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Vidal PJ, Pérez AP, Yahya G, Aldea M. Transcriptomic balance and optimal growth are determined by cell size. Mol Cell 2024:S1097-2765(24)00581-1. [PMID: 39084218 DOI: 10.1016/j.molcel.2024.07.005] [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: 03/04/2024] [Revised: 06/11/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
Cell size and growth are intimately related across the evolutionary scale, but whether cell size is important to attain maximal growth or fitness is still an open question. We show that growth rate is a non-monotonic function of cell volume, with maximal values around the critical size of wild-type yeast cells. The transcriptome of yeast and mouse cells undergoes a relative inversion in response to cell size, which we associate theoretically and experimentally with the necessary genome-wide diversity in RNA polymerase II affinity for promoters. Although highly expressed genes impose strong negative effects on fitness when the DNA/mass ratio is reduced, transcriptomic alterations mimicking the relative inversion by cell size strongly restrain cell growth. In all, our data indicate that cells set the critical size to obtain a properly balanced transcriptome and, as a result, maximize growth and fitness during proliferation.
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Affiliation(s)
- Pedro J Vidal
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
| | - Alexis P Pérez
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain; Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain
| | - Galal Yahya
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain; Department of Microbiology and Immunology, School of Pharmacy, Zagazig University, 44511 Zagazig, Egypt.
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain; Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain.
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2
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Yang N, Zhang J, Guo J, Xiang Q, Huang Y, Wen J, Liu Q, Hu T, Chen Y, Rao C. Revealing the mechanism of Zanthoxylum armatum DC. extract-induced liver injury in mice based on lipidomics. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117086. [PMID: 37634752 DOI: 10.1016/j.jep.2023.117086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/19/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Zanthoxylum armatum DC. (Z. armatum) is an herbal medicine with various active ingredients and pharmacological effects. However, modern studies found that Z. armatum is hepatotoxic. The liver is the target organ for toxic effects and an important site for lipid metabolism. The effects of Z. armatum on lipid level and metabolism in the liver are still unclear. AIM OF THE STUDY This study aimed to analyze hepatic lipid levels, lipid metabolites and metabolic pathways of action of Z. armatum based on lipidomics, to investigate the potential hepatotoxic mechanism of Z. armatum. MATERIALS AND METHODS Different doses (62, 96, and 150 mg/kg) of the methanolic extract of Z. armatum (MZADC) were administered to ICR mice by gavage. The hepatotoxicity of MZADC was assessed by the liver index, serum biochemical measurements, and histopathological examination. Lipid levels measured by the serum lipid index were evaluated in the mice. Lipidomics was used to screen for differential lipid metabolism markers and lipid metabolism pathways in the liver. Western blot analysis was performed to investigate the effects of MZADC on the liver. RESULTS Liver index values and serum alanine transaminase and aspartate transaminase levels were increased in the MZADC group. Histopathology examination revealed hepatocyte necrosis, watery degeneration of the hepatocytes, and hepatic cord rupture in the livers of mice. Serum levels of low-density lipoprotein cholesterol, cholesterol, and triglycerides were elevated, and high-density lipoprotein cholesterol levels were decreased. Lipidomics screening for markers of differential lipid metabolism in the liver, and altered profiles of differential metabolites indicated that glycerophospholipid metabolism, linoleic acid metabolism, alpha-linolenic acid metabolism, glycosylphosphatidylinositol-anchored biosynthesis, sphingolipid metabolism and arachidonic acid metabolic pathways were significantly associated with MZADC-induced liver injury. Western blots confirmed that the protein expression of LC3, Beclin-1, ATG5, ATG12 and ATG16L1 was decreased, and p62 was increased in the MZADC group. The proportion of p-PI3K/PI3K and p-AKT/AKT was increased. CONCLUSIONS The liver injury induced by MZADC involved many different lipid metabolites and lipid metabolic pathways, which may be related to autophagy. This study provides a new perspective on the hepatotoxicity study of Z. armatum and provides a reference for the safe application of Z. armatum in the medicine and food fields.
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Affiliation(s)
- Nannan Yang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Jian Zhang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Jiafu Guo
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Qiwen Xiang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Yan Huang
- Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Jiayu Wen
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Qiuyan Liu
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Tingting Hu
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Yan Chen
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China; Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China.
| | - Chaolong Rao
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China; Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China; R&D Center for Efficiency, Safety and Application in Chinese Materia Medica with Medical and Edible Values, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China.
