1
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Morozumi Y, Hayashi Y, Chu CM, Sofyantoro F, Akikusa Y, Fukuda T, Shiozaki K. Fission yeast Pib2 localizes to vacuolar membranes and regulates TOR complex 1 through evolutionarily conserved domains. FEBS Lett 2024. [PMID: 39010328 DOI: 10.1002/1873-3468.14980] [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: 04/15/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 07/17/2024]
Abstract
TOR complex 1 (TORC1) is a multi-protein kinase complex that coordinates cellular growth with environmental cues. Recent studies have identified Pib2 as a critical activator of TORC1 in budding yeast. Here, we show that loss of Pib2 causes severe growth defects in fission yeast cells, particularly when basal TORC1 activity is diminished by hypomorphic mutations in tor2, the gene encoding the catalytic subunit of TORC1. Consistently, TORC1 activity is significantly compromised in the tor2 hypomorphic mutants lacking Pib2. Moreover, as in budding yeast, fission yeast Pib2 localizes to vacuolar membranes via its FYVE domain, with its tail motif indispensable for TORC1 activation. These results strongly suggest that Pib2-mediated positive regulation of TORC1 is evolutionarily conserved between the two yeast species.
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Affiliation(s)
- Yuichi Morozumi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yumi Hayashi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Cuong Minh Chu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Fajar Sofyantoro
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Department of Animal Physiology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yutaka Akikusa
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Tomoyuki Fukuda
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Kazuhiro Shiozaki
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
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2
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Tang T, Sun J, Li C. The role of Phafin proteins in cell signaling pathways and diseases. Open Life Sci 2024; 19:20220896. [PMID: 38947768 PMCID: PMC11211877 DOI: 10.1515/biol-2022-0896] [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: 02/11/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Membrane-associated proteins are important membrane readers that mediate and facilitate the signaling and trafficking pathways in eukaryotic membrane-bound compartments. The protein members in the Phafin family are membrane readers containing two phosphoinositide recognition domains: the Pleckstrin Homology domain and the FYVE (Fab1, YOTB, Vac1, and early endosome antigen 1) domain. Phafin proteins, categorized into two subfamilies, Phafin1 and Phafin2, associate with cellular membranes through interactions involving membrane-embedded phosphoinositides and phosphoinositide-binding domains. These membrane-associated Phafin proteins play pivotal roles by recruiting binding partners and forming complexes, which contribute significantly to apoptotic, autophagic, and macropinocytotic pathways. Elevated expression levels of Phafin1 and Phafin2 are observed in various cancers. A recent study highlights a significant increase in Phafin1 protein levels in the lungs of idiopathic pulmonary fibrosis patients compared to normal subjects, suggesting a crucial role for Phafin1 in the pathogenesis of pulmonary fibrosis. Additionally, phosphatidylinositol-3-phosphate-binding 2 (Pib2), a close relative of the Phafin1 protein, functions as an amino acid sensor activating the TOCR1 pathway in yeasts. This review focuses on delineating the involvement of Phafin proteins in cellular signaling and their implications in diseases and briefly discusses the latest research findings concerning Pib2.
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Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jing Sun
- Department of Biostatistics and Epidemiology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin, Germany
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3
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Moulton MJ, Atala K, Zheng Y, Dutta D, Grange DK, Lin WW, Wegner DJ, Wambach JA, Duker AL, Bober MB, Kratz L, Wise CA, Oxendine I, Khanshour A, Wangler MF, Yamamoto S, Cole FS, Rios J, Bellen HJ. Dominant missense variants in SREBF2 are associated with complex dermatological, neurological, and skeletal abnormalities. Genet Med 2024; 26:101174. [PMID: 38847193 DOI: 10.1016/j.gim.2024.101174] [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: 01/30/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/21/2024] Open
Abstract
PURPOSE We identified 2 individuals with de novo variants in SREBF2 that disrupt a conserved site 1 protease (S1P) cleavage motif required for processing SREBP2 into its mature transcription factor. These individuals exhibit complex phenotypic manifestations that partially overlap with sterol regulatory element binding proteins (SREBP) pathway-related disease phenotypes, but SREBF2-related disease has not been previously reported. Thus, we set out to assess the effects of SREBF2 variants on SREBP pathway activation. METHODS We undertook ultrastructure and gene expression analyses using fibroblasts from an affected individual and utilized a fly model of lipid droplet (LD) formation to investigate the consequences of SREBF2 variants on SREBP pathway function. RESULTS We observed reduced LD formation, endoplasmic reticulum expansion, accumulation of aberrant lysosomes, and deficits in SREBP2 target gene expression in fibroblasts from an affected individual, indicating that the SREBF2 variant inhibits SREBP pathway activation. Using our fly model, we discovered that SREBF2 variants fail to induce LD production and act in a dominant-negative manner, which can be rescued by overexpression of S1P. CONCLUSION Taken together, these data reveal a mechanism by which SREBF2 pathogenic variants that disrupt the S1P cleavage motif cause disease via dominant-negative antagonism of S1P, limiting the cleavage of S1P targets, including SREBP1 and SREBP2.
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Affiliation(s)
- Matthew J Moulton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Kristhen Atala
- Center for Translational Research, Scottish Rite for Children, Dallas, TX
| | - Yiming Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX; Current address: State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Dorothy K Grange
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine and St. Louis Children's Hospital, St. Louis, MO
| | - Wen-Wen Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Daniel J Wegner
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine and St. Louis Children's Hospital, St. Louis, MO
| | - Jennifer A Wambach
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine and St. Louis Children's Hospital, St. Louis, MO
| | - Angela L Duker
- Skeletal Dysplasia Program, Orthogenetics, Nemours Children's Hospital, Wilmington, DE
| | - Michael B Bober
- Skeletal Dysplasia Program, Orthogenetics, Nemours Children's Hospital, Wilmington, DE
| | - Lisa Kratz
- Kennedy Krieger Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Carol A Wise
- Center for Translational Research, Scottish Rite for Children, Dallas, TX; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX; Department of Orthopedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ila Oxendine
- Center for Translational Research, Scottish Rite for Children, Dallas, TX
| | - Anas Khanshour
- Center for Translational Research, Scottish Rite for Children, Dallas, TX
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - F Sessions Cole
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine and St. Louis Children's Hospital, St. Louis, MO
| | - Jonathan Rios
- Center for Translational Research, Scottish Rite for Children, Dallas, TX; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX; Department of Orthopedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX.
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Liu Y, Wang R, Liu J, Fan M, Ye Z, Hao Y, Xie F, Wang T, Jiang Y, Liu N, Cui X, Lv Q, Yan L. The vacuolar fusion regulated by HOPS complex promotes hyphal initiation and penetration in Candida albicans. Nat Commun 2024; 15:4131. [PMID: 38755250 PMCID: PMC11099166 DOI: 10.1038/s41467-024-48525-5] [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: 10/11/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
The transition between yeast and hyphae is crucial for regulating the commensalism and pathogenicity in Candida albicans. The mechanisms that affect the invasion of hyphae in solid media, whose deficiency is more related to the pathogenicity of C. albicans, have not been elucidated. Here, we found that the disruption of VAM6 or VPS41 which are components of the homotypic vacuolar fusion and protein sorting (HOPS) complex, or the Rab GTPase YPT72, all responsible for vacuole fusion, led to defects in hyphal growth in both liquid and solid media, but more pronounced on solid agar. The phenotypes of vac8Δ/Δ and GTR1OE-vam6Δ/Δ mutants indicated that these deficiencies are mainly caused by the reduced mechanical forces that drive agar and organs penetration, and confirmed that large vacuoles are required for hyphal mechanical penetration. In summary, our study revealed that large vacuoles generated by vacuolar fusion support hyphal penetration and provided a perspective to refocus attention on the role of solid agar in evaluating C. albicans invasion.
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Affiliation(s)
- Yu Liu
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Ruina Wang
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Jiacun Liu
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Mengting Fan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, PR China
| | - Zi Ye
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Yumeng Hao
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Fei Xie
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Ting Wang
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China
| | - Yuanying Jiang
- School of Medicine, Tongji University, Shanghai, 200092, PR China
| | - Ningning Liu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China.
| | - Xiaoyan Cui
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, PR China.
| | - Quanzhen Lv
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China.
| | - Lan Yan
- Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai, 200433, PR China.
