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Lipiński O, Sonani RR, Dubin G. Crystal structure of glycerol kinase from Trypanosoma cruzi, a potential molecular target in Chagas disease. Acta Crystallogr D Struct Biol 2024; 80:629-638. [PMID: 39052317 DOI: 10.1107/s2059798324006594] [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: 04/10/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. It bears a significant global health burden with limited treatment options, thus calling for the development of new and effective drugs. Certain trypanosomal metabolic enzymes have been suggested to be druggable and valid for subsequent inhibition. In this study, the crystal structure of glycerol kinase from T. cruzi, a key enzyme in glycerol metabolism in this parasite, is presented. Structural analysis allowed a detailed description of the glycerol binding pocket, while comparative assessment pinpointed a potential regulatory site which may serve as a target for selective inhibition. These findings advance the understanding of glycerol metabolism in eukaryotes and provide a solid basis for the future treatment of Chagas disease.
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Affiliation(s)
- Oskar Lipiński
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ravi R Sonani
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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Qi X, Liu C, Si J, Yin B, Huang J, Wang X, Huang J, Sun H, Zhu C, Zhang W. A bioenergetically-active ploy (glycerol sebacate)-based multiblock hydrogel improved diabetic wound healing through revitalizing mitochondrial metabolism. Cell Prolif 2024; 57:e13613. [PMID: 38351579 PMCID: PMC11216945 DOI: 10.1111/cpr.13613] [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: 12/11/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 07/03/2024] Open
Abstract
Diabetic wounds impose significant burdens on patients' quality of life and healthcare resources due to impaired healing potential. Factors like hyperglycemia, oxidative stress, impaired angiogenesis and excessive inflammation contribute to the delayed healing trajectory. Mounting evidence indicates a close association between impaired mitochondrial function and diabetic complications, including chronic wounds. Mitochondria are critical for providing energy essential to wound healing processes. However, mitochondrial dysfunction exacerbates other pathological factors, creating detrimental cycles that hinder healing. This study conducted correlation analysis using clinical specimens, revealing a positive correlation between mitochondrial dysfunction and oxidative stress, inflammatory response and impaired angiogenesis in diabetic wounds. Restoring mitochondrial function becomes imperative for developing targeted therapies. Herein, we synthesized a biodegradable poly (glycerol sebacate)-based multiblock hydrogel, named poly (glycerol sebacate)-co-poly (ethylene glycol)-co-poly (propylene glycol) (PEPGS), which can be degraded in vivo to release glycerol, a crucial component in cellular metabolism, including mitochondrial respiration. We demonstrate the potential of PEPGS-based hydrogels to improve outcomes in diabetic wound healing by revitalizing mitochondrial metabolism. Furthermore, we investigate the underlying mechanism through proteomics analysis, unravelling the regulation of ATP and nicotinamide adenine dinucleotide metabolic processes, biosynthetic process and generation during mitochondrial metabolism. These findings highlight the therapeutic potential of PEPGS-based hydrogels as advanced wound dressings for diabetic wound healing.
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Affiliation(s)
- Xin Qi
- Department of Orthopedic SurgeryShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Department of Orthopedic Surgery, Shanghai Institute of Microsurgery on ExtremitiesShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Chenjun Liu
- Department of Orthopedic SurgeryShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jingyi Si
- Department of Gastroenterology and Hepatology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Bohao Yin
- Department of Orthopedic SurgeryShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jingjing Huang
- Department of Orthopedic SurgeryShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xin Wang
- Department of Orthopedic SurgeryShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jinghuan Huang
- Department of Orthopedic SurgeryShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hui Sun
- Department of Orthopedic SurgeryShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Changfeng Zhu
- Department of Gastroenterology and Hepatology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Wei Zhang
- Department of Orthopedic SurgeryShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
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Elnegaard JJ, Iena FM, Herold J, Lebeck J. Sex-specific effect of AQP9 deficiency on hepatic triglyceride metabolism in mice with diet-induced obesity. J Physiol 2024; 602:3131-3149. [PMID: 37026573 DOI: 10.1113/jp284188] [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: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023] Open
Abstract
Studies in obese rats and human cell models of non-alcoholic fatty liver disease have indicated that knockdown of the hepatic glycerol channel aquaporin 9 (AQP9) leads to decreased hepatic steatosis. However, a study in leptin receptor-deficient mice did not find that knockout (KO) of AQP9 alleviated hepatic steatosis. The aim of this study was to investigate the effect of high-fat diet (HFD) on hepatic glycerol and triglyceride metabolism in male and female AQP9 KO mice. Male and female AQP9 KO mice and wild-type (WT) littermates were fed a HFD for 12 weeks. Weight, food intake and blood glucose were monitored throughout the study and tissue analysis included determination of hepatic triglyceride content and triglyceride secretion. The expression of key molecules for hepatic glycerol and triglyceride metabolism was evaluated using qPCR and western blotting. AQP9 KO and WT mice demonstrated a similar weight gain throughout the study period, and we found no evidence for AQP9 deficiency being associated with a reduced hepatic accumulation of triglyceride or a reduced blood glucose level. Instead, we show that the effect of AQP9 deficiency on hepatic lipid metabolism is sex-specific, with only male AQP9 KO mice having a reduced hepatic secretion of triglycerides and an elevated expression of peroxisome proliferator-activated receptor α. Male AQP9 KO mice had an elevated blood glucose level after 12 weeks of HFD when compared to baseline levels. Thus, we found no evidence for AQP9 inhibition being a target for alleviating the development of hepatic steatosis in mice with diet-induced obesity. KEY POINTS: This study investigates the effect of AQP9 deficiency on hepatic triglyceride metabolism in both male and female mice fed a high-fat diet (HFD) for 12 weeks. No evidence was found for AQP9 deficiency being associated with a reduced hepatic accumulation of triglyceride or a reduced blood glucose level. The effect of AQP9 deficiency on hepatic triglyceride metabolism is sex-specific. Male AQP9 KO mice had a reduced hepatic secretion of triglycerides and an elevated expression of peroxisome proliferator-activated receptor α, which likely promotes an increased hepatic fatty acid oxidation. Male AQP9 KO had an elevated blood glucose level after 12 weeks of HFD when compared to baseline levels.
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Affiliation(s)
| | | | | | - Janne Lebeck
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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4
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Sankaran DG, Zhu H, Maymi VI, Forlastro IM, Jiang Y, Laniewski N, Scheible KM, Rudd BD, Grimson AW. Gene Regulatory Programs that Specify Age-Related Differences during Thymocyte Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599011. [PMID: 38948840 PMCID: PMC11212896 DOI: 10.1101/2024.06.14.599011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
T cell development is fundamental to immune system establishment, yet how this development changes with age remains poorly understood. Here, we construct a transcriptional and epigenetic atlas of T cell developmental programs in neonatal and adult mice, revealing the ontogeny of divergent gene regulatory programs and their link to age-related differences in phenotype and function. Specifically, we identify a gene module that diverges with age from the earliest stages of genesis and includes programs that govern effector response and cell cycle regulation. Moreover, we reveal that neonates possess more accessible chromatin during early thymocyte development, likely establishing poised gene expression programs that manifest later in thymocyte development. Finally, we leverage this atlas, employing a CRISPR-based perturbation approach coupled with single-cell RNA sequencing as a readout to uncover a conserved transcriptional regulator, Zbtb20, that contributes to age-dependent differences in T cell development. Altogether, our study defines transcriptional and epigenetic programs that regulate age-specific differences in T cell development.
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Kim DK, Rajan P, Cuong DM, Choi JH, Yoon TH, Go GM, Lee JW, Noh SW, Choi HK, Cho SK. Melosira nummuloides Ethanol Extract Ameliorates Alcohol-Induced Liver Injury by Affecting Metabolic Pathways. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8476-8490. [PMID: 38588403 DOI: 10.1021/acs.jafc.3c06261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Melosira nummuloides is a microalga with a nutritionally favorable polyunsaturated fatty acid profile. In the present study, M. nummuloides ethanol extract (MNE) was administered to chronic-binge alcohol-fed mice and alcohol-treated HepG2 cells, and its hepatoprotective effects and underlying mechanisms were investigated. MNE administration reduced triglyceride (TG), total cholesterol (T-CHO), and liver injury markers, including aspartate transaminase (AST) and alanine transaminase (ALT), in the serum of chronic-binge alcohol-fed mice. However, MNE administration increased the levels of phosphorylated adenosine monophosphate-activated protein kinase (P-AMPK/AMPK) and PPARα, which was accompanied by a decrease in SREBP-1; this indicates that MNE can inhibit adipogenesis and improve fatty acid oxidation. Moreover, MNE administration upregulated the expression of antioxidant enzymes, including SOD, NAD(P)H quinone dehydrogenase 1, and GPX, and ameliorated alcohol-induced inflammation by repressing the Akt/NFκB/COX-2 pathway. Metabolomic analysis revealed that MNE treatment modulated many lipid metabolites in alcohol-treated HepG2 cells. Our study findings provide evidence for the efficacy and mechanisms of MNE in ameliorating alcohol-induced liver injury.
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Affiliation(s)
- Dae Kyeong Kim
- Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 63243, Republic of Korea
| | - Priyanka Rajan
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju 63243, Republic of Korea
| | - Do Manh Cuong
- Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 63243, Republic of Korea
| | - Jae Ho Choi
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon 16499, Republic of Korea
| | - Tae Hyeon Yoon
- College of Applied Life Sciences, SARI, Jeju National University, Jeju 63243, Republic of Korea
| | - Gyung Min Go
- JDKBIO lnc., Jeju-si, Jeju 63023, Republic of Korea
| | - Ji Won Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Soon-Wook Noh
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyung-Kyoon Choi
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Somi Kim Cho
- Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 63243, Republic of Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju 63243, Republic of Korea
- College of Applied Life Sciences, Jeju National University, Jeju 63243, Republic of Korea
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Lackner S, Mahnert A, Moissl-Eichinger C, Madl T, Habisch H, Meier-Allard N, Kumpitsch C, Lahousen T, Kohlhammer-Dohr A, Mörkl S, Strobl H, Holasek S. Interindividual differences in aronia juice tolerability linked to gut microbiome and metabolome changes-secondary analysis of a randomized placebo-controlled parallel intervention trial. MICROBIOME 2024; 12:49. [PMID: 38461313 PMCID: PMC10924357 DOI: 10.1186/s40168-024-01774-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/05/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Aronia melanocarpa is a berry rich in polyphenols known for health benefits. However, the bioavailability of polyphenols has been questioned, and the individual taste acceptance of the fruit with its specific flavor varies. We recently observed substantial differences in the tolerability of aronia juice among healthy females, with half of the individuals tolerating aronia juice without complaints. Given the importance of the gut microbiome in food digestion, we investigated in this secondary analysis of the randomized placebo-controlled parallel intervention study (ClinicalTrials.gov registration: NCT05432362) if aronia juice tolerability was associated with changes in intestinal microbiota and bacterial metabolites, seeking for potential mechanistic insights into the impact on aronia polyphenol tolerance and metabolic outcomes. RESULTS Forty females were enrolled for this 6-week trial, receiving either 100 ml natural aronia juice (verum, V) twice daily or a polyphenol-free placebo (P) with a similar nutritional profile, followed by a 6-week washout. Within V, individuals were categorized into those who tolerated the juice well (Vt) or reported complaints (Vc). The gut microbiome diversity, as analyzed by 16S rRNA gene-based next-generation sequencing, remained unaltered in Vc but changed significantly in Vt. A MICOM-based flux balance analysis revealed pronounced differences in the 40 most predictive metabolites post-intervention. In Vc carbon-dioxide, ammonium and nine O-glycans were predicted due to a shift in microbial composition, while in Vt six bile acids were the most likely microbiota-derived metabolites. NMR metabolomics of plasma confirmed increased lipoprotein subclasses (LDL, VLDL) post-intervention, reverting after wash out. Stool samples maintained a stable metabolic profile. CONCLUSION In linking aronia polyphenol tolerance to gut microbiota-derived metabolites, our study explores adaptive processes affecting lipoprotein profiles during high polyphenol ingestion in Vt and examines effects on mucosal gut health in response to intolerance to high polyphenol intake in Vc. Our results underpin the importance of individualized hormetic dosing for beneficial polyphenol effects, demonstrate dynamic gut microbiome responses to aronia juice, and emphasize personalized responses in polyphenol interventions.
