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Laframboise SJ, Deneault LF, Denoncourt A, Downey M, Baetz K. Uncovering the Role of the Yeast Lysine Acetyltransferase NuA4 in the Regulation of Nuclear Shape and Lipid Metabolism. Mol Cell Biol 2024:1-16. [PMID: 38961766 DOI: 10.1080/10985549.2024.2366206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/19/2024] [Indexed: 07/05/2024] Open
Abstract
Here, we report a novel role for the yeast lysine acetyltransferase NuA4 in regulating phospholipid availability for organelle morphology. Disruption of the NuA4 complex results in 70% of cells displaying nuclear deformations and nearly 50% of cells exhibiting vacuolar fragmentation. Cells deficient in NuA4 also show severe defects in the formation of nuclear-vacuole junctions (NJV), as well as a decrease in piecemeal microautophagy of the nucleus (PMN). To determine the cause of these defects we focused on Pah1, an enzyme that converts phosphatidic acid into diacylglycerol, favoring accumulation of lipid droplets over phospholipids that are used for membrane expansion. NuA4 subunit Eaf1 was required for Pah1 localization to the inner nuclear membrane and artificially tethering of Pah1 to the nuclear membrane rescued nuclear deformation and vacuole fragmentation defects, but not defects related to the formation of NVJs. Mutation of a NuA4-dependent acetylation site on Pah1 also resulted in aberrant Pah1 localization and defects in nuclear morphology and NVJ. Our work suggests a critical role for NuA4 in organelle morphology that is partially mediated through the regulation of Pah1 subcellular localization.
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Affiliation(s)
- Sarah Jane Laframboise
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Lauren F Deneault
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Alix Denoncourt
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
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2
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Meng W, Lu X, Wang G, Xiao Q, Gao J. ZNF692 drives malignant development of hepatocellular carcinoma cells by promoting ALDOA-dependent glycolysis. Funct Integr Genomics 2024; 24:53. [PMID: 38453820 PMCID: PMC10920453 DOI: 10.1007/s10142-024-01326-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/30/2023] [Accepted: 02/20/2024] [Indexed: 03/09/2024]
Abstract
Hepatocellular carcinoma (HCC) is one of the malignancies with the worst prognosis worldwide, in the occurrence and development of which glycolysis plays a central role. This study uncovered a mechanism by which ZNF692 regulates ALDOA-dependent glycolysis in HCC cells. RT-qPCR and western blotting were used to detect the expression of ZNF692, KAT5, and ALDOA in HCC cell lines and a normal liver cell line. The influences of transfection-induced alterations in the expression of ZNF692, KAT5, and ALDOA on the functions of HepG2 cells were detected by performing MTT, flow cytometry, Transwell, cell scratch, and colony formation assays, and the levels of glucose and lactate were determined using assay kits. ChIP and luciferase reporter assays were conducted to validate the binding of ZNF692 to the KAT5 promoter, and co-IP assays to detect the interaction between KAT5 and ALDOA and the acetylation of ALDOA. ZNF692, KAT5, and ALDOA were highly expressed in human HCC samples and cell lines, and their expression levels were positively correlated in HCC. ZNF692, ALDOA, or KAT5 knockdown inhibited glycolysis, proliferation, invasion, and migration and promoted apoptosis in HepG2 cells. ZNF692 bound to the KAT5 promoter and promoted its activity. ALDOA acetylation levels were elevated in HCC cell lines. KAT5 bound to ALDOA and catalyzed ALDOA acetylation. ALDOA or KAT5 overexpression in the same time of ZNF692 knockdown, compared to ZNF692 knockdown only, stimulated glycolysis, proliferation, invasion, and migration and reduced apoptosis in HepG2 cells. ZNF692 promotes the acetylation modification and protein expression of ALDOA by catalyzing KAT5 transcription, thereby accelerating glycolysis to drive HCC cell development.
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Affiliation(s)
- Weiwei Meng
- Department of Laboratory, Shenzhen Baoan Shiyan People's Hospital, No. 11, Jixiang Road, Shiyan Street, Baoan District, Shenzhen, Guangdong, 518108, P.R. China
| | - Xiaojuan Lu
- Department of Laboratory, Shenzhen Baoan Shiyan People's Hospital, No. 11, Jixiang Road, Shiyan Street, Baoan District, Shenzhen, Guangdong, 518108, P.R. China
| | - Guanglei Wang
- Department of Laboratory, Shenzhen Baoan Shiyan People's Hospital, No. 11, Jixiang Road, Shiyan Street, Baoan District, Shenzhen, Guangdong, 518108, P.R. China
| | - Qingyu Xiao
- Department of Blood Transfusion, Shenzhen Baoan Shiyan People's Hospital, Shenzhen, Guangdong, 518108, P.R. China
| | - Jing Gao
- Department of Laboratory, Shenzhen Baoan Shiyan People's Hospital, No. 11, Jixiang Road, Shiyan Street, Baoan District, Shenzhen, Guangdong, 518108, P.R. China.
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3
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Yazaki J, Dal-Bianco M. In Situ Protein Microarray for Identifying the Geminivirus-Arabidopsis Interactome. Methods Mol Biol 2024; 2724:307-314. [PMID: 37987915 DOI: 10.1007/978-1-0716-3485-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The protein-protein interactions (PPI) by protein array technology complement other PPI assay technologies such as AP-MS and Y2H. The in situ protein array technology (NAPPA) enables low-cost, rapid, and comprehensive protein detection. It allows standardized and simultaneous assay of a wide range of proteins with a broad range of expression in cells. This technology facilitates the detection of protein-protein interactions within species and between heterologous species such as host-microbe. Here, we described the technique that identified a syntaxin-6 protein-mediated begomovirus infection using an array containing 4600 Arabidopsis genes. The protein microarray assay also identified several other viral protein-host protein interactions.
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Affiliation(s)
- Junshi Yazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan.
| | - Maximiller Dal-Bianco
- Plant Genetics and Biochemistry Laboratory, BIOAGRO, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.
- Department of Biochemistry and Molecular Biology, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.
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4
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Kim YH, Ryu JI, Devare MN, Jung J, Kim JY. The intricate role of Sir2 in oxidative stress response during the post-diauxic phase in Saccharomyces cerevisiae. Front Microbiol 2023; 14:1285559. [PMID: 38029141 PMCID: PMC10666771 DOI: 10.3389/fmicb.2023.1285559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Silent information regulator 2 (Sir2) is a conserved NAD+-dependent histone deacetylase crucial for regulating cellular stress response and the aging process in Saccharomyces cerevisiae. In this study, we investigated the molecular mechanism underlying how the absence of Sir2 can lead to altered stress susceptibilities in S. cerevisiae under different environmental and physiological conditions. In a glucose-complex medium, the sir2Δ strain showed increased sensitivity to H2O2 compared to the wild-type strain during the post-diauxic phase. In contrast, it displayed increased resistance during the exponential growth phase. Transcriptome analysis of yeast cells in the post-diauxic phase indicated that the sir2Δ mutant expressed several oxidative defense genes at lower levels than the wild-type, potentially accounting for its increased susceptibility to H2O2. Interestingly, however, the sir2Δras2Δ double mutant exhibited greater resistance to H2O2 than the ras2Δ single mutant counterpart. We found that the expression regulation of the cytoplasmic catalase encoded by CTT1 was critical for the increased resistance to H2O2 in the sir2Δras2Δ strain. The expression of the CTT1 gene was influenced by the combined effect of RAS2 deletion and the transcription factor Azf1, whose level was modulated by Sir2. These findings provide insights into the importance of understanding the intricate interactions among various factors contributing to cellular stress response.
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Affiliation(s)
| | | | | | | | - Jeong-Yoon Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
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Gonzalez-Rellan MJ, Fernández U, Parracho T, Novoa E, Fondevila MF, da Silva Lima N, Ramos L, Rodríguez A, Serrano-Maciá M, Perez-Mejias G, Chantada-Vazquez P, Riobello C, Veyrat-Durebex C, Tovar S, Coppari R, Woodhoo A, Schwaninger M, Prevot V, Delgado TC, Lopez M, Diaz-Quintana A, Dieguez C, Guallar D, Frühbeck G, Diaz-Moreno I, Bravo SB, Martinez-Chantar ML, Nogueiras R. Neddylation of phosphoenolpyruvate carboxykinase 1 controls glucose metabolism. Cell Metab 2023; 35:1630-1645.e5. [PMID: 37541251 PMCID: PMC10487638 DOI: 10.1016/j.cmet.2023.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/08/2023] [Accepted: 07/10/2023] [Indexed: 08/06/2023]
Abstract
Neddylation is a post-translational mechanism that adds a ubiquitin-like protein, namely neural precursor cell expressed developmentally downregulated protein 8 (NEDD8). Here, we show that neddylation in mouse liver is modulated by nutrient availability. Inhibition of neddylation in mouse liver reduces gluconeogenic capacity and the hyperglycemic actions of counter-regulatory hormones. Furthermore, people with type 2 diabetes display elevated hepatic neddylation levels. Mechanistically, fasting or caloric restriction of mice leads to neddylation of phosphoenolpyruvate carboxykinase 1 (PCK1) at three lysine residues-K278, K342, and K387. We find that mutating the three PCK1 lysines that are neddylated reduces their gluconeogenic activity rate. Molecular dynamics simulations show that neddylation of PCK1 could re-position two loops surrounding the catalytic center into an open configuration, rendering the catalytic center more accessible. Our study reveals that neddylation of PCK1 provides a finely tuned mechanism of controlling glucose metabolism by linking whole nutrient availability to metabolic homeostasis.
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Affiliation(s)
- María J Gonzalez-Rellan
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Uxía Fernández
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Tamara Parracho
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Eva Novoa
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Marcos F Fondevila
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Natalia da Silva Lima
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Lucía Ramos
- Department of Biochemistry, CIMUS, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
| | - Amaia Rodríguez
- CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Department of Endocrinology & Nutrition, Metabolic Research Laboratory, Clínica Universidad de Navarra, University of Navarra, IdiSNA, Pamplona, Navarra, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, BRTA CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - Gonzalo Perez-Mejias
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-CSIC. Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Pilar Chantada-Vazquez
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15705, A Coruña, Spain
| | - Cristina Riobello
- Gene Regulatory Control in Disease, CIMUS, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Christelle Veyrat-Durebex
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sulay Tovar
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Roberto Coppari
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ashwin Woodhoo
- Gene Regulatory Control in Disease, CIMUS, University of Santiago de Compostela, Santiago de Compostela, Spain; Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain
| | - Markus Schwaninger
- University of Lübeck, Institute for Experimental and Clinical Pharmacology and Toxicology, Lübeck, Germany
| | - Vincent Prevot
- University of Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience & Cognition, UMR-S 1172, European Genomic Institute for Diabetes (EGID), 59000 Lille, France
| | - Teresa C Delgado
- Liver Disease Lab, BRTA CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - Miguel Lopez
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Antonio Diaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-CSIC. Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Carlos Dieguez
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Diana Guallar
- Department of Biochemistry, CIMUS, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
| | - Gema Frühbeck
- CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Department of Endocrinology & Nutrition, Metabolic Research Laboratory, Clínica Universidad de Navarra, University of Navarra, IdiSNA, Pamplona, Navarra, Spain
| | - Irene Diaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-CSIC. Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Susana B Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15705, A Coruña, Spain
| | - Maria L Martinez-Chantar
- Liver Disease Lab, BRTA CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain.
| | - Ruben Nogueiras
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain.