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5
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Pavesic MW, Gale AN, Nickels TJ, Harrington AA, Bussey M, Cunningham KW. Calcineurin-dependent contributions to fitness in the opportunistic pathogen Candida glabrata. mSphere 2024; 9:e0055423. [PMID: 38171022 PMCID: PMC10826367 DOI: 10.1128/msphere.00554-23] [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: 09/22/2023] [Accepted: 11/19/2023] [Indexed: 01/05/2024] Open
Abstract
The protein phosphatase calcineurin is vital for the virulence of the opportunistic fungal pathogen Candida glabrata. The host-induced stresses that activate calcineurin signaling are unknown, as are the targets of calcineurin relevant to virulence. To potentially shed light on these processes, millions of transposon insertion mutants throughout the genome of C. glabrata were profiled en masse for fitness defects in the presence of FK506, a specific inhibitor of calcineurin. Eighty-seven specific gene deficiencies depended on calcineurin signaling for full viability in vitro both in wild-type and pdr1∆ null strains lacking pleiotropic drug resistance. Three genes involved in cell wall biosynthesis (FKS1, DCW1, FLC1) possess co-essential paralogs whose expression depended on calcineurin and Crz1 in response to micafungin, a clinical antifungal that interferes with cell wall biogenesis. Interestingly, 80% of the FK506-sensitive mutants were deficient in different aspects of vesicular trafficking, such as endocytosis, exocytosis, sorting, and biogenesis of secretory proteins in the endoplasmic reticulum (ER). In response to the experimental antifungal manogepix that blocks GPI-anchor biosynthesis in the ER, calcineurin signaling increased and strongly prevented cell death independent of Crz1, one of its major targets. Comparisons between manogepix, micafungin, and the ER-stressing tunicamycin reveal a correlation between the degree of calcineurin signaling and the degree of cell survival. These findings suggest that calcineurin plays major roles in mitigating stresses of vesicular trafficking. Such stresses may arise during host infection and in response to antifungal therapies.IMPORTANCECalcineurin plays critical roles in the virulence of most pathogenic fungi. This study sheds light on those roles in the opportunistic pathogen Candida glabrata using a genome-wide analysis in vitro. The findings could lead to antifungal developments that also avoid immunosuppression.
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Affiliation(s)
- Matthew W. Pavesic
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew N. Gale
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Timothy J. Nickels
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Maya Bussey
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kyle W. Cunningham
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
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6
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Zeng Q, Araki Y, Noda T. Pib2 is a cysteine sensor involved in TORC1 activation in Saccharomyces cerevisiae. Cell Rep 2024; 43:113599. [PMID: 38127619 DOI: 10.1016/j.celrep.2023.113599] [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: 07/11/2023] [Revised: 10/24/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Target of rapamycin complex 1 (TORC1) is a master regulator that monitors the availability of various amino acids to promote cell growth in Saccharomyces cerevisiae. It is activated via two distinct upstream pathways: the Gtr pathway, which corresponds to mammalian Rag, and the Pib2 pathway. This study shows that Ser3 was phosphorylated exclusively in a Pib2-dependent manner. Using Ser3 as an indicator of TORC1 activity, together with the established TORC1 substrate Sch9, we investigated which pathways were employed by individual amino acids. Different amino acids exhibited different dependencies on the Gtr and Pib2 pathways. Cysteine was most dependent on the Pib2 pathway and increased the interaction between TORC1 and Pib2 in vivo and in vitro. Moreover, cysteine directly bound to Pib2 via W632 and F635, two critical residues in the T(ail) motif that are necessary to activate TORC1. These results indicate that Pib2 functions as a sensor for cysteine in TORC1 regulation.
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Affiliation(s)
- Qingzhong Zeng
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Yasuhiro Araki
- Center for Frontier Oral Sciences, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan.
| | - Takeshi Noda
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan; Center for Frontier Oral Sciences, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.
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7
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Cecil JH, Padilla CM, Lipinski AA, Langlais PR, Luo X, Capaldi AP. The Molecular Logic of Gtr1/2 and Pib2 Dependent TORC1 Regulation in Budding Yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570342. [PMID: 38106135 PMCID: PMC10723367 DOI: 10.1101/2023.12.06.570342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The Target of Rapamycin kinase Complex I (TORC1) regulates cell growth and metabolism in eukaryotes. Previous studies have shown that, in Saccharomyces cerevisiae, nitrogen and amino acid signals activate TORC1 via the highly conserved small GTPases, Gtr1/2, and the phosphatidylinositol 3-phosphate binding protein, Pib2. However, it was unclear if/how Gtr1/2 and Pib2 cooperate to control TORC1. Here we report that this dual regulator system pushes TORC1 into three distinct signaling states: (i) a Gtr1/2 on, Pib2 on, rapid growth state in nutrient replete conditions; (ii) a Gtr1/2 off, Pib2 on, adaptive/slow growth state in poor-quality growth medium; and (iii) a Gtr1/2 off, Pib2 off, quiescent state in starvation conditions. We suggest that other signaling pathways work in a similar way, to drive a multi-level response via a single kinase, but the behavior has been overlooked since most studies follow signaling to a single reporter protein.
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Affiliation(s)
- Jacob H. Cecil
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721
| | - Cristina M. Padilla
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721
| | | | - Paul R. Langlais
- Department of Medicine, University of Arizona, Tucson, AZ, 85721
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721
| | - Andrew P. Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721
- Bio5 Institute, University of Arizona, Tucson, AZ, 85721
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8
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Kulkarni M, Hardwick JM. Programmed Cell Death in Unicellular Versus Multicellular Organisms. Annu Rev Genet 2023; 57:435-459. [PMID: 37722687 DOI: 10.1146/annurev-genet-033123-095833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Programmed cell death (self-induced) is intrinsic to all cellular life forms, including unicellular organisms. However, cell death research has focused on animal models to understand cancer, degenerative disorders, and developmental processes. Recently delineated suicidal death mechanisms in bacteria and fungi have revealed ancient origins of animal cell death that are intertwined with immune mechanisms, allaying earlier doubts that self-inflicted cell death pathways exist in microorganisms. Approximately 20 mammalian death pathways have been partially characterized over the last 35 years. By contrast, more than 100 death mechanisms have been identified in bacteria and a few fungi in recent years. However, cell death is nearly unstudied in most human pathogenic microbes that cause major public health burdens. Here, we consider how the current understanding of programmed cell death arose through animal studies and how recently uncovered microbial cell death mechanisms in fungi and bacteria resemble and differ from mechanisms of mammalian cell death.
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Affiliation(s)
- Madhura Kulkarni
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; ,
| | - J Marie Hardwick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; ,
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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9
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Tang T, Hasan M, Capelluto DGS. Phafins Are More Than Phosphoinositide-Binding Proteins. Int J Mol Sci 2023; 24:ijms24098096. [PMID: 37175801 PMCID: PMC10178739 DOI: 10.3390/ijms24098096] [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: 03/22/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Phafins are PH (Pleckstrin Homology) and FYVE (Fab1, YOTB, Vac1, and EEA1) domain-containing proteins. The Phafin protein family is classified into two groups based on their sequence homology and functional similarity: Phafin1 and Phafin2. This protein family is unique because both the PH and FYVE domains bind to phosphatidylinositol 3-phosphate [PtdIns(3)P], a phosphoinositide primarily found in endosomal and lysosomal membranes. Phafin proteins act as PtdIns(3)P effectors in apoptosis, endocytic cargo trafficking, and autophagy. Additionally, Phafin2 is recruited to macropinocytic compartments through coincidence detection of PtdIns(3)P and PtdIns(4)P. Membrane-associated Phafins serve as adaptor proteins that recruit other binding partners. In addition to the phosphoinositide-binding domains, Phafin proteins present a poly aspartic acid motif that regulates membrane binding specificity. In this review, we summarize the involvement of Phafins in several cellular pathways and their potential physiological functions while highlighting the similarities and differences between Phafin1 and Phafin2. Besides, we discuss research perspectives for Phafins.
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Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mahmudul Hasan
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Daniel G S Capelluto
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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10
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Lin JX, Xu CY, Wu XM, Che L, Li TY, Mo SM, Guo DB, Lin ZN, Lin YC. Rab7a-mTORC1 signaling-mediated cholesterol trafficking from the lysosome to mitochondria ameliorates hepatic lipotoxicity induced by aflatoxin B1 exposure. CHEMOSPHERE 2023; 320:138071. [PMID: 36754296 DOI: 10.1016/j.chemosphere.2023.138071] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/10/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Aflatoxin B1 (AFB1) is a common contaminant in many foodstuffs and is considered a public health concern worldwide due to its hepatotoxicity caused by lipid metabolism disorders. However, the molecular mechanism underlying AFB1-induced lipotoxicity-dependent liver injury via regulating cholesterol metabolism remains unclear. We established a cholesterol trafficking disorder-mediated hepatic lipotoxicity model with AFB1 mixture exposure in vitro (HepaRG and HepG2 cells, 1.6 μM for 36 h) and in vivo (C57BL/6 mice, 3 mg kg-1, i.g., every other day for 6 weeks). In vitro, the interaction between lysosomal Niemann-Pick type C1 (NPC1) protein and mitochondrial translocator protein (TSPO) regulated lipotoxicity induced by AFB1 mixture exposure, including lysosomal membrane permeabilization and mitochondria-dependent necroptosis. Moreover, the downregulation of lysosomal Ras-associated protein 7a (Rab7a) enhanced the mammalian target of rapamycin complex 1 (mTORC1)-mediated disorders of cholesterol trafficking from the lysosome to mitochondria. Furthermore, cholesterol trafficking disorder-mediated hepatic lipotoxicity induced by the low-dose level of AFB1 exposure was relieved by genetic or pharmaceutic activation of Rab7a to inhibit mTORC1 in vitro and ex vivo. In vivo, mTORC1 inhibitor (Torin1, 4 mg kg-1, i.p., every other day for 3 weeks) alleviated the cholesterol trafficking disorder-mediated hepatic lipotoxicity via upregulating the molecular machinery of lysosomes and mitochondria contact mediated by NPC1 and TSPO interaction in the low dose of AFB1 exposure. Altogether, our data suggested a novel mechanism that lysosomal Rab7a-mTORC1 signaling determined the cholesterol trafficking regulated by NPC1-TSPO from the lysosome to mitochondria, which promoted hepatic lipotoxicity via lysosomal quality control and mitochondria-dependent necroptosis signaling pathways in chemical mixture exposure.
