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Hano T, Ito M, Sato T, Sugaya T, Sato J, Jusup M, Iwasaki Y. Triple jeopardy: The combined effects of viral, chemical, and thermal stress on kuruma prawn (Penaeus japonicus) juveniles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175934. [PMID: 39218101 DOI: 10.1016/j.scitotenv.2024.175934] [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: 05/24/2024] [Revised: 07/15/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Growing concerns have emerged over the combined effects of multiple stressors on ecosystems. Empirical evidence shows that the sensitivity of aquatic invertebrates to insecticides varies under thermally fluctuating conditions. Additionally, field surveys in estuarine areas of western Japan confirmed the presence of juvenile kuruma prawns (Penaeus japonicus) carrying the white spot syndrome virus (WSSV). Given the potential of co-exposure to multiple stressors, we performed a combined exposure experiment using a full-factorial design with three stressors: WSSV infection (presence or absence: initial 2 h exposure), fipronil (insecticide) exposure (0 or 0.1 μg/L: 14 d exposure), and temperature (20, 25, or 30 °C). We observed the highest mortality (75 %) in the WSSV + Fipronil treatment at 30 °C, with the associated specimens showing significant changes in the internal load of WSSV and concentrations of fipronil and its metabolite, fipronil sulfone. Severe perturbations of metabolites associated with increased energy expenditure and fatty acid utilization have been identified as potential factors underlying lethality in juvenile kuruma prawns. The results demonstrate that WSSV infection increases the susceptibility of thermally stressed juvenile kuruma prawns to fipronil. Therefore, further studies are required to determine the combined effects of multiple stressors in environmentally relevant scenarios on juvenile kuruma prawns as well as in estuarine ecosystems.
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Affiliation(s)
- Takeshi Hano
- Environmental Conservation Division, Fisheries Technology Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 2-17-5, Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan.
| | - Mana Ito
- Environmental Conservation Division, Fisheries Technology Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 2-17-5, Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Taku Sato
- Production Engineering Division, Fisheries Technology Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 1760 Momoshima, Onomichi, Hiroshima 722-0061, Japan
| | - Takuma Sugaya
- Production Engineering Division, Fisheries Technology Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 1760 Momoshima, Onomichi, Hiroshima 722-0061, Japan
| | - Jun Sato
- Pathology Division, Fisheries Technology Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhamaura, Minamiise, Mie 722-0061, Japan
| | - Marko Jusup
- Highly Migratory Resource Division, Fisheries Resources Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 2-12-4, Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Yuichi Iwasaki
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology, 16-1, Onogawa Tsukuba, Ibaraki 305-8569, Japan
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Zou S, Liu J, Zhao K, Zhu X, Zhang B, Liu Z, Zheng Y. Metabolic engineering of Escherichia coli for enhanced production of D-pantothenic acid. BIORESOURCE TECHNOLOGY 2024; 412:131352. [PMID: 39186986 DOI: 10.1016/j.biortech.2024.131352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 08/08/2024] [Accepted: 08/23/2024] [Indexed: 08/28/2024]
Abstract
D-pantothenic acid (D-PA) is an essential vitamin that has been widely used in various industries. However, the low productivity caused by slow D-PA production in fermentation hinders its potential applications. In this study, strategies of engineering the synthetic pathway combined with regulating methyl recycle were employed in E. coli to enhance D-PA production. First, a self-induced promoter-mediated dynamic regulation of D-PA degradation pathway was carried out to improve D-PA accumulation. Then, to drive more carbon flux into D-PA synthesis, the key nodes of the R-pantoate pathway which encoded the essential enzyme were integrated into the genome. Subsequently, the further increase in D-PA production was achieved by promoting the regeneration of methyl donor. The strain L11T produced 86.03 g/L D-PA with a productivity of 0.797 g/L/h, which presented the highest D-PA titer and productivity to date. The strategies could be applied to constructing cell factories for producing other bio-based products.
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Affiliation(s)
- Shuping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jinlong Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Kuo Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xintao Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhiqiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
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Zhang W, Zhao Y, Yang H, Liu Y, Zhang Y, Zhang Z, Li Y, Wang X, Xu Z, Deng J. Comparison analysis of bioactive metabolites in soybean, pea, mung bean, and common beans: reveal the potential variations of their antioxidant property. Food Chem 2024; 457:140137. [PMID: 38908251 DOI: 10.1016/j.foodchem.2024.140137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/27/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024]
Abstract
This study showed the significantly differences of basic nutrients and metabolite compounds in nine types of beans involved in soybean, mung bean, pea, and common beans. The metabolomics results showed that serval metabolites such as histidine, proline, 3-alanine, and myricetin which could be used to identify different beans. The random forest model showed that amino acid and fatty acid could be used as special indexes to distinguish different types of beans in practice. The different expressed metabolites among different types of beans were involved in various pathways including alanine, aspartate and glutamate metabolism, arginine and proline metabolism, and purine metabolism. The antioxidant activity was significantly different among different types of beans, and the contents of amino acid, coumarin, and polyphenol contributed the antioxidant activities of beans. Together, these results will provide a comprehensive understanding of metabolites in different types of beans and theoretical guideline for the future application of beans.
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Affiliation(s)
- Wenyuan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaqi Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haixia Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yichen Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yanli Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhanquan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yunlong Li
- College of Food science and technology, Shanxi Agricultural University, Taiyuan 030031, China
| | - Xue Wang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhenzhen Xu
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianjun Deng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Tran TH, Escapa IF, Roberts AQ, Gao W, Obawemimo AC, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebact e rium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum , C. pseudodiphtheriticum, C. accolens , and C. tuberculostearicum . To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the USA. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the USA clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches. IMPORTANCE Pangenomic analysis with estimation of functional capabilities facilitates our understanding of the full biologic diversity of bacterial species. We performed systematic genomic, phylogenomic, and pangenomic analyses with qualitative estimation of the metabolic capabilities of four common human nasal Corynebacterium species, along with focused experimental validations, generating a foundational resource. The prevalence of each species in human nasal microbiota is consistent with the common coexistence of at least two species. We identified a notably high level of metabolic conservation within and among species indicating limited options for species to occupy distinct metabolic niches, highlighting the importance of investigating interactions among nasal Corynebacterium species. Comparing strains from two continents, C. pseudodiphtheriticum had restricted geographic strain distribution characterized by an evolutionarily recent loss of assimilatory sulfate reduction in USA strains. Our findings contribute to understanding the functions of Corynebacterium within human nasal microbiota and to evaluating their potential for future use as biotherapeutics.
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Zhang H, Wang Y, Zhao H, Wang W, Han F. The involvement of effector memory CD4 + T cells in mediating the impact of genus Oscillibacter gut microbiota on Alzheimer's disease: a Mendelian randomization study. Front Aging Neurosci 2024; 16:1423707. [PMID: 39170894 PMCID: PMC11335717 DOI: 10.3389/fnagi.2024.1423707] [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: 04/26/2024] [Accepted: 07/26/2024] [Indexed: 08/23/2024] Open
Abstract
Objective This study aimed to investigate the causal relationship between gut microbiota characteristics (207 taxa and 205 pathways) and Alzheimer's disease and determine and quantify the role of immune cells as potential mediators. Methods Gut microbiota characteristics (207 taxa and 205 pathways) were obtained from the NHGRI-EBI GWAS Catalog project, while Alzheimer's disease data and 731 immune cell characteristics were obtained from the IEU Open GWAS project. Two-sample Mendelian randomization (MR) was conducted to determine whether gut microbiota characteristics (207 taxa and 205 pathways) were causally related to Alzheimer's disease. Furthermore, two-step MR was employed to quantify the proportion of the effect of immune cell characteristics mediated by gut microbiota characteristics (207 taxa and 205 pathways) on Alzheimer's disease. Results A total of 17 immune cell characteristics were identified as potential mediators for 13 gut microbiota influencing Alzheimer's disease, with Effector Memory CD4+ T-cell Absolute Count accounted for 8.99% of the causal relationship between genus Oscillibacter and Alzheimer's disease. Conclusion In summary, our research confirms a causal relationship between gut microbiota and Alzheimer's disease, with immune cells contributing to a significant portion of the effect. However, the full mediators of gut microbiota's impact on Alzheimer's disease remain unclear. Further investigation is warranted to explore additional potential risk factors acting as mediators.
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Affiliation(s)
- Huachang Zhang
- The Institute for Tissue Engineering and Regenerative Medicine, Stem Cell and Regenerative Medicine Laboratory, Liaocheng People's Hospital/Liaocheng University, Liaocheng, Shandong, China
| | - Yudong Wang
- Department of Nursing, Liaocheng People’s Hospital, Liaocheng, Shandong, China
- Intensive Care Unit, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Hui Zhao
- Henan Academy of Sciences, Zhengzhou, Henan, China
- Henan High Tech Industrial Co., Ltd., Zhengzhou, Henan, China
| | - Wei Wang
- The Institute for Tissue Engineering and Regenerative Medicine, Stem Cell and Regenerative Medicine Laboratory, Liaocheng People's Hospital/Liaocheng University, Liaocheng, Shandong, China
| | - Fabin Han
- The Institute for Tissue Engineering and Regenerative Medicine, Stem Cell and Regenerative Medicine Laboratory, Liaocheng People's Hospital/Liaocheng University, Liaocheng, Shandong, China
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6
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Schomakers BV, Jillings SL, van Weeghel M, Vaz FM, Salomons GS, Janssens GE, Houtkooper RH. Ophthalmic acid is a glutathione regulating tripeptide. FEBS J 2024; 291:3317-3330. [PMID: 38245827 DOI: 10.1111/febs.17061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/30/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024]
Abstract
Since its discovery in 1958 in the lens of cows, ophthalmic acid (OPH) has stood in the shadow of its anti-oxidant analog: glutathione (GSH). Lacking the thiol group that gives GSH many of its important properties, ophthalmic acid's function has remained elusive, and it has been widely presumed to be an accidental product of the same enzymes. In this review, we compile evidence demonstrating that OPH is a ubiquitous metabolite found in bacteria, plants, fungi, and animals, produced through several layers of metabolic regulation. We discuss the limitations of the oft-repeated suggestions that aberrations in OPH levels should solely indicate GSH deficiency or oxidative stress. Finally, we discuss the available literature and suggest OPH's role in metabolism as a GSH-regulating tripeptide; controlling both cellular and organelle influx and efflux of GSH, as well as modulating GSH-dependent reactions and signaling. Ultimately, we hope that this review reinvigorates and directs more research into this versatile metabolite.
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Affiliation(s)
- Bauke V Schomakers
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC Location University of Amsterdam, The Netherlands
| | - Sonia L Jillings
- Green Biotechnology, Inholland University of Applied Sciences, Amsterdam, The Netherlands
| | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC Location University of Amsterdam, The Netherlands
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC Location University of Amsterdam, The Netherlands
| | - Gajja S Salomons
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, The Netherlands
| | - Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, The Netherlands
- Amsterdam Cardiovascular Sciences, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, The Netherlands
- Amsterdam Cardiovascular Sciences, The Netherlands
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7
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Sobh A, Encinas E, Patel A, Surapaneni G, Bonilla E, Kaestner C, Poullard J, Clerio M, Vasan K, Freeman T, Lv D, Dupéré-Richer D, Riva A, Barwick BG, Zhou D, Boise LH, Mitsiades CS, Kim B, Bennett RL, Chandel NS, Licht JD. NSD2 drives t(4;14) myeloma cell dependence on adenylate kinase 2 by diverting one-carbon metabolism to the epigenome. Blood 2024; 144:283-295. [PMID: 38598835 DOI: 10.1182/blood.2023022859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
ABSTRACT Chromosomal translocation (4;14), an adverse prognostic factor in multiple myeloma (MM), drives overexpression of the histone methyltransferase nuclear receptor binding SET domain protein 2 (NSD2). A genome-wide CRISPR screen in MM cells identified adenylate kinase 2 (AK2), an enzyme critical for high-energy phosphate transfer from the mitochondria, as an NSD2-driven vulnerability. AK2 suppression in t(4;14) MM cells decreased nicotinamide adenine dinucleotide phosphate (NADP[H]) critical for conversion of ribonucleotides to deoxyribonucleosides, leading to replication stress, DNA damage, and apoptosis. Driving a large genome-wide increase in chromatin methylation, NSD2 overexpression depletes S-adenosylmethionine, compromising the synthesis of creatine from its precursor, guanidinoacetate. Creatine supplementation restored NADP(H) levels, reduced DNA damage, and rescued AK2-deficient t(4;14) MM cells. As the creatine phosphate shuttle constitutes an alternative means for mitochondrial high-energy phosphate transport, these results indicate that NSD2-driven creatine depletion underlies the hypersensitivity of t(4;14) MM cells to AK2 loss. Furthermore, AK2 depletion in t(4;14) cells impaired protein folding in the endoplasmic reticulum, consistent with impaired use of mitochondrial adenosine triphosphate (ATP). Accordingly, AK2 suppression increased the sensitivity of MM cells to proteasome inhibition. These findings delineate a novel mechanism in which aberrant transfer of carbon to the epigenome creates a metabolic vulnerability, with direct therapeutic implications for t(4;14) MM.