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6
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Abbiati F, Garagnani SA, Orlandi I, Vai M. Sir2 and Glycerol Underlie the Pro-Longevity Effect of Quercetin during Yeast Chronological Aging. Int J Mol Sci 2023; 24:12223. [PMID: 37569599 PMCID: PMC10419316 DOI: 10.3390/ijms241512223] [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: 07/06/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Quercetin (QUER) is a natural polyphenolic compound endowed with beneficial properties for human health, with anti-aging effects. However, although this flavonoid is commercially available as a nutraceutical, target molecules/pathways underlying its pro-longevity potential have yet to be fully clarified. Here, we investigated QUER activity in yeast chronological aging, the established model for simulating the aging of postmitotic quiescent mammalian cells. We found that QUER supplementation at the onset of chronological aging, namely at the diauxic shift, significantly increases chronological lifespan (CLS). Consistent with the antioxidant properties of QUER, this extension takes place in concert with a decrease in oxidative stress. In addition, QUER triggers substantial changes in carbon metabolism. Specifically, it promotes an enhancement of a pro-longevity anabolic metabolism toward gluconeogenesis due to improved catabolism of C2 by-products of yeast fermentation and glycerol. The former is attributable to the Sir2-dependent activity of phosphoenolpyruvate carboxykinase and the latter to the L-glycerol 3-phosphate pathway. Such a combined increased supply of gluconeogenesis leads to an increase in the reserve carbohydrate trehalose, ensuring CLS extension. Moreover, QUER supplementation to chronologically aging cells in water alone amplifies their long-lived phenotype. This is associated with intracellular glycerol catabolism and trehalose increase, further indicating a QUER-specific influence on carbon metabolism that results in CLS extension.
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Affiliation(s)
- Francesco Abbiati
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
| | - Stefano Angelo Garagnani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
| | - Ivan Orlandi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
- SYSBIO Centre for Systems Biology, 20126 Milano, Italy
| | - Marina Vai
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
- SYSBIO Centre for Systems Biology, 20126 Milano, Italy
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7
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Barreto EA, Cruz AS, Veras FP, Martins R, Bernardelli RS, Paiva IM, Lima TM, Singh Y, Guimarães RC, Damasceno S, Pereira N, Alves JM, Gonçalves TT, Forato J, Muraro SP, Souza GF, Batah SS, Proenca-Modena JL, Mori MA, Cunha FQ, Louzada-Junior P, Cunha TM, Nakaya HI, Fabro A, de Oliveira RDR, Arruda E, Réa R, Réa Neto Á, Fernandes da Silva MM, Leiria LO. COVID-19-related hyperglycemia is associated with infection of hepatocytes and stimulation of gluconeogenesis. Proc Natl Acad Sci U S A 2023; 120:e2217119120. [PMID: 37186819 PMCID: PMC10214153 DOI: 10.1073/pnas.2217119120] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Occurrence of hyperglycemia upon infection is associated with worse clinical outcome in COVID-19 patients. However, it is still unknown whether SARS-CoV-2 directly triggers hyperglycemia. Herein, we interrogated whether and how SARS-CoV-2 causes hyperglycemia by infecting hepatocytes and increasing glucose production. We performed a retrospective cohort study including patients that were admitted at a hospital with suspicion of COVID-19. Clinical and laboratory data were collected from the chart records and daily blood glucose values were analyzed to test the hypothesis on whether COVID-19 was independently associated with hyperglycemia. Blood glucose was collected from a subgroup of nondiabetic patients to assess pancreatic hormones. Postmortem liver biopsies were collected to assess the presence of SARS-CoV-2 and its transporters in hepatocytes. In human hepatocytes, we studied the mechanistic bases of SARS-CoV-2 entrance and its gluconeogenic effect. SARS-CoV-2 infection was independently associated with hyperglycemia, regardless of diabetic history and beta cell function. We detected replicating viruses in human hepatocytes from postmortem liver biopsies and in primary hepatocytes. We found that SARS-CoV-2 variants infected human hepatocytes in vitro with different susceptibility. SARS-CoV-2 infection in hepatocytes yields the release of new infectious viral particles, though not causing cell damage. We showed that infected hepatocytes increase glucose production and this is associated with induction of PEPCK activity. Furthermore, our results demonstrate that SARS-CoV-2 entry in hepatocytes occurs partially through ACE2- and GRP78-dependent mechanisms. SARS-CoV-2 infects and replicates in hepatocytes and exerts a PEPCK-dependent gluconeogenic effect in these cells that potentially is a key cause of hyperglycemia in infected patients.
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Affiliation(s)
- Ester A. Barreto
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Amanda S. Cruz
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Flavio P. Veras
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Ronaldo Martins
- Department of Cell Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Rafaella S. Bernardelli
- Federal University of Paraná, Center for Study and Research in Intensive Care Medicine, Curitiba82530-200, Brazil
| | - Isadora M. Paiva
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Thais M. Lima
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Youvika Singh
- Hospital Israelita Albert Einstein, São Paulo05652-900, Brazil
| | - Raphael C. Guimarães
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
| | - Samara Damasceno
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Nayara Pereira
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - João Manoel Alves
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Tiago T. Gonçalves
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Julia Forato
- Department of Genetics, Microbiology and Immunology, Laboratory of Emerging Viruses, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
| | - Stéfanie P. Muraro
- Department of Genetics, Microbiology and Immunology, Laboratory of Emerging Viruses, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
| | - Gabriela F. Souza
- Department of Genetics, Microbiology and Immunology, Laboratory of Emerging Viruses, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
| | - Sabrina Setembre Batah
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - José L. Proenca-Modena
- Department of Genetics, Microbiology and Immunology, Laboratory of Emerging Viruses, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
- Experimental Medicine Research, Cluster University of Campinas, Campinas13083-970, Brazil
| | - Marcelo A. Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
- Experimental Medicine Research, Cluster University of Campinas, Campinas13083-970, Brazil
- Obesity and Comorbidities Research Center, University of Campinas, Campinas13083-864, Brazil
| | - Fernando Q. Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Paulo Louzada-Junior
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Divisions of Clinical Immunology, Emergency, Infectious Diseases, and Intensive Care Unit, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Thiago M. Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Helder I. Nakaya
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Hospital Israelita Albert Einstein, São Paulo05652-900, Brazil
| | - Alexandre Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Renê D. R. de Oliveira
- Divisions of Clinical Immunology, Emergency, Infectious Diseases, and Intensive Care Unit, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Eurico Arruda
- Department of Cell Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Rosângela Réa
- Federal University of Paraná, Center for Study and Research in Intensive Care Medicine, Curitiba82530-200, Brazil
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba80060-900, Brazil
| | - Álvaro Réa Neto
- Federal University of Paraná, Center for Study and Research in Intensive Care Medicine, Curitiba82530-200, Brazil
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba80060-900, Brazil
| | | | - Luiz Osório Leiria
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
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8
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Chen J, Ye Y, Chi Y, Hao X, Zhao Q. Transcriptomics and co-expression network analysis revealing candidate genes for the laccase activity of Trametes gibbosa. BMC Microbiol 2023; 23:29. [PMID: 36703110 PMCID: PMC9878871 DOI: 10.1186/s12866-022-02727-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 12/08/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Trametes gibbosa, which is a white-rot fungus of the Polyporaceae family found in the cold temperate zone, causes spongy white rot on wood. Laccase can oxidize benzene homologs and is one of the important oxidases for white rot fungi to degrade wood. However, the pathway of laccase synthesis in white rot fungi is unknown. RESULTS The peak value of laccase activity reached 135.75 U/min/L on the 9th day. For laccase activity and RNA-seq data, gene expression was segmented into 24 modules. Turquoise and blue modules had greater associations with laccase activity (positively 0.94 and negatively -0.86, respectively). For biology function, these genes were concentrated on the cell cycle, citrate cycle, nicotinate, and nicotinamide metabolism, succinate dehydrogenase activity, flavin adenine dinucleotide binding, and oxidoreductase activity which are highly related to the laccase synthetic pathway. Among them, gene_8826 (MW199767), gene_7458 (MW199766), gene_61 (MW199765), gene_1741 (MH257605), and gene_11087 (MK805159) were identified as central genes. CONCLUSION Laccase activity steadily increased in wood degradation. Laccase oxidation consumes oxygen to produce hydrogen ions and water during the degradation of wood. Some of the hydrogen ions produced can be combined by Flavin adenine dinucleotide (FAD) to form reduced Flavin dinucleotide (FADH2), which can be transmitted. Also, the fungus was starved of oxygen throughout fermentation, and the NADH and FADH2 are unable to transfer hydrogen under hypoxia, resulting in the inability of NAD and FAD to regenerate and inhibit the tricarboxylic acid cycle of cells. These key hub genes related to laccase activity play important roles in the molecular mechanisms of laccase synthesis for exploring industrial excellent strains.
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Affiliation(s)
- Jie Chen
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China ,grid.4818.50000 0001 0791 5666Wageningen University & Research, Wageningen, Netherlands
| | - Yi Ye
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China
| | - Yujie Chi
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China
| | - Xin Hao
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China
| | - Qingquan Zhao
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China
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9
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Mameri A, Côté J. JAZF1: A metabolic actor subunit of the NuA4/TIP60 chromatin modifying complex. Front Cell Dev Biol 2023; 11:1134268. [PMID: 37091973 PMCID: PMC10119425 DOI: 10.3389/fcell.2023.1134268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
The multisubunit NuA4/TIP60 complex is a lysine acetyltransferase, chromatin modifying factor and gene co-activator involved in diverse biological processes. The past decade has seen a growing appreciation for its role as a metabolic effector and modulator. However, molecular insights are scarce and often contradictory, underscoring the need for further mechanistic investigation. A particularly exciting route emerged with the recent identification of a novel subunit, JAZF1, which has been extensively linked to metabolic homeostasis. This review summarizes the major findings implicating NuA4/TIP60 in metabolism, especially in light of JAZF1 as part of the complex.
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10
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Structure of the NuA4 histone acetyltransferase complex. Proc Natl Acad Sci U S A 2022; 119:e2214313119. [PMID: 36417436 PMCID: PMC9860254 DOI: 10.1073/pnas.2214313119] [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] [Indexed: 11/24/2022] Open
Abstract
Nucleosome acetyltransferase of H4 (NuA4), one of two major histone acetyltransferase complexes in Saccharomyces cerevisiae specifically acetylates histone H2A and H4, resulting in increased transcriptional activity. Here we present a 3.8-4.0 Å resolution structure of the NuA4 complex from cryoelectron microscopy and associated biochemical studies. The determined structure comprises six subunits and appropriately 5,000 amino acids, with a backbone formed by subunits Eaf1 and Eaf2 spanning from an Actin-Arp4 module to a platform subunit Tra1. Seven subunits are missing from the cryo-EM map. The locations of missing components, Yaf9, and three subunits of the Piccolo module Esa1, Yng2, and Eaf6 were determined. Biochemical studies showed that the Piccolo module and the complete NuA4 exhibit comparable histone acetyltransferase activities, but the Piccolo module binds to nucleosomes, whereas the complete NuA4 does not. The interaction lifetime of NuA4 and nucleosome is evidently short, possibly because of subunits of the NuA4 complex that diminish the affinity of the Piccolo module for the nucleosome, enabling rapid movement from nucleosome to nucleosome.