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3
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Obsilova V, Obsil T. The yeast 14-3-3 proteins Bmh1 and Bmh2 regulate key signaling pathways. Front Mol Biosci 2024; 11:1327014. [PMID: 38328397 PMCID: PMC10847541 DOI: 10.3389/fmolb.2024.1327014] [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: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Cell signaling regulates several physiological processes by receiving, processing, and transmitting signals between the extracellular and intracellular environments. In signal transduction, phosphorylation is a crucial effector as the most common posttranslational modification. Selectively recognizing specific phosphorylated motifs of target proteins and modulating their functions through binding interactions, the yeast 14-3-3 proteins Bmh1 and Bmh2 are involved in catabolite repression, carbon metabolism, endocytosis, and mitochondrial retrograde signaling, among other key cellular processes. These conserved scaffolding molecules also mediate crosstalk between ubiquitination and phosphorylation, the spatiotemporal control of meiosis, and the activity of ion transporters Trk1 and Nha1. In humans, deregulation of analogous processes triggers the development of serious diseases, such as diabetes, cancer, viral infections, microbial conditions and neuronal and age-related diseases. Accordingly, the aim of this review article is to provide a brief overview of the latest findings on the functions of yeast 14-3-3 proteins, focusing on their role in modulating the aforementioned processes.
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Affiliation(s)
- Veronika Obsilova
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Structural Biology of Signaling Proteins, Division, BIOCEV, Vestec, Czechia
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czechia
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Mariner BL, Felker DP, Cantergiani RJ, Peterson J, McCormick MA. Multiomics of GCN4-Dependent Replicative Lifespan Extension Models Reveals Gcn4 as a Regulator of Protein Turnover in Yeast. Int J Mol Sci 2023; 24:16163. [PMID: 38003352 PMCID: PMC10671045 DOI: 10.3390/ijms242216163] [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: 10/03/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
We have shown that multiple tRNA synthetase inhibitors can increase lifespan in both the nematode C. elegans and the budding yeast S. cerevisiae by acting through the conserved transcription factor Gcn4 (yeast)/ATF-4 (worms). To further understand the biology downstream from this conserved transcription factor in the yeast model system, we looked at two different yeast models known to have upregulated Gcn4 and GCN4-dependent increased replicative lifespan. These two models were rpl31aΔ yeast and yeast treated with the tRNA synthetase inhibitor borrelidin. We used both proteomic and RNAseq analysis of a block experimental design that included both of these models to identify GCN4-dependent changes in these two long-lived strains of yeast. Proteomic analysis of these yeast indicate that the long-lived yeast have increased abundances of proteins involved in amino acid biosynthesis. The RNAseq of these same yeast uncovered further regulation of protein degradation, identifying the differential expression of genes associated with autophagy and the ubiquitin-proteasome system (UPS). The data presented here further underscore the important role that GCN4 plays in the maintenance of protein homeostasis, which itself is an important hallmark of aging. In particular, the changes in autophagy and UPS-related gene expression that we have observed could also have wide-ranging implications for the understanding and treatment of diseases of aging that are associated with protein aggregation.
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Affiliation(s)
- Blaise L. Mariner
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA (D.P.F.); (R.J.C.)
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Daniel P. Felker
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA (D.P.F.); (R.J.C.)
| | - Ryla J. Cantergiani
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA (D.P.F.); (R.J.C.)
| | - Jack Peterson
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA (D.P.F.); (R.J.C.)
| | - Mark A. McCormick
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA (D.P.F.); (R.J.C.)