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Affiliation(s)
- Amin Sobh
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Elena Encinas
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Alisha Patel
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Greeshma Surapaneni
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Emilie Bonilla
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Charlotte Kaestner
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Janai Poullard
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Monica Clerio
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Karthik Vasan
- Department of Medicine, Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Tzipporah Freeman
- Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Daphné Dupéré-Richer
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, The University of Florida, Gainesville, FL
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Richard L Bennett
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Navdeep S Chandel
- Department of Medicine, Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
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Hu H, Huang Y, Li A, Mi Q, Wang K, Chen L, Zhao Z, Zhang Q, Bai X, Pan H. Effects of different energy levels in low-protein diet on liver lipid metabolism in the late-phase laying hens through the gut-liver axis. J Anim Sci Biotechnol 2024; 15:98. [PMID: 38987834 PMCID: PMC11238517 DOI: 10.1186/s40104-024-01055-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/26/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND The energy/protein imbalance in a low-protein diet induces lipid metabolism disorders in late-phase laying hens. Reducing energy levels in the low-protein diet to adjust the energy-to-protein ratio may improve fat deposition, but this also decreases the laying performance of hens. This study investigated the mechanism by which different energy levels in the low-protein diet influences liver lipid metabolism in late-phase laying hens through the enterohepatic axis to guide feed optimization and nutrition strategies. A total of 288 laying hens were randomly allocated to the normal-energy and normal-protein diet group (positive control: CK) or 1 of 3 groups: low-energy and low-protein diet (LL), normal-energy and low-protein diet (NL), and high-energy and low-protein diet (HL) groups. The energy-to-protein ratios of the CK, LL, NL, and HL diets were 0.67, 0.74, 0.77, and 0.80, respectively. RESULTS Compared with the CK group, egg quality deteriorated with increasing energy intake in late-phase laying hens fed low-protein diet. Hens fed LL, NL, and HL diets had significantly higher triglyceride, total cholesterol, acetyl-CoA carboxylase, and fatty acid synthase levels, but significantly lower hepatic lipase levels compared with the CK group. Liver transcriptome sequencing revealed that genes involved in fatty acid beta-oxidation (ACOX1, HADHA, EHHADH, and ACAA1) were downregulated, whereas genes related to fatty acid synthesis (SCD, FASN, and ACACA) were upregulated in LL group compared with the CK group. Comparison of the cecal microbiome showed that in hens fed an LL diet, Lactobacillus and Desulfovibrio were enriched, whereas riboflavin metabolism was suppressed. Cecal metabolites that were most significantly affected by the LL diet included several vitamins, such as riboflavin (vitamin B2), pantethine (vitamin B5 derivative), pyridoxine (vitamin B6), and 4-pyridoxic acid. CONCLUSION A lipid metabolism disorder due to deficiencies of vitamin B2 and pantethine originating from the metabolism of the cecal microbiome may be the underlying reason for fat accumulation in the liver of late-phase laying hens fed an LL diet. Based on the present study, we propose that targeting vitamin B2 and pantethine (vitamin B5 derivative) might be an effective strategy for improving lipid metabolism in late-phase laying hens fed a low-protein diet.
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Affiliation(s)
- Hong Hu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Ying Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Anjian Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Qianhui Mi
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Kunping Wang
- College of Animal Science, Anhui Science and Technology University, Bengbu, 233000, China
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100193, China
| | - Zelong Zhao
- Shanghai BIOZERON Biotechnology Co., Ltd, Shanghai, 201800, China
| | - Qiang Zhang
- WOD Poultry Research Institute, Beijing, 100193, China
| | - Xi Bai
- College of Animal Science, Anhui Science and Technology University, Bengbu, 233000, China.
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
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9
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Song F, Qin Z, Qiu K, Huang Z, Wang L, Zhang H, Shan X, Meng H, Liu X, Zhou J. Development of a vitamin B 5 hyperproducer in Escherichia coli by multiple metabolic engineering. Metab Eng 2024; 84:158-168. [PMID: 38942195 DOI: 10.1016/j.ymben.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/06/2024] [Accepted: 06/14/2024] [Indexed: 06/30/2024]
Abstract
Vitamin B5 [D-pantothenic acid (D-PA)] is an essential water-soluble vitamin that is widely used in the food and feed industries. Currently, the relatively low fermentation efficiency limits the industrial application of D-PA. Here, a plasmid-free D-PA hyperproducer was constructed using systematic metabolic engineering strategies. First, pyruvate was enriched by deleting the non-phosphotransferase system, inhibiting pyruvate competitive branches, and dynamically controlling the TCA cycle. Next, the (R)-pantoate pathway was enhanced by screening the rate-limiting enzyme PanBC and regulating the other enzymes of this pathway one by one. Then, to enhance NADPH sustainability, NADPH regeneration was achieved through the novel "PEACES" system by (1) expressing the NAD + kinase gene ppnk from Clostridium glutamicum and the NADP + -dependent gapCcae from Clostridium acetobutyricum and (2) knocking-out the endogenous sthA gene, which interacts with ilvC and panE in the D-PA biosynthesis pathway. Combined with transcriptome analysis, it was found that the membrane proteins OmpC and TolR promoted D-PA efflux by increasing membrane fluidity. Strain PA132 produced a D-PA titer of 83.26 g/L by two-stage fed-batch fermentation, which is the highest D-PA titer reported so far. This work established competitive producers for the industrial production of D-PA and provided an effective strategy for the production of related products.
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Affiliation(s)
- Fuqiang Song
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhijie Qin
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Kun Qiu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Zhongshi Huang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Lian Wang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Heng Zhang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xiaoyu Shan
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Hao Meng
- Hunan Chengda Biotechnology Co., Ltd., Malukou, Anhua, Hunan, 413506, China
| | - Xirong Liu
- Hunan Chengda Biotechnology Co., Ltd., Malukou, Anhua, Hunan, 413506, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China.
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10
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Chi JT, Lin CC, Lin YT, Chen SY, Setayeshpour Y, Chen Y, Dunn D, Soderblom E, Zhang GF, Filonenko V, Jeong SY, Floyd S, Hayflick S, Gout I. Coenzyme A protects against ferroptosis via CoAlation of thioredoxin reductase 2. RESEARCH SQUARE 2024:rs.3.rs-4522617. [PMID: 38947036 PMCID: PMC11213209 DOI: 10.21203/rs.3.rs-4522617/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The Cystine-xCT transporter-Glutathione (GSH)-GPX4 axis is the canonical pathway to protect against ferroptosis. While not required for ferroptosis-inducing compounds (FINs) targeting GPX4, FINs targeting the xCT transporter require mitochondria and its lipid peroxidation to trigger ferroptosis. However, the mechanism underlying the difference between these FINs is still unknown. Given that cysteine is also required for coenzyme A (CoA) biosynthesis, here we show that CoA supplementation specifically prevents ferroptosis induced by xCT inhibitors but not GPX4 inhibitors. We find that, auranofin, a thioredoxin reductase inhibitor, abolishes the protective effect of CoA. We also find that CoA availability determines the enzymatic activity of thioredoxin reductase, but not thioredoxin. Importantly, the mitochondrial thioredoxin system, but not the cytosolic thioredoxin system, determines CoA-mediated ferroptosis inhibition. Our data show that the CoA regulates the in vitro enzymatic activity of mitochondrial thioredoxin reductase (TXNRD2) by covalently modifying the thiol group of cysteine (CoAlation) on Cys-483. Replacing Cys-483 with alanine on TXNRD2 abolishes its in vitro enzymatic activity and ability to protect cells from ferroptosis. Targeting xCT to limit cysteine import and, therefore, CoA biosynthesis reduced CoAlation on TXNRD2, an effect that was rescued by CoA supplementation. Furthermore, the fibroblasts from patients with disrupted CoA metabolism demonstrate increased mitochondrial lipid peroxidation. In organotypic brain slice cultures, inhibition of CoA biosynthesis leads to an oxidized thioredoxin system, mitochondrial lipid peroxidation, and loss in cell viability, which were all rescued by ferrostatin-1. These findings identify CoA-mediated post-translation modification to regulate the thioredoxin system as an alternative ferroptosis protection pathway with potential clinical relevance for patients with disrupted CoA metabolism.
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11
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Brahmachary P, Erdogan E, Myers E, June RK. Metabolomic Profiling and Characterization of a Novel 3D Culture System for Studying Chondrocyte Mechanotransduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598340. [PMID: 38915493 PMCID: PMC11195103 DOI: 10.1101/2024.06.10.598340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Articular chondrocytes synthesize and maintain the avascular and aneural articular cartilage. In vivo these cells are surrounded by a 3D pericellular matrix (PCM) containing predominantly collagen VI. The PCM protects chondrocytes and facilitates mechanotransduction, and PCM stiffness is critical in transmitting biomechanical signals to chondrocytes. Various culture systems with different hydrogels have been used to encapsulate chondrocytes for 3D culture, but many lack either the PCM or the in vivo stiffness of the cartilage matrix. Here, we demonstrate that primary chondrocytes cultured in alginate will form a pericellular matrix and display a phenotype similar to in vivo conditions. We found that primary human and bovine chondrocytes, when cultured in alginate beads with addition of sodium L-ascorbate for 7 days, had a pronounced PCM, retained their phenotype, and synthesized both collagens VI and II. This novel culture system enables alginate-encapsulated chondrocytes to develop a robust PCM thereby creating a model system to study mechanotransduction. We also observed distinct compression-induced changes in metabolomic profiles between the monolayer-agarose and alginate-released agarose-embedded chondrocytes indicating physiological changes in cell metabolism. Our data suggest that 3D preculture of chondrocytes in alginate before encapsulation in physiologically-stiff agarose leads to a pronounced development of pericellular matrix that is sustained in the presence of ascorbate. This novel model can be useful in studying the mechanism by which chondrocytes respond to cyclical compression and other types of loading simulating in vivo physiological conditions.
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Affiliation(s)
- Priyanka Brahmachary
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT 59717
| | - Ebru Erdogan
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT 59717
| | - Erik Myers
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT 59717
| | - Ronald K June
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT 59717
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT 59717
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12
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Cho H, Huh KM, Cho HJ, Kim B, Shim MS, Cho YY, Lee JY, Lee HS, Kwon YJ, Kang HC. Beyond nanoparticle-based oral drug delivery: transporter-mediated absorption and disease targeting. Biomater Sci 2024; 12:3045-3067. [PMID: 38712883 DOI: 10.1039/d4bm00313f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Various strategies at the microscale/nanoscale have been developed to improve oral absorption of therapeutics. Among them, gastrointestinal (GI)-transporter/receptor-mediated nanosized drug delivery systems (NDDSs) have drawn attention due to their many benefits, such as improved water solubility, improved chemical/physical stability, improved oral absorption, and improved targetability of their payloads. Their therapeutic potential in disease animal models (e.g., solid tumors, virus-infected lungs, metastasis, diabetes, and so on) has been investigated, and could be expanded to disease targeting after systemic/lymphatic circulation, although the detailed paths and mechanisms of endocytosis, endosomal escape, intracellular trafficking, and exocytosis through the epithelial cell lining in the GI tract are still unclear. Thus, this review summarizes and discusses potential GI transporters/receptors, their absorption and distribution, in vivo studies, and potential sequential targeting (e.g., oral absorption and disease targeting in organs/tissues).
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Affiliation(s)
- Hana Cho
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
| | - Kang Moo Huh
- Department of Polymer Science and Engineering & Materials Science and Engineering, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hyun Ji Cho
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
| | - Bogeon Kim
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
| | - Min Suk Shim
- Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Yong-Yeon Cho
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
- Regulated Cell Death (RCD) Control Material Research Institute, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Joo Young Lee
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
- Regulated Cell Death (RCD) Control Material Research Institute, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Hye Suk Lee
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
- Regulated Cell Death (RCD) Control Material Research Institute, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Young Jik Kwon
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Han Chang Kang
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
- Regulated Cell Death (RCD) Control Material Research Institute, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
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13
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Poljšak B, Milisav I. Decreasing Intracellular Entropy by Increasing Mitochondrial Efficiency and Reducing ROS Formation-The Effect on the Ageing Process and Age-Related Damage. Int J Mol Sci 2024; 25:6321. [PMID: 38928027 PMCID: PMC11203720 DOI: 10.3390/ijms25126321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
A hypothesis is presented to explain how the ageing process might be influenced by optimizing mitochondrial efficiency to reduce intracellular entropy. Research-based quantifications of entropy are scarce. Non-equilibrium metabolic reactions and compartmentalization were found to contribute most to lowering entropy in the cells. Like the cells, mitochondria are thermodynamically open systems exchanging matter and energy with their surroundings-the rest of the cell. Based on the calculations from cancer cells, glycolysis was reported to produce less entropy than mitochondrial oxidative phosphorylation. However, these estimations depended on the CO2 concentration so that at slightly increased CO2, it was oxidative phosphorylation that produced less entropy. Also, the thermodynamic efficiency of mitochondrial respiratory complexes varies depending on the respiratory state and oxidant/antioxidant balance. Therefore, in spite of long-standing theoretical and practical efforts, more measurements, also in isolated mitochondria, with intact and suboptimal respiration, are needed to resolve the issue. Entropy increases in ageing while mitochondrial efficiency of energy conversion, quality control, and turnover mechanisms deteriorate. Optimally functioning mitochondria are necessary to meet energy demands for cellular defence and repair processes to attenuate ageing. The intuitive approach of simply supplying more metabolic fuels (more nutrients) often has the opposite effect, namely a decrease in energy production in the case of nutrient overload. Excessive nutrient intake and obesity accelerate ageing, while calorie restriction without malnutrition can prolong life. Balanced nutrient intake adapted to needs/activity-based high ATP requirement increases mitochondrial respiratory efficiency and leads to multiple alterations in gene expression and metabolic adaptations. Therefore, rather than overfeeding, it is necessary to fine-tune energy production by optimizing mitochondrial function and reducing oxidative stress; the evidence is discussed in this paper.