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Affiliation(s)
- Jin-Xian Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Chi-Yu Xu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Xin-Mou Wu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Lin Che
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Ting-Yu Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Su-Min Mo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Dong-Bei Guo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Zhong-Ning Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China.
| | - Yu-Chun Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China.
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11
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Caligaris M, Nicastro R, Hu Z, Tripodi F, Hummel JE, Pillet B, Deprez MA, Winderickx J, Rospert S, Coccetti P, Dengjel J, De Virgilio C. Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation. eLife 2023; 12:84319. [PMID: 36749016 PMCID: PMC9937656 DOI: 10.7554/elife.84319] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/06/2023] [Indexed: 02/08/2023] Open
Abstract
The AMP-activated protein kinase (AMPK) and the target of rapamycin complex 1 (TORC1) are central kinase modules of two opposing signaling pathways that control eukaryotic cell growth and metabolism in response to the availability of energy and nutrients. Accordingly, energy depletion activates AMPK to inhibit growth, while nutrients and high energy levels activate TORC1 to promote growth. Both in mammals and lower eukaryotes such as yeast, the AMPK and TORC1 pathways are wired to each other at different levels, which ensures homeostatic control of growth and metabolism. In this context, a previous study (Hughes Hallett et al., 2015) reported that AMPK in yeast, that is Snf1, prevents the transient TORC1 reactivation during the early phase following acute glucose starvation, but the underlying mechanism has remained elusive. Using a combination of unbiased mass spectrometry (MS)-based phosphoproteomics, genetic, biochemical, and physiological experiments, we show here that Snf1 temporally maintains TORC1 inactive in glucose-starved cells primarily through the TORC1-regulatory protein Pib2. Our data, therefore, extend the function of Pib2 to a hub that integrates both glucose and, as reported earlier, glutamine signals to control TORC1. We further demonstrate that Snf1 phosphorylates the TORC1 effector kinase Sch9 within its N-terminal region and thereby antagonizes the phosphorylation of a C-terminal TORC1-target residue within Sch9 itself that is critical for its activity. The consequences of Snf1-mediated phosphorylation of Pib2 and Sch9 are physiologically additive and sufficient to explain the role of Snf1 in short-term inhibition of TORC1 in acutely glucose-starved cells.
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Affiliation(s)
- Marco Caligaris
- Department of Biology, University of FribourgFribourgSwitzerland
| | | | - Zehan Hu
- Department of Biology, University of FribourgFribourgSwitzerland
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-BicoccaMilanoItaly
| | - Johannes Erwin Hummel
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Benjamin Pillet
- Department of Biology, University of FribourgFribourgSwitzerland
| | | | | | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of FreiburgFreiburgGermany,Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-BicoccaMilanoItaly
| | - Jörn Dengjel
- Department of Biology, University of FribourgFribourgSwitzerland
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12
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Troutman KK, Varlakhanova NV, Tornabene BA, Ramachandran R, Ford MGJ. Conserved Pib2 regions have distinct roles in TORC1 regulation at the vacuole. J Cell Sci 2022; 135:276418. [PMID: 36000409 PMCID: PMC9584352 DOI: 10.1242/jcs.259994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/15/2022] [Indexed: 12/27/2022] Open
Abstract
TORC1 is a critical controller of cell growth in eukaryotes. In yeast (Saccharomyces cerevisiae), the presence of nutrients is signaled to TORC1 by several upstream regulatory sensors that together coordinate TORC1 activity. TORC1 localizes to both vacuolar and endosomal membranes, where differential signaling occurs. This localization is mimicked by Pib2, a key upstream TORC1 regulator that is essential for TORC1 reactivation after nutrient starvation or pharmacological inhibition. Pib2 has both positive and negative effects on TORC1 activity, but the mechanisms remain poorly understood. Here, we pinpoint the Pib2 inhibitory function on TORC1 to residues within short, conserved N-terminal regions. We also show that the Pib2 C-terminal regions, helical region E and tail, are essential for TORC1 reactivation. Furthermore, the Pib2 FYVE domain plays a role in vacuolar localization, but it is surprisingly unnecessary for recovery from rapamycin exposure. Using chimeric Pib2 targeting constructs, we show that endosomal localization is not necessary for TORC1 reactivation and cell growth after rapamycin treatment. Thus, a comprehensive molecular dissection of Pib2 demonstrates that each of its conserved regions differentially contribute to Pib2-mediated regulation of TORC1 activity.
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Affiliation(s)
- Kayla K. Troutman
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Natalia V. Varlakhanova
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Bryan A. Tornabene
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Rajesh Ramachandran
- Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Marijn G. J. Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA,Author for correspondence ()
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13
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Wallace RL, Lu E, Luo X, Capaldi AP. Ait1 regulates TORC1 signaling and localization in budding yeast. eLife 2022; 11:68773. [PMID: 36047762 PMCID: PMC9499541 DOI: 10.7554/elife.68773] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
The target of rapamycin complex I (TORC1) regulates cell growth and metabolism in eukaryotes. Previous studies have shown that nitrogen and amino acid signals activate TORC1 via the highly conserved small GTPases, Gtr1/2 (RagA/C in humans), and the GTPase activating complex SEAC/GATOR. However, it remains unclear if, and how, other proteins/pathways regulate TORC1 in simple eukaryotes like yeast. Here, we report that the previously unstudied GPCR-like protein, Ait1, binds to TORC1-Gtr1/2 in Saccharomyces cerevisiae and holds TORC1 around the vacuole during log-phase growth. Then, during amino acid starvation, Ait1 inhibits TORC1 via Gtr1/2 using a loop that resembles the RagA/C-binding domain in the human protein SLC38A9. Importantly, Ait1 is only found in the Saccharomycetaceae/codaceae, two closely related families of yeast that have lost the ancient TORC1 regulators Rheb and TSC1/2. Thus, the TORC1 circuit found in the Saccharomycetaceae/codaceae, and likely other simple eukaryotes, has undergone significant rewiring during evolution.
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Affiliation(s)
- Ryan L Wallace
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, United States
| | - Eric Lu
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, United States
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, United States
| | - Andrew P Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, United States
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14
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Wood TE, Westervelt KA, Yoon JM, Eshleman HD, Levy R, Burnes H, Slade DJ, Lesser CF, Goldberg MB. The Shigella Spp. Type III Effector Protein OspB Is a Cysteine Protease. mBio 2022; 13:e0127022. [PMID: 35638611 PMCID: PMC9239218 DOI: 10.1128/mbio.01270-22] [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: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
The type III secretion system is required for virulence of many pathogenic bacteria. Bacterial effector proteins delivered into target host cells by this system modulate host signaling pathways and processes in a manner that promotes infection. Here, we define the activity of the effector protein OspB of the human pathogen Shigella spp., the etiological agent of shigellosis and bacillary dysentery. Using the yeast Saccharomyces cerevisiae as a model organism, we show that OspB sensitizes cells to inhibition of TORC1, the central regulator of growth and metabolism. In silico analyses reveal that OspB bears structural homology to bacterial cysteine proteases that target mammalian cell processes, and we define a conserved cysteine-histidine catalytic dyad required for OspB function. Using yeast genetic screens, we identify a crucial role for the arginine N-degron pathway in the yeast growth inhibition phenotype and show that inositol hexakisphosphate is an OspB cofactor. We find that a yeast substrate for OspB is the TORC1 component Tco89p, proteolytic cleavage of which generates a C-terminal fragment that is targeted for degradation via the arginine N-degron pathway; processing and degradation of Tco89p is required for the OspB phenotype. In all, we demonstrate that the Shigella T3SS effector OspB is a cysteine protease and decipher its interplay with eukaryotic cell processes. IMPORTANCEShigella spp. are important human pathogens and among the leading causes of diarrheal mortality worldwide, especially in children. Virulence depends on the Shigella type III secretion system (T3SS). Definition of the roles of the bacterial effector proteins secreted by the T3SS is key to understanding Shigella pathogenesis. The effector protein OspB contributes to a range of phenotypes during infection, yet the mechanism of action is unknown. Here, we show that S. flexneri OspB possesses cysteine protease activity in both yeast and mammalian cells, and that enzymatic activity of OspB depends on a conserved cysteine-histidine catalytic dyad. We determine how its protease activity sensitizes cells to TORC1 inhibition in yeast, finding that OspB cleaves a component of yeast TORC1, and that the degradation of the C-terminal cleavage product is responsible for OspB-mediated hypersensitivity to TORC1 inhibitors. Thus, OspB is a cysteine protease that depends on a conserved cysteine-histidine catalytic dyad.