- Autophagy, Inflammation, and Metabolism Center of Biomedical Research Excellence, University of New Mexico, Albuquerque, NM 87131, USA
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5
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Wu E, Lian Y, Zhao S, Li Y, Xiang L, Qi J. Involvement of the Sch9/Rim15/Msn2 signaling pathway in the anti-aging activity of dendrobine from Dendrobium nobile Lindl. via modification of oxidative stress and autophagy. Chin Med 2023; 18:111. [PMID: 37670345 PMCID: PMC10481559 DOI: 10.1186/s13020-023-00827-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Aging is an important pathogenic factor of age-related diseases and has brought huge health threat and economic burden to the society. Dendrobium nobile Lindl., a valuable herb in China, promotes longevity according to the record of ancient Chinese materia medica. This study aimed to discover the material basis of D. nobile as an anti-aging herb and elucidate its action mechanism. METHODS K6001 yeast replicative lifespan assay was used to guide the isolation of D. nobile. The chronological lifespan assay of YOM36 yeast was further conducted to confirm the anti-aging activity of dendrobine. The mechanism in which dendrobine exerts anti-aging effect was determined by conducting anti-oxidative stress assay, quantitative real-time PCR, Western blot, measurements of anti-oxidant enzymes activities, determination of nuclear translocation of Rim15 and Msn2, and replicative lifespan assays of Δsod1, Δsod2, Δcat, Δgpx, Δatg2, Δatg32, and Δrim15 yeasts. RESULTS Under the guidance of K6001 yeast replicative lifespan system, dendrobine with anti-aging effect was isolated from D. nobile. The replicative and chronological lifespans of yeast were extended upon dendrobine treatment. In the study of action mechanism, dendrobine improved the survival rate of yeast under oxidative stress, decreased the levels of reactive oxygen species and malondialdehyde, and enhanced the enzyme activities and gene expression of superoxide dismutase and catalase, but it failed to elongate the replicative lifespans of Δsod1, Δsod2, Δcat, and Δgpx yeast mutants. Meanwhile, dendrobine enhanced autophagy occurrence in yeast but had no effect on the replicative lifespans of Δatg2 and Δatg32 yeast mutants. Moreover, the inhibition of Sch9 phosphorylation and the promotion of nuclear translocation of Rim15 and Msn2 were observed after treatment with denrobine. However, the effect of dendrobine disappeared from the Δrim15 yeast mutant after lifespan extension, oxidative stress reduction, and autophagy enhancement. CONCLUSIONS Dendrobine exerts anti-aging activity in yeast via the modification of oxidative stress and autophagy through the Sch9/Rim15/Msn2 signaling pathway. Our work provides a scientific basis for the exploitation of D. nobile as an anti-aging herb.
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Affiliation(s)
- Enchan Wu
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou, 310058 China
| | - Yiting Lian
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou, 310058 China
| | - Sali Zhao
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou, 310058 China
| | - Yajing Li
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou, 310058 China
| | - Lan Xiang
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou, 310058 China
| | - Jianhua Qi
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou, 310058 China
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6
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Lee Y, Kim B, Jang HS, Huh WK. Atg1-dependent phosphorylation of Vps34 is required for dynamic regulation of the phagophore assembly site and autophagy in Saccharomyces cerevisiae. Autophagy 2023; 19:2428-2442. [PMID: 36803233 PMCID: PMC10392759 DOI: 10.1080/15548627.2023.2182478] [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: 07/28/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Macroautophagy/autophagy is a key catabolic pathway in which double-membrane autophagosomes sequester various substrates destined for degradation, enabling cells to maintain homeostasis and survive under stressful conditions. Several autophagy-related (Atg) proteins are recruited to the phagophore assembly site (PAS) and cooperatively function to generate autophagosomes. Vps34 is a class III phosphatidylinositol 3-kinase, and Atg14-containing Vps34 complex I plays essential roles in autophagosome formation. However, the regulatory mechanisms of yeast Vps34 complex I are still poorly understood. Here, we demonstrate that Atg1-dependent phosphorylation of Vps34 is required for robust autophagy activity in Saccharomyces cerevisiae. Following nitrogen starvation, Vps34 in complex I is selectively phosphorylated on multiple serine/threonine residues in its helical domain. This phosphorylation is important for full autophagy activation and cell survival. The absence of Atg1 or its kinase activity leads to complete loss of Vps34 phosphorylation in vivo, and Atg1 directly phosphorylates Vps34 in vitro, regardless of its complex association type. We also demonstrate that the localization of Vps34 complex I to the PAS provides a molecular basis for the complex I-specific phosphorylation of Vps34. This phosphorylation is required for the normal dynamics of Atg18 and Atg8 at the PAS. Together, our results reveal a novel regulatory mechanism of yeast Vps34 complex I and provide new insights into the Atg1-dependent dynamic regulation of the PAS.Abbreviations: ATG: autophagy-related; BARA: the repeated, autophagy-specific Co-IP: co-immunoprecipitation; GFP: green fluorescent protein; IP-MS: immunoprecipitation followed by tandem mass spectrometry; NTD: the N-terminal domain; PAS: phagophore assembly site; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns3K: phosphatidylinositol 3-kinase; SUR: structurally uncharacterized region; Vps34[KD]: Vps34D731N.