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Affiliation(s)
- Borut Poljšak
- Laboratory of Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, SI-1000 Ljubljana, Slovenia;
| | - Irina Milisav
- Laboratory of Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, SI-1000 Ljubljana, Slovenia;
- Faculty of Medicine, Institute of Pathophysiology, University of Ljubljana, Zaloska 4, SI-1000 Ljubljana, Slovenia
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14
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Guimond AJ, Ke S, Tworoger SS, Huang T, Chan AT, Kubzansky LD, Liu YY. Fulfilled Mind, Healthy Gut? Relationships of Eudaimonic Psychological Well-Being With the Gut Microbiome in Postmenopausal Women. Psychosom Med 2024; 86:398-409. [PMID: 38345311 PMCID: PMC11142870 DOI: 10.1097/psy.0000000000001278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
OBJECTIVE Eudaimonic facets of psychological well-being (PWB), like purpose in life and sense of mastery, are associated with healthy aging. Variation in the gut microbiome may be one pathway by which mental health influences age-related health outcomes. However, associations between eudaimonic PWB and the gut microbiome are understudied. We examined whether purpose in life and sense of mastery, separately, were associated with features of the gut microbiome in older women. METHODS Participants were from the Mind-Body Study ( N = 206, mean age = 61 years), a substudy of the Nurses' Health Study II cohort. In 2013, participants completed the Life Engagement Test and the Pearlin Mastery Scale. Three months later, up to two pairs of stool samples were collected, 6 months apart. Covariates included sociodemographics, depression, health status, and health behaviors. Analyses examined associations of PWB with gut microbiome taxonomic diversity, overall community structure, and specific species/pathways. To account for multiple testing, statistical significance was established using Benjamini-Hochberg adjusted p values (i.e., q values ≤0.25). RESULTS We found no evidence of an association between PWB and gut microbiome alpha diversity. In multivariate analysis, higher purpose levels were significantly associated with lower abundance of species previously linked with poorer health outcomes, notably Blautia hydrogenotrophica and Eubacterium ventriosum ( q values ≤0.25). No significant associations were found between PWB and metabolic pathways. CONCLUSIONS These findings offer early evidence suggesting that eudaimonic PWB is linked with variation in the gut microbiome, and this might be one pathway by which PWB promotes healthy aging.
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Affiliation(s)
- Anne-Josee Guimond
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Lee Kum Sheung Center for Health and Happiness, Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Shelley S. Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Tianyi Huang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura D. Kubzansky
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Lee Kum Sheung Center for Health and Happiness, Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
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15
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Barritt SA, DuBois-Coyne SE, Dibble CC. Coenzyme A biosynthesis: mechanisms of regulation, function and disease. Nat Metab 2024; 6:1008-1023. [PMID: 38871981 DOI: 10.1038/s42255-024-01059-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/30/2024] [Indexed: 06/15/2024]
Abstract
The tricarboxylic acid cycle, nutrient oxidation, histone acetylation and synthesis of lipids, glycans and haem all require the cofactor coenzyme A (CoA). Although the sources and regulation of the acyl groups carried by CoA for these processes are heavily studied, a key underlying question is less often considered: how is production of CoA itself controlled? Here, we discuss the many cellular roles of CoA and the regulatory mechanisms that govern its biosynthesis from cysteine, ATP and the essential nutrient pantothenate (vitamin B5), or from salvaged precursors in mammals. Metabolite feedback and signalling mechanisms involving acetyl-CoA, other acyl-CoAs, acyl-carnitines, MYC, p53, PPARα, PINK1 and insulin- and growth factor-stimulated PI3K-AKT signalling regulate the vitamin B5 transporter SLC5A6/SMVT and CoA biosynthesis enzymes PANK1, PANK2, PANK3, PANK4 and COASY. We also discuss methods for measuring CoA-related metabolites, compounds that target CoA biosynthesis and diseases caused by mutations in pathway enzymes including types of cataracts, cardiomyopathy and neurodegeneration (PKAN and COPAN).
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Affiliation(s)
- Samuel A Barritt
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sarah E DuBois-Coyne
- Department of Medicine, Department of Biological Chemistry and Molecular Pharmacology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian C Dibble
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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16
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Hussein M, Mahboob MBH, Tait JR, Grace JL, Montembault V, Fontaine L, Quinn JF, Velkov T, Whittaker MR, Landersdorfer CB. Providing insight into the mechanism of action of cationic lipidated oligomers using metabolomics. mSystems 2024; 9:e0009324. [PMID: 38606960 PMCID: PMC11097639 DOI: 10.1128/msystems.00093-24] [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] [Received: 02/01/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
The increasing resistance of clinically relevant microbes against current commercially available antimicrobials underpins the urgent need for alternative and novel treatment strategies. Cationic lipidated oligomers (CLOs) are innovative alternatives to antimicrobial peptides and have reported antimicrobial potential. An understanding of their antimicrobial mechanism of action is required to rationally design future treatment strategies for CLOs, either in monotherapy or synergistic combinations. In the present study, metabolomics was used to investigate the potential metabolic pathways involved in the mechanisms of antibacterial activity of one CLO, C12-o-(BG-D)-10, which we have previously shown to be effective against methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300. The metabolomes of MRSA ATCC 43300 at 1, 3, and 6 h following treatment with C12-o-(BG-D)-10 (48 µg/mL, i.e., 3× MIC) were compared to those of the untreated controls. Our findings reveal that the studied CLO, C12-o-(BG-D)-10, disorganized the bacterial membrane as the first step toward its antimicrobial effect, as evidenced by marked perturbations in the bacterial membrane lipids and peptidoglycan biosynthesis observed at early time points, i.e., 1 and 3 h. Central carbon metabolism and the biosynthesis of DNA, RNA, and arginine were also vigorously perturbed, mainly at early time points. Moreover, bacterial cells were under osmotic and oxidative stress across all time points, as evident by perturbations of trehalose biosynthesis and pentose phosphate shunt. Overall, this metabolomics study has, for the first time, revealed that the antimicrobial action of C12-o-(BG-D)-10 may potentially stem from the dysregulation of multiple metabolic pathways.IMPORTANCEAntimicrobial resistance poses a significant challenge to healthcare systems worldwide. Novel anti-infective therapeutics are urgently needed to combat drug-resistant microorganisms. Cationic lipidated oligomers (CLOs) show promise as new antibacterial agents against Gram-positive pathogens like methicillin-resistant Staphylococcus aureus (MRSA). Understanding their molecular mechanism(s) of antimicrobial action may help design synergistic CLO treatments along with monotherapy. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of CLOs against MRSA. The results of our study indicate that the CLO, C12-o-(BG-D)-10, had a notable impact on the biosynthesis and organization of the bacterial cell envelope. C12-o-(BG-D)-10 also inhibits arginine, histidine, central carbon metabolism, and trehalose production, adding to its antibacterial characteristics. This work illuminates the unique mechanism of action of C12-o-(BG-D)-10 and opens an avenue to design innovative antibacterial oligomers/polymers for future clinical applications.
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Affiliation(s)
- Maytham Hussein
- Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Muhammad Bilal Hassan Mahboob
- Drug Delivery, Disposition, and Dynamics Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Jessica R. Tait
- Drug Delivery, Disposition, and Dynamics Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - James L. Grace
- Drug Delivery, Disposition, and Dynamics Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Véronique Montembault
- Institut des Molécules et Matériaux du Mans, UMR 6283 CNRS–Le Mans Université, Le Mans, France
| | - Laurent Fontaine
- Institut des Molécules et Matériaux du Mans, UMR 6283 CNRS–Le Mans Université, Le Mans, France
| | - John F. Quinn
- Drug Delivery, Disposition, and Dynamics Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Department of Chemical and Biological Engineering, Faculty of Engineering, Monash University, Clayton, Victoria, Australia
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Michael R. Whittaker
- Drug Delivery, Disposition, and Dynamics Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Cornelia B. Landersdorfer
- Drug Delivery, Disposition, and Dynamics Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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17
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Guden RM, Haegeman A, Ruttink T, Moens T, Derycke S. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach. Mol Ecol 2024; 33:e17331. [PMID: 38533629 DOI: 10.1111/mec.17331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.
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Affiliation(s)
- Rodgee Mae Guden
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Moens
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Oostende, Belgium
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18
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Carneiro T, Batista de Carvalho ALM, Vojtek M, Laginha RC, Marques MPM, Diniz C, Gil AM. Pd 2Spermine as an Alternative Therapeutics for Cisplatin-Resistant Triple-Negative Breast Cancer. J Med Chem 2024; 67:6839-6853. [PMID: 38590144 PMCID: PMC11056979 DOI: 10.1021/acs.jmedchem.4c00435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/25/2024] [Accepted: 04/02/2024] [Indexed: 04/10/2024]
Abstract
Cisplatin (cDDP) resistance is a matter of concern in triple-negative breast cancer therapeutics. We measured the metabolic response of cDDP-sensitive (S) and -resistant (R) MDA-MB-231 cells to Pd2Spermine(Spm) (a possible alternative to cDDP) compared to cDDP to investigate (i) intrinsic response/resistance mechanisms and (ii) the potential cytotoxic role of Pd2Spm. Cell extracts were analyzed by untargeted nuclear magnetic resonance metabolomics, and cell media were analyzed for particular metabolites. CDDP-exposed S cells experienced enhanced antioxidant protection and small deviations in the tricarboxylic acid cycle (TCA), pyrimidine metabolism, and lipid oxidation (proposed cytotoxicity signature). R cells responded more strongly to cDDP, suggesting a resistance signature of activated TCA cycle, altered AMP/ADP/ATP and adenine/uracil fingerprints, and phospholipid biosynthesis (without significant antioxidant protection). Pd2Spm impacted more markedly on R/S cell metabolisms, inducing similarities to cDDP/S cells (probably reflecting high cytotoxicity) and strong additional effects indicative of amino acid depletion, membrane degradation, energy/nucleotide adaptations, and a possible beneficial intracellular γ-aminobutyrate/glutathione-mediated antioxidant mechanism.
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Affiliation(s)
- Tatiana
J. Carneiro
- Department
of Chemistry and CICECO − Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
- Molecular
Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- LAQV/REQUIMTE,
Laboratory of Pharmacology, Department of Drug Sciences, Faculty of
Pharmacy, University of Porto, 4150-755 Porto, Portugal
| | | | - Martin Vojtek
- LAQV/REQUIMTE,
Laboratory of Pharmacology, Department of Drug Sciences, Faculty of
Pharmacy, University of Porto, 4150-755 Porto, Portugal
| | - Raquel C. Laginha
- Molecular
Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Maria Paula M. Marques
- Molecular
Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Department
of Life Sciences, Faculty of Science and Technology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Carmen Diniz
- LAQV/REQUIMTE,
Laboratory of Pharmacology, Department of Drug Sciences, Faculty of
Pharmacy, University of Porto, 4150-755 Porto, Portugal
| | - Ana M. Gil
- Department
of Chemistry and CICECO − Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
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19
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Welhaven HD, Viles E, Starke J, Wallace C, Bothner B, June RK, Hahn AK. Metabolomic profiles of cartilage and bone reflect tissue type, radiography-confirmed osteoarthritis, and spatial location within the joint. Biochem Biophys Res Commun 2024; 703:149683. [PMID: 38373382 DOI: 10.1016/j.bbrc.2024.149683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/21/2024]
Abstract
Osteoarthritis is the most common chronic joint disease, characterized by the abnormal remodeling of joint tissues including articular cartilage and subchondral bone. However, there are currently no therapeutic drug targets to slow the progression of disease because disease pathogenesis is largely unknown. Thus, the goals of this study were to identify metabolic differences between articular cartilage and subchondral bone, compare the metabolic shifts in osteoarthritic grade III and IV tissues, and spatially map metabolic shifts across regions of osteoarthritic hip joints. Articular cartilage and subchondral bone from 9 human femoral heads were obtained after total joint arthroplasty, homogenized and metabolites were extracted for liquid chromatography-mass spectrometry analysis. Metabolomic profiling revealed that distinct metabolic endotypes exist between osteoarthritic tissues, late-stage grades, and regions of the diseased joint. The pathways that contributed the most to these differences between tissues were associated with lipid and amino acid metabolism. Differences between grades were associated with nucleotide, lipid, and sugar metabolism. Specific metabolic pathways such as glycosaminoglycan degradation and amino acid metabolism, were spatially constrained to more superior regions of the femoral head. These results suggest that radiography-confirmed grades III and IV osteoarthritis are associated with distinct global metabolic and that metabolic shifts are not uniform across the joint. The results of this study enhance our understanding of osteoarthritis pathogenesis and may lead to potential drug targets to slow, halt, or reverse tissue damage in late stages of osteoarthritis.