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Affiliation(s)
- Thomas E. Wood
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathleen A. Westervelt
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jessica M. Yoon
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Heather D. Eshleman
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Roie Levy
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Henry Burnes
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Daniel J. Slade
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Cammie F. Lesser
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Marcia B. Goldberg
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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15
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Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization. Cell Rep 2022; 39:110647. [PMID: 35417721 PMCID: PMC9074372 DOI: 10.1016/j.celrep.2022.110647] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/17/2022] [Accepted: 03/16/2022] [Indexed: 12/24/2022] Open
Abstract
Unicellular eukaryotes have been suggested as undergoing self-inflicted destruction. However, molecular details are sparse compared with the mechanisms of programmed/regulated cell death known for human cells and animal models. Here, we report a molecular cell death pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization. Following a transient cell death stimulus, yeast cells die slowly over several hours, consistent with an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 complex, a vesicle trafficking adapter known to transport and install newly synthesized proteins on the vacuole/lysosome membrane. To promote cell death, AP-3 requires its Arf1-GTPase-dependent vesicle trafficking function and the kinase Yck3, which is selectively transported to the vacuole membrane by AP-3. Video microscopy revealed a sequence of events where vacuole permeability precedes the loss of plasma membrane integrity. AP-3-dependent death appears to be conserved in the human pathogenic yeast Cryptococcus neoformans. Details about how mammalian cells die have yielded effective cancer therapies. Similarly, details about fungal cell death may explain failed responses to anti-fungal agents and inform next-generation anti-fungal strategies. Stolp et al. describe a potential mechanism of yeast cell death subversion, by inhibiting AP-3 vesicle trafficking to block vacuole/lysosome permeability.
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16
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Reinheckel T, Tholen M. Low level lysosomal membrane permeabilization for limited release and sub-lethal functions of cathepsin proteases in the cytosol and nucleus. FEBS Open Bio 2022; 12:694-707. [PMID: 35203107 PMCID: PMC8972055 DOI: 10.1002/2211-5463.13385] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/21/2022] [Accepted: 02/15/2022] [Indexed: 11/12/2022] Open
Abstract
For a long time, lysosomes were purely seen as organelles in charge of garbage disposal within the cell. They destroy any cargo delivered into their lumen with a plethora of highly potent hydrolytic enzymes, including various proteases. In case of damage to their limiting membranes, the lysosomes release their soluble content with detrimental outcomes for the cell. In recent years however, this view of the lysosome changed towards acknowledging it as a platform for integration of manifold intra- and extracellular signals. Even impaired lysosomal membrane integrity is no longer considered to be a one-way street to cell death. Increasing evidence suggests that lysosomal enzymes, mainly cathepsin proteases, can be released in a spatially and temporarily restricted manner that is compatible with cellular survival. This way, cathepsins can act in the cytosol and the nucleus, where they affect important cellular processes such as cell division. Here, we review this evidence and discuss the routes and molecular mechanisms by which the cathepsins may reach their unusual destination.
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Affiliation(s)
- Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, Albert Ludwigs University, Freiburg, Germany.,German Cancer Consortium (DKTK) Partner Site Freiburg, Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center for Biological Signaling Studies BIOSS, Albert Ludwigs University, Freiburg, Germany
| | - Martina Tholen
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, Albert Ludwigs University, Freiburg, Germany
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17
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Hatakeyama R. Pib2 as an Emerging Master Regulator of Yeast TORC1. Biomolecules 2021; 11:biom11101489. [PMID: 34680122 PMCID: PMC8533233 DOI: 10.3390/biom11101489] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/18/2022] Open
Abstract
Cell growth is dynamically regulated in response to external cues such as nutrient availability, growth factor signals, and stresses. Central to this adaptation process is the Target of Rapamycin Complex 1 (TORC1), an evolutionarily conserved kinase complex that fine-tunes an enormous number of cellular events. How upstream signals are sensed and transmitted to TORC1 has been intensively studied in major model organisms including the budding yeast Saccharomyces cerevisiae. This field recently saw a breakthrough: the identification of yeast phosphatidylInositol(3)-phosphate binding protein 2 (Pib2) protein as a critical regulator of TORC1. Although the study of Pib2 is still in its early days, multiple groups have provided important mechanistic insights on how Pib2 relays nutrient signals to TORC1. There remain, on the other hand, significant gaps in our knowledge and mysteries that warrant further investigations. This is the first dedicated review on Pib2 that summarizes major findings and outstanding questions around this emerging key player in cell growth regulation.
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Affiliation(s)
- Riko Hatakeyama
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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18
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Tanigawa M, Yamamoto K, Nagatoishi S, Nagata K, Noshiro D, Noda NN, Tsumoto K, Maeda T. A glutamine sensor that directly activates TORC1. Commun Biol 2021; 4:1093. [PMID: 34535752 PMCID: PMC8448839 DOI: 10.1038/s42003-021-02625-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/31/2021] [Indexed: 01/08/2023] Open
Abstract
TOR complex 1 (TORC1) is an evolutionarily-conserved protein kinase that controls cell growth and metabolism in response to nutrients, particularly amino acids. In mammals, several amino acid sensors have been identified that converge on the multi-layered machinery regulating Rag GTPases to trigger TORC1 activation; however, these sensors are not conserved in many other organisms including yeast. Previously, we reported that glutamine activates yeast TORC1 via a Gtr (Rag ortholog)-independent mechanism involving the vacuolar protein Pib2, although the identity of the supposed glutamine sensor and the exact TORC1 activation mechanism remain unclear. In this study, we successfully reconstituted glutamine-responsive TORC1 activation in vitro using only purified Pib2 and TORC1. In addition, we found that glutamine specifically induced a change in the folding state of Pib2. These findings indicate that Pib2 is a glutamine sensor that directly activates TORC1, providing a new model for the metabolic control of cells.
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Affiliation(s)
- Mirai Tanigawa
- Departments of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Katsuyoshi Yamamoto
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Maeda
- Departments of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan. .,Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
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19
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Lakpa KL, Khan N, Afghah Z, Chen X, Geiger JD. Lysosomal Stress Response (LSR): Physiological Importance and Pathological Relevance. J Neuroimmune Pharmacol 2021; 16:219-237. [PMID: 33751445 PMCID: PMC8099033 DOI: 10.1007/s11481-021-09990-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/08/2021] [Indexed: 02/08/2023]
Abstract
Extensive work has characterized endoplasmic reticulum (ER) and mitochondrial stress responses. In contrast, very little has been published about stress responses in lysosomes; subcellular acidic organelles that are physiologically important and are of pathological relevance. The greater lysosomal system is dynamic and is comprised of endosomes, lysosomes, multivesicular bodies, autophagosomes, and autophagolysosomes. They are important regulators of cellular physiology, they represent about 5% of the total cellular volume, they are heterogeneous in their sizes and distribution patterns, they are electron dense, and their subcellular positioning within cells varies in response to stimuli, insults and pH. These organelles are also integral to the pathogenesis of lysosomal storage diseases and it is increasingly recognized that lysosomes play important roles in the pathogenesis of such diverse conditions as neurodegenerative disorders and cancer. The purpose of this review is to focus attention on lysosomal stress responses (LSR), compare LSR with better characterized stress responses in ER and mitochondria, and form a framework for future characterizations of LSR. We synthesized data into the concept of LSR and present it here such that the definition of LSR can be modified as new knowledge is added and specific therapeutics are developed.
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Affiliation(s)
- Koffi L Lakpa
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA
| | - Nabab Khan
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA
| | - Zahra Afghah
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA
| | - Xuesong Chen
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA
| | - Jonathan D Geiger
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA.