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Affiliation(s)
- Sonja Lackner
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Tobias Madl
- Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Hansjörg Habisch
- Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Nathalie Meier-Allard
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Theresa Lahousen
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Auenbruggerplatz 31, 8036, Graz, Austria
| | - Alexandra Kohlhammer-Dohr
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Auenbruggerplatz 31, 8036, Graz, Austria
| | - Sabrina Mörkl
- Division of Medical Psychology, Psychosomatics and Psychotherapeutic Medicine, Auenbruggerplatz 3, 8036, Graz, Austria
| | - Herbert Strobl
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Sandra Holasek
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria.
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de Fátima Cobre A, Alves AC, Gotine ARM, Domingues KZA, Lazo REL, Ferreira LM, Tonin FS, Pontarolo R. Novel COVID-19 biomarkers identified through multi-omics data analysis: N-acetyl-4-O-acetylneuraminic acid, N-acetyl-L-alanine, N-acetyltriptophan, palmitoylcarnitine, and glycerol 1-myristate. Intern Emerg Med 2024:10.1007/s11739-024-03547-1. [PMID: 38416303 DOI: 10.1007/s11739-024-03547-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
This study aims to apply machine learning models to identify new biomarkers associated with the early diagnosis and prognosis of SARS-CoV-2 infection.Plasma and serum samples from COVID-19 patients (mild, moderate, and severe), patients with other pneumonia (but with negative COVID-19 RT-PCR), and healthy volunteers (control) from hospitals in four different countries (China, Spain, France, and Italy) were analyzed by GC-MS, LC-MS, and NMR. Machine learning models (PCA and PLS-DA) were developed to predict the diagnosis and prognosis of COVID-19 and identify biomarkers associated with these outcomes.A total of 1410 patient samples were analyzed. The PLS-DA model presented a diagnostic and prognostic accuracy of around 95% of all analyzed data. A total of 23 biomarkers (e.g., spermidine, taurine, L-aspartic, L-glutamic, L-phenylalanine and xanthine, ornithine, and ribothimidine) have been identified as being associated with the diagnosis and prognosis of COVID-19. Additionally, we also identified for the first time five new biomarkers (N-Acetyl-4-O-acetylneuraminic acid, N-Acetyl-L-Alanine, N-Acetyltriptophan, palmitoylcarnitine, and glycerol 1-myristate) that are also associated with the severity and diagnosis of COVID-19. These five new biomarkers were elevated in severe COVID-19 patients compared to patients with mild disease or healthy volunteers.The PLS-DA model was able to predict the diagnosis and prognosis of COVID-19 around 95%. Additionally, our investigation pinpointed five novel potential biomarkers linked to the diagnosis and prognosis of COVID-19: N-Acetyl-4-O-acetylneuraminic acid, N-Acetyl-L-Alanine, N-Acetyltriptophan, palmitoylcarnitine, and glycerol 1-myristate. These biomarkers exhibited heightened levels in severe COVID-19 patients compared to those with mild COVID-19 or healthy volunteers.
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Affiliation(s)
| | - Alexessander Couto Alves
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | | | | | | | - Luana Mota Ferreira
- Department of Pharmacy, Universidade Federal do Paraná, Campus III, Av. Pref. Lothário Meissner, 632, Jardim Botânico, Curitiba, PR, 80210-170, Brazil
| | - Fernanda Stumpf Tonin
- H&TRC - Health & Technology Research Centre, ESTeSL, Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Roberto Pontarolo
- Department of Pharmacy, Universidade Federal do Paraná, Campus III, Av. Pref. Lothário Meissner, 632, Jardim Botânico, Curitiba, PR, 80210-170, Brazil.
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Iizuka Y, Hirako S, Kim H, Wada N, Ohsaki Y, Yanagisawa N. Fish oil-derived n-3 polyunsaturated fatty acids downregulate aquaporin 9 protein expression of liver and white adipose tissues in diabetic KK mice and 3T3-L1 adipocytes. J Nutr Biochem 2024; 124:109514. [PMID: 37918450 DOI: 10.1016/j.jnutbio.2023.109514] [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: 05/01/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Aquaporin 9 (AQP9) is an integral membrane protein that facilitates glycerol transport in hepatocytes and adipocytes. Glycerol is necessary as a substrate for gluconeogenesis in the physiological fasted state, suggesting that inhibiting AQP9 function may be beneficial for treating type 2 diabetes associated with fasting hyperglycemia. The n-3 polyunsaturated fatty acids (PUFAs), including eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are rich in fish oil and lower the risk of metabolic syndrome; however, the effects of EPA and DHA on AQP9 expression in obese and type 2 diabetes are unclear. The KK mouse is an animal model of obesity and type 2 diabetes because of the polymorphisms on leptin receptor gene, which results in a part of cause for obese and diabetic conditions. In this study, we determined the effect of fish oil-derived n-3 PUFA on AQP9 protein expression in the liver and white adipose tissue (WAT) of KK mice and mouse 3T3-L1 adipocytes. The expression of AQP9 protein in the liver, epididymal WAT, and inguinal WAT were markedly decreased following fish oil administration. We also demonstrated that n-3 PUFAs, such as DHA, and to a lesser extent EPA, downregulated AQP9 protein expression in 3T3-L1 adipocytes. Our results suggest that fish oil-derived n-3 PUFAs may regulate the protein expressions of AQP9 in glycerol metabolism-related organs in KK mice and 3T3-L1 adipocytes.
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Affiliation(s)
- Yuzuru Iizuka
- Department of Microbiology and Immunology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan.
| | - Satoshi Hirako
- Department of Health and Nutrition, University of Human Arts and Sciences, Saitama, Japan
| | - Hyounju Kim
- Department of Nutrition and Health Sciences, Faculty of Food and Nutritional Sciences, Toyo University, Gunma, Japan
| | - Nobuhiro Wada
- Department of Anatomy, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yuki Ohsaki
- Department of Anatomy, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Naoko Yanagisawa
- Department of Microbiology and Immunology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
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Abdulazeez I, Ismail IS, Mohd Faudzi SM, Christianus A, Chong SG. Study on the acute toxicity of sodium taurocholate via zebrafish mortality, behavioral response, and NMR-metabolomics analysis. Drug Chem Toxicol 2024; 47:115-130. [PMID: 37548163 DOI: 10.1080/01480545.2023.2242005] [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: 03/06/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Sodium taurocholate (NaT) is a hydrophobic bile salt that exhibits varying toxicity and antimicrobial activity. The accumulation of BSs during their entero-hepatic cycle causes cytotoxicity in the liver and intestine and could also alter the intestinal microbiome leading to various diseases. In this research, the acute toxicity of sodium taurocholate in different concentrations (3000 mg/L, 1500 mg/L, 750 mg/L, 375 mg/L, and 0 mg/L) was investigated on four months old zebrafish by immersion in water for 96 h. The results were determined based on the fish mortality, behavioral response, and NMR metabolomics analysis which revealed LC50 of 1760.32 mg/L and 1050.42 mg/L after 72 and 96 h treatment, respectively. However, the non-lethal NaT concentrations of 750 mg/L and 375 mg/L at 96 h exposure significantly (p ≤ 0.05) decreased the total distance traveled and the activity duration, also caused surface respiration on the zebrafish. Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) revealed that the metabolome of the fish treated with 750 mg/L was discriminated from that of the control by PC1. Major significantly downregulated metabolites by NaT-induction include valine, isoleucine, 2-hydroxyvalerate, glycine, glycerol, choline, glucose, pyruvate, anserine, threonine, carnitine and homoserine. On the contrary, taurine, creatine, lactate, acetate and 3-hydroxybutyrate were upregulated suggesting cellular consumption of lipids, glucose and amino acids for adenosine triphosphate (ATP) generation during immune and inflammatory response. whereby these metabolites were released in the process. In conclusion, the research revealed the toxic effect of NaT and its potential to trigger changes in zebrafish metabolism.
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Affiliation(s)
- Isah Abdulazeez
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang Selangor, Malaysia
| | - Intan Safinar Ismail
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang Selangor, Malaysia
- Natural Medicines and Product Research Laboratory (NaturMeds), Institute of Bioscience (IBS), Universiti Putra Malaysia, UPM Serdang Selangor, Malaysia
| | - Siti Munirah Mohd Faudzi
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang Selangor, Malaysia
| | - Annie Christianus
- Department of Aquaculture, Faculty of Agricultural Sciences, Universiti Putra Malaysia, UPM Serdang Selangor, Malaysia
| | - Seok-Giok Chong
- Natural Medicines and Product Research Laboratory (NaturMeds), Institute of Bioscience (IBS), Universiti Putra Malaysia, UPM Serdang Selangor, Malaysia
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10
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Li Z, Zhang G, Pan K, Niu X, Shu-Chien AC, Chen T, Zhang X, Wu X. Functional transcriptome reveals hepatopancreatic lipid metabolism during the molting cycle of the Chinese mitten crab Eriocheir sinensis. Comp Biochem Physiol A Mol Integr Physiol 2023; 284:111474. [PMID: 37406959 DOI: 10.1016/j.cbpa.2023.111474] [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: 02/08/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
Crustacean molting is highly related to energy and lipid metabolism. This study was conducted to detect the changes of total lipids (TL), triacylglyceride (TAG), phospholipid (PL) and lipid droplets in hepatopancreas, and then to investigate the gene expression patterns related to hepatopancreatic lipid metabolism during the molting cycle of Chinese mitten crab Eriocheir sinensis. Hepatopancreatic TL and TAG increased significantly from post-molt stage to pre-molt stage, then decreased significantly from pre-molt stage to ecdysis stage, which is consistent to the changes of neutral lipid-rich adipocytes in hepatopancreas. By transcriptomic analysis, 65,325 transcripts were sequenced and assembled, and 28,033 transcripts were annotated. Most genes were related to energy metabolism, and the enriched genes were involved in carbohydrate and lipid metabolism and biosynthesis, especially in de novo synthesis of fatty acids and TAG, and ketone body production. Compared to the inter-molt stages, acetyl-CoA carboxylase, fatty acid synthase and other genes related to the synthesis of fatty acids were upregulated in the pre-molt stage. TAG synthesis related genes, including Glycerol-3-phosphate acyltransferase and 1-acylglycerol-3-phosphate acyltransferases, were upregulated in the post-molt stage compared to the inter-molt stage. The expression of ketone body-related genes had no significant changes during the molting cycle. Compared to the TAG synthetic pathway, ketone body biosynthesis may contribute less/secondarily to fatty acid metabolic processes, which could be involved in the other physiological processes or metabolism. In conclusion, these results showed that TAG is the major lipid deposition during inter- and pre-molt stages, and the most genes are related to the fatty acids and TAG metabolism in the hepatopancreas during the molting cycle of E. sinensis.