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11
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Lu PYT, Kirlin AC, Aristizabal MJ, Brewis HT, Lévesque N, Setiaputra DT, Avvakumov N, Benschop JJ, Groot Koerkamp M, Holstege FCP, Krogan NJ, Yip CK, Côté J, Kobor MS. A balancing act: interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans. Genetics 2022; 222:iyac136. [PMID: 36066422 PMCID: PMC9630986 DOI: 10.1093/genetics/iyac136] [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: 10/12/2021] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The NuA4 lysine acetyltransferase complex acetylates histone and nonhistone proteins and functions in transcription regulation, cell cycle progression, and DNA repair. NuA4 harbors an interesting duality in that its catalytic module can function independently and distinctly as picNuA4. At the molecular level, picNuA4 anchors to its bigger brother via physical interactions between the C-terminus of Epl1 and the HSA domain of Eaf1, the NuA4 central scaffolding subunit. This is reflected at the regulatory level, as picNuA4 can be liberated genetically from NuA4 by disrupting the Epl1-Eaf1 interaction. As such, removal of either Eaf1 or the Epl1 C-terminus offers a unique opportunity to elucidate the contributions of Eaf1 and Epl1 to NuA4 biology and in turn their roles in balancing picNuA4 and NuA4 activities. Using high-throughput genetic and gene expression profiling, and targeted functional assays to compare eaf1Δ and epl1-CΔ mutants, we found that EAF1 and EPL1 had both overlapping and distinct roles. Strikingly, loss of EAF1 or its HSA domain led to a significant decrease in the amount of picNuA4, while loss of the Epl1 C-terminus increased picNuA4 levels, suggesting starkly opposing effects on picNuA4 regulation. The eaf1Δ epl1-CΔ double mutants resembled the epl1-CΔ single mutants, indicating that Eaf1's role in picNuA4 regulation depended on the Epl1 C-terminus. Key aspects of this regulation were evolutionarily conserved, as truncating an Epl1 homolog in human cells increased the levels of other picNuA4 subunits. Our findings suggested a model in which distinct aspects of the Epl1-Eaf1 interaction regulated picNuA4 amount and activity.
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Affiliation(s)
- Phoebe Y T Lu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Alyssa C Kirlin
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Hilary T Brewis
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Nancy Lévesque
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Dheva T Setiaputra
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nikita Avvakumov
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Joris J Benschop
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | | | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht 3584 CS, The Netherlands
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jacques Côté
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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12
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Vega M, Castillo D, de Cubas L, Wang Y, Huang Y, Hidalgo E, Cabrera M. Antagonistic effects of mitochondrial matrix and intermembrane space proteases on yeast aging. BMC Biol 2022; 20:160. [PMID: 35820914 PMCID: PMC9277893 DOI: 10.1186/s12915-022-01352-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/15/2022] [Indexed: 12/27/2022] Open
Abstract
Background In many organisms, aging is characterized by a loss of mitochondrial homeostasis. Multiple factors such as respiratory metabolism, mitochondrial fusion/fission, or mitophagy have been linked to cell longevity, but the exact impact of each one on the aging process is still unclear. Results Using the deletion mutant collection of the fission yeast Schizosaccharomyces pombe, we have developed a genome-wide screening for mutants with altered chronological lifespan. We have identified four mutants associated with proteolysis at the mitochondria that exhibit opposite effects on longevity. The analysis of the respiratory activity of these mutants revealed a positive correlation between increased respiration rate and prolonged lifespan. We also found that the phenotype of the long-lived protease mutants could not be explained by impaired mitochondrial fusion/fission activities, but it was dependent on mitophagy induction. The anti-aging role of mitophagy was supported by the effect of a mutant defective in degradation of mitochondria, which shortened lifespan of the long-lived mutants. Conclusions Our characterization of the mitochondrial protease mutants demonstrates that mitophagy sustains the lifespan extension of long-lived mutants displaying a higher respiration potential. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01352-w.
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Affiliation(s)
- Montserrat Vega
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003, Barcelona, Spain
| | | | - Laura de Cubas
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Yirong Wang
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Margarita Cabrera
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003, Barcelona, Spain. .,Department of Biology, Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, C/ Tulipán s/n, 28933, Móstoles, Madrid, Spain.
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13
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Ugbogu EA, Schweizer LM, Schweizer M. Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. Cells 2022; 11:1909. [PMID: 35741038 PMCID: PMC9221600 DOI: 10.3390/cells11121909] [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: 03/30/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphoribosyl pyrophosphate synthetase (PRS EC 2.7.6.1) is a rate-limiting enzyme that irreversibly catalyzes the formation of phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate and adenosine triphosphate (ATP). This key metabolite is required for the synthesis of purine and pyrimidine nucleotides, the two aromatic amino acids histidine and tryptophan, the cofactors nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), all of which are essential for various life processes. Despite its ubiquity and essential nature across the plant and animal kingdoms, PRPP synthetase displays species-specific characteristics regarding the number of gene copies and architecture permitting interaction with other areas of cellular metabolism. The impact of mutated PRS genes in the model eukaryote Saccharomyces cerevisiae on cell signalling and metabolism may be relevant to the human neuropathies associated with PRPS mutations. Human PRPS1 and PRPS2 gene products are implicated in drug resistance associated with recurrent acute lymphoblastic leukaemia and progression of colorectal cancer and hepatocellular carcinoma. The investigation of PRPP metabolism in accepted model organisms, e.g., yeast and zebrafish, has the potential to reveal novel drug targets for treating at least some of the diseases, often characterized by overlapping symptoms, such as Arts syndrome and respiratory infections, and uncover the significance and relevance of human PRPS in disease diagnosis, management, and treatment.
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Affiliation(s)
- Eziuche A. Ugbogu
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Lilian M. Schweizer
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Michael Schweizer
- Institute of Biological Chemistry, Biophysics & Engineering (IB3), School of Engineering &Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK
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14
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Lai Y, Wang L, Zheng W, Wang S. Regulatory Roles of Histone Modifications in Filamentous Fungal Pathogens. J Fungi (Basel) 2022; 8:jof8060565. [PMID: 35736048 PMCID: PMC9224773 DOI: 10.3390/jof8060565] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungal pathogens have evolved diverse strategies to infect a variety of hosts including plants and insects. The dynamic infection process requires rapid and fine-tuning regulation of fungal gene expression programs in response to the changing host environment and defenses. Therefore, transcriptional reprogramming of fungal pathogens is critical for fungal development and pathogenicity. Histone post-translational modification, one of the main mechanisms of epigenetic regulation, has been shown to play an important role in the regulation of gene expressions, and is involved in, e.g., fungal development, infection-related morphogenesis, environmental stress responses, biosynthesis of secondary metabolites, and pathogenicity. This review highlights recent findings and insights into regulatory mechanisms of histone methylation and acetylation in fungal development and pathogenicity, as well as their roles in modulating pathogenic fungi–host interactions.
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Affiliation(s)
- Yiling Lai
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.L.); (S.W.)
| | - Lili Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weilu Zheng
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sibao Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.L.); (S.W.)
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15
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Pham T, Walden E, Huard S, Pezacki J, Fullerton MD, Baetz K. Fine tuning Acetyl-CoA Carboxylase 1 activity through localization: Functional genomics reveal a role for the lysine acetyltransferase NuA4 and sphingolipid metabolism in regulating Acc1 activity and localization. Genetics 2022; 221:6591204. [PMID: 35608294 PMCID: PMC9339284 DOI: 10.1093/genetics/iyac086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Acetyl-CoA Carboxylase 1 catalyzes the conversion of acetyl-CoA to malonyl-CoA, the committed step of de novo fatty acid synthesis. As a master regulator of lipid synthesis, acetyl-CoA carboxylase 1 has been proposed to be a therapeutic target for numerous metabolic diseases. We have shown that acetyl-CoA carboxylase 1 activity is reduced in the absence of the lysine acetyltransferase NuA4 in Saccharomyces cerevisiae. This change in acetyl-CoA carboxylase 1 activity is correlated with a change in localization. In wild-type cells, acetyl-CoA carboxylase 1 is localized throughout the cytoplasm in small punctate and rod-like structures. However, in NuA4 mutants, acetyl-CoA carboxylase 1 localization becomes diffuse. To uncover mechanisms regulating acetyl-CoA carboxylase 1 localization, we performed a microscopy screen to identify other deletion mutants that impact acetyl-CoA carboxylase 1 localization and then measured acetyl-CoA carboxylase 1 activity in these mutants through chemical genetics and biochemical assays. Three phenotypes were identified. Mutants with hyper-active acetyl-CoA carboxylase 1 form 1 or 2 rod-like structures centrally within the cytoplasm, mutants with mid-low acetyl-CoA carboxylase 1 activity displayed diffuse acetyl-CoA carboxylase 1, while the mutants with the lowest acetyl-CoA carboxylase 1 activity (hypomorphs) formed thick rod-like acetyl-CoA carboxylase 1 structures at the periphery of the cell. All the acetyl-CoA carboxylase 1 hypomorphic mutants were implicated in sphingolipid metabolism or very long-chain fatty acid elongation and in common, their deletion causes an accumulation of palmitoyl-CoA. Through exogenous lipid treatments, enzyme inhibitors, and genetics, we determined that increasing palmitoyl-CoA levels inhibits acetyl-CoA carboxylase 1 activity and remodels acetyl-CoA carboxylase 1 localization. Together this study suggests yeast cells have developed a dynamic feed-back mechanism in which downstream products of acetyl-CoA carboxylase 1 can fine-tune the rate of fatty acid synthesis.
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Affiliation(s)
- Trang Pham
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Elizabeth Walden
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Sylvain Huard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - John Pezacki
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa K1N6N5 Canada
| | - Morgan D Fullerton
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary T2N 1N4, Canada
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16
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Zhao G, Rusche LN. Sirtuins in Epigenetic Silencing and Control of Gene Expression in Model and Pathogenic Fungi. Annu Rev Microbiol 2022; 76:157-178. [PMID: 35609947 DOI: 10.1146/annurev-micro-041020-100926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fungi, including yeasts, molds, and mushrooms, proliferate on decaying matter and then adopt quiescent forms once nutrients are depleted. This review explores how fungi use sirtuin deacetylases to sense and respond appropriately to changing nutrients. Because sirtuins are NAD+-dependent deacetylases, their activity is sensitive to intracellular NAD+ availability. This allows them to transmit information about a cell's metabolic state on to the biological processes they influence. Fungal sirtuins are primarily known to deacetylate histones, repressing transcription and modulating genome stability. Their target genes include those involved in NAD+ homeostasis, metabolism, sporulation, secondary metabolite production, and virulence traits of pathogenic fungi. By targeting different genes over evolutionary time, sirtuins serve as rewiring points that allow organisms to evolve novel responses to low NAD+ stress by bringing relevant biological processes under the control of sirtuins. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Guolei Zhao
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, USA; ,
| | - Laura N Rusche
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, USA; ,
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17
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Novel serological biomarker panel using protein microarray can distinguish active TB from latent TB infection. Microbes Infect 2022; 24:105002. [DOI: 10.1016/j.micinf.2022.105002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/22/2022]
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18
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Odoh CK, Guo X, Arnone JT, Wang X, Zhao ZK. The role of NAD and NAD precursors on longevity and lifespan modulation in the budding yeast, Saccharomyces cerevisiae. Biogerontology 2022; 23:169-199. [PMID: 35260986 PMCID: PMC8904166 DOI: 10.1007/s10522-022-09958-x] [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: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 11/26/2022]
Abstract
Molecular causes of aging and longevity interventions have witnessed an upsurge in the last decade. The resurgent interests in the application of small molecules as potential geroprotectors and/or pharmacogenomics point to nicotinamide adenine dinucleotide (NAD) and its precursors, nicotinamide riboside, nicotinamide mononucleotide, nicotinamide, and nicotinic acid as potentially intriguing molecules. Upon supplementation, these compounds have shown to ameliorate aging related conditions and possibly prevent death in model organisms. Besides being a molecule essential in all living cells, our understanding of the mechanism of NAD metabolism and its regulation remain incomplete owing to its omnipresent nature. Here we discuss recent advances and techniques in the study of chronological lifespan (CLS) and replicative lifespan (RLS) in the model unicellular organism Saccharomyces cerevisiae. We then follow with the mechanism and biology of NAD precursors and their roles in aging and longevity. Finally, we review potential biotechnological applications through engineering of microbial lifespan, and laid perspective on the promising candidature of alternative redox compounds for extending lifespan.