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20
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Hepowit NL, Macedo JKA, Young LEA, Liu K, Sun RC, MacGurn JA, Dickson RC. Enhancing lifespan of budding yeast by pharmacological lowering of amino acid pools. Aging (Albany NY) 2021; 13:7846-7871. [PMID: 33744865 PMCID: PMC8034917 DOI: 10.18632/aging.202849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/21/2021] [Indexed: 04/20/2023]
Abstract
The increasing prevalence of age-related diseases and resulting healthcare insecurity and emotional burden require novel treatment approaches. Several promising strategies seek to limit nutrients and promote healthy aging. Unfortunately, the human desire to consume food means this strategy is not practical for most people but pharmacological approaches might be a viable alternative. We previously showed that myriocin, which impairs sphingolipid synthesis, increases lifespan in Saccharomyces cerevisiae by modulating signaling pathways including the target of rapamycin complex 1 (TORC1). Since TORC1 senses cellular amino acids, we analyzed amino acid pools and identified 17 that are lowered by myriocin treatment. Studying the methionine transporter, Mup1, we found that newly synthesized Mup1 traffics to the plasma membrane and is stable for several hours but is inactive in drug-treated cells. Activity can be restored by adding phytosphingosine to culture medium thereby bypassing drug inhibition, thus confirming a sphingolipid requirement for Mup1 activity. Importantly, genetic analysis of myriocin-induced longevity revealed a requirement for the Gtr1/2 (mammalian Rags) and Vps34-Pib2 amino acid sensing pathways upstream of TORC1, consistent with a mechanism of action involving decreased amino acid availability. These studies demonstrate the feasibility of pharmacologically inducing a state resembling amino acid restriction to promote healthy aging.
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Affiliation(s)
- Nathaniel L. Hepowit
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Jessica K. A. Macedo
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Lyndsay E. A. Young
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Ke Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan University, Chengdu 610000, Sichuan, P. R. China
| | - Ramon C. Sun
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA
| | - Jason A. MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Robert C. Dickson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
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21
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Kira S, Noguchi M, Araki Y, Oikawa Y, Yoshimori T, Miyahara A, Noda T. Vacuolar protein Tag1 and Atg1-Atg13 regulate autophagy termination during persistent starvation in S. cerevisiae. J Cell Sci 2021; 134:jcs.253682. [PMID: 33536246 DOI: 10.1242/jcs.253682] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
Under starvation conditions, cells degrade their own components via autophagy in order to provide sufficient nutrients to ensure their survival. However, even if starvation persists, the cell is not completely degraded through autophagy, implying the existence of some kind of termination mechanism. In the yeast Saccharomyces cerevisiae, autophagy is terminated after 10-12 h of nitrogen starvation. In this study, we found that termination is mediated by re-phosphorylation of Atg13 by the Atg1 protein kinase, which is also affected by PP2C phosphatases, and the eventual dispersion of the pre-autophagosomal structure, also known as the phagophore assembly site (PAS). In a genetic screen, we identified an uncharacterized vacuolar membrane protein, Tag1, as a factor responsible for the termination of autophagy. Re-phosphorylation of Atg13 and eventual PAS dispersal were defective in the Δtag1 mutant. The vacuolar luminal domain of Tag1 and autophagic progression are important for the behaviors of Tag1. Together, our findings reveal the mechanism and factors responsible for termination of autophagy in yeast.
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Affiliation(s)
- Shintaro Kira
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Yamadaoka 1-8, Suita, Osaka 565-0871, Japan
| | - Masafumi Noguchi
- Department of Oral Frontier Biology, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-8, Suita, Osaka 565-0871, Japan.,Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Yasuhiro Araki
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Yamadaoka 1-8, Suita, Osaka 565-0871, Japan
| | - Yu Oikawa
- Research Center of Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama, Kanagawa 226-8503, Japan
| | - Tamotsu Yoshimori
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan.,Department of Genetics, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Aiko Miyahara
- Department of Oral Frontier Biology, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-8, Suita, Osaka 565-0871, Japan.,Department of Genetics, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Takeshi Noda
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Yamadaoka 1-8, Suita, Osaka 565-0871, Japan .,Department of Oral Frontier Biology, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-8, Suita, Osaka 565-0871, Japan
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22
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Morozumi Y, Shiozaki K. Conserved and Divergent Mechanisms That Control TORC1 in Yeasts and Mammals. Genes (Basel) 2021; 12:genes12010088. [PMID: 33445779 PMCID: PMC7828246 DOI: 10.3390/genes12010088] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/23/2022] Open
Abstract
Target of rapamycin complex 1 (TORC1), a serine/threonine-protein kinase complex highly conserved among eukaryotes, coordinates cellular growth and metabolism with environmental cues, including nutrients and growth factors. Aberrant TORC1 signaling is associated with cancers and various human diseases, and TORC1 also plays a key role in ageing and lifespan, urging current active research on the mechanisms of TORC1 regulation in a variety of model organisms. Identification and characterization of the RAG small GTPases as well as their regulators, many of which are highly conserved from yeast to humans, led to a series of breakthroughs in understanding the molecular bases of TORC1 regulation. Recruitment of mammalian TORC1 (mTORC1) by RAGs to lysosomal membranes is a key step for mTORC1 activation. Interestingly, the RAG GTPases in fission yeast are primarily responsible for attenuation of TORC1 activity on vacuoles, the yeast equivalent of lysosomes. In this review, we summarize our current knowledge about the functions of TORC1 regulators on yeast vacuoles, and illustrate the conserved and divergent mechanisms of TORC1 regulation between yeasts and mammals.
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Affiliation(s)
- Yuichi Morozumi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan;
- Correspondence: ; Tel.: +81-743-72-5543
| | - Kazuhiro Shiozaki
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan;
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
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23
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Chen Z, Malia PC, Hatakeyama R, Nicastro R, Hu Z, Péli-Gulli MP, Gao J, Nishimura T, Eskes E, Stefan CJ, Winderickx J, Dengjel J, De Virgilio C, Ungermann C. TORC1 Determines Fab1 Lipid Kinase Function at Signaling Endosomes and Vacuoles. Curr Biol 2020; 31:297-309.e8. [PMID: 33157024 DOI: 10.1016/j.cub.2020.10.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/25/2020] [Accepted: 10/08/2020] [Indexed: 01/17/2023]
Abstract
Organelles of the endomembrane system maintain their identity and integrity during growth or stress conditions by homeostatic mechanisms that regulate membrane flux and biogenesis. At lysosomes and endosomes, the Fab1 lipid kinase complex and the nutrient-regulated target of rapamycin complex 1 (TORC1) control the integrity of the endolysosomal homeostasis and cellular metabolism. Both complexes are functionally connected as Fab1-dependent generation of PI(3,5)P2 supports TORC1 activity. Here, we identify Fab1 as a target of TORC1 on signaling endosomes, which are distinct from multivesicular bodies, and provide mechanistic insight into their crosstalk. Accordingly, TORC1 can phosphorylate Fab1 proximal to its PI3P-interacting FYVE domain, which causes Fab1 to shift to signaling endosomes, where it generates PI(3,5)P2. This, in turn, regulates (1) vacuole morphology, (2) recruitment of TORC1 and the TORC1-regulatory Rag GTPase-containing EGO complex to signaling endosomes, and (3) TORC1 activity. Thus, our study unravels a regulatory feedback loop between TORC1 and the Fab1 complex that controls signaling at endolysosomes.
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Affiliation(s)
- Zilei Chen
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Pedro Carpio Malia
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Riko Hatakeyama
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Zehan Hu
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Marie-Pierre Péli-Gulli
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Jieqiong Gao
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Taki Nishimura
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Elja Eskes
- Functional Biology, KU Leuven, Kasteelpark Arensberg 31, 3000 Leuven, Belgium
| | - Christopher J Stefan
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Joris Winderickx
- Functional Biology, KU Leuven, Kasteelpark Arensberg 31, 3000 Leuven, Belgium
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland.
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany; Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany.
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24
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Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions. G3-GENES GENOMES GENETICS 2020; 10:3859-3870. [PMID: 32819971 PMCID: PMC7534453 DOI: 10.1534/g3.120.401595] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Within the budding yeasts, the opportunistic pathogen Candida glabrata and other members of the Nakaseomyces clade have developed virulence traits independently from C. albicans and C. auris. To begin exploring the genetic basis of C. glabrata virulence and its innate resistance to antifungals, we launched the Hermes transposon from a plasmid and sequenced more than 500,000 different semi-random insertions throughout the genome. With machine learning, we identified 1278 protein-encoding genes (25% of total) that could not tolerate transposon insertions and are likely essential for C. glabrata fitness in vitro. Interestingly, genes involved in mRNA splicing were less likely to be essential in C. glabrata than their orthologs in S. cerevisiae, whereas the opposite is true for genes involved in kinetochore function and chromosome segregation. When a pool of insertion mutants was challenged with the first-line antifungal fluconazole, insertions in several known resistance genes (e.g., PDR1, CDR1, PDR16, PDR17, UPC2A, DAP1, STV1) and 15 additional genes (including KGD1, KGD2, YHR045W) became hypersensitive to fluconazole. Insertions in 200 other genes conferred significant resistance to fluconazole, two-thirds of which function in mitochondria and likely down-regulate Pdr1 expression or function. Knockout mutants of KGD2 and IDH2, which consume and generate alpha-ketoglutarate in mitochondria, exhibited increased and decreased resistance to fluconazole through a process that depended on Pdr1. These findings establish the utility of transposon insertion profiling in forward genetic investigations of this important pathogen of humans.