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Affiliation(s)
- Zhi Li
- Shanghai Collaborative Innovation Centre for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Guangbao Zhang
- Shanghai Collaborative Innovation Centre for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Kewu Pan
- Shanghai Collaborative Innovation Centre for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Xingjian Niu
- Shanghai Collaborative Innovation Centre for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | | | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xin Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Xugan Wu
- Shanghai Collaborative Innovation Centre for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; School of Biological Sciences, Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia; Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
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11
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Liang S, Jiang Y, Zhang M. Integrative analysis of the effects of organic and conventional farming methods on peanut based on transcriptome and metabolomics. Food Res Int 2023; 171:113065. [PMID: 37330858 DOI: 10.1016/j.foodres.2023.113065] [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: 04/30/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/19/2023]
Abstract
To elucidate the nutritional quality of peanut under different farming methods, we selected two cultivars, "jihua13" and "jihua4", to grow in organic and conventional environments, respectively. After harvest, we measured physiological parameters and differential metabolites. Metabolomics showed that most of the amino acids, carbohydrates, and secondary metabolites in organically grown jihua4 were downregulated, which was completely the opposite in jihua13. Fatty acids associated with heart disease and hypertension are reduced in organically grown peanuts. In particular, the highly statistically significant tryptophan betaine seems to be used as a reference to distinguish between organic and conventional cultivation. Mechanisms leading to differences in crop chemical composition are explained by transcriptome analysis. The results of the transcriptome analysis indicated that organic cultivation largely affects the synthesis of amino acids and carbohydrates in jihua13. Combined analysis of transcriptome and metabolomics found that variety jihua13 is more sensitive to farming methods and produces more unsaturated fatty acids than jihua4.
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Affiliation(s)
- Shan Liang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Yangjie Jiang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Min Zhang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China.
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12
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Zhao X, Wang J, Xia N, Liu Y, Qu Y, Ming M, Zhan Y, Han Y, Zhao X, Li Y. Combined analysis of the metabolome and transcriptome provides insight into seed oil accumulation in soybean. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:70. [PMID: 37098528 PMCID: PMC10131312 DOI: 10.1186/s13068-023-02321-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/16/2023] [Indexed: 04/27/2023]
Abstract
BACKGROUND Soybean (Glycine max (L.) Merr) is an important source of human food, animal feed, and bio-energy. Although the genetic network of lipid metabolism is clear in Arabidopsis, the understanding of lipid metabolism in soybean is limited. RESULTS In this study, 30 soybean varieties were subjected to transcriptome and metabolome analysis. In total, 98 lipid-related metabolites were identified, including glycerophospholipid, alpha-linolenic acid, linoleic acid, glycolysis, pyruvate, and the sphingolipid pathway. Of these, glycerophospholipid pathway metabolites accounted for the majority of total lipids. Combining the transcriptomic and metabolomic analyses, we found that 33 lipid-related metabolites and 83 lipid-related genes, 14 lipid-related metabolites and 17 lipid-related genes, and 12 lipid-related metabolites and 25 lipid-related genes were significantly correlated in FHO (five high-oil varieties) vs. FLO (five low-oil varieties), THO (10 high-oil varieties) vs. TLO (10 low-oil varieties), and HO (15 high-oil varieties) vs. LO (15 low-oil varieties), respectively. CONCLUSIONS The GmGAPDH and GmGPAT genes were significantly correlated with lipid metabolism genes, and the result revealed the regulatory relationship between glycolysis and oil synthesis. These results improve our understanding of the regulatory mechanism of soybean seed oil improvement.
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Affiliation(s)
- Xunchao Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Jie Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Ning Xia
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Yuanyuan Liu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Yuewen Qu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Meng Ming
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
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13
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Theodosiou E. Engineering Strategies for Efficient Bioconversion of Glycerol to Value-Added Products by Yarrowia lipolytica. Catalysts 2023. [DOI: 10.3390/catal13040657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Yarrowia lipolytica has been a valuable biotechnological workhorse for the production of commercially important biochemicals for over 70 years. The knowledge gained so far on the native biosynthetic pathways, as well as the availability of numerous systems and synthetic biology tools, enabled not only the regulation and the redesign of the existing metabolic pathways, but also the introduction of novel synthetic ones; further consolidating the position of the yeast in industrial biotechnology. However, for the development of competitive and sustainable biotechnological production processes, bioengineering should be reinforced by bioprocess optimization strategies. Although there are many published reviews on the bioconversion of various carbon sources to value-added products by Yarrowia lipolytica, fewer works have focused on reviewing up-to-date strain, medium, and process engineering strategies with an aim to emphasize the significance of integrated engineering approaches. The ultimate goal of this work is to summarize the necessary knowledge and inspire novel routes to manipulate at a systems level the yeast biosynthetic machineries by combining strain and bioprocess engineering. Due to the increasing surplus of biodiesel-derived waste glycerol and the favored glycerol-utilization metabolic pathways of Y. lipolytica over other carbon sources, the present review focuses on pure and crude glycerol-based biomanufacturing.
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14
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Lee J, Shin JA, Lee EM, Nam M, Park EM. Noggin-mediated effects on metabolite profiles of microglia and oligodendrocytes after ischemic insult. J Pharm Biomed Anal 2023; 224:115196. [PMID: 36529041 DOI: 10.1016/j.jpba.2022.115196] [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: 07/01/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Recent studies show that shifts in energy metabolism in activated microglia are linked to their functions and immune responses in the ischemic brain. We previously reported that an antagonist of the bone morphogenetic protein, noggin, enhanced myelination in the ischemic brain during the chronic phase, and conditioned media (CM) from activated BV2 microglia treated with noggin after ischemia/reperfusion (I/R) increased the expression of myelin basic protein (MBP) in oligodendrocytes (MO3.13). To determine whether noggin induced changes in cell metabolism, metabolite profiles in BV2 and MO3.13 cells were analyzed by untargeted metabolomics using 1H nuclear magnetic resonance spectroscopy. Compared to vehicle-treated BV2 cells, noggin treatment (100 ng/mL for 3 h after I/R) suppressed the I/R-induced increase in intracellular glucose and lactate levels but increased extracellular levels of glucose and several amino acids. When MO3.13 cells were exposed to noggin CM from BV2 cells, most of the vehicle CM-induced changes in the levels of metabolites such as choline, formate, and intermediates of oxidative phosphorylation were reversed, while the glycerol level was markedly increased. An increase in glycerol level was also observed in the noggin-treated ischemic brain and was further supported by the expression of glycerol-3-phosphate dehydrogenase 1 (required for glycerol synthesis) in the cytoplasm of MBP-positive oligodendrocytes in the ischemic brains treated with noggin. These results suggest that noggin-induced changes in the metabolism of microglia provide a favorable environment for myelin synthesis in oligodendrocytes during the recovery phase after ischemic stroke.
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Affiliation(s)
- Jueun Lee
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea.
| | - Jin A Shin
- Department of Pharmacology, College of Medicine, Ewha Womans University, Seoul 07084, Republic of Korea
| | - Eun-Mi Lee
- Department of Pharmacology, College of Medicine, Ewha Womans University, Seoul 07084, Republic of Korea
| | - Miso Nam
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea; Food Analysis Research Center, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Eun-Mi Park
- Department of Pharmacology, College of Medicine, Ewha Womans University, Seoul 07084, Republic of Korea.
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15
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Chandler LM, Rodriguez M, Choe KP. RNAi screening for modulators of an osmo-sensitive gene response to extracellular matrix damage reveals negative feedback and interactions with translation inhibition. PLoS One 2023; 18:e0285328. [PMID: 37155688 PMCID: PMC10166495 DOI: 10.1371/journal.pone.0285328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
In epidermal tissues, extracellular matrices (ECMs) function as barriers between the organism and environment. Despite being at the interface with the environment, little is known about the role of animal barrier ECMs in sensing stress and communicating with cytoprotective gene pathways in neighboring cells. We and others have identified a putative damage sensor in the C. elegans cuticle that regulates osmotic, detoxification, and innate immune response genes. This pathway is associated with circumferential collagen bands called annular furrows; mutation or loss of furrow collagens causes constitutive activation of osmotic, detoxification, and innate immune response genes. Here, we performed a genome-wide RNAi screen for modulators of osmotic stress response gene gpdh-1 in a furrow collagen mutant strain. RNAi of six genes identified in this screen were tested under other conditions and for effects on other stress responses. The functions of these genes suggest negative feedback within osmolyte accumulation pathways and interactions with ATP homeostasis and protein synthesis. Loss of these gpdh-1 modulators had distinct effects on canonical detoxification and innate immune response genes.
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Affiliation(s)
- Luke M Chandler
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, United States of America
| | - Michael Rodriguez
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, United States of America
| | - Keith P Choe
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, United States of America
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16
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Liang Y, Wang Y, Zhu X, Cai J, Shi A, Huang J, Zhu Q, Si Y. Binding of Glycerol to Human Galectin-7 Expands Stability and Modulates Its Functions. Int J Mol Sci 2022; 23:ijms232012318. [PMID: 36293173 PMCID: PMC9604435 DOI: 10.3390/ijms232012318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Glycerol is seen in biological systems as an intermediate in lipid metabolism. In recent years, glycerol has been reported to act as a chemical chaperone to correct the conformation of proteins. Here, we investigate the role of glycerol in galectin-7 (Gal-7). The thermal shift and CD assays showed that the thermal stability of Gal-7 increased with glycerol concentration but with little secondary structure changes induced by glycerol. In addition, glycerol can inhibit Gal-7-mediated erythrocyte agglutination. We also solved the crystal structures of human Gal-7 in complex with glycerol in two different conditions. Glycerol binds at the carbohydrate-recognition binding sites of Gal-7, which indicates glycerol as a small ligand for Gal-7. Surprisingly, glycerol can bind a new pocket near the N-terminus of Gal-7, which can greatly reduce the flexibility and improve the stability of this region. Moreover, overexpression of Gal-7 decreased the intracellular triglyceride levels and increased mRNA expression of aquaporin-3 (AQP-3) when HeLa cells were incubated with glycerol. These findings indicate that Gal-7 might regulate glycerol metabolism. Overall, our results on human Gal-7 raise the perspective to systematically explore this so far unrecognized phenomenon for Gal-7 in glycerol metabolism.
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17
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Correia BSB, Ferreira VG, Piagge PMFD, Almeida MB, Assunção NA, Raimundo JRS, Fonseca FLA, Carrilho E, Cardoso DR. 1H qNMR-Based Metabolomics Discrimination of Covid-19 Severity. J Proteome Res 2022; 21:1640-1653. [PMID: 35674498 PMCID: PMC9212193 DOI: 10.1021/acs.jproteome.1c00977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Indexed: 01/08/2023]
Abstract
The coronavirus disease 2019 (Covid-19), which caused respiratory problems in many patients worldwide, led to more than 5 million deaths by the end of 2021. Experienced symptoms vary from mild to severe illness. Understanding the infection severity to reach a better prognosis could be useful to the clinics, and one study area to fulfill one piece of this biological puzzle is metabolomics. The metabolite profile and/or levels being monitored can help predict phenotype properties. Therefore, this study evaluated plasma metabolomes of 110 individual samples, 57 from control patients and 53 from recent positive cases of Covid-19 (IgM 98% reagent), representing mild to severe symptoms, before any clinical intervention. Polar metabolites from plasma samples were analyzed by quantitative 1H NMR. Glycerol, 3-aminoisobutyrate, formate, and glucuronate levels showed alterations in Covid-19 patients compared to those in the control group (Tukey's HSD p-value cutoff = 0.05), affecting the lactate, phenylalanine, tyrosine, and tryptophan biosynthesis and d-glutamine, d-glutamate, and glycerolipid metabolisms. These metabolic alterations show that SARS-CoV-2 infection led to disturbance in the energetic system, supporting the viral replication and corroborating with the severe clinical conditions of patients. Six polar metabolites (glycerol, acetate, 3-aminoisobutyrate, formate, glucuronate, and lactate) were revealed by PLS-DA and predicted by ROC curves and ANOVA to be potential prognostic metabolite panels for Covid-19 and considered clinically relevant for predicting infection severity due to their straight roles in the lipid and energy metabolism. Thus, metabolomics from samples of Covid-19 patients is a powerful tool for a better understanding of the disease mechanism of action and metabolic consequences of the infection in the human body and may corroborate allowing clinicians to intervene quickly according to the needs of Covid-19 patients.