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Affiliation(s)
- Hope D Welhaven
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT, 59717, United States.
| | - Ethan Viles
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT, 59717, United States.
| | - Jenna Starke
- Montana WWAMI, University of Washington School of Medicine, Seattle, WA, 98195, United States.
| | - Cameron Wallace
- Department of Orthopaedic Surgery, University of Utah Health, Salt Lake City, UT, 84103, United States.
| | - Brian Bothner
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT, 59717, United States.
| | - Ronald K June
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT, 59717, United States.
| | - Alyssa K Hahn
- Department of Biological and Environmental Sciences, Carroll College, Helena, MT, 59625, United States.
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20
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Zhang B, Zhang YQ, He ZL, Xiao YY, Tang MN, Zhou JP, Liu ZQ, Zheng YG. Engineered E. coli for D-pantothenic acid production with an acetolactate isomeroreductase mutant. 3 Biotech 2024; 14:117. [PMID: 38524241 PMCID: PMC10959892 DOI: 10.1007/s13205-024-03931-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/11/2024] [Indexed: 03/26/2024] Open
Abstract
D-Pantothenic acid, as a momentous vitamin, is extensively applied to feed, medicine, cosmetics and other fields. However, there are still limitations to produce D-pantothenic acid by microbial fermentation at present. In this paper, we constructed a recombinant strain for D-pantothenic acid production by blocking the organic acid pathway, boosting pyruvate biosynthesis, relieving feedback inhibition of acetolactate synthase, improving glucose intake capacity, and modifying essential genes in the metabolic pathway. In addition, a new acetolactate isomeroreductase mutant V412A origin from Escherichia coli (EcAHAIR) encoded by ilvC was obtained to explore its substrate promiscuity. Compared with the wild type, the variant EcAHAIR-V412A has reduced steric hindrance and enhanced intermolecular forces, resulting in a high affinity for 2-acetolactate. Eventually, the fermentation production of the final strain DPAN19/trc-ilvCV412A reached 4.65 g/L, increased by 192.5% compared with strain DPA8 in shake flask cultivation and produced 62.82 g/L D-pantothenic acid in a 5 L bioreactor. The metabolic engineering strategies and enzyme modification approaches described in this paper provide a particular perspective for the bio-manufacturing of D-pantothenic acid, branched-chain amino acids and its derivates.
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Affiliation(s)
- Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yu-Qiong Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Zhou-Lin He
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yun-Ying Xiao
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Meng-Na Tang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Jun-Ping Zhou
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
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21
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Sahu U, Villa E, Reczek CR, Zhao Z, O'Hara BP, Torno MD, Mishra R, Shannon WD, Asara JM, Gao P, Shilatifard A, Chandel NS, Ben-Sahra I. Pyrimidines maintain mitochondrial pyruvate oxidation to support de novo lipogenesis. Science 2024; 383:1484-1492. [PMID: 38547260 PMCID: PMC11325697 DOI: 10.1126/science.adh2771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 02/20/2024] [Indexed: 04/02/2024]
Abstract
Cellular purines, particularly adenosine 5'-triphosphate (ATP), fuel many metabolic reactions, but less is known about the direct effects of pyrimidines on cellular metabolism. We found that pyrimidines, but not purines, maintain pyruvate oxidation and the tricarboxylic citric acid (TCA) cycle by regulating pyruvate dehydrogenase (PDH) activity. PDH activity requires sufficient substrates and cofactors, including thiamine pyrophosphate (TPP). Depletion of cellular pyrimidines decreased TPP synthesis, a reaction carried out by TPP kinase 1 (TPK1), which reportedly uses ATP to phosphorylate thiamine (vitamin B1). We found that uridine 5'-triphosphate (UTP) acts as the preferred substrate for TPK1, enabling cellular TPP synthesis, PDH activity, TCA-cycle activity, lipogenesis, and adipocyte differentiation. Thus, UTP is required for vitamin B1 utilization to maintain pyruvate oxidation and lipogenesis.
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Affiliation(s)
- Umakant Sahu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Elodie Villa
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Colleen R Reczek
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Brendan P O'Hara
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Michael D Torno
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | | | | | - John M Asara
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Gao
- Metabolomics Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Navdeep S Chandel
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
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22
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Meliawati M, Volke DC, Nikel PI, Schmid J. Engineering the carbon and redox metabolism of Paenibacillus polymyxa for efficient isobutanol production. Microb Biotechnol 2024; 17:e14438. [PMID: 38529712 DOI: 10.1111/1751-7915.14438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Paenibacillus polymyxa is a non-pathogenic, Gram-positive bacterium endowed with a rich and versatile metabolism. However interesting, this bacterium has been seldom used for bioproduction thus far. In this study, we engineered P. polymyxa for isobutanol production, a relevant bulk chemical and next-generation biofuel. A CRISPR-Cas9-based genome editing tool facilitated the chromosomal integration of a synthetic operon to establish isobutanol production. The 2,3-butanediol biosynthesis pathway, leading to the main fermentation product of P. polymyxa, was eliminated. A mutant strain harbouring the synthetic isobutanol operon (kdcA from Lactococcus lactis, and the native ilvC, ilvD and adh genes) produced 1 g L-1 isobutanol under microaerobic conditions. Improving NADPH regeneration by overexpression of the malic enzyme subsequently increased the product titre by 50%. Network-wide proteomics provided insights into responses of P. polymyxa to isobutanol and revealed a significant metabolic shift caused by alcohol production. Glucose-6-phosphate 1-dehydrogenase, the key enzyme in the pentose phosphate pathway, was identified as a bottleneck that hindered efficient NADPH regeneration through this pathway. Furthermore, we conducted culture optimization towards cultivating P. polymyxa in a synthetic minimal medium. We identified biotin (B7), pantothenate (B5) and folate (B9) to be mutual essential vitamins for P. polymyxa. Our rational metabolic engineering of P. polymyxa for the production of a heterologous chemical sheds light on the metabolism of this bacterium towards further biotechnological exploitation.
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Affiliation(s)
- Meliawati Meliawati
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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23
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Chen SY, Lin CC, Wu J, Chen Y, Wang YE, Setayeshpour Y, Mestre A, Chi JT. NINJ1 regulates ferroptosis via xCT antiporter interaction and CoA modulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.581432. [PMID: 38464226 PMCID: PMC10925083 DOI: 10.1101/2024.02.22.581432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Ninjurin-1 (NINJ1), initially identified as a stress-induced protein in neurons, recently emerged as a key mediator of plasma membrane rupture during apoptosis, necrosis, and pyroptosis. However, its involvement in ferroptosis remains unknown. Here, we demonstrate that NINJ1 also plays a crucial role in ferroptosis, but through a distinct mechanism. NINJ1 knockdown significantly protected cancer cells against ferroptosis induced by xCT inhibitors but no other classes of ferroptosis-inducing compounds (FINs). Glycine, known to inhibit canonical NINJ1-mediated membrane rupture in other cell deaths, had no impact on ferroptosis. A compound screen revealed that NINJ1-mediated ferroptosis protection can be abolished by pantothenate kinase inhibitor (PANKi), buthionine sulfoximine (BSO), and diethylmaleate (DEM). These results suggest that this ferroptosis protection is mediated via Coenzyme A (CoA) and glutathione (GSH), both of which were found to be elevated upon NINJ1 knockdown. Furthermore, we discovered that NINJ1 interacts with the xCT antiporter, which is responsible for cystine uptake for the biosynthesis of CoA and GSH. The removal of NINJ1 increased xCT levels and stability, enhanced cystine uptake, and contributed to elevated CoA and GSH levels, collectively contributing to ferroptosis protection. These findings reveal that NINJ1 regulates ferroptosis via a non-canonical mechanism, distinct from other regulated cell deaths.
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Affiliation(s)
- Ssu-Yu Chen
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chao-Chieh Lin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jianli Wu
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yubin Chen
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ya-En Wang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yasaman Setayeshpour
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alexander Mestre
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC 27710, USA
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24
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Brown KL, Krekhno JMC, Xing S, Huan T, Eltis LD. Cholesterol-Mediated Coenzyme A Depletion in Catabolic Mutants of Mycobacteria Leads to Toxicity. ACS Infect Dis 2024; 10:107-119. [PMID: 38054469 DOI: 10.1021/acsinfecdis.3c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Cholesterol is a critical growth substrate for Mycobacterium tuberculosis (Mtb) during infection, and the cholesterol catabolic pathway has been targeted for the development of new antimycobacterial agents. A key metabolite in cholesterol catabolism is 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP). Many of the HIP metabolites are acyl-coenzyme A (CoA) thioesters, whose accumulation in deletion mutants can cause cholesterol-mediated toxicity. We used LC-MS/MS analysis to demonstrate that deletion of genes involved in HIP catabolism leads to acyl-CoA accumulation with concomitant depletion of free CoASH, leading to dysregulation of central metabolic pathways. CoASH and acyl-CoAs inhibited PanK, the enzyme that catalyzes the first step in the transformation of pantothenate to CoASH. Inhibition was competitive with respect to ATP with Kic values ranging from 9 μM for CoASH to 57 μM for small acyl-CoAs and 180 ± 30 μM for cholesterol-derived acyl-CoA. These findings link two critical metabolic pathways and suggest that therapeutics targeting cholesterol catabolic enzymes could both prevent the utilization of an important growth substrate and simultaneously sequester CoA from essential cellular processes, leading to bacterial toxicity.
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Affiliation(s)
- Kirstin L Brown
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Jessica M C Krekhno
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Shipei Xing
- Department of Chemistry, The University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Tao Huan
- Department of Chemistry, The University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
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25
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Xu Y, Guan X, Wang S. Synergistic bactericidal mechanisms of RF energy simultaneously combined with cinnamon essential oil or epsilon-polylysine against Salmonella revealed at cellular and metabolic levels. Int J Food Microbiol 2024; 408:110447. [PMID: 37907022 DOI: 10.1016/j.ijfoodmicro.2023.110447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/13/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023]
Abstract
Radio frequency (RF) heating and antimicrobials are considered to be effective methods for inactivating food pathogens. This study explored the bactericidal effects against Salmonella of RF heating combined with two kinds of natural antimicrobials possessing different hydrophobic properties and their synergistic bactericidal mechanisms. Results showed that RF heating caused sublethal damage to bacterial cells and enhanced the interaction of cells and antimicrobials, leading to synergistic bactericidal effects of the simultaneous combination of RF heating and antimicrobials. The combination of RF heating and ε-polylysine (ε-PL) further promoted cell morphological alteration, raised membrane permeability, intracellular adenosine triphosphate (ATP) leakage and intracellular reactive oxygen species (ROS) accumulation compared to individual treatment. The simultaneous combination of RF heating and cinnamon essential oil nanoemulsion (CEON) also further enhanced membrane permeability and ROS accumulation compared to individual treatment, but impacts were less than those in the combination of RF heating and ε-PL. The major synergistic bactericidal mechanism of RF heating and CEON was significantly inhibiting intracellular ATP synthesis. The untargeted metabolomics analysis revealed that the combined treatments enhanced disturbances to multiple intracellular metabolisms compared to individual treatment, thus leading to synergistic bactericidal effects against Salmonella. These results provide an in-depth understanding of the synergistic bactericidal mechanisms of the combination of RF heating and natural antimicrobials from cellular and metabolic levels.
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Affiliation(s)
- Yuanmei Xu
- College of Biological and Food Engineering, Changshu Institute of Technology, 99 South Third Ring Road, Changshu 215500, China
| | - Xiangyu Guan
- College of Food Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Shaojin Wang
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling 712100, China; Washington State University, Department of Biological Systems Engineering, Pullman, WA 99164-6120, USA.
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26
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Bacigalupa ZA, Landis MD, Rathmell JC. Nutrient inputs and social metabolic control of T cell fate. Cell Metab 2024; 36:10-20. [PMID: 38118440 PMCID: PMC10872404 DOI: 10.1016/j.cmet.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/25/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023]
Abstract
Cells in multicellular organisms experience diverse neighbors, signals, and evolving physical environments that drive functional and metabolic demands. To maintain proper development and homeostasis while avoiding inappropriate cell proliferation or death, individual cells interact with their neighbors via "social" cues to share and partition available nutrients. Metabolic signals also contribute to cell fate by providing biochemical links between cell-extrinsic signals and available resources. In addition to metabolic checkpoints that sense nutrients and directly supply molecular intermediates for biosynthetic pathways, many metabolites directly signal or provide the basis for post-translational modifications of target proteins and chromatin. In this review, we survey the landscape of T cell nutrient sensing and metabolic signaling that supports proper immunity while avoiding immunodeficiency or autoimmunity. The integration of cell-extrinsic microenvironmental cues with cell-intrinsic metabolic signaling provides a social metabolic control model to integrate cell signaling, metabolism, and fate.