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Affiliation(s)
- Chuks Kenneth Odoh
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaojia Guo
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
| | - James T Arnone
- Department of Biology, William Paterson University, Wayne, NJ, 07470, USA
| | - Xueying Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
| | - Zongbao K Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
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19
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Yu X, Meng Z, Fang T, Liu X, Cheng Y, Xu L, Liu X, Li X, Xue M, Li T, Sun B, Chen L. Empagliflozin Inhibits Hepatic Gluconeogenesis and Increases Glycogen Synthesis by AMPK/CREB/GSK3β Signalling Pathway. Front Physiol 2022; 13:817542. [PMID: 35299662 PMCID: PMC8921641 DOI: 10.3389/fphys.2022.817542] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/07/2022] [Indexed: 01/14/2023] Open
Abstract
Increases in glucose production and decreases in hepatic glycogen storage induce glucose metabolic abnormalities in type 2 diabetes (T2DM). Empagliflozin, a sodium-dependent glucose transporter 2 (SGLT2) inhibitor, is an effective hypoglycemic drug; however, the effects of empagliflozin on hepatic gluconeogenesis and glycogenesis are still unclear. In this study, we investigated the effects and mechanisms of empagliflozin on hepatic gluconeogenesis and glycogenesis in vivo and in vitro. Empagliflozin was administered via gavage to db/db mice for 8 weeks, and human hepatocyte HL7702 cells were treated with empagliflozin after palmitic acid (PA) stimulation. Compared with the control db/db mice, empagliflozin-treated mice showed a significant reduction in urine glucose levels, blood glucose levels, body weight and intraperitoneal glucose tolerance test (IPGTT) blood glucose levels. Moreover, the expression levels and activities of key gluconeogenesis enzymes PEPCK and G6Pase were dramatically reduced in the empagliflozin-treated mice, and the protein expression levels of AMPK/CREB/GSK3β signalling pathway-related molecules were significantly changed. In HL7702 cells, empagliflozin ameliorated glucose production and PEPCK and G6Pase expression and activity. Empagliflozin could also prevent the decreases in glycogen content and regulate the protein expression levels of AMPK/CREB/GSK3β signalling pathway-related molecules. Then, we selected the AMPK agonist AICAR and inhibitor compound C to further verify the effects of the AMPK signalling pathway on hepatic gluconeogenesis and glycogen synthesis. The results of the 5-Aminoimidazole-4-carboxamide1-β-D-ribofuranoside (AIACR) intervention in HL7702 cells were consistent with those of empagliflozin treatment, and the effects of empagliflozin were abolished by compound C. In summary, empagliflozin could maintain glucose homoeostasis by reducing gluconeogenesis and increasing glycogenesis through the AMPK/CREB/GSK3β signalling pathway.
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Marín-Hernández Á, Rodríguez-Zavala JS, Jasso-Chávez R, Saavedra E, Moreno-Sánchez R. Protein acetylation effects on enzyme activity and metabolic pathway fluxes. J Cell Biochem 2021; 123:701-718. [PMID: 34931340 DOI: 10.1002/jcb.30197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/11/2022]
Abstract
Acetylation of proteins seems a widespread process found in the three domains of life. Several studies have shown that besides histones, acetylation of lysine residues also occurs in non-nuclear proteins. Hence, it has been suggested that this covalent modification is a mechanism that might regulate diverse metabolic pathways by modulating enzyme activity, stability, and/or subcellular localization or interaction with other proteins. However, protein acetylation levels seem to have low correlation with modification of enzyme activity and pathway fluxes. In addition, the results obtained with mutant enzymes that presumably mimic acetylation have frequently been over-interpreted. Moreover, there is a generalized lack of rigorous enzyme kinetic analysis in parallel to acetylation level determinations. The purpose of this review is to analyze the current findings on the impact of acetylation on metabolic enzymes and its repercussion on metabolic pathways function/regulation.
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Affiliation(s)
| | | | - Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico
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21
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Chen X, Wu L, Lan H, Sun R, Wen M, Ruan D, Zhang M, Wang S. Histone acetyltransferases MystA and MystB contribute to morphogenesis and aflatoxin biosynthesis by regulating acetylation in fungus Aspergillus flavus. Environ Microbiol 2021; 24:1340-1361. [PMID: 34863014 DOI: 10.1111/1462-2920.15856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/19/2021] [Indexed: 11/28/2022]
Abstract
Myst family is highly conserved histone acetyltransferases in eukaryotic cells and is known to play crucial roles in various cellular processes; however, acetylation catalysed by acetyltransferases is unclear in filamentous fungi. Here, we identified two classical nonessential Myst enzymes and analysed their functions in Aspergillus flavus, which generates aflatoxin B1, one of the most carcinogenic secondary metabolites. MystA and MystB located in nuclei and cytoplasm, and mystA could acetylate H4K16ac, while mystB acetylates H3K14ac, H3K18ac and H3K23ac. Deletion mystA resulted in decreased conidiation, increased sclerotia formation and aflatoxin production. Deletion of mystB leads to significant defects in conidiation, sclerotia formation and aflatoxin production. Additionally, double-knockout mutant (ΔmystA/mystB) display a stronger and similar defect to ΔmystB mutant, indicating that mystB plays a major role in regulating development and aflatoxin production. Both mystA and mystB play important role in crop colonization. Moreover, catalytic domain MOZ and the catalytic site E199/E243 were important for the acetyltransferase function of Myst. Notably, chromatin immunoprecipitation results indicated that mystB participated in oxidative detoxification by regulating the acetylation level of H3K14, and further regulated nsdD to affect sclerotia formation and aflatoxin production. This study provides new evidences to discover the biological functions of histone acetyltransferase in A. flavus.
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Affiliation(s)
- Xuan Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianghuan Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huahui Lan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruilin Sun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meifang Wen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Danrui Ruan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengjuan Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shihua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Kato T, Azegami J, Kano M, El Enshasy HA, Park EY. Effects of sirtuins on the riboflavin production in Ashbya gossypii. Appl Microbiol Biotechnol 2021; 105:7813-7823. [PMID: 34559286 DOI: 10.1007/s00253-021-11595-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 12/01/2022]
Abstract
This study focuses on sirtuins, which catalyze the reaction of NAD+-dependent protein deacetylase, for riboflavin production in A. gossypii. Nicotinamide, a known inhibitor of sirtuin, made the color of A. gossypii colonies appear a deeper yellow at 5 mM. A. gossypii has 4 sirtuin genes (AgHST1, AgHST2, AgHST3, AgHST4) and these were disrupted to investigate the role of sirtuins in riboflavin production in A. gossypii. AgHST1∆, AgHST3∆, and AgHST4∆ strains were obtained, but AgHST2∆ was not. The AgHST1∆ and AgHST3∆ strains produced approximately 4.3- and 2.9-fold higher amounts of riboflavin than the WT strain. The AgHST3∆ strain showed a lower human sirtuin 6 (SIRT6)-like activity than the WT strain and only in the AgHST3∆ strain was a higher amount of acetylation of histone H3 K9 and K56 (H3K9ac and H3K56ac) observed compared to the WT strain. These results indicate that AgHst3 is SIRT6-like sirtuin in A. gossypii and the activity has an influence on the riboflavin production in A. gossypii. In the presence of 5 mM hydroxyurea and 50 µM camptothecin, which causes DNA damage, especially double-strand DNA breaks, the color of the WT strain colonies turned a deeper yellow. Additionally, hydroxyurea significantly led to the production of approximately 1.5 higher amounts of riboflavin and camptothecin also enhanced the riboflavin production even through the significant difference was not detected. Camptothecin tended to increase the amount of H3K56ac, but the amount of H3K56ac was not increased by hydroxyurea treatment. This study revealed that AgHst1 and AgHst3 are involved in the riboflavin production in A. gossypii through NAD metabolism and the acetylation of H3, respectively. This new finding is a step toward clarifying the role of sirtuins in riboflavin over-production by A. gossypii.Key points• Nicotinamide enhanced the riboflavin production in Ashbya gossypii.• Disruption of AgHST1 or AgHST3 gene also enhanced the riboflavin production in Ashbya gossypii.• Acetylation of H3K56 led to the enhancement of the riboflavin production in Ashbya gossypii.
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Affiliation(s)
- Tatsuya Kato
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan. .,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan. .,Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.
| | - Junya Azegami
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Mai Kano
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Hesham A El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81310 UTM, Johor Bahru, Malaysia.,City of Scientific Research and Technology Applications, New Borg Al Arab, Alexandria, Egypt
| | - Enoch Y Park
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.,Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
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23
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Ahmad S, Côté V, Cheng X, Bourriquen G, Sapountzi V, Altaf M, Côté J. Antagonistic relationship of NuA4 with the non-homologous end-joining machinery at DNA damage sites. PLoS Genet 2021; 17:e1009816. [PMID: 34543274 PMCID: PMC8483352 DOI: 10.1371/journal.pgen.1009816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 09/30/2021] [Accepted: 09/09/2021] [Indexed: 11/19/2022] Open
Abstract
The NuA4 histone acetyltransferase complex, apart from its known role in gene regulation, has also been directly implicated in the repair of DNA double-strand breaks (DSBs), favoring homologous recombination (HR) in S/G2 during the cell cycle. Here, we investigate the antagonistic relationship of NuA4 with non-homologous end joining (NHEJ) factors. We show that budding yeast Rad9, the 53BP1 ortholog, can inhibit NuA4 acetyltransferase activity when bound to chromatin in vitro. While we previously reported that NuA4 is recruited at DSBs during the S/G2 phase, we can also detect its recruitment in G1 when genes for Rad9 and NHEJ factors Yku80 and Nej1 are mutated. This is accompanied with the binding of single-strand DNA binding protein RPA and Rad52, indicating DNA end resection in G1 as well as recruitment of the HR machinery. This NuA4 recruitment to DSBs in G1 depends on Mre11-Rad50-Xrs2 (MRX) and Lcd1/Ddc2 and is linked to the hyper-resection phenotype of NHEJ mutants. It also implicates NuA4 in the resection-based single-strand annealing (SSA) repair pathway along Rad52. Interestingly, we identified two novel non-histone acetylation targets of NuA4, Nej1 and Yku80. Acetyl-mimicking mutant of Nej1 inhibits repair of DNA breaks by NHEJ, decreases its interaction with other core NHEJ factors such as Yku80 and Lif1 and favors end resection. Altogether, these results establish a strong reciprocal antagonistic regulatory function of NuA4 and NHEJ factors in repair pathway choice and suggests a role of NuA4 in alternative repair mechanisms in situations where some DNA-end resection can occur in G1. DNA double-strand breaks (DSBs) are one of the most harmful form of DNA damage. Cells employ two major repair pathways to resolve DSBs: Homologous Recombination (HR) and Non-Homologous End Joining (NHEJ). Here we wanted to dissect further the role played by the NuA4 (Nucleosome acetyltransferase of histone H4) complex in the repair of DSBs. Budding yeast NuA4 complex, like its mammalian homolog TIP60 complex, has been shown to favor repair by HR. Here, we show that indeed budding yeast NuA4 and components of the NHEJ repair pathway share an antagonistic relationship. Deletion of NHEJ components enables increased recruitment of NuA4 in the vicinity of DSBs, possible through two independent mechanisms, where NuA4 favors the end resection process which implicates it in repair by single-strand annealing (SSA), an alternate homology-based repair pathway. Additionally, we also present two NHEJ core components as new targets of NuA4 acetyltransferase activity and suggest that these acetylation events can disassemble the NHEJ repair complex from DSBs, favoring repair by HR. Our study demonstrates the importance of NuA4 in the modulation of DSB repair pathway choice.