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Affiliation(s)
- Banny S. B. Correia
- Instituto de Química de São Carlos,
Universidade de São Paulo, São Carlos, SP
13566-590, Brazil
| | - Vinicius G. Ferreira
- Instituto de Química de São Carlos,
Universidade de São Paulo, São Carlos, SP
13566-590, Brazil
- Instituto Nacional de Ciência e Tecnologia de
Bioanalítica, INCTBio, Campinas, SP 13083-861,
Brazil
| | | | - Mariana B. Almeida
- Instituto de Química de São Carlos,
Universidade de São Paulo, São Carlos, SP
13566-590, Brazil
- Instituto Nacional de Ciência e Tecnologia de
Bioanalítica, INCTBio, Campinas, SP 13083-861,
Brazil
| | - Nilson A. Assunção
- Instituto de Ciências Ambientais, Químicas
e Farmacêuticas, Universidade Federal de São
Paulo, São Paulo, SP 09972-270, Brazil
| | | | - Fernando L. A. Fonseca
- Faculdade de Medicina do
ABC, Santo André, SP 09060-870, Brazil
- Departamento de Ciências Farmacêuticas,
Universidade Federal de São Paulo, Diadema, SP
09972-270, Brazil
| | - Emanuel Carrilho
- Instituto de Química de São Carlos,
Universidade de São Paulo, São Carlos, SP
13566-590, Brazil
- Instituto Nacional de Ciência e Tecnologia de
Bioanalítica, INCTBio, Campinas, SP 13083-861,
Brazil
| | - Daniel R. Cardoso
- Instituto de Química de São Carlos,
Universidade de São Paulo, São Carlos, SP
13566-590, Brazil
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Teng GC, Boo MV, Lam SH, Pang CZ, Chew SF, Ip YK. Molecular characterization and light-dependent expression of glycerol facilitator (GlpF) in coccoid Symbiodiniaceae dinoflagellates of the giant clam Tridacna squamosa. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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McLendon BA, Kramer AC, Seo H, Burghardt RC, Bazer FW, Wu G, Johnson GA. Temporal and spatial expression of aquaporins 1, 5, 8, and 9: Potential transport of water across the endometrium and chorioallantois of pigs. Placenta 2022; 124:28-36. [DOI: 10.1016/j.placenta.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
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20
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Lemieux H, Blier PU. Exploring Thermal Sensitivities and Adaptations of Oxidative Phosphorylation Pathways. Metabolites 2022; 12:metabo12040360. [PMID: 35448547 PMCID: PMC9025460 DOI: 10.3390/metabo12040360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Temperature shifts are a major challenge to animals; they drive adaptations in organisms and species, and affect all physiological functions in ectothermic organisms. Understanding the origin and mechanisms of these adaptations is critical for determining whether ectothermic organisms will be able to survive when faced with global climate change. Mitochondrial oxidative phosphorylation is thought to be an important metabolic player in this regard, since the capacity of the mitochondria to produce energy greatly varies according to temperature. However, organism survival and fitness depend not only on how much energy is produced, but, more precisely, on how oxidative phosphorylation is affected and which step of the process dictates thermal sensitivity. These questions need to be addressed from a new perspective involving a complex view of mitochondrial oxidative phosphorylation and its related pathways. In this review, we examine the effect of temperature on the commonly measured pathways, but mainly focus on the potential impact of lesser-studied pathways and related steps, including the electron-transferring flavoprotein pathway, glycerophosphate dehydrogenase, dihydroorotate dehydrogenase, choline dehydrogenase, proline dehydrogenase, and sulfide:quinone oxidoreductase. Our objective is to reveal new avenues of research that can address the impact of temperature on oxidative phosphorylation in all its complexity to better portray the limitations and the potential adaptations of aerobic metabolism.
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Affiliation(s)
- Hélène Lemieux
- Faculty Saint-Jean, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6C 4G9, Canada
- Correspondence: (H.L.); (P.U.B.)
| | - Pierre U. Blier
- Department Biologie, Université du Québec à Rimouski, Rimouski, QC G5L 3A1, Canada
- Correspondence: (H.L.); (P.U.B.)
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21
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Glycerol-3-phosphate phosphatase operates a glycerol shunt in pancreatic β-cells that controls insulin secretion and metabolic stress. Mol Metab 2022; 60:101471. [PMID: 35272070 PMCID: PMC8972011 DOI: 10.1016/j.molmet.2022.101471] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/20/2022] [Accepted: 03/03/2022] [Indexed: 11/23/2022] Open
Abstract
Objective The recently identified glycerol-3-phosphate (Gro3P) phosphatase (G3PP) in mammalian cells, encoded by the PGP gene, was shown to regulate glucose, lipid and energy metabolism by hydrolyzing Gro3P and to control glucose-stimulated insulin secretion (GSIS) in β-cells, in vitro. However, whether G3PP regulates β-cell function and insulin secretion in vivo is not known. Methods We now examined the role of G3PP in the control of insulin secretion in vivo, β-cell function and glucotoxicity in inducible β-cell specific G3PP-KO (BKO) mice. Inducible BKO mice were generated by crossing floxed-G3PP mice with Mip-Cre-ERT (MCre) mice. All the in vivo studies were done using BKO and control mice fed normal diet and the ex vivo studies were done using pancreatic islets from these mice. Results BKO mice, compared to MCre controls, showed increased body weight, adiposity, fed insulinemia, enhanced in vivo GSIS, reduced plasma triglycerides and mild glucose intolerance. Isolated BKO mouse islets incubated at high (16.7 mM), but not at low or intermediate glucose (3 and 8 mM), showed elevated GSIS, Gro3P content as well as increased levels of metabolites and signaling coupling factors known to reflect β-cell activation for insulin secretion. BKO islets also showed reduced glycerol release and increased O2 consumption and ATP production at high glucose only. BKO islets chronically exposed to elevated glucose levels showed increased apoptosis, reduced insulin content and decreased mRNA expression of β-cell differentiation markers, Pdx-1, MafA and Ins-2. Conclusions The results demonstrate that β-cells are endowed with a “glycerol shunt”, operated by G3PP that regulates β-cell metabolism, signaling and insulin secretion in vivo, primarily at elevated glucose concentrations. We propose that the glycerol shunt plays a role in preventing insulin hypersecretion and excess body weight gain and contributes to β-cell mass preservation in the face of hyperglycemia. G3PP operates a glycerol shunt in β-cells to remove excess glucose as glycerol. Inducible β-cell specific G3PP-KO (BKO) mice show hyperinsulinemia. BKO mice show enhanced body weight and glucose induced insulin secretion. BKO isolated islets show elevated insulin secretion only at high glucose. Chronic exposure of BKO isolated islets to high glucose enhances glucotoxicity.
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22
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Localization of aquaglyceroporins in human and murine white adipose tissue. Histochem Cell Biol 2022; 157:623-639. [PMID: 35235046 DOI: 10.1007/s00418-022-02090-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2022] [Indexed: 11/04/2022]
Abstract
The glycerol channel AQP7 facilitates glycerol efflux from adipose tissue (AT), and AQP7 deficiency has been suggested to promote obesity. However, the release of glycerol from AT is not fully blocked in AQP7-deficient mice, which suggests that either alternative glycerol channels are present in AT or significant simple diffusion of glycerol occurs. Previous investigations of the expression of other aquaglyceroporins (AQP3, AQP9, AQP10) than AQP7 in AT are contradictory. Therefore, we here aim at determining the cellular localization of AQP3 and AQP9 in addition to AQP7 in human and mouse AT using well-characterized antibodies for immunohistochemistry (IHC) and immunoblotting as well as available single-cell transcriptomic data from human and mouse AT. We confirm that AQP7 is expressed in endothelial cells and adipocytes in human AT and find ex vivo evidence for interaction between AQP7 and perilipin-1 in adipocytes. In addition, labeling for AQP7 in human AT also includes CD68-positive cells. No labeling for AQP3 or AQP9 was identified in endothelial cells or adipocytes in human or mouse AT using IHC. Instead, in human AT, AQP3 was predominantly found in erythrocytes, whereas AQP9 expression was observed in a small number of CD15-positive cells. The transcriptomic data revealed that AQP3 mRNA was found in a low number of cells in most of the identified cell clusters, whereas AQP9 mRNA was found in myeloid cell clusters as well as in clusters likely representing mesothelial progenitor cells. No AQP10 mRNA was identified in human AT. In conclusion, the presented results do not suggest a functional overlap between AQP3/AQP9/AQP10 and AQP7 in human or mouse white AT.
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Zhang X, Wu Q, Zheng W, Liu C, Huang L, Zuo X, Xiao W, Han X, Ye H, Wang W, Zhu Y, Yang L. Exogenous Linoleic Acid Intervention Alters Hepatic Glucose Metabolism in an Avian Embryo Model. Front Physiol 2022; 13:844148. [PMID: 35264980 PMCID: PMC8899105 DOI: 10.3389/fphys.2022.844148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/31/2022] [Indexed: 11/28/2022] Open
Abstract
In the present study, developmental changes of gluconeogenesis and glycolysis in an avian model were measured, and then the intervention effects of in ovo feeding (IOF) linoleic acid (LA) on hepatic glucose metabolism were evaluated. In Experiment 1, thirty fertilized eggs were sampled on embryonic days (E) of 16, 19, 22, 25, 28, 31, and thirty newly-hatched ducklings at hatch (E34 and E35). In Experiment 2, a total of 120 fertilized eggs (60 eggs for each group) were injected into the yolk sac with PBS as the control group and LA as the IOF LA group on E25. Twelve eggs were selected for sample collection on E28 and E31. Serum contents of glucose, pyruvate, and lactate increased ( p < 0.05) linearly or quadratically from E16 to hatch, as well as hepatic glycogen and pyruvate contents. Hepatic mRNA expression related to energy homeostasis, gluconeogenesis, and glycolysis increased ( p < 0.05) in embryogenesis, and the plateau period was presented on E25–E31. IOF LA decreased ( p < 0.05) serum contents of glucose, triacylglycerol, cholesterol, and hepatic oleic acid, unsaturated fatty acids on E28, as well as the gene expression relative to gluconeogenesis. IOF LA increased ( p < 0.05) pyruvate content in serum and liver, and hepatic gene expression relative to glycolysis on E31. In summary, hepatic gluconeogenesis and glycolysis were enhanced to meet the increasing energy demands of embryonic development during E25 – hatch. Exogenous LA intervention on E25 could inhibit hepatic gluconeogenesis and enhance glycolysis during the later developmental period, disrupting glucose embryonic homeostasis and energy status.
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Affiliation(s)
- Xiufen Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qilin Wu
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wenxuan Zheng
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Chuang Liu
- Wen’s Food Group Co., Ltd., Yunfu, China
| | - Liang Huang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xin Zuo
- Wen’s Food Group Co., Ltd., Yunfu, China
| | | | | | - Hui Ye
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wence Wang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yongwen Zhu
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
- Yongwen Zhu,
| | - Lin Yang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
- *Correspondence: Lin Yang,
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Ning Z, Lang K, Xia K, Linhardt RJ, Gross RA. Lipase-Catalyzed Synthesis and Characterization of Poly(glycerol sebacate). Biomacromolecules 2021; 23:398-408. [PMID: 34936341 DOI: 10.1021/acs.biomac.1c01351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study demonstrated that immobilized Candida antarctica lipase B (N435) catalysis in bulk leads to higher molecular weight poly(glycerol sebacate), PGS, than self-catalyzed condensation polymerization. Since the glass-transition temperature, fragility, modulus, and strength for rubbery networks are inversely dependent on the concentration of chain ends, higher molecular weight PGS prepolymers will enable the preparation of cross-linked PGS matrices with unique mechanical properties. The evolution of molecular species during the prepolymerization step conducted at 120 °C for 24 h, prior to enzyme addition, revealed regular decreases in sebacic acid and glycerol-sebacate dimer with corresponding increases in oligomers with chain lengths from 3 to 7 units such that a homogeneous liquid substrate has resulted. At 67 h, for N435-catalyzed PGS synthesis, the carboxylic acid conversion reached 82% without formation of a gel fraction, and number-average molecular weight (Mn) and weight-average molecular weight (Mw) values reached 6000 and 59 400 g/mol, respectively. In contrast, self-catalyzed PGS condensation polymerizations required termination at 55 h to avoid gelation, reached 72% conversion, and Mn and Mw values of 2600 and 13 800 g/mol, respectively. We also report the extent that solvent fractionation can enrich PGS in higher molecular weight chains. The use of methanol as a nonsolvent increased Mn and Mw by 131.7 and 18.3%, respectively, and narrower dispersity (Đ) decreased by 47.7% relative to the nonfractionated product.