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Affiliation(s)
- Yongook Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Bongkeun Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hae-Soo Jang
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Won-Ki Huh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
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7
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Xiao L, Tang C, Klosterman SJ, Wang Y. VdTps2 Modulates Plant Colonization and Symptom Development in Verticillium dahliae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:572-583. [PMID: 36989041 DOI: 10.1094/mpmi-03-23-0024-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The trehalose biosynthesis pathway is a potential target for antifungal drugs development. Trehalose phosphate synthase (TPS) and phosphatase are widely conserved components of trehalose biosynthesis in fungi. However, the role of trehalose biosynthesis in the vascular plant-pathogenic fungus Verticillium dahliae remains unclear. Here, we investigated the functions of the TPS complex, including VdTps1, VdTps2, and VdTps3 in V. dahliae. Unlike VdTps2, deletion of VdTps1 or VdTps3 did not alter any phenotypes compared with the wild-type strain. In contrast, the ΔVdTps2 strain showed severely depressed radial growth due to the abnormal swelling of the hyphal tips. Further, deletion of VdTps2 increased microsclerotia formation, melanin biosynthesis, and resistance to cell-wall perturbation and high-temperature stress. Virulence assays and quantification of fungal biomass revealed that deletion of VdTps2 delayed disease symptom development, as evident by the reduced virulence and decreased biomass of the ΔVdTps2 strain in plant stem tissue following inoculation. Additionally, increases in penetration peg formation observed in the ΔVdTps2 strain in the presence of H2O2 suggested that VdTps2 suppresses initial colonization. Our results also revealed the role of VdTps2 as a regulator of autophagy. Together, these results indicate that VdTps2 contributes to plant colonization and disease development. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Luyao Xiao
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Chen Tang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, U.S.A
| | - Yonglin Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
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8
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Li G, Gong Z, Dulal N, Marroquin-Guzman M, Rocha RO, Richter M, Wilson RA. A protein kinase coordinates cycles of autophagy and glutaminolysis in invasive hyphae of the fungus Magnaporthe oryzae within rice cells. Nat Commun 2023; 14:4146. [PMID: 37438395 DOI: 10.1038/s41467-023-39880-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
The blast fungus Magnaporthe oryzae produces invasive hyphae in living rice cells during early infection, separated from the host cytoplasm by plant-derived interfacial membranes. However, the mechanisms underpinning this intracellular biotrophic growth phase are poorly understood. Here, we show that the M. oryzae serine/threonine protein kinase Rim15 promotes biotrophic growth by coordinating cycles of autophagy and glutaminolysis in invasive hyphae. Alongside inducing autophagy, Rim15 phosphorylates NAD-dependent glutamate dehydrogenase, resulting in increased levels of α-ketoglutarate that reactivate target-of-rapamycin (TOR) kinase signaling, which inhibits autophagy. Deleting RIM15 attenuates invasive hyphal growth and triggers plant immunity; exogenous addition of α-ketoglutarate prevents these effects, while glucose addition only suppresses host defenses. Our results indicate that Rim15-dependent cycles of autophagic flux liberate α-ketoglutarate - via glutaminolysis - to reactivate TOR signaling and fuel biotrophic growth while conserving glucose for antioxidation-mediated host innate immunity suppression.
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Affiliation(s)
- Gang Li
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ziwen Gong
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nawaraj Dulal
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Margarita Marroquin-Guzman
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Bayer CropScience, Chesterfield, MO, USA
| | - Raquel O Rocha
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Michael Richter
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Richard A Wilson
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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9
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Lei Y, Klionsky DJ. Transcriptional regulation of autophagy and its implications in human disease. Cell Death Differ 2023; 30:1416-1429. [PMID: 37045910 PMCID: PMC10244319 DOI: 10.1038/s41418-023-01162-9] [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: 01/11/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023] Open
Abstract
Macroautophagy/autophagy is a conserved catabolic pathway that is vital for maintaining cell homeostasis and promoting cell survival under stressful conditions. Dysregulation of autophagy is associated with a variety of human diseases, such as cancer, neurodegenerative diseases, and metabolic disorders. Therefore, this pathway must be precisely regulated at multiple levels, involving epigenetic, transcriptional, post-transcriptional, translational, and post-translational mechanisms, to prevent inappropriate autophagy activity. In this review, we focus on autophagy regulation at the transcriptional level, summarizing the transcription factors that control autophagy gene expression in both yeast and mammalian cells. Because the expression and/or subcellular localization of some autophagy transcription factors are altered in certain diseases, we also discuss how changes in transcriptional regulation of autophagy are associated with human pathophysiologies.