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Affiliation(s)
- Salar Ahmad
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Valérie Côté
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Gaëlle Bourriquen
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Vasileia Sapountzi
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Mohammed Altaf
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
- * E-mail:
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24
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Cheng X, Côté V, Côté J. NuA4 and SAGA acetyltransferase complexes cooperate for repair of DNA breaks by homologous recombination. PLoS Genet 2021; 17:e1009459. [PMID: 34228704 PMCID: PMC8284799 DOI: 10.1371/journal.pgen.1009459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/16/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Chromatin modifying complexes play important yet not fully defined roles in DNA repair processes. The essential NuA4 histone acetyltransferase (HAT) complex is recruited to double-strand break (DSB) sites and spreads along with DNA end resection. As predicted, NuA4 acetylates surrounding nucleosomes upon DSB induction and defects in its activity correlate with altered DNA end resection and Rad51 recombinase recruitment. Importantly, we show that NuA4 is also recruited to the donor sequence during recombination along with increased H4 acetylation, indicating a direct role during strand invasion/D-loop formation after resection. We found that NuA4 cooperates locally with another HAT, the SAGA complex, during DSB repair as their combined action is essential for DNA end resection to occur. This cooperation of NuA4 and SAGA is required for recruitment of ATP-dependent chromatin remodelers, targeted acetylation of repair factors and homologous recombination. Our work reveals a multifaceted and conserved cooperation mechanism between acetyltransferase complexes to allow repair of DNA breaks by homologous recombination. DNA double-strand breaks (DSBs) are among the most dangerous types of DNA lesions as they can produce genomic instability that leads to cancer and genetic diseases. It is therefore crucial to understand the precise molecular mechanisms used by cells to detect and repair this type of damages. Homologous recombination using sister chromatid as template is the most accurate pathway to repair these breaks but has to occur within the context of the DNA compacted structure in chromosomes. Here, we show that two enzymes, NuA4 and SAGA, that acetylate the structural components of chromosomes in the vicinity of the DNA breaks are together essential for recombination-mediated repair to occur. We found that they are recruited at an early step after damage detection and their action allows subsequent remodeling of local structural organisation by other enzymes, providing DNA access to the recombination machinery. These results highlight the cooperation of enzymes for a same goal, providing robustness in the repair process as only the loss of both leads to major defects.
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Affiliation(s)
- Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Valérie Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
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25
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Arabidopsis RPD3-like histone deacetylases form multiple complexes involved in stress response. J Genet Genomics 2021; 48:369-383. [PMID: 34144927 DOI: 10.1016/j.jgg.2021.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/31/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022]
Abstract
The Arabidopsis thaliana RPD3-type histone deacetylases have been known to form conserved SIN3-type histone deacetylase complexes, but whether they form other types of complexes is unknown. Here, we perform affinity purification followed by mass spectrometry and demonstrate that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 interact with several previously uncharacterized proteins, thereby forming three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicates that the newly identified components function together with HDA6 and HDA19 and coregulate the expression of a number of genes. HDA6 and HDA19 were previously thought to repress gene transcription by histone deacetylation. We find that the histone deacetylase complexes can repress gene expression via both histone deacetylation-dependent and -independent mechanisms. In the mutants of histone deacetylase complexes, the expression of a number of stress-induced genes is up-regulated, and several mutants of the histone deacetylase complexes show severe retardation in growth. Considering that growth retardation is thought to be a trade-off for an increase in stress tolerance, we infer that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under nonstress conditions.
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Wang T, Chen K, Yao W, Zheng R, He Q, Xia J, Li J, Shao Y, Zhang L, Huang L, Qin L, Xu M, Zhang Z, Pan D, Li Z, Huang F. Acetylation of lactate dehydrogenase B drives NAFLD progression by impairing lactate clearance. J Hepatol 2021; 74:1038-1052. [PMID: 33248168 DOI: 10.1016/j.jhep.2020.11.028] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS Lactate has recently been reported to accumulate in the livers of patients progressing from simple steatosis to non-alcoholic steatohepatitis (NASH). However, the underlying mechanism(s) of lactate accumulation and the role of lactate in the progression of non-alcoholic fatty liver disease (NAFLD) are essentially unknown. METHODS We compared the acetylome in liver samples taken from healthy individuals, patients with simple steatosis and patients with NASH to identify potential targets of acetylation with a role in lactate metabolism. Interactions between the acetylated target and acetyltransferases were measured in multiple cell lines. An acetyltransferase inhibitor was injected into high-fat diet (HFD)-fed mice to determine the role of lactate on NAFLD progression in vivo. RESULTS Hyperacetylation of lactate dehydrogenase B (LDHB) was found to be associated with lactate accumulation in NAFL and NASH livers in humans and mice. P300/CBP-associated factor (PCAF)-mediated acetylation of LDHB K82 was found to significantly decrease LDHB activity and impair hepatic lactate clearance, resulting in lactate accumulation. Acetylated LDHB induced lactate accumulation which exacerbated lipid deposition and inflammatory responses by activating histone hyperacetylation in HFD-induced NASH. The administration of embelin, a PCAF inhibitor, and the generation of an acetylation-deficient mutant of LDHB ameliorated NASH. CONCLUSION PCAF-dependent LDHB acetylation plays a key role in hepatic lipid accumulation and inflammatory responses by impairing lactate clearance; this process might be a potential therapeutic target for the treatment of NASH. LAY SUMMARY Lactate is known to accumulate in the livers of patients during the progression of non-alcoholic fatty liver disease (NAFLD); however, the underlying mechanism(s) of this accumulation and its importance in disease progression are unknown. Herein, we show that the acetylation of an enzyme involved in lactate metabolism leads to impaired lactate clearance and exacerbates NAFLD progression.
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Affiliation(s)
- Tongxin Wang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Kai Chen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Weilei Yao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Ruilong Zheng
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Qiongyu He
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Jun Xia
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Juan Li
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Yafei Shao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Li Zhang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Lu Huang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Longshan Qin
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Mingming Xu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Zheng Zhang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Dingyu Pan
- Department of hepatobiliary and pancreatic Surgery, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China
| | - Zhen Li
- Department of hepatobiliary and pancreatic Surgery, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China
| | - Feiruo Huang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China; Key laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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Latorre-Muro P, Baeza J, Hurtado-Guerrero R, Hicks T, Delso I, Hernández-Ruiz C, Velázquez-Campoy A, Lawton AJ, Angulo J, Denu JM, Carrodeguas JA. Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity. J Biol Chem 2021; 296:100205. [PMID: 33334880 PMCID: PMC7948413 DOI: 10.1074/jbc.ra120.015103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/12/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Acetylation is known to regulate the activity of cytosolic phosphoenolpyruvate carboxykinase (PCK1), a key enzyme in gluconeogenesis, by promoting the reverse reaction of the enzyme (converting phosphoenolpyruvate to oxaloacetate). It is also known that the histone acetyltransferase p300 can induce PCK1 acetylation in cells, but whether that is a direct or indirect function was not known. Here we initially set out to determine whether p300 can acetylate directly PCK1 in vitro. We report that p300 weakly acetylates PCK1, but surprisingly, using several techniques including protein crystallization, mass spectrometry, isothermal titration calorimetry, saturation-transfer difference nuclear magnetic resonance and molecular docking, we found that PCK1 is also able to acetylate itself using acetyl-CoA independently of p300. This reaction yielded an acetylated recombinant PCK1 with a 3-fold decrease in kcat without changes in Km for all substrates. Acetylation stoichiometry was determined for 14 residues, including residues lining the active site. Structural and kinetic analyses determined that site-directed acetylation of K244, located inside the active site, altered this site and rendered the enzyme inactive. In addition, we found that acetyl-CoA binding to the active site is specific and metal dependent. Our findings provide direct evidence for acetyl-CoA binding and chemical reaction with the active site of PCK1 and suggest a newly discovered regulatory mechanism of PCK1 during metabolic stress.
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Affiliation(s)
- Pedro Latorre-Muro
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain.
| | - Josue Baeza
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health-Madison, Madison, Wisconsin, USA
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark; Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, Zaragoza, Spain; Fundación ARAID, Zaragoza, Spain
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - Ignacio Delso
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, Zaragoza, Spain
| | - Cristina Hernández-Ruiz
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Adrian Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Fundación ARAID, Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Biomedical Research Network Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain; IIS Aragón, Zaragoza, Spain
| | - Alexis J Lawton
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health-Madison, Madison, Wisconsin, USA
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich, UK; Departamento de Química Orgánica, Universidad de Sevilla, Sevilla, Spain; Instituto de Investigaciones Químicas (CSIC-Universidad de Sevilla), Sevilla, Spain
| | - John M Denu
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health-Madison, Madison, Wisconsin, USA
| | - José A Carrodeguas
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; IIS Aragón, Zaragoza, Spain.
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Walden EA, Fong RY, Pham TT, Knill H, Laframboise SJ, Huard S, Harper ME, Baetz K. Phenomic screen identifies a role for the yeast lysine acetyltransferase NuA4 in the control of Bcy1 subcellular localization, glycogen biosynthesis, and mitochondrial morphology. PLoS Genet 2020; 16:e1009220. [PMID: 33253187 PMCID: PMC7728387 DOI: 10.1371/journal.pgen.1009220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 12/10/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022] Open
Abstract
Cellular metabolism is tightly regulated by many signaling pathways and processes, including lysine acetylation of proteins. While lysine acetylation of metabolic enzymes can directly influence enzyme activity, there is growing evidence that lysine acetylation can also impact protein localization. As the Saccharomyces cerevisiae lysine acetyltransferase complex NuA4 has been implicated in a variety of metabolic processes, we have explored whether NuA4 controls the localization and/or protein levels of metabolic proteins. We performed a high-throughput microscopy screen of over 360 GFP-tagged metabolic proteins and identified 23 proteins whose localization and/or abundance changed upon deletion of the NuA4 scaffolding subunit, EAF1. Within this, three proteins were required for glycogen synthesis and 14 proteins were associated with the mitochondria. We determined that in eaf1Δ cells the transcription of glycogen biosynthesis genes is upregulated resulting in increased proteins and glycogen production. Further, in the absence of EAF1, mitochondria are highly fused, increasing in volume approximately 3-fold, and are chaotically distributed but remain functional. Both the increased glycogen synthesis and mitochondrial elongation in eaf1Δ cells are dependent on Bcy1, the yeast regulatory subunit of PKA. Surprisingly, in the absence of EAF1, Bcy1 localization changes from being nuclear to cytoplasmic and PKA activity is altered. We found that NuA4-dependent localization of Bcy1 is dependent on a lysine residue at position 313 of Bcy1. However, the glycogen accumulation and mitochondrial elongation phenotypes of eaf1Δ, while dependent on Bcy1, were not fully dependent on Bcy1-K313 acetylation state and subcellular localization of Bcy1. As NuA4 is highly conserved with the human Tip60 complex, our work may inform human disease biology, revealing new avenues to investigate the role of Tip60 in metabolic diseases.