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Affiliation(s)
- Zhuoyuan Ning
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, Henan, P. R. China
| | - Kening Lang
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Ke Xia
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department of Biomedical Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Richard A Gross
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department of Biomedical Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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25
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Pedersen S, Hansen JB, Maltesen RG, Szejniuk WM, Andreassen T, Falkmer U, Kristensen SR. Identifying metabolic alterations in newly diagnosed small cell lung cancer patients. Metabol Open 2021; 12:100127. [PMID: 34585134 PMCID: PMC8455369 DOI: 10.1016/j.metop.2021.100127] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Small cell lung cancer (SCLC) is a malignant disease with poor prognosis. At the time of diagnosis most patients are already in a metastatic stage. Current diagnosis is based on imaging, histopathology, and immunohistochemistry, but no blood-based biomarkers have yet proven to be clinically successful for diagnosis and screening. The precise mechanisms of SCLC are not fully understood, however, several genetic mutations, protein and metabolic aberrations have been described. We aim at identifying metabolite alterations related to SCLC and to expand our knowledge relating to this aggressive cancer. METHODS A total of 30 serum samples of patients with SCLC, collected at the time of diagnosis, and 25 samples of healthy controls were included in this study. The samples were analyzed with nuclear magnetic resonance spectroscopy. Multivariate, univariate and pathways analyses were performed. RESULTS Several metabolites were identified to be altered in the pre-treatment serum samples of small-cell lung cancer patients compared to healthy individuals. Metabolites involved in tricarboxylic acid cycle (succinate: fold change (FC) = 2.4, p = 0.068), lipid metabolism (LDL triglyceride: FC = 1.3, p = 0.001; LDL-1 triglyceride: FC = 1.3, p = 0.012; LDL-2 triglyceride: FC = 1.4, p = 0.009; LDL-6 triglyceride: FC = 1.5, p < 0.001; LDL-4 cholesterol: FC = 0.5, p = 0.007; HDL-3 free cholesterol: FC = 0.7, p = 0.002; HDL-4 cholesterol FC = 0.8, p < 0.001; HDL-4 apolipoprotein-A1: FC = 0.8, p = 0.005; HDL-4 apolipoprotein-A2: FC ≥ 0.7, p ≤ 0.001), amino acids (glutamic acid: FC = 1.7, p < 0.001; glutamine: FC = 0.9, p = 0.007, leucine: FC = 0.8, p < 0.001; isoleucine: FC = 0.8, p = 0.016; valine: FC = 0.9, p = 0.032; lysine: FC = 0.8, p = 0.004; methionine: FC = 0.8, p < 0.001; tyrosine: FC = 0.7, p = 0.002; creatine: FC = 0.9, p = 0.030), and ketone body metabolism (3-hydroxybutyric acid FC = 2.5, p < 0.001; acetone FC = 1.6, p < 0.001), among other, were found deranged in SCLC. CONCLUSIONS This study provides novel insight into the metabolic disturbances in pre-treatment SCLC patients, expanding our molecular understanding of this malignant disease.
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Affiliation(s)
- Shona Pedersen
- Department of Basic Medical Science, College of Medicine, Qatar University, QU Health, Doha, Qatar
| | | | - Raluca Georgiana Maltesen
- Translational Radiation Biology and Oncology Laboratory, Centre for Cancer Research, Westmead Institute of Medical Research, Westmead, 2145, Australia
| | - Weronika Maria Szejniuk
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Oncology, Aalborg University Hospital, Aalborg, Denmark
| | - Trygve Andreassen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ursula Falkmer
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Oncology, Aalborg University Hospital, Aalborg, Denmark
| | - Søren Risom Kristensen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
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26
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Biosynthetic Mechanisms and Biological Significance of Glycerol Phosphate-Containing Glycan in Mammals. Molecules 2021; 26:molecules26216675. [PMID: 34771084 PMCID: PMC8587909 DOI: 10.3390/molecules26216675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022] Open
Abstract
Bacteria contain glycerol phosphate (GroP)-containing glycans, which are important constituents of cell-surface glycopolymers such as the teichoic acids of Gram-positive bacterial cell walls. These glycopolymers comprising GroP play crucial roles in bacterial physiology and virulence. Recently, the first identification of a GroP-containing glycan in mammals was reported as a variant form of O-mannosyl glycan on α-dystroglycan (α-DG). However, the biological significance of such GroP modification remains largely unknown. In this review, we provide an overview of this new discovery of GroP-containing glycan in mammals and then outline the recent progress in elucidating the biosynthetic mechanisms of GroP-containing glycans on α-DG. In addition, we discuss the potential biological role of GroP modification along with the challenges and prospects for further research. The progress in this newly identified glycan modification will provide insights into the phylogenetic implications of glycan.
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27
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Qiu L, Daniell TJ, Banwart SA, Nafees M, Wu J, Du W, Yin Y, Guo H. Insights into the mechanism of the interference of sulfadiazine on soil microbial community and function. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126388. [PMID: 34171664 DOI: 10.1016/j.jhazmat.2021.126388] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/18/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
The accumulation of sulfonamides in the soil environment possessed the potential to change soil microbial community and function. Metabolomics is capable of providing insights into the carbon metabolic pool and molecular mechanisms associated with external stressors. Here we evaluated alternations in soil bacterial community and soil metabolites profiles under sulfadiazine (SDZ) exposure and proposed a potential mechanism that SDZ accumulation in soil affected soil organic matter (SOM) cycling. Sequencing analysis showed that the relative abundance of bacterial species associated with carbon cycling significantly decreased under high concentrations of SDZ exposure. Untargeted metabolomics analysis showed that 78 metabolites were significantly changed with the presence of SDZ in soil. The combination of functional predictions and pathway analysis both demonstrated that high concentrations of SDZ exposure could cause disturbance in anabolism and catabolism. Moreover, the noticeable decline in the relative content of carbohydrates under high concentrations of SDZ exposure might weaken physical separation and provide more chances for microbes to degrade SOM. The above results provided evidence that SDZ accumulation in soil held the potential to disturb SOM cycling. These findings spread our understanding about the environmental risk of antibiotic in the soil environment beyond the dissemination of antibiotic resistance.
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Affiliation(s)
- Linlin Qiu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Tim J Daniell
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Steven A Banwart
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK; Global Food and Environment Institute, University of Leeds, Leeds LS2 9JT, UK
| | - Muhammad Nafees
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jingjing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Wenchao Du
- School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Ying Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongyan Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China; Joint International Research Centre for Critical Zone Science-University of Leeds and Nanjing University, Nanjing University, Nanjing 210023, China.
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28
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Tracing Key Molecular Regulators of Lipid Biosynthesis in Tuber Development of Cyperus esculentus Using Transcriptomics and Lipidomics Profiling. Genes (Basel) 2021; 12:genes12101492. [PMID: 34680888 PMCID: PMC8535953 DOI: 10.3390/genes12101492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Cyperus esculentus is widely representing one of the important oil crops around the world, which provides valuable resources of edible tubers called tiger nut. The chemical composition and high ability to produce fats emphasize the role of tiger nut in promoting oil crop productivity. However, the underlying molecular mechanism of the production and accumulation of lipids in tiger nut development still remains unclear. Here, we conducted comprehensive transcriptomics and lipidomics analyses at different developmental stages of tuber in Cyperus esculentus. Lipidomic analyses confirmed that the accumulation of lipids including glycolipids, phospholipids, and glycerides were significantly enriched during tuber development from early to mature stage. The proportion of phosphatidylcholines (PC) declined during all stages and phosphatidyl ethanolamine (PE) was significantly declined in early and middle stages. These findings implied that PC is actively involved in triacylglycerol (TAG) biosynthesis during the tubers development, whereas PE may participate in TAG metabolism during early and middle stages. Comparative transcriptomics analyses indicated several genomic and metabolic pathways associated with lipid metabolism during tuber development in tiger nut. The Pearson correlation analysis showed that TAG synthesis in different developmental stages was attributed to 37 candidate transcripts including CePAH1. The up-regulation of diacylglycerol (DAG) and oil content in yeast, resulted from the inducible expression of exogenous CePAH1 confirmed the central role of this candidate gene in lipid metabolism. Our results demonstrated the foundation of an integrative metabolic model for understanding the molecular mechanism of tuber development in tiger nut, in which lipid biosynthesis plays a central role.
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29
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Falconer J, Pucino V, Clayton SA, Marshall JL, Raizada S, Adams H, Philp A, Clark AR, Filer A, Raza K, Young SP, Buckley CD. Spontaneously Resolving Joint Inflammation Is Characterised by Metabolic Agility of Fibroblast-Like Synoviocytes. Front Immunol 2021; 12:725641. [PMID: 34512657 PMCID: PMC8426599 DOI: 10.3389/fimmu.2021.725641] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/09/2021] [Indexed: 01/01/2023] Open
Abstract
Fibroblast-like synoviocytes (FLS) play an important role in maintaining joint homeostasis and orchestrating local inflammatory processes. When activated during injury or inflammation, FLS undergo transiently increased bioenergetic and biosynthetic demand. We aimed to identify metabolic changes which occur early in inflammatory disease pathogenesis which might support sustained cellular activation in persistent inflammation. We took primary human FLS from synovial biopsies of patients with very early rheumatoid arthritis (veRA) or resolving synovitis, and compared them with uninflamed control samples from the synovium of people without arthritis. Metabotypes were compared using NMR spectroscopy-based metabolomics and correlated with serum C-reactive protein levels. We measured glycolysis and oxidative phosphorylation by Seahorse analysis and assessed mitochondrial morphology by immunofluorescence. We demonstrate differences in FLS metabolism measurable after ex vivo culture, suggesting that disease-associated metabolic changes are long-lasting. We term this phenomenon 'metabolic memory'. We identify changes in cell metabolism after acute TNFα stimulation across disease groups. When compared to FLS from patients with early rheumatoid arthritis, FLS from patients with resolving synovitis have significantly elevated mitochondrial respiratory capacity in the resting state, and less fragmented mitochondrial morphology after TNFα treatment. Our findings indicate the potential to restore cell metabotypes by modulating mitochondrial function at sites of inflammation, with implications for treatment of RA and related inflammatory conditions in which fibroblasts play a role.