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Affiliation(s)
- Yuchen Lei
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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10
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Sun Q, Zhang H, Du HB, Zhao ZA, Li CJ, Chen SJ, Li YM, Zhang SL, Liu JC, Niu CY, Zhao ZG. ESTROGEN ALLEVIATES POSTHEMORRHAGIC SHOCK MESENTERIC LYMPH-MEDIATED LUNG INJURY THROUGH AUTOPHAGY INHIBITION. Shock 2023; 59:754-762. [PMID: 36840514 DOI: 10.1097/shk.0000000000002102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
ABSTRACT Background: Hemorrhagic shock-induced acute lung injury (ALI) is commonly associated with the posthemorrhagic shock mesenteric lymph (PHSML) return. Whether excessive autophagy is involved in PHSML-mediated ALI remains unclear. The relationship between estrogen treatment and PHSML or autophagy needs to verify. The current study will clarify the role of estrogen in reducing PHSML-mediated ALI through inhibition of autophagy. Methods: First, a hemorrhagic shock model in conscious rats was used to observe the effects of 17β-estradiol (E2) on intestinal blood flow, pulmonary function, intestinal and pulmonary morphology, and expression of autophagy marker proteins. Meanwhile, the effect of PHSML and autophagy agonist during E2 treatment was also investigated. Secondly, rat primary pulmonary microvascular endothelial cells were used to observe the effect of PHSML, PHSML plus E2, and E2-PHSML (PHSML obtained from rats treated by E2) on the cell viability. Results: Hemorrhagic shock induced intestinal and pulmonary tissue damage and increased wet/dry ratio, reduced intestinal blood flow, along with pulmonary dysfunction characterized by increased functional residual capacity and lung resistance and decreased inspiratory capacity and peak expiratory flow. Hemorrhagic shock also enhanced the autophagy levels in intestinal and pulmonary tissue, which was characterized by increased expressions of LC3 II/I and Beclin-1 and decreased expression of p62. E2 treatment significantly attenuated these adverse changes after hemorrhagic shock, which was reversed by PHSML or rapamycin administration. Importantly, PHSML incubation decreased the viability of pulmonary microvascular endothelial cells, while E2 coincubation or E2-treated lymph counteracted the adverse roles of PHSML. Conclusions: The role of estrogen reducing PHSML-mediated ALI is associated with the inhibition of autophagy.
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Affiliation(s)
| | | | | | | | | | - Si-Jie Chen
- Institute of Microcirculation and Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Yi-Ming Li
- Institute of Microcirculation and Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Sen-Lu Zhang
- Institute of Microcirculation and Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Jun-Chao Liu
- The First Affiliated Hospital, Hebei North University, Zhangjiakou, China
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11
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Sun G, Wase N, Shu S, Jenkins J, Zhou B, Torres-Rodríguez JV, Chen C, Sandor L, Plott C, Yoshinga Y, Daum C, Qi P, Barry K, Lipzen A, Berry L, Pedersen C, Gottilla T, Foltz A, Yu H, O'Malley R, Zhang C, Devos KM, Sigmon B, Yu B, Obata T, Schmutz J, Schnable JC. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Nat Commun 2022; 13:7731. [PMID: 36513676 PMCID: PMC9747981 DOI: 10.1038/s41467-022-35507-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation.
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Affiliation(s)
- Guangchao Sun
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Nishikant Wase
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Biomolecular Analysis Facility. School of Medicine, University of Virginia, Charlottesville, VA, 22903, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Bangjun Zhou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - J Vladimir Torres-Rodríguez
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Cindy Chen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Yuko Yoshinga
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Luke Berry
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Connor Pedersen
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Thomas Gottilla
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Ashley Foltz
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Huihui Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Ronan O'Malley
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Toshihiro Obata
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA.