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Affiliation(s)
- Zachary A Bacigalupa
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madelyn D Landis
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey C Rathmell
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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27
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Zhao D, Zhuang W, Wang Y, Xu X, Qiao L. In-depth mass spectrometry analysis of rhGH administration altered energy metabolism and steroidogenesis. Talanta 2024; 266:125069. [PMID: 37574608 DOI: 10.1016/j.talanta.2023.125069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Growth hormone, as a proteohormone, is primarily known of its dramatic effect on longitudinal growth. Recombinant DNA technology has provided a safe, abundant and comparatively cheap supply of human GH for growth hormone-deficient individuals. However, many healthy subjects, especially athletics, administrate GH for enhanced athletic performance or strength. A better and more comprehensive understanding of rhGH effect in healthy individuals is urgent and essential. In this study, we recruited 14 healthy young male and injected rhGH once. Untargeted LC-MS metabolomics profiling of serum and urine was performed before and after the rhGH injection. The GH-induced dysregulation of energy related pathways, such as amino acid metabolism, nucleotide metabolism, glycolysis and TCA cycle, was revealed. Moreover, individuals supplemented with micro-doses of rhGH exhibited significantly changed urinary steroidal profiles, suggesting a role of rhGH in both energy metabolism and steroidogenesis. We expect that our results will be helpful to provide new evidence on the effects of rhGH injection and provide potential biomarkers for rhGH administration.
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Affiliation(s)
- Dan Zhao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Wenqian Zhuang
- Research Institute for Doping Control, Shanghai University of Sport, Shanghai, 200000, China
| | - Yang Wang
- Research Institute for Doping Control, Shanghai University of Sport, Shanghai, 200000, China
| | - Xin Xu
- Research Institute for Doping Control, Shanghai University of Sport, Shanghai, 200000, China.
| | - Liang Qiao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China.
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28
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George N, Joshi MB, Satyamoorthy K. DNA damage-induced senescence is associated with metabolomic reprogramming in breast cancer cells. Biochimie 2024; 216:71-82. [PMID: 37758157 DOI: 10.1016/j.biochi.2023.09.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023]
Abstract
Senescence due to exogenous and endogenous stresses triggers metabolic reprogramming and is associated with many pathologies, including cancer. In solid tumors, senescence promotes tumorigenesis, facilitates relapse, and changes the outcomes of anti-cancer therapies. Hence, cellular and molecular mechanisms regulating senescent pathways make attractive therapeutic targets. Cancer cells undergo metabolic reprogramming to sustain the growth-arrested state of senescence. In the present study, we aimed to understand the metabolic reprogramming in MCF-7 breast tumor cells in response to two independent inducers of DNA damage-mediated senescence, including ionizing radiation and doxorubicin. Increased DNA double-strand breaks, as demonstrated by γH2AX staining, showed a senescence phenotype, with expression of senescence-associated β-galactosidase accompanied by the upregulation of p21 and p16 in both groups. Further, untargeted analysis of the senescence-related extracellular metabolome profile of MCF-7 cells showed significantly reduced concentrations of carnitine and pantothenic acid and increased levels of S-adenosylhomocysteine in doxorubicin-treated cells, indicating the accumulation of ROS mediated DNA damage and impaired mitochondrial membrane potential. Similarly, a significant decline in the creatine level was observed in radiation-exposed cells, suggesting an increase in oxidative stress-mediated DNA damage. Our study, therefore, provides key effectors of the metabolic changes in doxorubicin and radiation-induced early senescence in MCF-7 breast cancer cells.
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Affiliation(s)
- Neena George
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576 104, India.
| | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576 104, India.
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576 104, India; Shri Dharmasthala Manjunatheshwara (SDM) University, SDM College of Medical Sciences and Hospital, Manjushree Nagar, Sattur, Dharwad, 580009, Karnataka, India.
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29
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Dai H, Xu L, Jiang M, Zhang W, Han Q. Comparative proteomic analysis of the protein profile in the cuttlefish Sepia pharaonis associated with skin ulceration syndrome. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109265. [PMID: 38040138 DOI: 10.1016/j.fsi.2023.109265] [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: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Skin ulceration syndrome (SUS) is becoming a severe problem in the breeding and culturing process of the cuttlefish Sepia pharaonis. However, limited knowledge is available about the occurrence of this devastating disease. In this study, proteomic analysis was used to identify the differentially expressed proteins (DEPs) and the biological pathways enriched in SUS-diseased S. pharaonis. Both the healthy group and diseased group were analyzed in triplicate, with 4 cuttlefish in each replicate. The results showed that 85 DEPs were identified between the two groups, including 36 upregulated proteins and 49 downregulated proteins in the diseased group compared to the healthy group. GO enrichment analysis revealed that the DEPs were mainly enriched in cellular component organization or biogenesis, nucleus and ion binding processes. The results of the KEGG pathway analysis indicated that extracellular matrix (ECM)-receptor interaction was the most enriched upregulated pathway. Real-time reverse transcriptase PCR was used to identify the expression of two differentially expressed matrix metalloproteinases (MMPs), and the results showed that the mRNA expression of MMP14 and MMP19 was significantly upregulated in the skin tissue of the diseased group. Furthermore, the protease activity of the diseased group was higher than that of the healthy group. Our results offer basic knowledge on the changes in protein profiles during the occurrence of SUS in the cuttlefish S. pharaonis.
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Affiliation(s)
- Haijuan Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315832, PR China
| | - Liting Xu
- School of Marine Sciences, Ningbo University, Ningbo, 315832, PR China
| | - Maowang Jiang
- School of Marine Sciences, Ningbo University, Ningbo, 315832, PR China
| | - Weiwei Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315832, PR China
| | - Qingxi Han
- School of Marine Sciences, Ningbo University, Ningbo, 315832, PR China.
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Bircher L, Sourabié AM, Paurevic M, Hochuli J, Geirnaert A, Navas C, Drogue B, Lacroix C. Faecalibacterium duncaniae A2-165 growth is strongly promoted by yeast extract and vitamin B5 in cGMP medium. Microb Biotechnol 2024; 17:e14374. [PMID: 38019136 PMCID: PMC10832529 DOI: 10.1111/1751-7915.14374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023] Open
Abstract
Several gut microbial species within the Faecalibacterium genus have emerged as promising next-generation probiotics (NGP) due to their multifunctional protective effects against gastrointestinal and systemic disorders. To enable clinical studies and further applications, improved methods for cultivating Faecalibacterium must be developed in compliance with current Good Manufacturing Practice regulations, which is complicated by its oxygen sensitivity and complex nutritional requirements. Different yeast-based nutrients (YBNs), including yeast extracts (YEs) and yeast peptones (YPs), are ubiquitously used when cultivating microbes to supply a broad range of macro- and micronutrients. In this study, we evaluated six experimental YBNs, namely three YEs, two YPs and a yeast cell wall product (YCW), and eight B-vitamins in the cultivation of Faecalibacterium duncaniae A2-165, former Faecalibacterium prausnitzii, using growth assays in microtitre plates, dose-effect studies in Hungate tube fermentations and fully controlled bioreactor experiments. We demonstrated that YEs promote F. duncaniae A2-165 growth in a nutritionally limited medium, while YPs and YCW lacked essential growth factors for enabling cell propagation. High cell density was obtained in controlled bioreactors using a medium containing 2-4% of a selected YE and 1% casein peptone (3.4 ± 1.7 × 109 -5.1 ± 1.3 × 109 cells mL-1 ). Among all tested B-vitamins, we identified B5 as a strong growth promoter. Replacing casein peptone with YP and supplementing with vitamin B5 further increased biomass by approximately 50% (6.8 ± 1.7 × 109 cells mL-1 ). Hence, empirical selection of YE, YP and B5 allowed formulation of a high-yielding animal allergen-free nutritive medium to produce F. duncaniae A2-165. Selecting nutritionally suitable YBNs and combining these with other key nutrients are important steps for optimizing production of NGP with high yields and lower cost.
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Affiliation(s)
- Lea Bircher
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Alain M. Sourabié
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Marijana Paurevic
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Janina Hochuli
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Annelies Geirnaert
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Chloé Navas
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Benoît Drogue
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Christophe Lacroix
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
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Li J, Chen Z, Bai Y, Wei Y, Guo D, Liu Z, Niu Y, Shi B, Zhang X, Cai Y, Zhao Z, Hu J, Wang J, Liu X, Li S, Zhao F. Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak. Int J Mol Sci 2023; 25:158. [PMID: 38203329 PMCID: PMC10779322 DOI: 10.3390/ijms25010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (ANKRD2, ANKRD1, BTG2 and LMOD3) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Sanchez-Rodriguez L, Galvez-Fernandez M, Rojas-Benedicto A, Domingo-Relloso A, Amigo N, Redon J, Monleon D, Saez G, Tellez-Plaza M, Martin-Escudero JC, Ramis R. Traffic Density Exposure, Oxidative Stress Biomarkers and Plasma Metabolomics in a Population-Based Sample: The Hortega Study. Antioxidants (Basel) 2023; 12:2122. [PMID: 38136241 PMCID: PMC10740723 DOI: 10.3390/antiox12122122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Exposure to traffic-related air pollution (TRAP) generates oxidative stress, with downstream effects at the metabolic level. Human studies of traffic density and metabolomic markers, however, are rare. The main objective of this study was to evaluate the cross-sectional association between traffic density in the street of residence with oxidative stress and metabolomic profiles measured in a population-based sample from Spain. We also explored in silico the potential biological implications of the findings. Secondarily, we assessed the contribution of oxidative stress to the association between exposure to traffic density and variation in plasma metabolite levels. Traffic density was defined as the average daily traffic volume over an entire year within a buffer of 50 m around the participants' residence. Plasma metabolomic profiles and urine oxidative stress biomarkers were measured in samples from 1181 Hortega Study participants by nuclear magnetic resonance spectroscopy and high-performance liquid chromatography, respectively. Traffic density was associated with 7 (out of 49) plasma metabolites, including amino acids, fatty acids, products of bacterial and energy metabolism and fluid balance metabolites. Regarding urine oxidative stress biomarkers, traffic associations were positive for GSSG/GSH% and negative for MDA. A total of 12 KEGG pathways were linked to traffic-related metabolites. In a protein network from genes included in over-represented pathways and 63 redox-related candidate genes, we observed relevant proteins from the glutathione cycle. GSSG/GSH% and MDA accounted for 14.6% and 12.2% of changes in isobutyrate and the CH2CH2CO fatty acid moiety, respectively, which is attributable to traffic exposure. At the population level, exposure to traffic density was associated with specific urine oxidative stress and plasma metabolites. Although our results support a role of oxidative stress as a biological intermediary of traffic-related metabolic alterations, with potential implications for the co-bacterial and lipid metabolism, additional mechanistic and prospective studies are needed to confirm our findings.
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Affiliation(s)
- Laura Sanchez-Rodriguez
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, 28029 Madrid, Spain; (L.S.-R.); (A.D.-R.); (R.R.)
- Joint Research Institute-National School of Health (IMIENS), National Distance Education University, 28029 Madrid, Spain
| | - Marta Galvez-Fernandez
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, 28029 Madrid, Spain; (L.S.-R.); (A.D.-R.); (R.R.)
| | - Ayelén Rojas-Benedicto
- Joint Research Institute-National School of Health (IMIENS), National Distance Education University, 28029 Madrid, Spain
- Department of Communicable Diseases, National Center for Epidemiology, Instituto de Salud Carlos III, 28029 Madrid, Spain
- CIBER on Epidemiology and Public Health, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Arce Domingo-Relloso
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, 28029 Madrid, Spain; (L.S.-R.); (A.D.-R.); (R.R.)
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Nuria Amigo
- Biosfer Teslab, 43201 Reus, Spain;
- Department of Basic Medical Sciences, Universidad de Rovira i Virgili, 43007 Tarragona, Spain
| | - Josep Redon
- Institute for Biomedical Research, Hospital Clinic de Valencia (INCLIVA), 46010 Valencia, Spain
| | - Daniel Monleon
- Institute for Biomedical Research, Hospital Clinic de Valencia (INCLIVA), 46010 Valencia, Spain
| | - Guillermo Saez
- Department of Biochemistry and Molecular Biology, Faculty of Medicine and Dentistry, Clinical Analysis Service, Hospital Universitario Dr. Peset-FISABIO, Universitat de Valencia, 46020 Valencia, Spain;
| | - Maria Tellez-Plaza
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, 28029 Madrid, Spain; (L.S.-R.); (A.D.-R.); (R.R.)
| | - Juan Carlos Martin-Escudero
- Department of Internal Medicine, Hospital Universitario Rio Hortega, University of Valladolid, 47012 Valladolid, Spain;
| | - Rebeca Ramis
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, 28029 Madrid, Spain; (L.S.-R.); (A.D.-R.); (R.R.)