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Affiliation(s)
- Jane Falconer
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom.,School of Medicine, Institute of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
| | - Valentina Pucino
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Sally A Clayton
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom.,Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jennifer L Marshall
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Sabrina Raizada
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Holly Adams
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Andrew Philp
- Healthy Ageing Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, UNSW Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Andrew R Clark
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Karim Raza
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom.,Department of Rheumatology, Sandwell and West Birmingham NHS Trust, Birmingham, United Kingdom
| | - Stephen P Young
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Christopher D Buckley
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom.,Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
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30
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Chang L, Lu H, Chen H, Tang X, Zhao J, Zhang H, Chen YQ, Chen W. Lipid metabolism research in oleaginous fungus Mortierella alpina: Current progress and future prospects. Biotechnol Adv 2021; 54:107794. [PMID: 34245810 DOI: 10.1016/j.biotechadv.2021.107794] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 06/11/2021] [Accepted: 07/04/2021] [Indexed: 12/19/2022]
Abstract
The oleaginous fungus Mortierella alpina has distinct advantages in long-chain PUFAs production, and it is the only source for dietary arachidonic acid (ARA) certificated by FDA and European Commission. This review provides an overall introduction to M. alpina, including its major research methods, key factors governing lipid biosynthesis, metabolic engineering and omics studies. Currently, the research interests in M. alpina focus on improving lipid yield and fatty acid desaturation degree by enhancing fatty acid precursors and the reducing power NADPH, and genetic manipulation on PUFAs synthetic pathways is carried to optimise fatty acid composition. Besides, multi-omics studies have been applied to elucidate the global regulatory mechanism of lipogenesis in M. alpina. However, research challenges towards achieving a lipid cell factory lie in strain breeding and cost control due to the coenocytic mycelium, long fermentation period and insufficient conversion rate from carbon to lipid. We also proposed future research goals based on a multilevel regulating strategy: obtaining ideal chassis by directional evolution and high-throughput screening; rewiring central carbon metabolism and inhibiting competitive pathways by multi-gene manipulation system to enhance carbon to lipid conversion rate; optimisation of protein function based on post-translational modification; application of dynamic fermentation strategies suitable for different fermentation phases. By reviewing the comprehensive research progress of this oleaginous fungus, we aim to further comprehend the fungal lipid metabolism and provide reference information and guidelines for the exploration of microbial oils from the perspectives of fundamental research to industrial application.
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Affiliation(s)
- Lulu Chang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Hengqian Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China; Wuxi Translational Medicine Research Center, Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, Jiangsu 214122, PR China; Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
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31
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Zhao Y, Cao P, Cui Y, Liu D, Li J, Zhao Y, Yang S, Zhang B, Zhou R, Sun M, Guo X, Yang M, Xin D, Zhang Z, Li X, Lv C, Liu C, Qi Z, Xu J, Wu X, Chen Q. Enhanced production of seed oil with improved fatty acid composition by overexpressing NAD + -dependent glycerol-3-phosphate dehydrogenase in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1036-1053. [PMID: 33768659 DOI: 10.1111/jipb.13094] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
There is growing interest in expanding the production of soybean oils (mainly triacylglycerol, or TAG) to meet rising feed demand and address global energy concerns. We report that a plastid-localized glycerol-3-phosphate dehydrogenase (GPDH), encoded by GmGPDHp1 gene, catalyzes the formation of glycerol-3-phosphate (G3P), an obligate substrate required for TAG biosynthesis. Overexpression of GmGPDHp1 increases soybean seed oil content with high levels of unsaturated fatty acids (FAs), especially oleic acid (C18:1), without detectably affecting growth or seed protein content or seed weight. Based on the lipidomic analyses, we found that the increase in G3P content led to an elevated diacylglycerol (DAG) pool, in which the Kennedy pathway-derived DAG was mostly increased, followed by PC-derived DAG, thereby promoting the synthesis of TAG containing relatively high proportion of C18:1. The increased G3P levels induced several transcriptional alterations of genes involved in the glycerolipid pathways. In particular, genes encoding the enzymes responsible for de novo glycerolipid synthesis were largely upregulated in the transgenic lines, in-line with the identified biochemical phenotype. These results reveal a key role for GmGPDHp1-mediated G3P metabolism in enhancing TAG synthesis and demonstrate a strategy to modify the FA compositions of soybean oils for improved nutrition and biofuel.
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Affiliation(s)
- Ying Zhao
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Pan Cao
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Yifan Cui
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Dongxu Liu
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Jiapeng Li
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Yabin Zhao
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Siqi Yang
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Bo Zhang
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Runnan Zhou
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Minghao Sun
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Xuetian Guo
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Mingliang Yang
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Dawei Xin
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Zhanguo Zhang
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Xin Li
- Key Lab of Maize Genetics and Breeding, Heilongjiang Academy of Agricultural Sciences, Harbin, 150000, China
- Department of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Chen Lv
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Chunyan Liu
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Zhaoming Qi
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Jingyu Xu
- Department of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Xiaoxia Wu
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Qingshan Chen
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
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32
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Piras C, Pibiri M, Leoni VP, Balsamo A, Tronci L, Arisci N, Mariotti S, Atzori L. Analysis of metabolomics profile in hypothyroid patients before and after thyroid hormone replacement. J Endocrinol Invest 2021; 44:1309-1319. [PMID: 33025552 DOI: 10.1007/s40618-020-01434-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE The serum metabolic changes occurring during the transition from hypothyroidism to euthyroidism are not known. This study aimed to determine the metabolomic profile in hypothyroid patients before (HypoT0) and after (HypoT1) euthyroidism achieved through levothyroxine (L-T4) treatment. METHODS Eighteen patients with overt primary hypothyroidism were recruited for the study. All patients were treated with L-T4 to achieve euthyroidism. Thyrotropin (TSH), free thyroxine (FT4), free triiodothyronine (FT3) and metabolomics profiles were measured before and after 3 months of treatment. The euthyroid control group consisted of 28 healthy volunteers. Metabolomics analysis was performed using Nuclear Magnetic Resonance (NMR) spectroscopy. RESULTS 1H NMR-based metabolomics profiling of patients with newly diagnosed hypothyroidism (HypoT0) showed significantly higher levels of citrate, creatinine, glycerol, myo-inositol and serine, and lower levels of proline and taurine compared to controls. Interestingly, some metabolic changes were persistent three months after pharmacological treatments, despite normal serum TSH and thyroid hormone concentrations (HypoT1). When an Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) model was built to evaluate possible differences in the metabolic profile between HypoT0 and HypoT1, the data obtained were not significantly different. CONCLUSION These results suggest that metabolic changes in the patients with hypothyroidism may persist after normalization of serum levels of FT3, FT4, and TSH, which currently represent the gold standard in laboratory testing for diagnosis and evaluation of thyroid pathology. So, the metabolomics approach may contribute to integrate classical hormone assays and to determine the euthyroid status achievement with greater efficacy.
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Affiliation(s)
- C Piras
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - M Pibiri
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - V P Leoni
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - A Balsamo
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - L Tronci
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - N Arisci
- Department of Medical Sciences and Public Health, University of Cagliari, 09042, Monserrato, Italy
| | - S Mariotti
- Department of Medical Sciences and Public Health, University of Cagliari, 09042, Monserrato, Italy.
| | - L Atzori
- Department of Biomedical Sciences, University of Cagliari, 09042, Monserrato, Italy
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Kotecka K, Kawalek A, Kobylecki K, Bartosik AA. The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:5066. [PMID: 34064685 PMCID: PMC8151288 DOI: 10.3390/ijms22105066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa encodes a large set of transcriptional regulators (TRs) that modulate and manage cellular metabolism to survive in variable environmental conditions including that of the human body. The AraC family regulators are an abundant group of TRs in bacteria, mostly acting as gene expression activators, controlling diverse cellular functions (e.g., carbon metabolism, stress response, and virulence). The PA3027 protein from P. aeruginosa has been classified in silico as a putative AraC-type TR. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3027 revealed a spectacular increase in the mRNA levels of PA3026-PA3024 (divergent to PA3027), PA3464, and PA3342 genes encoding proteins potentially involved in glycerolipid metabolism. Concomitantly, chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that at least 22 regions are bound by PA3027 in the PAO1161 genome. These encompass promoter regions of PA3026, PA3464, and PA3342, showing the major increase in expression in response to PA3027 excess. In Vitro DNA binding assay confirmed interactions of PA3027 with these regions. Furthermore, promoter-reporter assays in a heterologous host showed the PA3027-dependent activation of the promoter of the PA3026-PA3024 operon. Two motifs representing the preferred binding sites for PA3027, one localized upstream and one overlapping with the -35 promoter sequence, were identified in PA3026p and our data indicate that both motifs are required for full activation of this promoter by PA3027. Overall, the presented data show that PA3027 acts as a transcriptional regulator in P. aeruginosa, activating genes likely engaged in glycerolipid metabolism. The GliR name, from a glycerolipid metabolism regulator, is proposed for PA3027 of P. aeruginosa.
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Affiliation(s)
| | | | | | - Aneta Agnieszka Bartosik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (K.K.); (A.K.); (K.K.)
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Jaiswal SK, Agarwal SM, Thodum P, Sharma VK. SkinBug: an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics. iScience 2021; 24:101925. [PMID: 33385118 PMCID: PMC7772573 DOI: 10.1016/j.isci.2020.101925] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/08/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022] Open
Abstract
In addition to being pivotal for the host health, the skin microbiome possesses a large reservoir of metabolic enzymes, which can metabolize molecules (cosmetics, medicines, pollutants, etc.) that form a major part of the skin exposome. Therefore, to predict the complete metabolism of any molecule by skin microbiome, a curated database of metabolic enzymes (1,094,153), reactions, and substrates from ∼900 bacterial species from 19 different skin sites were used to develop “SkinBug.” It integrates machine learning, neural networks, and chemoinformatics methods, and displays a multiclass multilabel accuracy of up to 82.4% and binary accuracy of up to 90.0%. SkinBug predicts all possible metabolic reactions and associated enzymes, reaction centers, skin microbiome species harboring the enzyme, and the respective skin sites. Thus, SkinBug will be an indispensable tool to predict xenobiotic/biotic metabolism by skin microbiome and will find applications in exposome and microbiome studies, dermatology, and skin cancer research. SkinBug is AI/ML-based tool to predict metabolism of molecules by Skin microbiome Database of 1,094,153 metabolic enzymes from 897 pangenomes of skin microbiome Predicts enzymes, bacterial species, and skin sites for the predicted reactions 82.4% multilabel and 90.0% binary accuracy, and validated on 28 diverse real cases
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Affiliation(s)
- Shubham K Jaiswal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Shitij Manojkumar Agarwal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Parikshit Thodum
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
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Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum. Int J Mol Sci 2020; 21:ijms21249570. [PMID: 33339113 PMCID: PMC7765489 DOI: 10.3390/ijms21249570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/05/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Glycerol is an organic compound that can be utilized as an alternative source of carbon by various organisms. One of the ways to assimilate glycerol by the cell is the phosphorylative catabolic pathway in which its activation is catalyzed by glycerol kinase (GK) and glycerol-3-phosphate (G3P) is formed. To date, several GK crystal structures from bacteria, archaea, and unicellular eukaryotic parasites have been solved. Herein, we present a series of crystal structures of GK from Chaetomium thermophilum (CtGK) in apo and glycerol-bound forms. In addition, we show the feasibility of an ADP-dependent glucokinase (ADPGK)-coupled enzymatic assay to measure the CtGK activity. New structures described in our work provide structural insights into the GK catalyzed reaction in the filamentous fungus and set the foundation for understanding the glycerol metabolism in eukaryotes.