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
| | - James C Schnable
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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12
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Soberanes-Gutiérrez CV, Castillo-Jiménez A, Pérez-Rueda E, Galán-Vásquez E. Construction and analysis of gene co-expression network in the pathogenic fungus Ustilago maydis. Front Microbiol 2022; 13:1048694. [PMID: 36569046 PMCID: PMC9767968 DOI: 10.3389/fmicb.2022.1048694] [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: 09/19/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Biological systems respond to environmental disturbances and a wide range of compounds through complex gene interaction networks. The enormous growth of experimental information obtained using large-scale genomic techniques such as microarrays and RNA sequencing led to the construction of a wide variety of gene co-expression networks in recent years. These networks allow the discovery of clusters of co-expressed genes that potentially work in the same process linking them to biological processes often of interest to industrial, medicinal, and academic research. Methods In this study, we built the gene co-expression network of Ustilago maydis from the gene expression data of 168 samples belonging to 19 series, which correspond to the GPL3681 platform deposited in the NCBI using WGCNA software. This network was analyzed to identify clusters of co-expressed genes, gene hubs and Gene Ontology terms. Additionally, we identified relevant modules through a hypergeometric approach based on a predicted set of transcription factors and virulence genes. Results and Discussion We identified 13 modules in the gene co-expression network of U. maydis. The TFs enriched in the modules of interest belong to the superfamilies of Nucleic acid-binding proteins, Winged helix DNA-binding, and Zn2/Cys6 DNA-binding. On the other hand, the modules enriched with virulence genes were classified into diseases related to corn smut, Invasive candidiasis, among others. Finally, a large number of hypothetical, a large number of hypothetical genes were identified as highly co-expressed with virulence genes, making them possible experimental targets.
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Affiliation(s)
- Cinthia V. Soberanes-Gutiérrez
- Laboratorio de Ciencias Agrogenómicas, de la Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, León, Guanajuato, Mexico
| | - Alfredo Castillo-Jiménez
- Licenciatura en Biología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Ernesto Pérez-Rueda
- Unidad Académica Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mérida, Mexico
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigación en Matemáticas Aplicadas y en Sistemas. Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico,*Correspondence: Edgardo Galán-Vásquez,
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13
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Huang T, Jiang G, Zhang Y, Lei Y, Liu S, Li H, Lu K. The RNA polymerase II subunit Rpb9 activates ATG1 transcription and autophagy. EMBO Rep 2022; 23:e54993. [PMID: 36102592 PMCID: PMC9638876 DOI: 10.15252/embr.202254993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 08/01/2023] Open
Abstract
Macroautophagy/autophagy is a conserved process in eukaryotic cells that mediates the degradation and recycling of intracellular substrates. Proteins encoded by autophagy-related (ATG) genes are essentially involved in the autophagy process and must be tightly regulated in response to various circumstances, such as nutrient-rich and starvation conditions. However, crucial transcriptional activators of ATG genes have remained obscure. Here, we identify the RNA polymerase II subunit Rpb9 as an essential regulator of autophagy by a high-throughput screen of a Saccharomyces cerevisiae gene knockout library. Rpb9 plays a crucial and specific role in upregulating ATG1 transcription, and its deficiency decreases autophagic activities. Rpb9 promotes ATG1 transcription by binding to its promoter region, which is mediated by Gcn4. Furthermore, the function of Rpb9 in autophagy and its regulation of ATG1/ULK1 transcription are conserved in mammalian cells. Together, our results indicate that Rpb9 specifically activates ATG1 transcription and thus positively regulates the autophagy process.
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Affiliation(s)
- Ting Huang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Gaoyue Jiang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Yabin Zhang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Yuqing Lei
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Shiyan Liu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Huihui Li
- West China Second University HospitalSichuan UniversityChengduChina
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
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14
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Willis SD, Hanley SE, Doyle SJ, Beluch K, Strich R, Cooper KF. Cyclin C-Cdk8 Kinase Phosphorylation of Rim15 Prevents the Aberrant Activation of Stress Response Genes. Front Cell Dev Biol 2022; 10:867257. [PMID: 35433688 PMCID: PMC9008841 DOI: 10.3389/fcell.2022.867257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cells facing adverse environmental cues respond by inducing signal transduction pathways resulting in transcriptional reprograming. In the budding yeast Saccharomyces cerevisiae, nutrient deprivation stimulates stress response gene (SRG) transcription critical for entry into either quiescence or gametogenesis depending on the cell type. The induction of a subset of SRGs require nuclear translocation of the conserved serine-threonine kinase Rim15. However, Rim15 is also present in unstressed nuclei suggesting that additional activities are required to constrain its activity in the absence of stress. Here we show that Rim15 is directly phosphorylated by cyclin C-Cdk8, the conserved kinase module of the Mediator complex. Several results indicate that Cdk8-dependent phosphorylation prevents Rim15 activation in unstressed cells. First, Cdk8 does not control Rim15 subcellular localization and rim15∆ is epistatic to cdk8∆ with respect to SRG transcription and the execution of starvation programs required for viability. Next, Cdk8 phosphorylates a residue in the conserved PAS domain in vitro. This modification appears important as introducing a phosphomimetic at Cdk8 target residues reduces Rim15 activity. Moreover, the Rim15 phosphomimetic only compromises cell viability in stresses that induce cyclin C destruction as well as entrance into meiosis. Taken together, these findings suggest a model in which Cdk8 phosphorylation contributes to Rim15 repression whilst it cycles through the nucleus. Cyclin C destruction in response to stress inactivates Cdk8 which in turn stimulates Rim15 to maximize SRG transcription and cell survival.