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Affiliation(s)
- Elizabeth A. Walden
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Roger Y. Fong
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Trang T. Pham
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Hana Knill
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sarah Jane Laframboise
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sylvain Huard
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
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29
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Chen J, Liu Q, Zeng L, Huang X. Protein Acetylation/Deacetylation: A Potential Strategy for Fungal Infection Control. Front Microbiol 2020; 11:574736. [PMID: 33133044 PMCID: PMC7579399 DOI: 10.3389/fmicb.2020.574736] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
Protein acetylation is a universal post-translational modification that fine-tunes the major cellular processes of many life forms. Although the mechanisms regulating protein acetylation have not been fully elucidated, this modification is finely tuned by both enzymatic and non-enzymatic mechanisms. Protein deacetylation is the reverse process of acetylation and is mediated by deacetylases. Together, protein acetylation and deacetylation constitute a reversible regulatory protein acetylation network. The recent application of mass spectrometry-based proteomics has led to accumulating evidence indicating that reversible protein acetylation may be related to fungal virulence because a substantial amount of virulence factors are acetylated. Additionally, the relationship between protein acetylation/deacetylation and fungal drug resistance has also been proven and the potential of deacetylase inhibitors as an anti-infective treatment has attracted attention. This review aimed to summarize the research progress in understanding fungal protein acetylation/deacetylation and discuss the mechanism of its mediation in fungal virulence, providing novel targets for the treatment of fungal infection.
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Affiliation(s)
- Junzhu Chen
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Qiong Liu
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Lingbing Zeng
- The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaotian Huang
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
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30
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Tan KN, Avery VM, Carrasco-Pozo C. Metabolic Roles of Androgen Receptor and Tip60 in Androgen-Dependent Prostate Cancer. Int J Mol Sci 2020; 21:ijms21186622. [PMID: 32927797 PMCID: PMC7555377 DOI: 10.3390/ijms21186622] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 01/10/2023] Open
Abstract
Androgen receptor (AR)-mediated signaling is essential for the growth and differentiation of the normal prostate and is the primary target for androgen deprivation therapy in prostate cancer. Tat interactive protein 60 kDa (Tip60) is a histone acetyltransferase that is critical for AR activation. It is well known that cancer cells rewire their metabolic pathways in order to sustain aberrant proliferation. Growing evidence demonstrates that the AR and Tip60 modulate key metabolic processes to promote the survival of prostate cancer cells, in addition to their classical roles. AR activation enhances glucose metabolism, including glycolysis, tricarboxylic acid cycle and oxidative phosphorylation, as well as lipid metabolism in prostate cancer. The AR also interacts with other metabolic regulators, including calcium/calmodulin-dependent kinase kinase 2 and mammalian target of rapamycin. Several studies have revealed the roles of Tip60 in determining cell fate indirectly by modulating metabolic regulators, such as c-Myc, hypoxia inducible factor 1α (HIF-1α) and p53 in various cancer types. Furthermore, Tip60 has been shown to regulate the activity of key enzymes in gluconeogenesis and glycolysis directly through acetylation. Overall, both the AR and Tip60 are master metabolic regulators that mediate cellular energy metabolism in prostate cancer, providing a framework for the development of novel therapeutic targets in androgen-dependent prostate cancer.
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Affiliation(s)
- Kah Ni Tan
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia; (K.N.T.); (V.M.A.)
- CRC for Cancer Therapeutics, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Vicky M. Avery
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia; (K.N.T.); (V.M.A.)
- CRC for Cancer Therapeutics, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Catalina Carrasco-Pozo
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia; (K.N.T.); (V.M.A.)
- CRC for Cancer Therapeutics, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
- Correspondence: ; Tel.: +617-3735-6034
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31
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Syu GD, Dunn J, Zhu H. Developments and Applications of Functional Protein Microarrays. Mol Cell Proteomics 2020; 19:916-927. [PMID: 32303587 PMCID: PMC7261817 DOI: 10.1074/mcp.r120.001936] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/24/2020] [Indexed: 12/19/2022] Open
Abstract
Protein microarrays are crucial tools in the study of proteins in an unbiased, high-throughput manner, as they allow for characterization of up to thousands of individually purified proteins in parallel. The adaptability of this technology has enabled its use in a wide variety of applications, including the study of proteome-wide molecular interactions, analysis of post-translational modifications, identification of novel drug targets, and examination of pathogen-host interactions. In addition, the technology has also been shown to be useful in profiling antibody specificity, as well as in the discovery of novel biomarkers, especially for autoimmune diseases and cancers. In this review, we will summarize the developments that have been made in protein microarray technology in both in basic and translational research over the past decade. We will also introduce a novel membrane protein array, the GPCR-VirD array, and discuss the future directions of functional protein microarrays.
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Affiliation(s)
- Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan R.O.C..
| | - Jessica Dunn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231.
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32
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Disruption in phosphate transport affects membrane lipid and lipid droplet homeostasis in Saccharomyces cerevisiae. J Bioenerg Biomembr 2020; 52:215-227. [PMID: 32462239 DOI: 10.1007/s10863-020-09837-5] [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: 10/01/2019] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
Phosphate plays a crucial role in phospholipid metabolism and it is transported by the phosphate (Pi) transporters. Phospholipids are building blocks of the cell membrane, and essential for cell growth; however, the role of phosphate transporters in lipid metabolism remains elusive. The present study shows that the deletion of Pi transporters exhibited an increase in both phospholipid and neutral lipid levels when compared to wild type. The mRNA expressions of genes involved in phospholipid synthesis (CKI1, EKI1, CHO2, and OPI3) were increased due to de-repression of the transcription factors (INO2 and INO4). Neutral lipid levels (triacylglycerol and sterol ester) and their synthesizing genes (LRO1, ARE2, ACC1, and FAS1) were also increased, resulting in lipid droplet accumulation in Pi transporter mutants. Interestingly, phospholipase (PLC1) and histone acetyltransferase genes (ESA1, EAF1, YNG1, YNG2, and GCN5) were also found to be significantly increased, leading to dysregulation of lipid levels in Pi transporter mutants. In summary, our results suggest that the Pi transporters are involved in lipid droplet and membrane lipid homeostasis.
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Evans LW, Stratton MS, Ferguson BS. Dietary natural products as epigenetic modifiers in aging-associated inflammation and disease. Nat Prod Rep 2020; 37:653-676. [PMID: 31993614 PMCID: PMC7577396 DOI: 10.1039/c9np00057g] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to 2020Chronic, low-grade inflammation is linked to aging and has been termed "inflammaging". Inflammaging is considered a key contributor to the development of metabolic dysfunction and a broad spectrum of diseases or disorders including declines in brain and heart function. Genome-wide association studies (GWAS) coupled with epigenome-wide association studies (EWAS) have shown the importance of diet in the development of chronic and age-related diseases. Moreover, dietary interventions e.g. caloric restriction can attenuate inflammation to delay and/or prevent these diseases. Common themes in these studies entail the use of phytochemicals (plant-derived compounds) or the production of short chain fatty acids (SCFAs) as epigenetic modifiers of DNA and histone proteins. Epigenetic modifications are dynamically regulated and as such, serve as potential therapeutic targets for the treatment or prevention of age-related disease. In this review, we will focus on the role for natural products that include phytochemicals and short chain fatty acids (SCFAs) as regulators of these epigenetic adaptations. Specifically, we discuss regulators of methylation, acetylation and acylation, in the protection from chronic inflammation driven metabolic dysfunction and deterioration of neurocognitive and cardiac function.
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Affiliation(s)
- Levi W Evans
- Department of Nutrition, University of Nevada, Reno, NV 89557, USA.
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34
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Orlandi I, Alberghina L, Vai M. Nicotinamide, Nicotinamide Riboside and Nicotinic Acid-Emerging Roles in Replicative and Chronological Aging in Yeast. Biomolecules 2020; 10:E604. [PMID: 32326437 PMCID: PMC7226615 DOI: 10.3390/biom10040604] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
Nicotinamide, nicotinic acid and nicotinamide riboside are vitamin B3 precursors of NAD+ in the human diet. NAD+ has a fundamental importance for cellular biology, that derives from its essential role as a cofactor of various metabolic redox reactions, as well as an obligate co-substrate for NAD+-consuming enzymes which are involved in many fundamental cellular processes including aging/longevity. During aging, a systemic decrease in NAD+ levels takes place, exposing the organism to the risk of a progressive inefficiency of those processes in which NAD+ is required and, consequently, contributing to the age-associated physiological/functional decline. In this context, dietary supplementation with NAD+ precursors is considered a promising strategy to prevent NAD+ decrease and attenuate in such a way several metabolic defects common to the aging process. The metabolism of NAD+ precursors and its impact on cell longevity have benefited greatly from studies performed in the yeast Saccharomyces cerevisiae, which is one of the most established model systems used to study the aging processes of both proliferating (replicative aging) and non-proliferating cells (chronological aging). In this review we summarize important aspects of the role played by nicotinamide, nicotinic acid and nicotinamide riboside in NAD+ metabolism and how each of these NAD+ precursors contribute to the different aspects that influence both replicative and chronological aging. Taken as a whole, the findings provided by the studies carried out in S. cerevisiae are informative for the understanding of the complex dynamic flexibility of NAD+ metabolism, which is essential for the maintenance of cellular fitness and for the development of dietary supplements based on NAD+ precursors.
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Affiliation(s)
- Ivan Orlandi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 2016 Milan, Italy;
| | | | - Marina Vai
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 2016 Milan, Italy;
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35
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Yazaki J, Kawashima Y, Ogawa T, Kobayashi A, Okoshi M, Watanabe T, Yoshida S, Kii I, Egami S, Amagai M, Hosoya T, Shiroguchi K, Ohara O. HaloTag-based conjugation of proteins to barcoding-oligonucleotides. Nucleic Acids Res 2020; 48:e8. [PMID: 31752022 PMCID: PMC6954424 DOI: 10.1093/nar/gkz1086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/29/2019] [Accepted: 11/18/2019] [Indexed: 11/12/2022] Open
Abstract
Highly sensitive protein quantification enables the detection of a small number of protein molecules that serve as markers/triggers for various biological phenomena, such as cancer. Here, we describe the development of a highly sensitive protein quantification system called HaloTag protein barcoding. The method involves covalent linking of a target protein to a unique molecule counting oligonucleotide at a 1:1 conjugation ratio based on an azido-cycloalkyne click reaction. The sensitivity of the HaloTag-based barcoding was remarkably higher than that of a conventional luciferase assay. The HaloTag system was successfully validated by analyzing a set of protein-protein interactions, with the identification rate of 44% protein interactions between positive reference pairs reported in the literature. Desmoglein 3, the target antigen of pemphigus vulgaris, an IgG-mediated autoimmune blistering disease, was used in a HaloTag protein barcode assay to detect the anti-DSG3 antibody. The dynamic range of the assay was over 104-times wider than that of a conventional enzyme-linked immunosorbent assay (ELISA). The technology was used to detect anti-DSG3 antibody in patient samples with much higher sensitivity compared to conventional ELISA. Our detection system, with its superior sensitivity, enables earlier detection of diseases possibly allowing the initiation of care/treatment at an early disease stage.