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25
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Uemura S, Mochizuki T, Amemiya K, Kurosaka G, Yazawa M, Nakamoto K, Ishikawa Y, Izawa S, Abe F. Amino acid homeostatic control by TORC1 in Saccharomyces cerevisiae under high hydrostatic pressure. J Cell Sci 2020; 133:jcs245555. [PMID: 32801125 DOI: 10.1242/jcs.245555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/05/2020] [Indexed: 12/30/2022] Open
Abstract
Mechanical stresses, including high hydrostatic pressure, elicit diverse physiological effects on organisms. Gtr1, Gtr2, Ego1 (also known as Meh1) and Ego3 (also known as Slm4), central regulators of the TOR complex 1 (TORC1) nutrient signaling pathway, are required for the growth of Saccharomyces cerevisiae cells under high pressure. Here, we showed that a pressure of 25 MPa (∼250 kg/cm2) stimulates TORC1 to promote phosphorylation of Sch9, which depends on the EGO complex (EGOC) and Pib2. Incubation of cells at this pressure aberrantly increased glutamine and alanine levels in the ego1Δ, gtr1Δ, tor1Δ and pib2Δ mutants, whereas the polysome profiles were unaffected. Moreover, we found that glutamine levels were reduced by combined deletions of EGO1, GTR1, TOR1 and PIB2 with GLN3 These results suggest that high pressure leads to the intracellular accumulation of amino acids. Subsequently, Pib2 loaded with glutamine stimulates the EGOC-TORC1 complex to inactivate Gln3, downregulating glutamine synthesis. Our findings illustrate the regulatory circuit that maintains intracellular amino acid homeostasis and suggest critical roles for the EGOC-TORC1 and Pib2-TORC1 complexes in the growth of yeast under high hydrostatic pressure.
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Affiliation(s)
- Satoshi Uemura
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
- Division of Medical Biochemistry, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi 983-8536, Japan
| | - Takahiro Mochizuki
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Kengo Amemiya
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Goyu Kurosaka
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Miho Yazawa
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Keiko Nakamoto
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
| | - Yu Ishikawa
- Laboratory of Microbial Technology, Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Shingo Izawa
- Laboratory of Microbial Technology, Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Fumiyoshi Abe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan
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26
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Milanesi R, Coccetti P, Tripodi F. The Regulatory Role of Key Metabolites in the Control of Cell Signaling. Biomolecules 2020; 10:biom10060862. [PMID: 32516886 PMCID: PMC7356591 DOI: 10.3390/biom10060862] [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: 05/08/2020] [Revised: 05/29/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
Robust biological systems are able to adapt to internal and environmental perturbations. This is ensured by a thick crosstalk between metabolism and signal transduction pathways, through which cell cycle progression, cell metabolism and growth are coordinated. Although several reports describe the control of cell signaling on metabolism (mainly through transcriptional regulation and post-translational modifications), much fewer information is available on the role of metabolism in the regulation of signal transduction. Protein-metabolite interactions (PMIs) result in the modification of the protein activity due to a conformational change associated with the binding of a small molecule. An increasing amount of evidences highlight the role of metabolites of the central metabolism in the control of the activity of key signaling proteins in different eukaryotic systems. Here we review the known PMIs between primary metabolites and proteins, through which metabolism affects signal transduction pathways controlled by the conserved kinases Snf1/AMPK, Ras/PKA and TORC1. Interestingly, PMIs influence also the mitochondrial retrograde response (RTG) and calcium signaling, clearly demonstrating that the range of this phenomenon is not limited to signaling pathways related to metabolism.
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27
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Meng D, Yang Q, Wang H, Melick CH, Navlani R, Frank AR, Jewell JL. Glutamine and asparagine activate mTORC1 independently of Rag GTPases. J Biol Chem 2020; 295:2890-2899. [PMID: 32019866 DOI: 10.1074/jbc.ac119.011578] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/24/2020] [Indexed: 12/14/2022] Open
Abstract
Nutrient sensing by cells is crucial, and when this sensing mechanism is disturbed, human disease can occur. mTOR complex 1 (mTORC1) senses amino acids to control cell growth, metabolism, and autophagy. Leucine, arginine, and methionine signal to mTORC1 through the well-characterized Rag GTPase signaling pathway. In contrast, glutamine activates mTORC1 through a Rag GTPase-independent mechanism that requires ADP-ribosylation factor 1 (Arf1). Here, using several biochemical and genetic approaches, we show that eight amino acids filter through the Rag GTPase pathway. Like glutamine, asparagine signals to mTORC1 through Arf1 in the absence of the Rag GTPases. Both the Rag-dependent and Rag-independent pathways required the lysosome and lysosomal function for mTORC1 activation. Our results show that mTORC1 is differentially regulated by amino acids through two distinct pathways.
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Affiliation(s)
- Delong Meng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Qianmei Yang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Huanyu Wang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Chase H Melick
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Rishika Navlani
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Anderson R Frank
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Jenna L Jewell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390.
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28
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Brito AS, Soto Diaz S, Van Vooren P, Godard P, Marini AM, Boeckstaens M. Pib2-Dependent Feedback Control of the TORC1 Signaling Network by the Npr1 Kinase. iScience 2019; 20:415-433. [PMID: 31622882 PMCID: PMC6817644 DOI: 10.1016/j.isci.2019.09.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 05/10/2019] [Accepted: 09/13/2019] [Indexed: 01/21/2023] Open
Abstract
To adjust cell growth and metabolism according to environmental conditions, the conserved TORC1 signaling network controls autophagy, protein synthesis, and turnover. Here, we dissected the signals controlling phosphorylation and activity of the TORC1-effector kinase Npr1, involved in tuning the plasma membrane permeability to nitrogen sources. By evaluating a role of pH as a signal, we show that, although a transient cytosolic acidification accompanies nitrogen source entry and is correlated to a rapid TORC1-dependent phosphorylation of Npr1, a pH drop is not a prerequisite for TORC1 activation. We show that the Gtr1/Gtr2 and Pib2 regulators of TORC1 both independently and differently contribute to regulate Npr1 phosphorylation and activity. Finally, our data reveal that Npr1 mediates nitrogen-dependent phosphorylation of Pib2, as well as a Pib2-dependent inhibition of TORC1. This work highlights a feedback control loop likely enabling efficient downregulation and faster re-activation of TORC1 in response to a novel stimulating signal.
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Affiliation(s)
- Ana Sofia Brito
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium
| | - Silvia Soto Diaz
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium
| | - Pascale Van Vooren
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium
| | - Patrice Godard
- UCB Pharma, Chemin du Foriest, 1420 Braine-l'Alleud, Belgium
| | - Anna Maria Marini
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium
| | - Mélanie Boeckstaens
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium.
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29
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Kessi-Pérez EI, Salinas F, González A, Su Y, Guillamón JM, Hall MN, Larrondo LF, Martínez C. KAE1 Allelic Variants Affect TORC1 Activation and Fermentation Kinetics in Saccharomyces cerevisiae. Front Microbiol 2019; 10:1686. [PMID: 31417508 PMCID: PMC6685402 DOI: 10.3389/fmicb.2019.01686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
The eukaryotic domain-conserved TORC1 signalling pathway connects growth with nutrient sufficiency, promoting anabolic processes such as ribosomal biogenesis and protein synthesis. In Saccharomyces cerevisiae, TORC1 is activated mainly by the nitrogen sources. Recently, this pathway has gotten renewed attention but now in the context of the alcoholic fermentation, due to its key role in nitrogen metabolism regulation. Although the distal and proximal effectors downstream TORC1 are well characterised in yeast, the mechanism by which TORC1 is activated by nitrogen sources is not fully understood. In this work, we took advantage of a previously developed microculture-based methodology, which indirectly evaluates TORC1 activation in a nitrogen upshift experiment, to identify genetic variants affecting the activation of this pathway. We used this method to phenotype a recombinant population derived from two strains (SA and WE) with different geographic origins, which show opposite phenotypes for TORC1 activation by glutamine. Using this phenotypic information, we performed a QTL mapping that allowed us to identify several QTLs for TORC1 activation. Using a reciprocal hemizygous analysis, we validated GUS1, KAE1, PIB2, and UTH1 as genes responsible for the natural variation in the TORC1 activation. We observed that reciprocal hemizygous strains for KAE1 (ATPase required for t6A tRNA modification) gene showed the greatest phenotypic differences for TORC1 activation, with the hemizygous strain carrying the SA allele (KAE1SA) showing the higher TORC1 activation. In addition, we evaluated the fermentative capacities of the hemizygous strains under low nitrogen conditions, observing an antagonistic effect for KAE1SA allele, where the hemizygous strain containing this allele presented the lower fermentation rate. Altogether, these results highlight the importance of the tRNA processing in TORC1 activation and connects this pathway with the yeasts fermentation kinetics under nitrogen-limited conditions.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.,Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco Salinas
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile (UACH), Valdivia, Chile
| | | | - Ying Su
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | | | - Luis F Larrondo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudio Martínez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.,Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
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30
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Ahmed K, Carter DE, Lajoie P. Hyperactive
TORC
1 sensitizes yeast cells to endoplasmic reticulum stress by compromising cell wall integrity. FEBS Lett 2019; 593:1957-1973. [DOI: 10.1002/1873-3468.13463] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Khadija Ahmed
- Department of Anatomy and Cell Biology The University of Western Ontario London Canada
| | - David E. Carter
- Robarts Research Institute The University of Western Ontario London Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology The University of Western Ontario London Canada
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31
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Deprez MA, Eskes E, Winderickx J, Wilms T. The TORC1-Sch9 pathway as a crucial mediator of chronological lifespan in the yeast Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:4980911. [PMID: 29788208 DOI: 10.1093/femsyr/foy048] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/19/2018] [Indexed: 12/18/2022] Open
Abstract
The concept of ageing is one that has intrigued mankind since the beginning of time and is now more important than ever as the incidence of age-related disorders is increasing in our ageing population. Over the past decades, extensive research has been performed using various model organisms. As such, it has become apparent that many fundamental aspects of biological ageing are highly conserved across large evolutionary distances. In this review, we illustrate that the unicellular eukaryotic organism Saccharomyces cerevisiae has proven to be a valuable tool to gain fundamental insights into the molecular mechanisms of cellular ageing in multicellular eukaryotes. In addition, we outline the current knowledge on how downregulation of nutrient signaling through the target of rapamycin (TOR)-Sch9 pathway or reducing calorie intake attenuates many detrimental effects associated with ageing and leads to the extension of yeast chronological lifespan. Given that both TOR Complex 1 (TORC1) and Sch9 have mammalian orthologues that have been implicated in various age-related disorders, unraveling the connections of TORC1 and Sch9 with yeast ageing may provide additional clues on how their mammalian orthologues contribute to the mechanisms underpinning human ageing and health.