- CIBER on Epidemiology and Public Health, Instituto de Salud Carlos III, 28029 Madrid, Spain
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Lyu Y, Xu J, Verdoodt F, Vanhaecke L, Hemeryck LY, Hesta M. Faecal metabolome responses to an altered dietary protein:carbohydrate ratio in adult dogs. Vet Q 2023; 43:1-10. [PMID: 37869782 PMCID: PMC10614716 DOI: 10.1080/01652176.2023.2273891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023] Open
Abstract
High-protein diets may aid weight loss and weight maintenance programs in both humans and dogs, although the effect of dietary protein levels on gut metabolism and functionality has not been studied in depth. The current study aimed to investigate the effect of an altered dietary protein:carbohydrate ratio on gut function in adult dogs by means of faecal metabolomic fingerprinting. More specifically, functional metabolic differences in dogs fed a high-protein/low-carbohydrate (HPLC) vs. low-protein/high-carbohydrate (LPHC) diet were studied by equally allocating twelve clinically healthy (6 lean and 6 obese) Beagles into two groups in a cross-over design, with each group receiving two isocaloric diets for four weeks. The faecal metabolome revealed that different protein:carbohydrate ratio can influence host and/or gut microbiome metabolism and function, while no effect was observed on the body condition. Targeted analysis demonstrated that the HPLC diet significantly increased the concentration of indole, spermidine, and pipecolinic acid and decreased the concentration of azelaic acid, D-fructose, mannose, and galactose (p < 0.05). Multivariate modelling (OPLS-DA) of the untargeted faecal metabolome revealed distinctly different metabolomic profiles following the HPLC vs. LPHC diet, with 18 altered pathways. The HPLC diet influenced amino acid and lipid metabolism, potentially promoting weight loss and immune function, whereas the LPHC diet affected carbohydrate fermentation and may promote anti-oxidative function.
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Affiliation(s)
- Yang Lyu
- ECAN Equine and Companion Animal Nutrition, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Jia Xu
- ECAN Equine and Companion Animal Nutrition, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Fien Verdoodt
- ECAN Equine and Companion Animal Nutrition, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Lynn Vanhaecke
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Lieselot Y. Hemeryck
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Myriam Hesta
- ECAN Equine and Companion Animal Nutrition, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Li T, Chen H, Xu B, Yu M, Li J, Shi Y, Xia S, Wu S. Deciphering the interplay between LPS/TLR4 pathways, neurotransmitter, and deltamethrin-induced depressive-like behavior: Perspectives from the gut-brain axis. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 197:105697. [PMID: 38072552 DOI: 10.1016/j.pestbp.2023.105697] [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: 08/28/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
The improper use of deltamethrin (DM) can result in its accumulation in soil, water, food, and even the human body, which is associated with an elevated risk of neurotoxicity and behavioral abnormalities; however, the underlying mechanisms remain insufficiently investigated. Emerging evidence underscores the significance of the gut-brain axis in central nervous system (CNS) dysfunctions. Accordingly, this study investigates the role of the gut-brain axis in DM-induced behavioral anomalies in mice. The results showed that DM exposure induced depressive-like behavior, and the hippocampus, the region that is responsible for the modulation of emotional behavior, showed structural integrity disrupted (neuronal nuclear shrinkage and decreased tight junction protein expression). In addition, DM exposure led to compromised gut barrier integrity (disruptions on crypt surfaces and decreased tight junction protein expression), which might contribute to the gut bacterial-derived lipopolysaccharide (LPS) leakage into the bloodstream and reaching the brain, triggering LPS/toll-like receptor (TLR) 4 -mediated increases in brain pro-inflammatory cytokines. Subsequently, we observed a disturbance in neurotransmitter metabolic pathways following DM exposure, which inhibited the production of 5-hydroxytryptamine (5-HT). Additionally, DM exposure resulted in gut microbiota dysbiosis. Characteristic bacteria, such as Alistipes, Bifidobacterium, Gram-negative bacterium cTPY-13, and Odoribacter exhibited significant correlations with behavior, tight junction proteins, inflammatory response, and neurotransmitters. Further fecal microbiota transplantation (FMT) experiments suggested that DM-induced gut microbiota dysbiosis might contribute to depressive-like behavior. These results provide a new perspective on the toxicity mechanism of DM, indicating that its neurotoxicity may be partially regulated by the microbiota-gut-brain axis.
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Affiliation(s)
- Tongtong Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hao Chen
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Baohua Xu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Mengwei Yu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jun Li
- Jiangxi Key Laboratory of Natural Product and Functional Food, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ying Shi
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Shaohui Xia
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Shijin Wu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
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35
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Zhao K, Tang H, Zhang B, Zou S, Liu Z, Zheng Y. Microbial production of vitamin B5: current status and prospects. Crit Rev Biotechnol 2023; 43:1172-1192. [PMID: 36210178 DOI: 10.1080/07388551.2022.2104690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 07/01/2022] [Indexed: 11/03/2022]
Abstract
Vitamin B5, also called D-pantothenic acid (D-PA), is a necessary micronutrient that plays an essential role in maintaining the physiological function of an organism. It is widely used in: food, medicine, feed, cosmetics, and other fields. Currently, the production of D-PA in industry heavily relies on chemical processes and enzymatic catalysis. With an increasing demand on the market, replacing chemical-based production of D-PA with microbial fermentation utilizing renewable resources is necessary. In this review, the physiological role and applications of D-PA were firstly introduced, after which the biosynthesis pathways and enzymes will be summarized. Subsequently, a series of cell factory development strategies for excessive D-PA production are analyzed and discussed. Finally, the prospect of microbial production of D-PA production has been prospected.
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Affiliation(s)
- Kuo Zhao
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Heng Tang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Bo Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Shuping Zou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Zhiqiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Yuguo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
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36
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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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37
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Khan S, Kumar Y, Sharma C, Gupta SK, Goel A, Aggarwal R, Veerapu NS. Dysregulated metabolites and lipids in serum of patients with acute hepatitis E: A longitudinal study. J Viral Hepat 2023; 30:959-969. [PMID: 37697495 DOI: 10.1111/jvh.13885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 07/17/2023] [Accepted: 08/21/2023] [Indexed: 09/13/2023]
Abstract
Hepatitis E is a disease associated with acute inflammation of the liver. It is related to several dysregulated metabolic pathways and alterations in the concentration of several metabolites. However, longitudinal analysis of the alterations in metabolites and lipids is generally lacking. This study investigated the changes in levels of metabolites and lipids over time in sera from men with acute hepatitis E compared to healthy controls similar in age and gender. Untargeted measurement of levels of various metabolites and lipids was done using mass spectrometry on 65 sera sequentially sampled from 14 patients with acute hepatitis E and 25 serum samples from five controls. Temporal changes in intensities of metabolites and lipids were determined over different times at 3-day periods for the hepatitis E virus (HEV) group. In carbohydrate metabolism, glucose levels, fructose 1-6-bisphosphate and ribulose-5-phosphate were increased in the HEV-infected persons compared to the healthy controls. HEV infection is significantly associated with decreased levels of inosine, guanosine, adenosine and urate in purine metabolism and thymine, uracil and β-aminoisobutyrate in pyrimidine metabolism. Glutamate, alanine and valine levels were significantly lower in the HEV group than in healthy individuals. Homogentisate of tyrosine metabolism and cystathionine of serine metabolism were increased, whereas kynurenate of tryptophan metabolism decreased in the HEV group. Metabolites of the bile acid biosynthesis, urea cycle (arginine and citrulline) and ammonia recycling (urocanate) were significantly altered. Co-enzymes, pantothenate and pyridoxal, and co-factors, lipoamide and FAD, were elevated in the HEV group. The acylcarnitines, sphingomyelins, phosphatidylcholine (PC), phosphatidylethanolamine (PE), lysoPC and lysoPE tended to be lower in the HEV group. In conclusion, acute hepatitis E is associated with altered metabolite and lipid profiles, significantly increased catabolism of carbohydrates, purines/pyrimidines and amino acids, and decreased levels of several glycerophospholipids.
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Affiliation(s)
- Shaheen Khan
- Virology Section, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Charu Sharma
- Department of Mathematics, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, India
| | - Sonu Kumar Gupta
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Amit Goel
- Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Rakesh Aggarwal
- Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Naga Suresh Veerapu
- Virology Section, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, India
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Zhan T, Wu Y, Deng X, Li Q, Chen Y, Lv J, Wang J, Li S, Wu Z, Liu D, Tang Z. Multi-omics approaches reveal the molecular mechanisms underlying the interaction between Clonorchis sinensis and mouse liver. Front Cell Infect Microbiol 2023; 13:1286977. [PMID: 38076459 PMCID: PMC10710275 DOI: 10.3389/fcimb.2023.1286977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction Clonorchiasis remains a serious global public health problem, causing various hepatobiliary diseases. However, there is still a lack of overall understanding regarding the molecular events triggered by Clonorchis sinensis (C. sinensis) in the liver. Methods BALB/c mouse models infected with C. sinensis for 5, 10, 15, and 20 weeks were constructed. Liver pathology staining and observation were conducted to evaluate histopathology. The levels of biochemical enzymes, blood routine indices, and cytokines in the blood were determined. Furthermore, alterations in the transcriptome, proteome, and metabolome of mouse livers infected for 5 weeks were analyzed using multi-omics techniques. Results The results of this study indicated that adult C. sinensis can cause hepatosplenomegaly and liver damage, with the most severe symptoms observed at 5 weeks post-infection. However, as the infection persisted, the Th2 immune response increased and symptoms were relieved. Multi-omics analysis of liver infected for 5 weeks identified 191, 402 and 232 differentially expressed genes (DEGs), proteins (DEPs) and metabolites (DEMs), respectively. Both DEGs and DEPs were significantly enriched in liver fibrosis-related pathways such as ECM-receptor interaction and cell adhesion molecules. Key molecules associated with liver fibrosis and inflammation (Cd34, Epcam, S100a6, Fhl2, Itgax, and Retnlg) were up-regulated at both the gene and protein levels. The top three metabolic pathways, namely purine metabolism, arachidonic acid metabolism, and ABC transporters, were associated with liver cirrhosis, fibrosis, and cholestasis, respectively. Furthermore, metabolites that can promote liver inflammation and fibrosis, such as LysoPC(P-16:0/0:0), 20-COOH-leukotriene E4, and 14,15-DiHETrE, were significantly up-regulated. Conclusion Our study revealed that the most severe symptoms in mice infected with C. sinensis occurred at 5 weeks post-infection. Moreover, multi-omics analysis uncovered predominant molecular events related to fibrosis changes in the liver. This study not only enhances our understanding of clonorchiasis progression but also provides valuable insights into the molecular-level interaction mechanism between C. sinensis and its host liver.
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Affiliation(s)
- Tingzheng Zhan
- Department of Parasitology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yuhong Wu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Xueling Deng
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Qing Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Medical University, Nanning, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yu Chen
- Schistosomiasis Prevention and Control Department, Hengzhou Center for Disease Control and Prevention, Hengzhou, China
| | - Jiahui Lv
- Department of Parasitology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Jilong Wang
- Department of Parasitology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Shitao Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Zhanshuai Wu
- Department of Immunology, Guangxi University of Chinese Medicine, Nanning, China
- Guangxi Key Laboratory of Translational Medicine for treating High-Incidence Infectious Diseases with Integrative Medicine, Nanning, China
| | - Dengyu Liu
- Department of Parasitology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Medical University, Nanning, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zeli Tang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Medical University, Nanning, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
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Kanhai AA, Sánchez-López E, Kuipers TB, van Klinken JB, Dijkstra KL, van der Veen I, Baelde HJ, Song X, Pei Y, Mei H, Leonhard WN, Mayboroda OA, Peters DJ. Short salsalate administration affects cell proliferation, metabolism, and inflammation in polycystic kidney disease. iScience 2023; 26:108278. [PMID: 38026227 PMCID: PMC10665819 DOI: 10.1016/j.isci.2023.108278] [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: 03/20/2023] [Revised: 09/04/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Metabolic reprogramming is a driver of autosomal dominant polycystic kidney disease (ADPKD) progression and a potential therapeutic intervention route. We showed before that the AMP-associated protein kinase (AMPK) activator salsalate attenuates cystic disease progression. Here, we aim to study the early, direct effects of short salsalate treatment in adult-onset conditional Pkd1 deletion mice. Cystic mice were treated with salsalate for two weeks, after which NMR metabolomics and RNA sequencing analyses were performed. Pkd1 deletion resulted in clear metabolomic dysregulation. Short salsalate treatment has small, but significant, effects, reverting acetylcarnitine and phosphocholine concentrations back to wildtype levels, and showing associations with altered purine metabolism. RNA sequencing revealed that short salsalate treatment, next to restoring energy metabolism toward wildtype levels, also affects cell proliferation and inflammation, in PKD. We show that salsalate positively affects major dysregulated processes in ADPKD: energy metabolism, cell proliferation, and inflammation, providing more insights into its working mechanisms.