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15
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Wang L, Wang Y, Zhao W, Lin K, Li W, Wang G, Zhang Q. Library Screening to Identify Highly-Effective Autophagy Inhibitors for Improving Photothermal Cancer Therapy. NANO LETTERS 2021; 21:9476-9484. [PMID: 34730354 DOI: 10.1021/acs.nanolett.1c02825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The small molecular inhibitor-associated downregulation of autophagy can remarkably enhance the efficiency of photothermal cancer therapy. To identify a more effective autophagy inhibitor, we screened a library of 20 compounds and found chloroquine, hydroxychloroquine, dauricine, and daurisoline were more efficient than the others to improve the photothermal killing of cancer cells. Interestingly, the four agents all disturb the autophagosome formation and fusion process, indicating it is a promising target to enhance cancer therapeutic efficiency. Among the four agents, daurisoline was identified to be the most efficient one. It reduced the viability of cancer cells treated by low-energy photothermal therapy from 86.27% to 32.92%. Finally, the combination treatment mediated by nanodrugs loaded with daurisoline and indocyanine green was more efficient than the individual modalities, resulting in complete inhibition of tumor growth. The study gives new inspiration to autophagy modulation-associated photothermal therapy and other therapeutic modalities for cancer treatment.
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Affiliation(s)
- Li Wang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, P. R. China
| | - Yitong Wang
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University; School of Medicine; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai 200011, P. R. China
| | - Wei Zhao
- Department of Stomatology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P. R. China
| | - Kaili Lin
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University; School of Medicine; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai 200011, P. R. China
| | - Wei Li
- Department of Stomatology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P. R. China
| | - Guodong Wang
- Department of Stomatology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P. R. China
| | - Qiang Zhang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, P. R. China
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16
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Investigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approach. Appl Microbiol Biotechnol 2021; 105:5103-5112. [PMID: 34152451 DOI: 10.1007/s00253-021-11394-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 03/21/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022]
Abstract
Ure2 regulates nitrogen catabolite repression in Saccharomyces cerevisiae. Deletion of URE2 induces a physiological state mimicking the nitrogen starvation and autophagic responses. Previous work has shown that deletion of URE2 increases the fermentation rate of some wine-producing strains of S. cerevisiae. In this work, we investigated the effect of URE2 deletion (ΔURE2) on the metabolism of S. cerevisiae. During growth on glucose, the ΔURE2 mutant grew at a 40% slower rate than the wild type; however, it produced ethanol at a 31% higher rate. To better under the behavior of this mutant, we performed transcriptomics and metabolomics. Analysis of the RNA sequencing results and metabolite levels indicates that the mutant strain exhibited characteristics of both nitrogen starvation and autophagy, including the upregulation of allantoin, urea, and amino acid uptake and utilization pathways and selective autophagic machinery. In addition, pyruvate decarboxylase and alcohol dehydrogenase isoforms were expressed at higher rates than the wild type. The mutant also accumulated less trehalose and glycogen, and produced more lipids. The induction of a nitrogen starvation-like state and increase in lipid production in nitrogen-rich conditions suggest that URE2 may be a promising target for metabolic engineering in S. cerevisiae and other yeasts for the production of lipids and lipid-derived compounds. KEY POINTS: • Deletion of URE2 increases ethanol and lipid production in Saccharomyces cerevisiae. • Deletion of URE2 reduces glycogen and trehalose production. • Metabolic changes mimic nitrogen starvation and autophagic response.