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Affiliation(s)
- Junshi Yazaki
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama City 230-0045, Japan
| | - Yusuke Kawashima
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama City 230-0045, Japan
| | - Taisaku Ogawa
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka 565-0874, Japan
| | - Atsuo Kobayashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama City 230-0045, Japan
| | - Mayu Okoshi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama City 230-0045, Japan
| | - Takashi Watanabe
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama City 230-0045, Japan
| | - Suguru Yoshida
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo 101-0062, Japan
| | - Isao Kii
- Common Facilities Unit, Compass to Healthy Life Research Complex Program, RIKEN Cluster for Science, Technology and Innovation Hub, Kobe 650-0047, Japan
| | - Shohei Egami
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan.,Department of Dermatology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masayuki Amagai
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan.,Department of Dermatology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Takamitsu Hosoya
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo 101-0062, Japan.,Laboratory for Chemical Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Katsuyuki Shiroguchi
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka 565-0874, Japan.,Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama City 230-0045, Japan
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36
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Croft T, Venkatakrishnan P, Lin SJ. NAD + Metabolism and Regulation: Lessons From Yeast. Biomolecules 2020; 10:E330. [PMID: 32092906 PMCID: PMC7072712 DOI: 10.3390/biom10020330] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/15/2020] [Accepted: 02/16/2020] [Indexed: 12/13/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite involved in various cellular processes. The cellular NAD+ pool is maintained by three biosynthesis pathways, which are largely conserved from bacteria to human. NAD+ metabolism is an emerging therapeutic target for several human disorders including diabetes, cancer, and neuron degeneration. Factors regulating NAD+ homeostasis have remained incompletely understood due to the dynamic nature and complexity of NAD+ metabolism. Recent studies using the genetically tractable budding yeast Saccharomyces cerevisiae have identified novel NAD+ homeostasis factors. These findings help provide a molecular basis for how may NAD+ and NAD+ homeostasis factors contribute to the maintenance and regulation of cellular function. Here we summarize major NAD+ biosynthesis pathways, selected cellular processes that closely connect with and contribute to NAD+ homeostasis, and regulation of NAD+ metabolism by nutrient-sensing signaling pathways. We also extend the discussions to include possible implications of NAD+ homeostasis factors in human disorders. Understanding the cross-regulation and interconnections of NAD+ precursors and associated cellular pathways will help elucidate the mechanisms of the complex regulation of NAD+ homeostasis. These studies may also contribute to the development of effective NAD+-based therapeutic strategies specific for different types of NAD+ deficiency related disorders.
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Affiliation(s)
| | | | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA; (T.C.); (P.V.)
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PCK1 Deficiency Shortens the Replicative Lifespan of Saccharomyces cerevisiae through Upregulation of PFK1. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3858465. [PMID: 32104690 PMCID: PMC7037958 DOI: 10.1155/2020/3858465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/29/2019] [Accepted: 01/11/2020] [Indexed: 12/25/2022]
Abstract
The cytosolic isozyme of phosphoenolpyruvate carboxykinase (PCK1) was the first rate-limiting enzyme in the gluconeogenesis pathway, which exerted a critical role in maintaining the blood glucose levels. PCK1 has been established to be involved in various physiological and pathological processes, including glucose metabolism, lipid metabolism, diabetes, and tumorigenesis. Nonetheless, the association of PCK1 with aging process and the detailed underlying mechanisms of PCK1 on aging are still far to be elucidated. Hence, we herein constructed the PCK1-deficient (pck1Δ) and PCK1 overexpression (PCK1 OE) Saccharomyces cerevisiae. The results unveiled that PCK1 deficiency significantly shortened the replicative lifespan (RLS) in the S. cerevisiae, while overexpression of PCK1 prolonged the RLS. Additionally, we noted that the ROS level was significantly enhanced in PCK1-deficient strain and decreased in PCK1 OE strain. Then, a high throughput analysis by deep sequencing was performed in the pck1Δ and wild-type strains, in an attempt to shed light on the effect of PCK1 on the lifespan of aging process. The data showed that the most downregulated mRNAs were enriched in the regulatory pathways of glucose metabolism. Fascinatingly, among the differentially expressed mRNAs, PFK1 was one of the most upregulated genes, which was involved in the glycolysis process and ROS generation. Thus, we further constructed the pfk1Δpck1Δ strain by deletion of PFK1 in the PCK1-deficient strain. The results unraveled that pfk1Δpck1Δ strain significantly suppressed the ROS level and restored the RLS of pck1Δ strain. Taken together, our data suggested that PCK1 deficiency enhanced the ROS level and shortened the RLS of S. cerevisiae via PFK1.
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Espinosa-Cores L, Bouza-Morcillo L, Barrero-Gil J, Jiménez-Suárez V, Lázaro A, Piqueras R, Jarillo JA, Piñeiro M. Insights Into the Function of the NuA4 Complex in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:125. [PMID: 32153620 PMCID: PMC7047200 DOI: 10.3389/fpls.2020.00125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/28/2020] [Indexed: 05/14/2023]
Abstract
Chromatin remodeling plays a key role in the establishment and maintenance of gene expression patterns essential for plant development and responses to environmental factors. Post-translational modification of histones, including acetylation, is one of the most relevant chromatin remodeling mechanisms that operate in eukaryotic cells. Histone acetylation is an evolutionarily conserved chromatin signature commonly associated with transcriptional activation. Histone acetylation levels are tightly regulated through the antagonistic activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In plants, different families of HATs are present, including the MYST family, which comprises homologs of the catalytic subunit of the Nucleosome Acetyltransferase of H4 (NuA4) complex in yeast. This complex mediates acetylation of histones H4, H2A, and H2A.Z, and is involved in transcriptional regulation, heterochromatin silencing, cell cycle progression, and DNA repair in yeast. In Arabidopsis and, other plant species, homologs for most of the yeast NuA4 subunits are present and although the existence of this complex has not been demonstrated yet, compelling evidence supports the notion that this type of HAT complex functions from mosses to angiosperms. Recent proteomic studies show that several Arabidopsis homologs of NuA4 components, including the assembly platform proteins and the catalytic subunit, are associated in vivo with additional members of this complex suggesting that a NuA4-like HAT complex is present in plants. Furthermore, the functional characterization of some Arabidopsis NuA4 subunits has uncovered the involvement of these proteins in the regulation of different plant biological processes. Interestingly, for most of the mutant plants deficient in subunits of this complex characterized so far, conspicuous defects in flowering time are observed, suggesting a role for NuA4 in the control of this plant developmental program. Moreover, the participation of Arabidopsis NuA4 homologs in other developmental processes, such as gametophyte development, as well as in cell proliferation and stress and hormone responses, has also been reported. In this review, we summarize the current state of knowledge on plant putative NuA4 subunits and discuss the latest progress concerning the function of this chromatin modifying complex.
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Song J, Zheng YG. Bioorthogonal Reporters for Detecting and Profiling Protein Acetylation and Acylation. SLAS DISCOVERY 2019; 25:148-162. [PMID: 31711353 DOI: 10.1177/2472555219887144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein acylation, exemplified by lysine acetylation, is a type of indispensable and widespread protein posttranslational modification in eukaryotes. Functional annotation of various lysine acetyltransferases (KATs) is critical to understanding their regulatory roles in abundant biological processes. Traditional radiometric and immunosorbent assays have found broad use in KAT study but have intrinsic limitations. Designing acyl-coenzyme A (CoA) reporter molecules bearing chemoselective chemical warhead groups as surrogates of the native cofactor acetyl-CoA for bioorthogonal labeling of KAT substrates has come into a technical innovation in recent years. This chemical biology platform equips molecular biologists with empowering tools in acyltransferase activity detection and substrate profiling. In the bioorthogonal labeling, protein substrates are first enzymatically modified with a functionalized acyl group. Subsequently, the chemical warhead on the acyl chain conjugates with either an imaging chromophore or an affinity handle or any other appropriate probes through an orthogonal chemical ligation. This bioorganic strategy reformats the chemically inert acetylation and acylation marks into a chemically maneuverable functionality and generates measurable signals without recourse to radioisotopes or antibodies. It offers ample opportunities for facile sensitive detection of KAT activity with temporal and spatial resolutions as well as allows for chemoproteomic profiling of protein acetylation pertaining to specific KATs of interest on the global scale. We reviewed here the past and current advances in bioorthogonal protein acylations and highlighted their wide-spectrum applications. We also discussed the design of other related acyl-CoA and CoA-based chemical probes and their deployment in illuminating protein acetylation and acylation biology.
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Affiliation(s)
- Jiabao Song
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
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Wakatsuki T, Sasaki M, Kobayashi T. Defects in the NuA4 acetyltransferase complex increase stability of the ribosomal RNA gene and extend replicative lifespan. Genes Genet Syst 2019; 94:197-206. [PMID: 31694990 DOI: 10.1266/ggs.19-00022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genome instability is a cause of cellular senescence. The ribosomal RNA gene repeat (rDNA) is one of the most unstable regions in the genome and its instability is proposed to be a major inducer of cellular senescence and restricted lifespan. We previously conducted a genome-wide screen using a budding yeast deletion library to identify mutants that exhibit a change in the stability of the rDNA region, compared to the wild-type. To investigate the correlation between rDNA stability and lifespan, we examined deletion mutants with very stable rDNA and found that deletion of EAF3, encoding a component of the NuA4 histone acetyltransferase complex, reproducibly resulted in increased stabilization of the rDNA. In the absence of Eaf3, and of other subunits of the NuA4 complex, we observed lower levels of extrachromosomal rDNA circles that are produced by recombination in the rDNA and are thus an indicator of rDNA instability. The replicative lifespan in the eaf3 mutant was extended by ~30%, compared to the wild-type strain. Our findings provide evidence that rDNA stability is correlated with extended replicative lifespan. The eaf3 mutation possibly affects the non-coding transcription in rDNA that regulates rDNA recombination through cohesin dissociation.
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Affiliation(s)
- Tsuyoshi Wakatsuki
- Institute for Quantitative Biosciences, The University of Tokyo.,Department of Life Science and Technology, Tokyo Institute of Technology
| | - Mariko Sasaki
- Institute for Quantitative Biosciences, The University of Tokyo
| | - Takehiko Kobayashi
- Institute for Quantitative Biosciences, The University of Tokyo.,Department of Life Science and Technology, Tokyo Institute of Technology.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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Cell organelles and yeast longevity: an intertwined regulation. Curr Genet 2019; 66:15-41. [PMID: 31535186 DOI: 10.1007/s00294-019-01035-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022]
Abstract
Organelles are dynamic structures of a eukaryotic cell that compartmentalize various essential functions and regulate optimum functioning. On the other hand, ageing is an inevitable phenomenon that leads to irreversible cellular damage and affects optimum functioning of cells. Recent research shows compelling evidence that connects organelle dysfunction to ageing-related diseases/disorders. Studies in several model systems including yeast have led to seminal contributions to the field of ageing in uncovering novel pathways, proteins and their functions, identification of pro- and anti-ageing factors and so on. In this review, we present a comprehensive overview of findings that highlight the role of organelles in ageing and ageing-associated functions/pathways in yeast.
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Roles of the INO80 and SWR1 Chromatin Remodeling Complexes in Plants. Int J Mol Sci 2019; 20:ijms20184591. [PMID: 31533258 PMCID: PMC6770637 DOI: 10.3390/ijms20184591] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic genes are packed into a dynamic but stable nucleoprotein structure called chromatin. Chromatin-remodeling and modifying complexes generate a dynamic chromatin environment that ensures appropriate DNA processing and metabolism in various processes such as gene expression, as well as DNA replication, repair, and recombination. The INO80 and SWR1 chromatin remodeling complexes (INO80-c and SWR1-c) are ATP-dependent complexes that modulate the incorporation of the histone variant H2A.Z into nucleosomes, which is a critical step in eukaryotic gene regulation. Although SWR1-c has been identified in plants, plant INO80-c has not been successfully isolated and characterized. In this review, we will focus on the functions of the SWR1-c and putative INO80-c (SWR1/INO80-c) multi-subunits and multifunctional complexes in Arabidopsis thaliana. We will describe the subunit compositions of the SWR1/INO80-c and the recent findings from the standpoint of each subunit and discuss their involvement in regulating development and environmental responses in Arabidopsis.