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Affiliation(s)
- Anish A. Kanhai
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Elena Sánchez-López
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Thomas B. Kuipers
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Jan B. van Klinken
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Laboratory Genetic Metabolic Diseases of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Kyra L. Dijkstra
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Inge van der Veen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans J. Baelde
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Xuewen Song
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - York Pei
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Wouter N. Leonhard
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Oleg A. Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dorien J.M. Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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Ke S, Guimond AJ, Tworoger SS, Huang T, Chan AT, Liu YY, Kubzansky LD. Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women. Psychol Med 2023; 53:7151-7160. [PMID: 36942524 PMCID: PMC10511660 DOI: 10.1017/s0033291723000612] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 02/09/2023] [Accepted: 02/20/2023] [Indexed: 03/23/2023]
Abstract
BACKGROUND Accumulating evidence suggests that positive and negative emotions, as well as emotion regulation, play key roles in human health and disease. Recent work has shown the gut microbiome is important in modulating mental and physical health through the gut-brain axis. Yet, its association with emotions and emotion regulation are understudied. Here we examined whether positive and negative emotions, as well as two emotion regulation strategies (i.e. cognitive reappraisal and suppression), were associated with the gut microbiome composition and functional pathways in healthy women. METHODS Participants were from the Mind-Body Study (N = 206, mean age = 61), a sub-study of the Nurses' Health Study II cohort. In 2013, participants completed measures of emotion-related factors. Two pairs of stool samples were collected, 6 months apart, 3 months after emotion-related factors measures were completed. Analyses examined associations of emotion-related factors with gut microbial diversity, overall microbiome structure, and specific species/pathways and adjusted for relevant covariates. RESULTS Alpha diversity was negatively associated with suppression. In multivariate analysis, positive emotions were inversely associated with the relative abundance of Firmicutes bacterium CAG 94 and Ruminococcaceae bacterium D16, while negative emotions were directly correlated with the relative abundance of these same species. At the metabolic pathway level, negative emotions were inversely related to the biosynthesis of pantothenate, coenzyme A, and adenosine. CONCLUSIONS These findings offer human evidence supporting linkages of emotions and related regulatory processes with the gut microbiome and highlight the importance of incorporating the gut microbiome in our understanding of emotion-related factors and their associations with physical health.
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Affiliation(s)
- Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Anne-Josee Guimond
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Lee Kum Sheung Center for Health and Happiness, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Shelley S. Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Tianyi Huang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
| | - Laura D. Kubzansky
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Ochoa-Hernández ME, Reynoso-Varela A, Martínez-Córdova LR, Rodelas B, Durán U, Alcántara-Hernández RJ, Serrano-Palacios D, Calderón K. Linking the shifts in the metabolically active microbiota in a UASB and hybrid anaerobic-aerobic bioreactor for swine wastewater treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118435. [PMID: 37379625 DOI: 10.1016/j.jenvman.2023.118435] [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: 12/20/2022] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Due to the high concentration of pollutants, swine wastewater needs to be treated prior to disposal. The combination of anaerobic and aerobic technologies in one hybrid system allows to obtain higher removal efficiencies compared to those achieved via conventional biological treatment, and the performance of a hybrid system depends on the microbial community in the bioreactor. Here, we evaluated the community assembly of an anaerobic-aerobic hybrid reactor for swine wastewater treatment. Sequencing of partial 16S rRNA coding genes was performed using Illumina from DNA and retrotranscribed RNA templates (cDNA) extracted from samples from both sections of the hybrid system and from a UASB bioreactor fed with the same swine wastewater influent. Proteobacteria and Firmicutes were the dominant phyla and play a key role in anaerobic fermentation, followed by Methanosaeta and Methanobacterium. Several differences were found in the relative abundances of some genera between the DNA and cDNA samples, indicating an increase in the diversity of the metabolically active community, highlighting Chlorobaculum, Cladimonas, Turicibacter and Clostridium senso stricto. Nitrifying bacteria were more abundant in the hybrid bioreactor. Beta diversity analysis revealed that the microbial community structure significantly differed among the samples (p < 0.05) and between both anaerobic treatments. The main predicted metabolic pathways were the biosynthesis of amino acids and the formation of antibiotics. Also, the metabolism of C5-branched dibasic acid, Vit B5 and CoA, exhibited an important relationship with the main nitrogen-removing microorganisms. The anaerobic-aerobic hybrid bioreactor showed a higher ammonia removal rate compared to the conventional UASB system. However, further research and adjustments are needed to completely remove nitrogen from wastewater.
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Affiliation(s)
- María E Ochoa-Hernández
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Andrea Reynoso-Varela
- Departamento de Ciencias del Agua y Medio Ambiente, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur., Ciudad Obregón, Sonora, CP.85000, Mexico
| | - Luis R Martínez-Córdova
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Belén Rodelas
- Department of Microbiology and Institute of Water Research, University of Granada, Spain
| | - Ulises Durán
- Universidad Autónoma Metropolitana, Biotechnology Dept., P.A. 55-535, 09340, Iztapalapa, Mexico City, Mexico
| | - Rocío J Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, Mexico
| | - Denisse Serrano-Palacios
- Departamento de Ciencias del Agua y Medio Ambiente, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur., Ciudad Obregón, Sonora, CP.85000, Mexico.
| | - Kadiya Calderón
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico.
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Choudhary A, Yu J, Kouznetsova VL, Kesari S, Tsigelny IF. Two-Stage Deep-Learning Classifier for Diagnostics of Lung Cancer Using Metabolites. Metabolites 2023; 13:1055. [PMID: 37887380 PMCID: PMC10609149 DOI: 10.3390/metabo13101055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
We developed a machine-learning system for the selective diagnostics of adenocarcinoma (AD), squamous cell carcinoma (SQ), and small-cell carcinoma lung (SC) cancers based on their metabolomic profiles. The system is organized as two-stage binary classifiers. The best accuracy for classification is 92%. We used the biomarkers sets that contain mostly metabolites related to cancer development. Compared to traditional methods, which exclude hierarchical classification, our method splits a challenging multiclass task into smaller tasks. This allows a two-stage classifier, which is more accurate in the scenario of lung cancer classification. Compared to traditional methods, such a "divide and conquer strategy" gives much more accurate and explainable results. Such methods, including our algorithm, allow for the systematic tracking of each computational step.
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Affiliation(s)
- Ashvin Choudhary
- School of Life Science, University of California, Los Angeles, CA 90095, USA;
| | - Jianpeng Yu
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
| | - Valentina L. Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, CA 92093, USA;
- IUL, La Jolla, CA 92038, USA
- CureScience Institute, San Diego, CA 92121, USA
| | - Santosh Kesari
- Pacific Neuroscience Institute, Santa Monica, CA 90404, USA;
| | - Igor F. Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, CA 92093, USA;
- IUL, La Jolla, CA 92038, USA
- CureScience Institute, San Diego, CA 92121, USA
- Department of Neurosciences, University of California, San Diego, CA 92093, USA
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Zhou Z, Wattiez R, Constant P, Marrakchi H, Soetaert K, Mathys V, Fontaine V, Zeng S. Telacebec Interferes with Virulence Lipid Biosynthesis Protein Expression and Sensitizes to Other Antibiotics. Microorganisms 2023; 11:2469. [PMID: 37894127 PMCID: PMC10609169 DOI: 10.3390/microorganisms11102469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a public health issue, particularly due to multi-drug-resistant Mtb. The bacillus is wrapped in a waxy envelope containing lipids acting as essential virulence factors, accounting for the natural antibiotic resistance of mycobacteria. Telacebec (previously known as Q203) is a promising new anti-TB agent inhibiting the cytochrome bc1 complex of a mycobacterial electron transport chain (ETC). Here, we show that the telacebec-challenged M. bovis BCG exhibited a reduced expression of proteins involved in the synthesis of phthiocerol dimycocerosates (PDIMs)/phenolic glycolipids (PGLs), lipid virulence factors associated with cell envelope impermeability. Consistently, telacebec, at concentrations lower than its MIC, downregulated the transcription of a PDIM/PGL-synthesizing operon, suggesting a metabolic vulnerability triggered by the drug. The drug was able to synergize on BCG with rifampicin or vancomycin, the latter being a drug exerting a marginal effect on PDIM-bearing bacilli. Telacebec at a concentration higher than its MIC had no detectable effect on cell wall PDIMs, as shown by TLC analysis, a finding potentially explained by the retaining of previously synthesized PDIMs due to the inhibition of growth. The study extends the potential of telacebec, demonstrating an effect on mycobacterial virulence lipids, allowing for the development of new anti-TB strategies.
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Affiliation(s)
- Zhiyu Zhou
- Microbiology, Bioorganic & Macromolecular Chemistry Research Unit, Faculté de Pharmacie, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Patricia Constant
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31077 Toulouse, France
| | - Hedia Marrakchi
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31077 Toulouse, France
| | - Karine Soetaert
- National Reference Laboratory "Mycobacterium", Sciensano, 1180 Uccle, Belgium
| | - Vanessa Mathys
- National Reference Laboratory "Mycobacterium", Sciensano, 1180 Uccle, Belgium
| | - Véronique Fontaine
- Microbiology, Bioorganic & Macromolecular Chemistry Research Unit, Faculté de Pharmacie, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Sheng Zeng
- School of Nursing and Health, Nanfang College Guangzhou, Guangzhou 510970, China
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Das S, Bhattacharjee MJ, Mukherjee AK, Khan MR. Comprehensive bacterial-metabolite profiles of Hawaijar, Bekang, and Akhone: a comparative study on traditional fermented soybeans of north-east India. World J Microbiol Biotechnol 2023; 39:315. [PMID: 37736853 DOI: 10.1007/s11274-023-03773-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/19/2023] [Indexed: 09/23/2023]
Abstract
Preparation of traditionally fermented soybeans varies across ethnicities with distinct tastes, flavour, and nutritional values. The fermented soybean varieties Hawaijar, Bekang, and Akhone of north-east India are associated with diverse ethnic groups from Manipur, Mizoram, and Nagaland, respectively. These varieties differ in substrate and traditional practice that exerts differential bacterial-metabolite profile, which needs an in-depth analysis i. Culture-dependent and independent techniques investigated the bacterial diversity of the fermented soybean varieties. Gas chromatography and mass spectroscopy (GC-MS) studied these varieties' metabolite profiles. The common dominant bacterial genera detected in Hawaijar, Bekang, and Akhone were Bacillus, Ignatzschinaria, and Corynebacterium, with the presence of Brevibacillus and Staphylococcus exclusively in Hawaijar and Oceanobacillus in Bekang and Akhone. The metabolite analysis identified a higher abundance of essential amino acids, amino and nucleotide sugars, and vitamins in Hawaijar, short-chain fatty acids in Bekang, polyunsaturated fatty acids in Akhone and Hawaijar, and prebiotics in Akhone. The bacteria-metabolite correlation analysis predicted four distinct bacterial clusters associated with the differential synthesis of the functional metabolites. While B. subtilis is ubiquitous, cluster-1 comprised B. thermoamylovorans/B. amyloliquefaciens, cluster-2 comprised B. tropicus, cluster-3 comprised B. megaterium/B. borstelensis, and cluster-4 comprised B. rugosus. To the best of our knowledge, this is the first comparative study on traditional fermented soybean varieties of north-east India linking bacterial-metabolite profiles which may help in designing starters for desired functionalities in the future.
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Affiliation(s)
- Sushmita Das
- Division of Life Science, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, Assam, 781035, India
- Department of Biotechnology, Gauhati University, Guwahati, Assam, 781014, India
| | - Maloyjo Joyraj Bhattacharjee
- Division of Life Science, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, Assam, 781035, India
| | - Ashis K Mukherjee
- Division of Life Science, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, Assam, 781035, India
| | - Mojibur Rohman Khan
- Division of Life Science, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, Assam, 781035, India.
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Riske BF, Luckhart S, Riehle MA. Starving the Beast: Limiting Coenzyme A Biosynthesis to Prevent Disease and Transmission in Malaria. Int J Mol Sci 2023; 24:13915. [PMID: 37762222 PMCID: PMC10530615 DOI: 10.3390/ijms241813915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Malaria parasites must acquire all necessary nutrients from the vertebrate and mosquito hosts to successfully complete their life cycle. Failure to acquire these nutrients can limit or even block parasite development and presents a novel target for malaria control. One such essential nutrient is pantothenate, also known as vitamin B5, which the parasite cannot synthesize de novo and is required for the synthesis of coenzyme A (CoA) in the parasite. This review examines pantothenate and the CoA biosynthesis pathway in the human-mosquito-malaria parasite triad and explores possible approaches to leverage the CoA biosynthesis pathway to limit malaria parasite development in both human and mosquito hosts. This includes a discussion of sources for pantothenate for the mosquito, human, and parasite, examining the diverse strategies used by the parasite to acquire substrates for CoA synthesis across life stages and host resource pools and a discussion of drugs and alternative approaches being studied to disrupt CoA biosynthesis in the parasite. The latter includes antimalarial pantothenate analogs, known as pantothenamides, that have been developed to target this pathway during the human erythrocytic stages. In addition to these parasite-targeted drugs, we review studies of mosquito-targeted allosteric enzymatic regulators known as pantazines as an approach to limit pantothenate availability in the mosquito and subsequently deprive the parasite of this essential nutrient.