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17
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Casting iron into the cell fate mold. Biochem J 2021; 478:1879-1883. [PMID: 34029365 DOI: 10.1042/bcj20210108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 11/17/2022]
Abstract
This commentary discusses general concepts introduced in the article 'Bulk autophagy induction and life extension is achieved when iron is the only limited nutrient in Saccharomyces cerevisiae' by Montella-Manuel et al. (Biochem J (2021) 478: 811-837). Montella-Manuel et al. show that like central carbon metabolism, iron metabolism is also closely implicated in autophagy-mediated life extension via the TORC2 activator Ypk1p and the iron regulator Aft1p. While not being an iron-sulfur cluster protein, Aft1p interacts with such proteins and thus senses the redox status of the cell, which, similar to amino acids and AMP, reports its energetic status. Furthermore, glucose and iron deficiencies are interrelated as the diauxic shift in glucose depleted cells requires iron uptake for activating respiration in the absence of fermentation.
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18
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Raj SD, Fann DY, Wong E, Kennedy BK. Natural products as geroprotectors: An autophagy perspective. Med Res Rev 2021; 41:3118-3155. [PMID: 33973253 DOI: 10.1002/med.21815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/09/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022]
Abstract
Over the past decade, significant attention has been given to repurposing Food and Drug Administration approved drugs to treat age-related diseases. In contrast, less consideration has been given to natural bioactive compounds. Consequently, there have been limited attempts to translate these compounds. Autophagy is a fundamental biological pathway linked to aging, and numerous strategies to enhance autophagy have been shown to extend lifespan. Interestingly, there are a number of natural products that are reported to modulate autophagy, and here we describe a number of them that activate autophagy through diverse molecular and cellular mechanisms. Among these, Urolithin A, Spermidine, Resveratrol, Fatty Acids and Phospholipids, Trehalose and Lithium are featured in detail. Finally, we outline possible strategies to optimise and increase the translatability of natural products, with the overall aim of delaying the ageing process and improving human healthspan.
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Affiliation(s)
- Stephen D Raj
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Centre For Healthy Longevity, National University Health System, National University of Singapore, Singapore
| | - David Y Fann
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Centre For Healthy Longevity, National University Health System, National University of Singapore, Singapore
| | - Esther Wong
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Centre For Healthy Longevity, National University Health System, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Brian K Kennedy
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Centre For Healthy Longevity, National University Health System, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Agency for Science, Technology and Research (A*STAR), Singapore Institute for Clinical Sciences, Singapore
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19
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Bulk autophagy induction and life extension is achieved when iron is the only limited nutrient in Saccharomyces cerevisiae. Biochem J 2021; 478:811-837. [DOI: 10.1042/bcj20200849] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/21/2023]
Abstract
We have investigated the effects that iron limitation provokes in Saccharomyces cerevisiae exponential cultures. We have demonstrated that one primary response is the induction of bulk autophagy mediated by TORC1. Coherently, Atg13 became dephosphorylated whereas Atg1 appeared phosphorylated. The signal of iron deprivation requires Tor2/Ypk1 activity and the inactivation of Tor1 leading to Atg13 dephosphorylation, thus triggering the autophagy process. Iron replenishment in its turn, reduces autophagy flux through the AMPK Snf1 and the subsequent activity of the iron-responsive transcription factor, Aft1. This signalling converges in Atg13 phosphorylation mediated by Tor1. Iron limitation promotes accumulation of trehalose and the increase in stress resistance leading to a quiescent state in cells. All these effects contribute to the extension of the chronological life, in a manner totally dependent on autophagy activation.
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20
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Wan T, Li X, Li Y. The role of TRIM family proteins in autophagy, pyroptosis, and diabetes mellitus. Cell Biol Int 2021; 45:913-926. [PMID: 33438267 DOI: 10.1002/cbin.11550] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 01/22/2023]
Abstract
The ubiquitin-proteasome system, which is one of the systems for cell protein homeostasis and degradation, happens through the ordered and coordinated action of three types of enzymes, E1 ubiquitin-activating enzyme, E2 ubiquitin-carrier enzyme, E3 ubiquitin-protein ligase. Tripartite motif-containing (TRIM) family proteins are the richest subfamily of really interesting new gene E3 ubiquitin ligases, which play a critical role not only in many biological processes, including proliferation, apoptosis, pyroptosis, innate immunity, and autophagy, but also many diseases like cancer, diabetes mellitus, and neurodegenerative disease. Increasing evidence suggests that TRIM family proteins play a vital role in modulating autophagy, pyroptosis, and diabetes mellitus. The aim of this review is to discuss the role of TRIM proteins in the regulation of autophagy, pyroptosis, diabetes mellitus, and diabetic complications.
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Affiliation(s)
- Tingting Wan
- Department of Endocrinology, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiudan Li
- Department of Endocrinology, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanbo Li
- Department of Endocrinology, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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