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Wang F, Chang C, Li R, Zhang Z, Jiang H, Zeng N, Li D, Chen L, Xiao Y, Chen W, Wang Q. Retinol binding protein 4 mediates MEHP-induced glucometabolic abnormalities in HepG2 cells. Toxicology 2019; 424:152236. [DOI: 10.1016/j.tox.2019.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/12/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022]
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Christensen DG, Xie X, Basisty N, Byrnes J, McSweeney S, Schilling B, Wolfe AJ. Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions. Front Microbiol 2019; 10:1604. [PMID: 31354686 PMCID: PMC6640162 DOI: 10.3389/fmicb.2019.01604] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Post-translational modifications (PTM) decorate proteins to provide functional heterogeneity to an existing proteome. The large number of known PTMs highlights the many ways that cells can modify their proteins to respond to diverse stimuli. Recently, PTMs have begun to receive increased interest because new sensitive proteomics workflows and structural methodologies now allow researchers to obtain large-scale, in-depth and unbiased information concerning PTM type and site localization. However, few PTMs have been extensively assessed for functional consequences, leaving a large knowledge gap concerning the inner workings of the cell. Here, we review understanding of N-𝜀-lysine acetylation in bacteria, a PTM that was largely ignored in bacteria until a decade ago. Acetylation is a modification that can dramatically change the function of a protein through alteration of its properties, including hydrophobicity, solubility, and surface properties, all of which may influence protein conformation and interactions with substrates, cofactors and other macromolecules. Most bacteria carry genes predicted to encode the lysine acetyltransferases and lysine deacetylases that add and remove acetylations, respectively. Many bacteria also exhibit acetylation activities that do not depend on an enzyme, but instead on direct transfer of acetyl groups from the central metabolites acetyl coenzyme A or acetyl phosphate. Regardless of mechanism, most central metabolic enzymes possess lysines that are acetylated in a regulated fashion and many of these regulated sites are conserved across the spectrum of bacterial phylogeny. The interconnectedness of acetylation and central metabolism suggests that acetylation may be a response to nutrient availability or the energy status of the cell. However, this and other hypotheses related to acetylation remain untested.
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Affiliation(s)
- David G. Christensen
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Xueshu Xie
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, CA, United States
| | - James Byrnes
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | - Sean McSweeney
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | | | - Alan J. Wolfe
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
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Cheng F, Han L, Xiao Y, Pan C, Li Y, Ge X, Zhang Y, Yan S, Wang M. d- chiro-Inositol Ameliorates High Fat Diet-Induced Hepatic Steatosis and Insulin Resistance via PKCε-PI3K/AKT Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5957-5967. [PMID: 31066268 DOI: 10.1021/acs.jafc.9b01253] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
d- chiro-Inositol (DCI) is a biologically active component found in tartary buckwheat, which can reduce hyperglycemia and ameliorate insulin resistance. However, the mechanism underlying the antidiabetic effects of DCI remains largely unclear. This study investigated the effects and underlying molecular mechanisms of DCI on hepatic gluconeogenesis in mice fed a high fat diet and saturated palmitic acid-treated hepatocytes. DCI attenuated free fatty acid uptake by the liver via lipid trafficking inhibition, reduced diacylglycerol deposition, and hepatic PKCε translocation. Thus, DCI could improve insulin sensitivity by suppressing hepatic gluconeogenesis. Subsequent analyses revealed that DCI decreased hepatic glucose output and the expression levels of PEPCK and G6 Pase in insulin resistant mice through PKCε-IRS/PI3K/AKT signaling pathway. Likewise, such effects of DCI were confirmed in HepG2 cells with palmitate-induced insulin resistance. These findings indicate a novel pathway by which DCI prevents hepatic gluconeogenesis, reduces lipid deposition, and ameliorates insulin resistance via regulation of PKCε-PI3K/AKT axis.
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Affiliation(s)
- Feier Cheng
- College of Food Science and Engineering , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Lin Han
- College of Food Science and Engineering , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Yao Xiao
- College of Food Science and Engineering , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Chuanying Pan
- College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Yunlong Li
- Institute of Agricultural Products Processing , Shanxi Academy of Agriculture Sciences , Taiyuan 030031 , People's Republic of China
| | - Xinhui Ge
- College of Food Science and Engineering , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Yao Zhang
- College of Food Science and Engineering , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Shaoqing Yan
- College of Food Science and Engineering , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Min Wang
- College of Food Science and Engineering , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
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Vall-Llaura N, Mir N, Garrido L, Vived C, Cabiscol E. Redox control of yeast Sir2 activity is involved in acetic acid resistance and longevity. Redox Biol 2019; 24:101229. [PMID: 31153040 PMCID: PMC6543126 DOI: 10.1016/j.redox.2019.101229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/10/2019] [Accepted: 05/19/2019] [Indexed: 01/07/2023] Open
Abstract
Yeast Sir2 is an NAD-dependent histone deacetylase related to oxidative stress and aging. In a previous study, we showed that Sir2 is regulated by S-glutathionylation of key cysteine residues located at the catalytic domain. Mutation of these residues results in strains with increased resistance to disulfide stress. In the present study, these mutant cells were highly resistant to acetic acid and had an increased chronological life span. Mutant cells had increased acetyl-CoA synthetase activity, which converts acetic acid generated by yeast metabolism to acetyl.CoA. This could explain the acetic acid resistance and lower levels of this toxic acid in the extracellular media during aging. Increased acetyl-CoA levels would raise lipid droplets, a source of energy during aging, and fuel glyoxylate-dependent gluconeogenesis. The key enzyme of this pathway, phosphoenolpyruvate carboxykinase (Pck1), showed increased activity in these Sir2 mutant cells during aging. Sir2 activity decreased when cells shifted to the diauxic phase in the mutant strains, compared to the WT strain. Since Pck1 is inactivated through Sir2-dependent deacetylation, the decline in Sir2 activity explained the rise in Pck1 activity. As a consequence, storage of sugars such as trehalose would increase. We conclude that extended longevity observed in the mutants was a combination of increased lipid droplets and trehalose, and decreased acetic acid in the extracellular media. These results offer a deeper understanding of the redox regulation of Sir2 in acetic acid resistance, which is relevant in some food and industrial biotechnology and also in the metabolism associated to calorie restriction, aging and pathologies such as diabetes.
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Affiliation(s)
- Núria Vall-Llaura
- Department de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, Catalonia, Spain.
| | - Noèlia Mir
- Department de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, Catalonia, Spain.
| | - Lourdes Garrido
- Department de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, Catalonia, Spain.
| | - Celia Vived
- Department de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, Catalonia, Spain.
| | - Elisa Cabiscol
- Department de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, Catalonia, Spain.
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Abstract
The acetylation of the ε-amine of lysine residues has significant impacts on the cellular functions of proteins. Through the combination of unbiased and targeted analysis of acetylated proteins, biological insights on lysine acetylation are now routinely generated. To help in this endeavor, we describe detailed protocols for the identification of acetylated lysine residues and the preparation of multiple reagents for the characterization of these sites in order to obtain functional insights on this widespread modification.
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Geisler CE, Ghimire S, Bogan RL, Renquist BJ. Role of ketone signaling in the hepatic response to fasting. Am J Physiol Gastrointest Liver Physiol 2019; 316:G623-G631. [PMID: 30767679 PMCID: PMC6580236 DOI: 10.1152/ajpgi.00415.2017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ketosis is a metabolic adaptation to fasting, nonalcoholic fatty liver disease (NAFLD), and prolonged exercise. β-OH butyrate acts as a transcriptional regulator and at G protein-coupled receptors to modulate cellular signaling pathways in a hormone-like manner. While physiological ketosis is often adaptive, chronic hyperketonemia may contribute to the metabolic dysfunction of NAFLD. To understand how β-OH butyrate signaling affects hepatic metabolism, we compared the hepatic fasting response in control and 3-hydroxy-3-methylglutaryl-CoA synthase II (HMGCS2) knockdown mice that are unable to elevate β-OH butyrate production. To establish that rescue of ketone metabolic/endocrine signaling would restore the normal hepatic fasting response, we gave intraperitoneal injections of β-OH butyrate (5.7 mmol/kg) to HMGCS2 knockdown and control mice every 2 h for the final 9 h of a 16-h fast. In hypoketonemic, HMGCS2 knockdown mice, fasting more robustly increased mRNA expression of uncoupling protein 2 (UCP2), a protein critical for supporting fatty acid oxidation and ketogenesis. In turn, exogenous β-OH butyrate administration to HMGCS2 knockdown mice decreased fasting UCP2 mRNA expression to that observed in control mice. Also supporting feedback at the transcriptional level, β-OH butyrate lowered the fasting-induced expression of HMGCS2 mRNA in control mice. β-OH butyrate also regulates the glycemic response to fasting. The fast-induced fall in serum glucose was absent in HMGCS2 knockdown mice but was restored by β-OH butyrate administration. These data propose that endogenous β-OH butyrate signaling transcriptionally regulates hepatic fatty acid oxidation and ketogenesis, while modulating glucose tolerance. NEW & NOTEWORTHY Ketogenesis regulates whole body glucose metabolism and β-OH butyrate produced by the liver feeds back to inhibit hepatic β-oxidation and ketogenesis during fasting.
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Affiliation(s)
- Caroline E. Geisler
- School of Animal and Comparative Biomedical Science, University of Arizona, Tucson, Arizona
| | - Susma Ghimire
- School of Animal and Comparative Biomedical Science, University of Arizona, Tucson, Arizona
| | - Randy L. Bogan
- School of Animal and Comparative Biomedical Science, University of Arizona, Tucson, Arizona
| | - Benjamin J. Renquist
- School of Animal and Comparative Biomedical Science, University of Arizona, Tucson, Arizona
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Lei Y, Gong L, Tan F, Liu Y, Li S, Shen H, Zhu M, Cai W, Xu F, Hou B, Zhou Y, Han H, Qiu L, Sun H. Vaccarin ameliorates insulin resistance and steatosis by activating the AMPK signaling pathway. Eur J Pharmacol 2019; 851:13-24. [DOI: 10.1016/j.ejphar.2019.02.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/26/2022]
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Xu M, Deng J, Xu K, Zhu T, Han L, Yan Y, Yao D, Deng H, Wang D, Sun Y, Chang C, Zhang X, Dai J, Yue L, Zhang Q, Cai X, Zhu Y, Duan H, Liu Y, Li D, Zhu Y, Radstake TRDJ, Balak DM, Xu D, Guo T, Lu C, Yu X. In-depth serum proteomics reveals biomarkers of psoriasis severity and response to traditional Chinese medicine. Theranostics 2019; 9:2475-2488. [PMID: 31131048 PMCID: PMC6526001 DOI: 10.7150/thno.31144] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/22/2019] [Indexed: 12/23/2022] Open
Abstract
Serum and plasma contain abundant biological information that reflect the body's physiological and pathological conditions and are therefore a valuable sample type for disease biomarkers. However, comprehensive profiling of the serological proteome is challenging due to the wide range of protein concentrations in serum. Methods: To address this challenge, we developed a novel in-depth serum proteomics platform capable of analyzing the serum proteome across ~10 orders or magnitude by combining data obtained from Data Independent Acquisition Mass Spectrometry (DIA-MS) and customizable antibody microarrays. Results: Using psoriasis as a proof-of-concept disease model, we screened 50 serum proteomes from healthy controls and psoriasis patients before and after treatment with traditional Chinese medicine (YinXieLing) on our in-depth serum proteomics platform. We identified 106 differentially-expressed proteins in psoriasis patients involved in psoriasis-relevant biological processes, such as blood coagulation, inflammation, apoptosis and angiogenesis signaling pathways. In addition, unbiased clustering and principle component analysis revealed 58 proteins discriminating healthy volunteers from psoriasis patients and 12 proteins distinguishing responders from non-responders to YinXieLing. To further demonstrate the clinical utility of our platform, we performed correlation analyses between serum proteomes and psoriasis activity and found a positive association between the psoriasis area and severity index (PASI) score with three serum proteins (PI3, CCL22, IL-12B). Conclusion: Taken together, these results demonstrate the clinical utility of our in-depth serum proteomics platform to identify specific diagnostic and predictive biomarkers of psoriasis and other immune-mediated diseases.
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