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Affiliation(s)
- Brendan F. Riske
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA;
| | - Shirley Luckhart
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83843, USA;
- Department of Biological Sciences, University of Idaho, Moscow, ID 83843, USA
| | - Michael A. Riehle
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA;
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Seeley EH, Liu Z, Yuan S, Stroope C, Cockerham E, Rashdan NA, Delgadillo L, Finney AC, Kumar D, Das S, Razani B, Liu W, Traylor J, Orr AW, Rom O, Pattillo CB, Yurdagul A. Spatially Resolved Metabolites in Stable and Unstable Human Atherosclerotic Plaques Identified by Mass Spectrometry Imaging. Arterioscler Thromb Vasc Biol 2023; 43:1626-1635. [PMID: 37381983 PMCID: PMC10527524 DOI: 10.1161/atvbaha.122.318684] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Impairments in carbohydrate, lipid, and amino acid metabolism drive features of plaque instability. However, where these impairments occur within the atheroma remains largely unknown. Therefore, we sought to characterize the spatial distribution of metabolites within stable and unstable atherosclerosis in both the fibrous cap and necrotic core. METHODS Atherosclerotic tissue specimens from 9 unmatched individuals were scored based on the Stary classification scale and subdivided into stable and unstable atheromas. After performing mass spectrometry imaging on these samples, we identified over 850 metabolite-related peaks. Using MetaboScape, METASPACE, and Human Metabolome Database, we confidently annotated 170 of these metabolites and found over 60 of these were different between stable and unstable atheromas. We then integrated these results with an RNA-sequencing data set comparing stable and unstable human atherosclerosis. RESULTS Upon integrating our mass spectrometry imaging results with the RNA-sequencing data set, we discovered that pathways related to lipid metabolism and long-chain fatty acids were enriched in stable plaques, whereas reactive oxygen species, aromatic amino acid, and tryptophan metabolism were increased in unstable plaques. In addition, acylcarnitines and acylglycines were increased in stable plaques whereas tryptophan metabolites were enriched in unstable plaques. Evaluating spatial differences in stable plaques revealed lactic acid in the necrotic core, whereas pyruvic acid was elevated in the fibrous cap. In unstable plaques, 5-hydroxyindoleacetic acid was enriched in the fibrous cap. CONCLUSIONS Our work here represents the first step to defining an atlas of metabolic pathways involved in plaque destabilization in human atherosclerosis. We anticipate this will be a valuable resource and open new avenues of research in cardiovascular disease.
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Affiliation(s)
- Erin H. Seeley
- Department of Chemistry, University of Texas at Austin, TX, USA
| | - Zhipeng Liu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, IN, USA
| | - Shuai Yuan
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, PA, USA
| | - Chad Stroope
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Elizabeth Cockerham
- Department of Pathology and Translational Pathobiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Nabil A Rashdan
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Luisa Delgadillo
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Alexandra C Finney
- Department of Pathology and Translational Pathobiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Dhananjay Kumar
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Sandeep Das
- Department of Pathology and Translational Pathobiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Babak Razani
- Cardiovascular Division, Department of Medicine and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- John Cochran VA Medical Center, St. Louis, MO, USA
| | - Wanqing Liu
- Department of Pharmaceutical Sciences and Department of Pharmacology, Wayne State University, MI, USA
| | - James Traylor
- Department of Pathology and Translational Pathobiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - A Wayne Orr
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center at Shreveport, LA, USA
- Department of Pathology and Translational Pathobiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Oren Rom
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center at Shreveport, LA, USA
- Department of Pathology and Translational Pathobiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Christopher B Pattillo
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center at Shreveport, LA, USA
| | - Arif Yurdagul
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center at Shreveport, LA, USA
- Department of Pathology and Translational Pathobiology, LSU Health Sciences Center at Shreveport, LA, USA
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47
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Gowtham L, Halder N, Angmo D, Singh SB, Jayasundar R, Dada T, Velpandian T. Untargeted metabolomics in the aqueous humor reveals the involvement of TAAR pathway in glaucoma. Exp Eye Res 2023; 234:109592. [PMID: 37474016 DOI: 10.1016/j.exer.2023.109592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
Understanding the metabolic dysfunctions and underlying complex pathological mechanisms of neurodegeneration in glaucoma could help discover disease pathways, identify novel biomarkers, and rationalize newer therapeutics. Therefore, we aimed to investigate the local metabolomic alterations in the aqueous humor and plasma of primary glaucomatous patients. This study cohort comprised primary open-angle glaucoma (POAG), primary angle-closure glaucoma (PACG), and cataract control groups. Aqueous humor and plasma samples were collected from patients undergoing trabeculectomy or cataract surgery and subjected to high-resolution mass spectrometry (HRMS) analysis. Spectral information was processed, and the acquired data were subjected to uni-variate as well as multi-variate statistical analyses using MetaboAnalyst ver5.0. To further understand the localized metabolic abnormalities in glaucoma, metabolites affected in aqueous humor were distinguished from metabolites altered in plasma in this study. Nine and twelve metabolites were found to be significantly altered (p < 0.05, variable importance of projection >1 and log2 fold change ≥0.58/≤ -0.58) in the aqueous humor of PACG and POAG patients, respectively. The galactose and amino acid metabolic pathways were locally affected in the PACG and POAG groups, respectively. Based on the observation of the previous findings, gene expression profiles of trace amine-associated receptor-1 (TAAR-1) were studied in rat ocular tissues. The pharmacodynamics of TAAR-1 were explored in rabbits using topical administration of its agonist, β-phenyl-ethylamine (β-PEA). TAAR-1 was expressed in the rat's iris-ciliary body, optic nerve, lens, and cornea. β-PEA elicited a mydriatic response in rabbit eyes, without altering intraocular pressure. Targeted analysis of β-PEA levels in the aqueous humor of POAG patients showed an insignificant elevation. This study provides new insights regarding alterations in both localized and systemic metabolites in primary glaucomatous patients. This study also demonstrated the propensity of β-PEA to cause an adrenergic response through the TAAR-1 pathway.
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Affiliation(s)
- Lakshminarayanan Gowtham
- Department of Ocular Pharmacology and Pharmacy Division, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Nabanita Halder
- Department of Ocular Pharmacology and Pharmacy Division, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Dewang Angmo
- Department of Ophthalmology, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | | | - Rama Jayasundar
- Department of NMR, All India Institute of Medical Sciences, New Delhi, India
| | - Tanuj Dada
- Department of Ophthalmology, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Thirumurthy Velpandian
- Department of Ocular Pharmacology and Pharmacy Division, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India.
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48
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Brooks SM, Marsan C, Reed KB, Yuan SF, Nguyen DD, Trivedi A, Altin-Yavuzarslan G, Ballinger N, Nelson A, Alper HS. A tripartite microbial co-culture system for de novo biosynthesis of diverse plant phenylpropanoids. Nat Commun 2023; 14:4448. [PMID: 37488111 PMCID: PMC10366228 DOI: 10.1038/s41467-023-40242-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023] Open
Abstract
Plant-derived phenylpropanoids, in particular phenylpropenes, have diverse industrial applications ranging from flavors and fragrances to polymers and pharmaceuticals. Heterologous biosynthesis of these products has the potential to address low, seasonally dependent yields hindering ease of widespread manufacturing. However, previous efforts have been hindered by the inherent pathway promiscuity and the microbial toxicity of key pathway intermediates. Here, in this study, we establish the propensity of a tripartite microbial co-culture to overcome these limitations and demonstrate to our knowledge the first reported de novo phenylpropene production from simple sugar starting materials. After initially designing the system to accumulate eugenol, the platform modularity and downstream enzyme promiscuity was leveraged to quickly create avenues for hydroxychavicol and chavicol production. The consortia was found to be compatible with Engineered Living Material production platforms that allow for reusable, cold-chain-independent distributed manufacturing. This work lays the foundation for further deployment of modular microbial approaches to produce plant secondary metabolites.
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Affiliation(s)
- Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Celeste Marsan
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kevin B Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Shuo-Fu Yuan
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Dustin-Dat Nguyen
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Adit Trivedi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gokce Altin-Yavuzarslan
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, 98195, USA
| | - Nathan Ballinger
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, USA
| | - Alshakim Nelson
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, 98195, USA
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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49
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Gholamalizadeh M, Jonoush M, Mobarakeh KA, Amjadi A, Alami F, Valisoltani N, Askarpour SA, Azizi-Tabesh G, Mohammadian MK, Akbari ME, Rajabibazl M, Alemrajabi M, Poodineh J, Sadeghi H, Hosseinzadeh P, Dahka SM, Badeli M, Jarrahi SAM, Doaei S. The effects of FTO gene rs9939609 polymorphism on the association between colorectal cancer and dietary intake. Front Nutr 2023; 10:1215559. [PMID: 37545585 PMCID: PMC10399810 DOI: 10.3389/fnut.2023.1215559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/21/2023] [Indexed: 08/08/2023] Open
Abstract
Background FTO gene is associated with obesity, dietary intake, and the risk of colorectal cancer (CRC). In this study, patients with colorectal cancer were assessed for the interactions between FTO gene polymorphisms and dietary intake. Methods This case-control study was carried out on 450 participants aged 35-70 years including 150 patients with colorectal cancer and 300 healthy controls. Blood samples were collected in order to extract DNA and genotyping of FTO gene for rs9939609 polymorphism. A validated 168-item food frequency questionnaire (FFQ) and the Nutritionist-IV software were used to assess dietary intake. Results In the participants with the TT genotype of FTO rs9939609 polymorphism, CRC risk was significantly associated with higher intake of dietary fat (OR:1.87 CI95%:1.76-1.99, p = 0.04), vitamin B3 (OR:1.20 CI95%:1.08-1.65, p = 0.04), and vitamin C (OR:1.06 CI95%:1.03-1.15, p = 0.04) and lower intake of β-carotene (OR:0.98 CI95%:0.97-0.99, p = 0.03), vitamin E (OR:0.77 CI95%:0.62-0.95, p = 0.02), vitamin B1 (OR:0.15 CI95%:0.04-0.50, p < 0.01), and biotin (OR:0.72 CI95%:0.0.57-0.92, p = 0.01). No significant association was found between CRC and dietary intake in carriers of AA/AT genotypes after adjustments for the confounders. Conclusion CRC risk may be decreased by β-carotene, vitamins E, B1, and biotin only in those without the risk allele of the FTO gene. The association of CRC and diet may be influenced by FTO genotype. Further studies are warranted.
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Affiliation(s)
- Maryam Gholamalizadeh
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mona Jonoush
- Department of Clinical Nutrition and Dietetics, Faculty of Nutrition and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Khadijeh Abbasi Mobarakeh
- Food Security Research Center and Department of Community Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Arezoo Amjadi
- Department of Nutrition, School of Nutritional Sciences and Food Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farkhondeh Alami
- Student Research Committee, Department of Nutrition, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Neda Valisoltani
- Department of Clinical Nutrition. School of Nutrition Science and Dietetics. Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Askarpour
- Division of Food Safety and Hygiene, Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghasem Azizi-Tabesh
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | | | - Masoumeh Rajabibazl
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdi Alemrajabi
- Clinical Research Development Center (CRDC), Firoozgar Hospital, School of Medicine, Iran University of Medical Sciences, Zabol, Iran
| | - Jafar Poodineh
- Department of Clinical Biochemistry, School of Medicine, Zabol University of Medical Sciences, Tehran, Iran
| | - Hossein Sadeghi
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Payam Hosseinzadeh
- Gastrointestinal and Liver Diseases Research Center (GLDRC), Iran University of Medical Sciences, Tehran, Iran
| | | | - Mostafa Badeli
- Department of Nutrition, Urmia University of Medical Science, Urmia, Iran
| | | | - Saeid Doaei
- Department of Community Nutrition, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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50
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Cronan JE. How an overlooked gene in coenzyme a synthesis solved an enzyme mechanism predicament. Mol Microbiol 2023; 119:687-694. [PMID: 37140060 PMCID: PMC10330860 DOI: 10.1111/mmi.15070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
Coenzyme A (CoA) is an essential cofactor throughout biology. The first committed step in the CoA synthetic pathway is synthesis of β-alanine from aspartate. In Escherichia coli and Salmonella enterica panD encodes the responsible enzyme, aspartate-1-decarboxylase, as a proenzyme. To become active, the E. coli and S. enterica PanD proenzymes must undergo an autocatalytic cleavage to form the pyruvyl cofactor that catalyzes decarboxylation. A problem was that the autocatalytic cleavage was too slow to support growth. A long-neglected gene (now called panZ) was belatedly found to encode the protein that increases autocatalytic cleavage of the PanD proenzyme to a physiologically relevant rate. PanZ must bind CoA or acetyl-CoA to interact with the PanD proenzyme and accelerate cleavage. The CoA/acetyl-CoA dependence has led to proposals that the PanD-PanZ CoA/acetyl-CoA interaction regulates CoA synthesis. Unfortunately, regulation of β-alanine synthesis is very weak or absent. However, the PanD-PanZ interaction provides an explanation for the toxicity of the CoA anti-metabolite, N5-pentyl pantothenamide.
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Affiliation(s)
- John E. Cronan
- Departments of Microbiology and Biochemistry, University of Illinois, Urbana 61801, USA
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