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Kuhlisch C, Althammer J, Sazhin AF, Jakobsen HH, Nejstgaard JC, Pohnert G. Metabolomics-derived marker metabolites to characterize Phaeocystis pouchetii physiology in natural plankton communities. Sci Rep 2020; 10:20444. [PMID: 33235278 PMCID: PMC7686483 DOI: 10.1038/s41598-020-77169-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 10/28/2020] [Indexed: 01/07/2023] Open
Abstract
Phaeocystis pouchetii (Hariot) Lagerheim, 1893 regularly dominates phytoplankton blooms in higher latitudes spanning from the English Channel to the Arctic. Through zooplankton grazing and microbial activity, it is considered to be a key resource for the entire marine food web, but the actual relevance of biomass transfer to higher trophic levels is still under discussion. Cell physiology and algal nutritional state are suggested to be major factors controlling the observed variability in zooplankton grazing. However, no data have so far yielded insights into the metabolic state of Phaeocystis populations that would allow testing this hypothesis. Therefore, endometabolic markers of different growth phases were determined in laboratory batch cultures using comparative metabolomics and quantified in different phytoplankton blooms in the field. Metabolites, produced during exponential, early and late stationary growth of P. pouchetii, were profiled using gas chromatography-mass spectrometry. Then, metabolites were characterized that correlate with the growth phases using multivariate statistical analysis. Free amino acids characterized the exponential growth, whereas the early stationary phase was correlated with sugar alcohols, mono- and disaccharides. In the late stationary phase, free fatty acids, sterols and terpenes increased. These marker metabolites were then traced in Phaeocystis blooms during a cruise in the Barents Sea and North Norwegian fjords. About 50 endometabolites of P. pouchetii were detected in natural phytoplankton communities. Mannitol, scyllo-inositol, 24-methylcholesta-5,22-dien-3β-ol, and several free fatty acids were characteristic for Phaeocystis-dominated blooms but showed variability between them. Distinct metabolic profiles were detected in the nutrient-depleted community in the inner Porsangerfjord (< 0.5 µM NO3-, < 0.1 µM PO 4 3- ), with high relative amounts of free mono- and disaccharides indicative for a limited culture. This study thereby shows how the variable physiology of phytoplankton can alter the metabolic landscape of entire plankton communities.
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Affiliation(s)
- Constanze Kuhlisch
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.,Department of Plant and Environmental Sciences, Weizmann Institute of Science, 234 Herzl Street, 7610001, Rehovot, Israel
| | - Julia Althammer
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.,JenaBios GmbH, Löbstedter Straße 80, 07749, Jena, Germany
| | - Andrey F Sazhin
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovsky Prospect 36, Moscow, Russia
| | - Hans H Jakobsen
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Jens C Nejstgaard
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Dep. 3, Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.
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Proteomics and Lipidomics Investigations to Decipher the Behavior of Willaertia magna C2c Maky According to Different Culture Modes. Microorganisms 2020; 8:microorganisms8111791. [PMID: 33207645 PMCID: PMC7696429 DOI: 10.3390/microorganisms8111791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 11/17/2022] Open
Abstract
Willaertia magna C2c Maky is a free-living amoeba that has demonstrated its ability to inhibit the intracellular multiplication of some Legionella pneumophila strains, which are pathogenic bacteria inhabiting the aquatic environment. The Amoeba, an industry involved in the treatment of microbiological risk in the water and plant protection sectors, has developed a natural biocide based on the property of W. magna to manage the proliferation of the pathogen in cooling towers. In axenic liquid medium, amoebas are usually cultivated in adhesion on culture flask. However, we implemented a liquid culture in suspension using bioreactors in order to produce large quantities of W. magna. In order to investigate the culture condition effects on W. magna, we conducted a study based on microscopic, proteomics and lipidomics analyzes. According to the culture condition, amoeba exhibited two different phenotypes. The differential proteomics study showed that amoebas seemed to promote the lipid metabolism pathway in suspension culture, whereas we observed an upregulation of the carbohydrate pathway in adherent culture. Furthermore, we observed an over-regulation of proteins related to the cytoskeleton for W. magna cells grown in adhesion. Regarding the lipid analysis, suspension and adhesion cell growth showed comparable lipid class compositions. However, the differential lipid analysis revealed differences that confirmed cell phenotype differences observed by microscopy and predicted by proteomics. Overall, this study provides us with a better insight into the biology and molecular processes of W. magna in different culture lifestyles.
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Panserat S, Plagnes-Juan E, Gazzola E, Palma M, Magnoni LJ, Marandel L, Viegas I. Hepatic Glycerol Metabolism-Related Genes in Carnivorous Rainbow Trout ( Oncorhynchus mykiss): Insights Into Molecular Characteristics, Ontogenesis, and Nutritional Regulation. Front Physiol 2020; 11:882. [PMID: 32848841 PMCID: PMC7413064 DOI: 10.3389/fphys.2020.00882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/29/2020] [Indexed: 12/29/2022] Open
Abstract
Glycerol metabolism in rainbow trout is poorly studied even though it is at the interface between lipid and glucose metabolism. Moreover, glycerol can be an important ingredient in new aquafeed formulation to decrease the catabolism of dietary amino acids. Thus, the present study aimed to characterize for the first time the different genes coding for key enzymes and proteins involved in hepatic glycerol metabolism. From the trout genomes, all the paralogous genes coding for glycerol transport (aqp9b), glycerol kinase (gk2a and gk5), glycerol-3-phosphate phosphatase (pgp), and glycerol-3-phosphate dehydrogenase (gpd1a, gpd1b, and gpd1c) were identified. The ontogenesis determined that the capacity to metabolize glycerol begins with the apparition of the liver during the development (stage 22) and are more expressed at the endogenous–exogenous feeding period (stage 35). The postprandial regulation of the expression of these genes in juvenile trout showed that the postprandial peak of expression is between 4 and 24 h after the last meal for many of the genes, demonstrating that glycerol metabolism could be nutritionally regulated at a molecular level. However, surprisingly, no regulation of the mRNA abundance for the glycerol metabolism-related genes by different levels of dietary glycerol (0, 2.5, and 5%) have been detected, showing that hepatic glycerol metabolism is poorly regulated at a molecular level by dietary glycerol in rainbow trout juveniles.
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Affiliation(s)
- Stephane Panserat
- INRAE, Université de Pau et des Pays de l'Adour, E2S UPPA, NuMéA, Saint-Pée-sur-Nivelle, France
| | - Elisabeth Plagnes-Juan
- INRAE, Université de Pau et des Pays de l'Adour, E2S UPPA, NuMéA, Saint-Pée-sur-Nivelle, France
| | - Elsa Gazzola
- INRAE, Université de Pau et des Pays de l'Adour, E2S UPPA, NuMéA, Saint-Pée-sur-Nivelle, France
| | - Mariana Palma
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Leonardo J Magnoni
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Lucie Marandel
- INRAE, Université de Pau et des Pays de l'Adour, E2S UPPA, NuMéA, Saint-Pée-sur-Nivelle, France
| | - Ivan Viegas
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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IsoSearch: An Untargeted and Unbiased Metabolite and Lipid Isotopomer Tracing Strategy from HR-LC-MS/MS Datasets. Methods Protoc 2020; 3:mps3030054. [PMID: 32751454 PMCID: PMC7563207 DOI: 10.3390/mps3030054] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022] Open
Abstract
Stable isotopic tracer analysis is a technique used to determine carbon or nitrogen atom incorporation into biological systems. A number of mass spectrometry based approaches have been developed for this purpose, including high-resolution tandem mass spectrometry (HR-LC-MS/MS), selected reaction monitoring (SRM) and parallel reaction monitoring (PRM). We have developed an approach for analyzing untargeted metabolomic and lipidomic datasets using high-resolution mass spectrometry with polarity switching and implemented our approach in the open-source R script IsoSearch and in Scaffold Elements software. Using our strategy, which requires an unlabeled reference dataset and isotope labeled datasets across various biological conditions, we traced metabolic isotopomer alterations in breast cancer cells (MCF-7) treated with the metabolic drugs 2-deoxy-glucose, 6-aminonicotinamide, compound 968, and rapamycin. Metabolites and lipids were first identified by the commercial software Scaffold Elements and LipidSearch, then IsoSearch successfully profiled the 13C-isotopomers extracted metabolites and lipids from 13C-glucose labeled MCF-7 cells. The results interpreted known models, such as glycolysis and pentose phosphate pathway inhibition, but also helped to discover new metabolic/lipid flux patterns, including a reactive oxygen species (ROS) defense mechanism induced by 6AN and triglyceride accumulation in rapamycin treated cells. The results suggest the IsoSearch/Scaffold Elements platform is effective for studying metabolic tracer analysis in diseases, drug metabolism, and metabolic engineering for both polar metabolites and non-polar lipids.
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Poddar N, Elahee Doomun SN, Callahan DL, Kowalski GM, Martin GJO. The assimilation of glycerol into lipid acyl chains and associated carbon backbones of Nannochloropsis salina varies under nitrogen replete and deplete conditions. Biotechnol Bioeng 2020; 117:3299-3309. [PMID: 32662891 DOI: 10.1002/bit.27498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 11/07/2022]
Abstract
Mixotrophic cultivation can increase microalgae productivity, yet the associated lipid metabolism remains mostly unknown. Stable isotope labeling was used to track assimilation of glycerol into the triacylglyceride (TAG) and membrane lipids of Nannochloropsis salina. In N-replete media, glycerol uptake and 13 C incorporation into acyl chains were, respectively, 6-fold and 12-fold higher than in N-deplete conditions. In N-replete cultures, 42% of the carbon in the consumed glycerol was assimilated into lipid acyl chains, mostly in membrane lipids rather than TAG. In N-deplete cultures, only 11% of the limited amount of consumed glycerol was fixed into lipid acyl chains. Labeled lipid-associated glycerol backbones were predominantly 13 C3 labeled, suggesting that intact glycerol molecules were directly esterified with fatty acids/polar head groups. However, the presence of singly and doubly labeled lipid-bound glycerol species suggested that some glycerol also went through the central carbon metabolism before forming glycerol-3-phosphate destined for lipid esterification. 13 C incorporation was higher in the saturated and monounsaturated than the polyunsaturated acyl chains of TAG, indicating the flux of carbon from glycerol went first to de novo fatty acid synthesis before acyl editing reactions. The results demonstrate that nitrogen availability influences both glycerol consumption and utilization for lipid synthesis in Nannochloropsis, providing novel insights for developing mixotrophic cultivation strategies.
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Affiliation(s)
- Nature Poddar
- Department of Chemical Engineering, Algal Processing Group, The University of Melbourne, Parkville, Victoria, Australia
| | - Sheik N Elahee Doomun
- School of Life and Environmental Science, Deakin University, Burwood, Victoria, Australia
| | - Damien L Callahan
- School of Life and Environmental Science, Deakin University, Burwood, Victoria, Australia
| | - Greg M Kowalski
- Institute for Physical Activity and Nutrition, School of Exercise Sciences, Deakin, Geelong, Australia
| | - Gregory J O Martin
- Department of Chemical Engineering, Algal Processing Group, The University of Melbourne, Parkville, Victoria, Australia
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41
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Cronobacter sakazakii CICC 21544 responds to the combination of carvacrol and citral by regulating proton motive force. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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42
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Zhang L, Zhang C, Liu J, Yang N. A strategy for stimulating astaxanthin and lipid production in Haematococcus pluvialis by exogenous glycerol application under low light. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101779] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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43
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Effect of dissolved oxygen on L-methionine production from glycerol by Escherichia coli W3110BL using metabolic flux analysis method. J Ind Microbiol Biotechnol 2020; 47:287-297. [PMID: 32052230 DOI: 10.1007/s10295-020-02264-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/30/2020] [Indexed: 12/15/2022]
Abstract
L-Methionine is an essential amino acid in humans, which plays an important role in the synthesis of some important amino acids and proteins. In this work, metabolic flux of batch fermentation of L-methionine with recombinant Escherichia coli W3110BL was analyzed using the flux balance analysis method, which estimated the intracellular flux distributions under different dissolved oxygen conditions. The results revealed the producing L-methionine flux of 4.8 mmol/(g cell·h) [based on the glycerol uptake flux of 100 mmol/(g cell·h)] was obtained at 30% dissolved oxygen level which was higher than that of other dissolved oxygen levels. The carbon fluxes for synthesizing L-methionine were mainly obtained from the pathway of phosphoenolpyruvate to oxaloacetic acid [15.6 mmol/(g cell·h)] but not from the TCA cycle. Hence, increasing the flow from phosphoenolpyruvate to oxaloacetic acid by enhancing the enzyme activity of phosphoenolpyruvate carboxylase might be conducive to the production of L-methionine. Additionally, pentose phosphate pathway could provide a large amount of reducing power NADPH for the synthesis of amino acids and the flux could increase from 41 mmol/(g cell·h) to 51 mmol/(g cell·h) when changing the dissolved oxygen levels, thus meeting the requirement of NADPH for L-methionine production and biomass synthesis. Therefore, the following modification of the strains should based on the improvement of the key pathway and the NAD(P)/NAD(P)H metabolism.