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Affiliation(s)
- Marie-Anne Deprez
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Elja Eskes
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Tobias Wilms
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
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32
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Rutherford JC, Bahn YS, van den Berg B, Heitman J, Xue C. Nutrient and Stress Sensing in Pathogenic Yeasts. Front Microbiol 2019; 10:442. [PMID: 30930866 PMCID: PMC6423903 DOI: 10.3389/fmicb.2019.00442] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/20/2019] [Indexed: 12/23/2022] Open
Abstract
More than 1.5 million fungal species are estimated to live in vastly different environmental niches. Despite each unique host environment, fungal cells sense certain fundamentally conserved elements, such as nutrients, pheromones and stress, for adaptation to their niches. Sensing these extracellular signals is critical for pathogens to adapt to the hostile host environment and cause disease. Hence, dissecting the complex extracellular signal-sensing mechanisms that aid in this is pivotal and may facilitate the development of new therapeutic approaches to control fungal infections. In this review, we summarize the current knowledge on how two important pathogenic yeasts, Candida albicans and Cryptococcus neoformans, sense nutrient availability, such as carbon sources, amino acids, and ammonium, and different stress signals to regulate their morphogenesis and pathogenicity in comparison with the non-pathogenic model yeast Saccharomyces cerevisiae. The molecular interactions between extracellular signals and their respective sensory systems are described in detail. The potential implication of analyzing nutrient and stress-sensing systems in antifungal drug development is also discussed.
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Affiliation(s)
- Julian C Rutherford
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yong-Sun Bahn
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, United States
| | - Chaoyang Xue
- Public Health Research Institute, Rutgers University, Newark, NJ, United States.,Department of Molecular Genetics, Biochemistry and Microbiology, Rutgers University, Newark, NJ, United States
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33
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Auxin-Inducible Depletion of the Essentialome Suggests Inhibition of TORC1 by Auxins and Inhibition of Vrg4 by SDZ 90-215, a Natural Antifungal Cyclopeptide. G3-GENES GENOMES GENETICS 2019; 9:829-840. [PMID: 30670608 PMCID: PMC6404609 DOI: 10.1534/g3.118.200748] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Gene knockout and knockdown strategies have been immensely successful probes of gene function, but small molecule inhibitors (SMIs) of gene products allow much greater time resolution and are particularly useful when the targets are essential for cell replication or survival. SMIs also serve as lead compounds for drug discovery. However, discovery of selective SMIs is costly and inefficient. The action of SMIs can be modeled simply by tagging gene products with an auxin-inducible degron (AID) that triggers rapid ubiquitylation and proteasomal degradation of the tagged protein upon exposure of live cells to auxin. To determine if this approach is broadly effective, we AID-tagged over 750 essential proteins in Saccharomyces cerevisiae and observed growth inhibition by low concentrations of auxin in over 66% of cases. Polytopic transmembrane proteins in the plasma membrane, Golgi complex, and endoplasmic reticulum were efficiently depleted if the AID-tag was exposed to cytoplasmic OsTIR1 ubiquitin ligase. The auxin analog 1-napthylacetic acid (NAA) was as potent as auxin on AID-tags, but surprisingly NAA was more potent than auxin at inhibiting target of rapamycin complex 1 (TORC1) function. Auxin also synergized with known SMIs when acting on the same essential protein, indicating that AID-tagged strains can be useful for SMI screening. Auxin synergy, resistance mutations, and cellular assays together suggest the essential GMP/GDP-mannose exchanger in the Golgi complex (Vrg4) as the target of a natural cyclic peptide of unknown function (SDZ 90-215). These findings indicate that AID-tagging can efficiently model the action of SMIs before they are discovered and can facilitate SMI discovery.
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Sullivan A, Wallace RL, Wellington R, Luo X, Capaldi AP. Multilayered regulation of TORC1-body formation in budding yeast. Mol Biol Cell 2019; 30:400-410. [PMID: 30485160 PMCID: PMC6589571 DOI: 10.1091/mbc.e18-05-0297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/08/2018] [Accepted: 11/20/2018] [Indexed: 02/05/2023] Open
Abstract
The target of rapamycin kinase complex 1 (TORC1) regulates cell growth and metabolism in eukaryotes. In Saccharomyces cerevisiae, TORC1 activity is known to be controlled by the conserved GTPases, Gtr1/2, and movement into and out of an inactive agglomerate/body. However, it is unclear whether/how these regulatory steps are coupled. Here we show that active Gtr1/2 is a potent inhibitor of TORC1-body formation, but cells missing Gtr1/2 still form TORC1-bodies in a glucose/nitrogen starvation-dependent manner. We also identify 13 new activators of TORC1-body formation and show that seven of these proteins regulate the Gtr1/2-dependent repression of TORC1-body formation, while the remaining proteins drive the subsequent steps in TORC1 agglomeration. Finally, we show that the conserved phosphatidylinositol-3-phosphate (PI(3)P) binding protein, Pib2, forms a complex with TORC1 and overrides the Gtr1/2-dependent repression of TORC1-body formation during starvation. These data provide a unified, systems-level model of TORC1 regulation in yeast.
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Affiliation(s)
- Arron Sullivan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
| | - Ryan L. Wallace
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
| | - Rachel Wellington
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
| | - Andrew P. Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
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Teng X, Hardwick JM. Whi2: a new player in amino acid sensing. Curr Genet 2019; 65:701-709. [PMID: 30701278 DOI: 10.1007/s00294-018-00929-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/30/2018] [Accepted: 12/31/2018] [Indexed: 12/26/2022]
Abstract
A critical function of human, yeast, and bacterial cells is the ability to sense and respond to available nutrients such as glucose and amino acids. Cells must also detect declining nutrient levels to adequately prepare for starvation conditions by inhibiting cell growth and activating autophagy. The evolutionarily conserved protein complex TORC1 regulates these cellular responses to nutrients, and in particular to amino acid availability. Recently, we found that yeast Whi2 (Saccharomyces cerevisiae) and a human counterpart, KCTD11, that shares a conserved BTB structural domain, are required to suppress TORC1 activity under low amino acid conditions. Using yeast, the mechanisms were more readily dissected. Unexpectedly, Whi2 suppresses TORC1 activity independently of the well-known SEACIT-GTR pathway, analogous to the GATOR1-RAG pathway in mammals. Instead, Whi2 requires the plasma membrane-associated phosphatases Psr1 and Psr2, which were known to bind Whi2, although their role was unknown. Yeast WHI2 was previously reported to be involved in regulating several fundamental cellular processes including cell cycle arrest, general stress responses, the Ras-cAMP-PKA pathway, autophagy, and mitophagy, and to be frequently mutated in the yeast knockout collections and in genome evolution studies. Most of these observations are likely explained by the ability of Whi2 to inhibit TORC1. Thus, understanding the function of yeast Whi2 will provide deeper insights into the disease-related KCTD family proteins and the pathogenesis of plant and human fungal infections.
