/ijms221910787] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 12/23/2022] Open
Abstract
Toxoplasma gondii is an apicomplexan parasite that infects and proliferates within many different types of host cells and infects virtually all warm-blooded animals and humans. Trypanosoma brucei is an extracellular kinetoplastid that causes human African trypanosomiasis and Nagana disease in cattle, primarily in rural sub-Saharan Africa. Current treatments against both parasites have limitations, e.g., suboptimal efficacy and adverse side effects. Here, we investigate the potential cellular and molecular targets of a trithiolato-bridged arene ruthenium complex conjugated to 9-(2-hydroxyethyl)-adenine (1), which inhibits both parasites with IC50s below 10−7 M. Proteins that bind to 1 were identified using differential affinity chromatography (DAC) followed by shotgun-mass spectrometry. A trithiolato-bridged ruthenium complex decorated with hypoxanthine (2) and 2-hydroxyethyl-adenine (3) were included as controls. Transmission electron microscopy (TEM) revealed distinct ultrastructural modifications in the mitochondrion induced by (1) but not by (2) and (3) in both species. DAC revealed 128 proteins in T. gondii and 46 proteins in T. brucei specifically binding to 1 but not 2 or 3. In T. gondii, the most abundant was a protein with unknown function annotated as YOU2. This protein is a homolog to the human mitochondrial inner membrane translocase subunit Tim10. In T. brucei, the most abundant proteins binding specifically to 1 were mitochondrial ATP-synthase subunits. Exposure of T. brucei bloodstream forms to 1 resulted in rapid breakdown of the ATP-synthase complex. Moreover, both datasets contained proteins involved in key steps of metabolism and nucleic acid binding proteins.
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Affiliation(s)
- Nicoleta Anghel
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (N.A.); (G.B.); (D.I.); (J.R.)
| | - Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (N.A.); (G.B.); (D.I.); (J.R.)
- Correspondence: (J.M.); (A.H.)
| | - Mauro Serricchio
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland; (M.S.); (J.J.); (P.B.)
| | - Jennifer Jelk
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland; (M.S.); (J.J.); (P.B.)
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland; (M.S.); (J.J.); (P.B.)
| | - Ghalia Boubaker
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (N.A.); (G.B.); (D.I.); (J.R.)
| | - Dennis Imhof
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (N.A.); (G.B.); (D.I.); (J.R.)
| | - Jessica Ramseier
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (N.A.); (G.B.); (D.I.); (J.R.)
| | - Oksana Desiatkina
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; (O.D.); (E.P.); (J.F.)
| | - Emilia Păunescu
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; (O.D.); (E.P.); (J.F.)
| | - Sophie Braga-Lagache
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, 3012 Bern, Switzerland; (S.B.-L.); (M.H.)
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, 3012 Bern, Switzerland; (S.B.-L.); (M.H.)
| | - Julien Furrer
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; (O.D.); (E.P.); (J.F.)
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (N.A.); (G.B.); (D.I.); (J.R.)
- Correspondence: (J.M.); (A.H.)
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Zhang R, Yao Y, Tu L, Luan T, Chen B. Non-targeted metabolomics of multiple human cells revealing differential toxic effects of perfluorooctanoic acid. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:125017. [PMID: 33421881 DOI: 10.1016/j.jhazmat.2020.125017] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/26/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Differences in toxic effects of contaminants among human cells are essential for evaluating their health risks to humans. In this study, non-targeted metabolomics of multiple human cell lines (A549 (lung), DLD-1 (intestine) and L-02 (liver) cells) was used to address the differential toxicity of perfluorooctanoic acid (PFOA). The number of differential metabolites (DMs) identified in the PFOA-treated A549 cells (67) was highest, followed by DLD-1 (12) and L-02 cells (10). The categorization of DMs was almost uniquely specific to each of cell lines. PFOA significantly promoted linoleic acid metabolism in L-02 cells whereas this metabolism was inhibited in the PFOA-treated A549 cells. The levels of interleukin (IL)-1β, IL-6, IL-8 and IL-13 were about 1.5 times higher in the PFOA-treated A549 and L-02 cells than in the controls. PFOA stimulated the biosynthesis of arginine and the metabolism of vitamin B6 in A549 cells. Arginine and vitamin B6 supplemented into cell culture effectively decreased the levels of IL-6 and IL-8. The inhibition of purine metabolism by PFOA resulted in the arrestation of DLD-1 cells at the G0/G1-phase. Our results suggest that the differential toxicity of PFOA related to exposure pathways could be elucidated by metabolic profiles specific to various human cells.
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Affiliation(s)
- Ruijia Zhang
- Sate Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yao Yao
- Sate Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Lanyin Tu
- Sate Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tiangang Luan
- Sate Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Baowei Chen
- Southern Marine Science and Engineering Guangdong Laboratory, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China.
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Bora N, Jha AN. In silico Metabolic Pathway Analysis Identifying Target Against Leishmaniasis - A Kinetic Modeling Approach. Front Genet 2020; 11:179. [PMID: 32211028 PMCID: PMC7068213 DOI: 10.3389/fgene.2020.00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 02/14/2020] [Indexed: 01/14/2023] Open
Abstract
The protozoan Leishmania donovani, from trypanosomatids family is a deadly human pathogen responsible for causing Visceral Leishmaniasis. Unavailability of proper treatment in the developing countries has served as a major threat to the people. The absence of vaccines has made treatment possibilities to rely solely over chemotherapy. Also, reduced drug efficacy due to emerging resistant strains magnifies the threat. Despite years of formulations for an effective drug therapy, complexity of the disease is also unfortunately increasing. Absence of potential drug targets has worsened the scenario. Therefore exploring new therapeutic approach is a priority for the scientific community to combat the disease. One of the most reliable ways to alter the adversities of the infection is finding new biological targets for designing potential drugs. An era of computational biology allows identifying targets, assisting experimental studies. It includes sorting the parasite’s metabolic pathways that pins out proteins essential for its survival. We have directed our study towards a computational methodology for determining targets against L. donovani from the “purine salvage” pathway. This is a mainstay pathway towards the maintenance of purine amounts in the parasitic pool of nutrients proving to be mandatory for its survival. This study represents an integration of metabolic pathway and Protein-Protein Interactions analysis. It consists of incorporating the available experimental data to the theoretical methods with a prospective to develop a kinetic model of Purine salvage pathway. Simulation data revealed the time course mechanism of the enzymes involved in the synthesis of the metabolites. Modeling of the metabolic pathway helped in marking of crucial enzymes. Additionally, the PPI analysis of the pathway assisted in building a static interaction network for the proteins. Topological analysis of the PPI network through centrality measures (MCC and Closeness) detected targets found common with Dynamic Modeling. Therefore our analysis reveals the enzymes ADSL (Adenylosuccinate lyase) and IMPDH (Inosine-5′-monophosphate dehydrogenase) to be important having a central role in the modeled network based on PPI and kinetic modeling techniques. Further the available three dimensional structure of the enzyme “ADSL” aided towards the search for potential inhibitors against the protein. Hence, the study presented the significance of integrating methods to identify key proteins which might be putative targets against the treatment of Visceral Leishmaniasis and their potential inhibitors.
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Affiliation(s)
- Nikita Bora
- Computational Biophysics Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Anupam Nath Jha
- Computational Biophysics Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
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