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Lan X, Yuan W, Wang M, Xiao H. Efficient biosynthesis of antitumor ganoderic acid HLDOA using a dual tunable system for optimizing the expression of CYP5150L8 and aGanodermaP450 reductase. Biotechnol Bioeng 2019; 116:3301-3311. [DOI: 10.1002/bit.27154] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/22/2019] [Accepted: 08/22/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Xiaoting Lan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and Laboratory of Molecular Biochemical Engineering, School of Life Sciences and BiotechnologyShanghai Jiao Tong University Shanghai China
| | - Wei Yuan
- College of Life SciencesUniversity of Chinese Academy of Sciences Beijing China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of Sciences Tianjin China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Meng Wang
- College of Life SciencesUniversity of Chinese Academy of Sciences Beijing China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of Sciences Tianjin China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Han Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and Laboratory of Molecular Biochemical Engineering, School of Life Sciences and BiotechnologyShanghai Jiao Tong University Shanghai China
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Li-Beisson Y, Thelen JJ, Fedosejevs E, Harwood JL. The lipid biochemistry of eukaryotic algae. Prog Lipid Res 2019; 74:31-68. [PMID: 30703388 DOI: 10.1016/j.plipres.2019.01.003] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 02/06/2023]
Abstract
Algal lipid metabolism fascinates both scientists and entrepreneurs due to the large diversity of fatty acyl structures that algae produce. Algae have therefore long been studied as sources of genes for novel fatty acids; and, due to their superior biomass productivity, algae are also considered a potential feedstock for biofuels. However, a major issue in a commercially viable "algal oil-to-biofuel" industry is the high production cost, because most algal species only produce large amounts of oils after being exposed to stress conditions. Recent studies have therefore focused on the identification of factors involved in TAG metabolism, on the subcellular organization of lipid pathways, and on interactions between organelles. This has been accompanied by the development of genetic/genomic and synthetic biological tools not only for the reference green alga Chlamydomonas reinhardtii but also for Nannochloropsis spp. and Phaeodactylum tricornutum. Advances in our understanding of enzymes and regulatory proteins of acyl lipid biosynthesis and turnover are described herein with a focus on carbon and energetic aspects. We also summarize how changes in environmental factors can impact lipid metabolism and describe present and potential industrial uses of algal lipids.
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Affiliation(s)
- Yonghua Li-Beisson
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, CEA Cadarache, Saint-Paul-lez Durance F-13108, France.
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, United States.
| | - Eric Fedosejevs
- Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, United States.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
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Liu XX, Luo XF, Luo KX, Liu YL, Pan T, Li ZZ, Duns GJ, He FL, Qin ZD. Small RNA sequencing reveals dynamic microRNA expression of important nutrient metabolism during development of Camellia oleifera fruit. Int J Biol Sci 2019; 15:416-429. [PMID: 30745831 PMCID: PMC6367553 DOI: 10.7150/ijbs.26884] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/10/2018] [Indexed: 12/13/2022] Open
Abstract
To obtain insight into the function of miRNAs in the synthesis and storage of important nutrients during the development of Camellia oleifera fruit, Illumina sequencing of flower and fruit small-RNA was conducted. The results revealed that 797 miRNAs were significantly differentially expressed between flower and fruit samples of Camellia oleifera. Through integrated GO and KEGG function annotations, it was determined that the miRNA target genes were mainly involved in metabolic pathways, plant hormone signal transduction, fruit development, mitosis and regulation of biosynthetic processes. Carbohydrate accumulation genes were differentially regulated by miR156, miR390 and miR395 in the fruit growth and development process. MiR477 is the key miRNA functioning in regulation of genes and involved in fatty acid synthesis. Additionally, miR156 also has the function of regulating glycolysis and nutrient transformation genes.
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Affiliation(s)
- Xiao-Xia Liu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Xiao-Fang Luo
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ke-Xin Luo
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ya-Lin Liu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ting Pan
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Zhi-Zhang Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Gregory J Duns
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Fu-Lin He
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Zuo-Dong Qin
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
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Pinto ABF, Naves LDP, Lima IG, Garbossa CAP, Silva Júnior SR, Barbosa AMS, Maluf CL, Rosa PV, Zangeronimo MG, Cantarelli VDS, Sousa RV. Metabolism of glycerol in pigs fed diets containing mixed crude glycerin and β-adrenergic agonist. ANIMAL PRODUCTION SCIENCE 2019. [DOI: 10.1071/an18210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The optimised use of mixed crude glycerin (MCG) and ractopamine hydrochloride (RH) in diets for finishing pigs requires a better understanding of glycerol metabolism. Therefore, the present study evaluated the performance, blood parameters, metabolite concentrations in the Longissimus lumborum muscle and the activity of enzymes in the liver, subcutaneous adipose tissue and kidney of pigs fed diets containing MCG and/or RH. According to the initial weight, 64 barrows were distributed in a 4 × 2 factorial design, corresponding to four concentrations of MCG (0, 100, 150, and 200 g/kg) in diets containing 0 or 10 mg/kg of RH. There was no MCG × RH interaction for any of the evaluated parameters (P > 0.05). Moreover, there was no isolated effect of dietary MCG or RH on the weight gain and the blood concentrations of glucose, insulin, triacylglycerols, total cholesterol, total protein, albumin, creatinine, cortisol and lactate (P > 0.05). There was a higher rate of phosphorylation of glycerol in the liver, stimulation of lipogenesis in adipose tissue and a likely increase in the utilisation of glycerol by muscle fibres in response to an increased concentration of circulating glycerol from the diet (P < 0.05). In contrast, when the diet contained up to 200 g/kg MCG and 10 mg/kg RH, there were indications of a lower utilisation of glycerol for the synthesis of triacylglycerols in muscle, liver and adipose tissue, in addition to increased oxidation of amino acids in the liver followed by improved feed conversion of pigs (P < 0.05).
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Watanabe M, Netzer F, Tohge T, Orf I, Brotman Y, Dubbert D, Fernie AR, Rennenberg H, Hoefgen R, Herschbach C. Metabolome and Lipidome Profiles of Populus × canescens Twig Tissues During Annual Growth Show Phospholipid-Linked Storage and Mobilization of C, N, and S. FRONTIERS IN PLANT SCIENCE 2018; 9:1292. [PMID: 30233628 PMCID: PMC6133996 DOI: 10.3389/fpls.2018.01292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/16/2018] [Indexed: 05/06/2023]
Abstract
The temperate climax tree species Fagus sylvatica and the floodplain tree species Populus × canescens possess contrasting phosphorus (P) nutrition strategies. While F. sylvatica has been documented to display P storage and mobilization (Netzer et al., 2017), this was not observed for Populus × canescens (Netzer et al., 2018b). Nevertheless, changes in the abundance of organic bound P in gray poplar trees indicated adaptation of the P nutrition to different needs during annual growth. The present study aimed at characterizing seasonal changes in metabolite and lipid abundances in gray poplar and uncovering differences in metabolite requirement due to specific needs depending on the season. Seasonal variations in the abundance of (i) sugar-Ps and phospholipids, (ii) amino acids, (iii) sulfur compounds, and (iv) carbon metabolites were expected. It was hypothesized that seasonal changes in metabolite levels relate to N, S, and C storage and mobilization. Changes in organic metabolites binding Pi (Porg) are supposed to support these processes. Variation in triacylglycerols, in sugar-phosphates, in metabolites of the TCA cycle and in the amino acid abundance of poplar twig buds, leaves, bark, and wood were found to be linked to changes in metabolite abundances as well as to C, N, and S storage and mobilization processes. The observed changes support the view of a lack of any P storage in poplar. Yet, during dormancy, contents of phospholipids in twig bark and wood were highest probably due to frost-hardening and to its function in extra-plastidic membranes such as amyloplasts, oleosomes, and protein bodies. Consistent with this assumption, in spring sugar-Ps increased when phospholipids declined and poplar plants entering the vegetative growth period and, hence, metabolic activity increases. These results indicate that poplar trees adopt a policy of P nutrition without P storage and mobilization that is different from their N- and S-nutrition strategies.
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Affiliation(s)
- Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Potsdam, Germany
- NARA Institute of Science and Technology, Ikoma, Japan
| | - Florian Netzer
- Chair of Tree Physiology, Institute of Forest Sciences, Albert Ludwigs University of Freiburg, Freiburg, Germany
- Chair of Ecosystem Physiology, Institute of Forest Sciences, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Potsdam, Germany
- NARA Institute of Science and Technology, Ikoma, Japan
| | - Isabel Orf
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Potsdam, Germany
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - David Dubbert
- Chair of Ecosystem Physiology, Institute of Forest Sciences, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Potsdam, Germany
| | - Heinz Rennenberg
- Chair of Tree Physiology, Institute of Forest Sciences, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Potsdam, Germany
| | - Cornelia Herschbach
- Chair of Tree Physiology, Institute of Forest Sciences, Albert Ludwigs University of Freiburg, Freiburg, Germany
- Chair of Ecosystem Physiology, Institute of Forest Sciences, Albert Ludwigs University of Freiburg, Freiburg, Germany
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Benlebna M, Ruesgas-Ramón M, Bonafos B, Fouret G, Casas F, Coudray C, Durand E, Cruz Figueroa-Espinoza M, Feillet-Coudray C. Toxicity of Natural Deep Eutectic Solvent Betaine:Glycerol in Rats. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6205-6212. [PMID: 29807424 DOI: 10.1021/acs.jafc.8b01746] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Natural deep eutectic solvents (NaDES) are new natural solvents in green chemistry that in some cases have been shown to allow better extraction of plant bioactive molecules compared to conventional solvents and higher phenolic compound absorption in rodents. However, there is a serious lack of information regarding their in vivo safety. The purpose of this study was to verify the safety of a NaDES (betaine:glycerol (1:2 mole ratio) of water) extract from green coffee beans, rich in polyphenols. Twelve 6-week-old male Wistar rats were randomized into two groups of 6 animals each and twice daily gavaged for 14 days either with 3 mL of water or 3 mL of phenolic NaDES extract. Oral administration of phenolic NaDES extract induced mortality in two rats. In addition, it induced excessive water consumption, reduced dietary intake and weight loss, hepatomegaly, and plasma oxidative stress associated with high blood lipid levels. In conclusion, this work demonstrated the toxicity of oral administration of the selected NaDES under a short-term condition. This occurs despite the fact that this NaDES extract contains polyphenols, whose beneficial effects have been shown. Therefore, complementary work is needed to find the best dose and formulation of NaDES that are safe for the environment and animals and ultimately for humans.
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Affiliation(s)
- Melha Benlebna
- DMEM, INRA , University of Montpellier , Montpellier , France
| | - Mariana Ruesgas-Ramón
- IATE, Montpellier SupAgro, INRA, CIRAD , University of Montpellier , Montpellier , France
| | | | - Gilles Fouret
- DMEM, INRA , University of Montpellier , Montpellier , France
| | - François Casas
- DMEM, INRA , University of Montpellier , Montpellier , France
| | - Charles Coudray
- DMEM, INRA , University of Montpellier , Montpellier , France
| | - Erwann Durand
- CIRAD, UMR IATE , Montpellier F-34398 , France
- IATE, University of Montpellier, CIRAD, INRA, Montpellier SupAgro , Montpellier , France
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Kinetics, composition and antioxidant activity of burdock (Arctium lappa) root extracts obtained with supercritical CO2 and co-solvent. J Supercrit Fluids 2018. [DOI: 10.1016/j.supflu.2017.12.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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