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Affiliation(s)
- Xinchen Teng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China. .,W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - J Marie Hardwick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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36
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Spatially Distinct Pools of TORC1 Balance Protein Homeostasis. Mol Cell 2019; 73:325-338.e8. [DOI: 10.1016/j.molcel.2018.10.040] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/03/2018] [Accepted: 10/25/2018] [Indexed: 11/19/2022]
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37
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Kessi-Pérez EI, Salinas F, Molinet J, González A, Muñiz S, Guillamón JM, Hall MN, Larrondo LF, Martínez C. Indirect monitoring of TORC1 signalling pathway reveals molecular diversity among different yeast strains. Yeast 2018; 36:65-74. [PMID: 30094872 DOI: 10.1002/yea.3351] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/07/2018] [Accepted: 07/29/2018] [Indexed: 11/08/2022] Open
Abstract
Saccharomyces cerevisiae is the main species responsible for the alcoholic fermentation in wine production. One of the main problems in this process is the deficiency of nitrogen sources in the grape must, which can lead to stuck or sluggish fermentations. Currently, yeast nitrogen consumption and metabolism are under active inquiry, with emphasis on the study of the TORC1 signalling pathway, given its central role responding to nitrogen availability and influencing growth and cell metabolism. However, the mechanism by which different nitrogen sources activates TORC1 is not completely understood. Existing methods to evaluate TORC1 activation by nitrogen sources are time-consuming, making difficult the analyses of large numbers of strains. In this work, a new indirect method for monitoring TORC1 pathway was developed on the basis of the luciferase reporter gene controlled by the promoter region of RPL26A gene, a gene known to be expressed upon TORC1 activation. The method was tested in strains representative of the clean lineages described so far in S. cerevisiae. The activation of the TORC1 pathway by a proline-to-glutamine upshift was indirectly evaluated using our system and the traditional direct methods based on immunoblot (Sch9 and Rps6 phosphorylation). Regardless of the different molecular readouts obtained with both methodologies, the general results showed a wide phenotypic variation between the representative strains analysed. Altogether, this easy-to-use assay opens the possibility to study the molecular basis for the differential TORC1 pathway activation, allowing to interrogate a larger number of strains in the context of nitrogen metabolism phenotypic differences.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco Salinas
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jennifer Molinet
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | | | - Sara Muñiz
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Paterna, Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Paterna, Valencia, Spain
| | | | - Luis F Larrondo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudio Martínez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.,Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
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Varlakhanova NV, Tornabene BA, Ford MGJ. Feedback regulation of TORC1 by its downstream effectors Npr1 and Par32. Mol Biol Cell 2018; 29:2751-2765. [PMID: 30156471 PMCID: PMC6249832 DOI: 10.1091/mbc.e18-03-0158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
TORC1 (target of rapamycin complex) integrates complex nutrient signals to generate and fine-tune a growth and metabolic response. Npr1 (nitrogen permease reactivator) is a downstream effector kinase of TORC1 that regulates the stability, activity, and trafficking of various nutrient permeases including the ammonium permeases Mep1, Mep2, and Mep3 and the general amino acid permease Gap1. Npr1 exerts its regulatory effects on Mep1 and Mep3 via Par32 (phosphorylated after rapamycin). Activation of Npr1 leads to phosphorylation of Par32, resulting in changes in its subcellular localization and function. Here we demonstrate that Par32 is a positive regulator of TORC1 activity. Loss of Par32 renders cells unable to recover from exposure to rapamycin and reverses the resistance to rapamycin of Δ npr1 cells. The sensitivity to rapamycin of cells lacking Par32 is dependent on Mep1 and Mep3 and the presence of ammonium, linking ammonium metabolism to TORC1 activity. Par32 function requires its conserved repeated glycine-rich motifs to be intact but, surprisingly, does not require its localization to the plasma membrane. In all, this work elucidates a novel mechanism by which Npr1 and Par32 exert regulatory feedback on TORC1.
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Affiliation(s)
- Natalia V Varlakhanova
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Bryan A Tornabene
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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Abstract
This question of whether fungi undergo apoptosis-like programmed cell death can be separated into two questions. One question is about applying the term "apoptosis" to fungi, and the other is a more challenging question of whether fungi have evolved mechanisms that inflict self-injury. The answers to both questions depend on the definitions applied to "apoptosis" and "programmed cell death." Considering how these and other cell death terms originated and are currently defined for animals, some confusion arises when the terms are applied to fungi. While it is difficult to defend the concept of fungal apoptosis, the more interesting issue is whether fungi will eventually be found to encode programmed or extemporaneous self-destructive processes, as suggested by intriguing new findings.
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Affiliation(s)
- J Marie Hardwick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
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40
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Liu Y, Okamoto K. The TORC1 signaling pathway regulates respiration-induced mitophagy in yeast. Biochem Biophys Res Commun 2018; 502:76-83. [DOI: 10.1016/j.bbrc.2018.05.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 01/02/2023]
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41
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Antifungal tolerance is a subpopulation effect distinct from resistance and is associated with persistent candidemia. Nat Commun 2018; 9:2470. [PMID: 29941885 PMCID: PMC6018213 DOI: 10.1038/s41467-018-04926-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/05/2018] [Indexed: 11/23/2022] Open
Abstract
Tolerance to antifungal drug concentrations above the minimal inhibitory concentration (MIC) is rarely quantified, and current clinical recommendations suggest it should be ignored. Here, we quantify antifungal tolerance in Candida albicans isolates as the fraction of growth above the MIC, and find that it is distinct from susceptibility/resistance. Instead, tolerance is due to the slow growth of subpopulations of cells that overcome drug stress more efficiently than the rest of the population, and correlates inversely with intracellular drug accumulation. Many adjuvant drugs used in combination with fluconazole, a widely used fungistatic drug, reduce tolerance without affecting resistance. Accordingly, in an invertebrate infection model, adjuvant combination therapy is more effective than fluconazole in treating infections with highly tolerant isolates and does not affect infections with low tolerance isolates. Furthermore, isolates recovered from immunocompetent patients with persistent candidemia display higher tolerance than isolates readily cleared by fluconazole. Thus, tolerance correlates with, and may help predict, patient responses to fluconazole therapy. The authors show that antifungal tolerance, defined as the fraction of growth of a fungal pathogen above the minimal inhibitory concentration, is due to the slow growth of subpopulations of cells that overcome drug stress, and that high tolerance is often associated with persistent infections.
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Ukai H, Araki Y, Kira S, Oikawa Y, May AI, Noda T. Gtr/Ego-independent TORC1 activation is achieved through a glutamine-sensitive interaction with Pib2 on the vacuolar membrane. PLoS Genet 2018; 14:e1007334. [PMID: 29698392 PMCID: PMC5919408 DOI: 10.1371/journal.pgen.1007334] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 03/15/2018] [Indexed: 12/18/2022] Open
Abstract
TORC1 is a central regulator of cell growth in response to amino acids. The role of the evolutionarily conserved Gtr/Rag pathway in the regulation of TORC1 is well-established. Recent genetic studies suggest that an additional regulatory pathway, depending on the activity of Pib2, plays a role in TORC1 activation independently of the Gtr/Rag pathway. However, the interplay between the Pib2 pathway and the Gtr/Rag pathway remains unclear. In this study, we show that Pib2 and Gtr/Ego form distinct complexes with TORC1 in a mutually exclusive manner, implying dedicated functional relationships between TORC1 and Pib2 or Gtr/Rag in response to specific amino acids. Furthermore, simultaneous depletion of Pib2 and the Gtr/Ego system abolishes TORC1 activity and completely compromises the vacuolar localization of TORC1. Thus, the amino acid-dependent activation of TORC1 is achieved through the Pib2 and Gtr/Ego pathways alone. Finally, we show that glutamine induces a dose-dependent increase in Pib2-TORC1 complex formation, and that glutamine binds directly to the Pib2 complex. These data provide strong preliminary evidence for Pib2 functioning as a putative glutamine sensor in the regulation of TORC1. TORC1 is a central regulator of cell growth in response to amino acids. The evolutionarily conserved Gtr/Rag pathway is a well-established TORC1 regulatory pathway. In this study, we show that two molecular machineries, Pib2 and Gtr/Ego, form distinct complexes with TORC1 in a mutually exclusive manner, implying an exclusive functional relationship between TORC1 and Pib2 or Gtr/Rag in response to various amino acids. We also show that the amino acid-dependent activation of TORC1 is achieved through the Pib2 and Gtr/Ego pathways by anchoring them to the vacuolar membrane. Finally, we show that glutamine binds directly to the Pib2 complex and that glutamine enhances Pib2-TORC1 complex formation. Collectively we provide evidence supporting a role for Pib2 as an element of a putative glutamine sensor.
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Affiliation(s)
- Hirofumi Ukai
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Yasuhiro Araki
- Graduate School of Dentistry, Osaka University, Osaka, Japan
- * E-mail: (TN); (YA)
| | - Shintaro Kira
- Graduate School of Dentistry, Osaka University, Osaka, Japan
| | - Yu Oikawa
- Research Center of Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Alexander I. May
- Research Center of Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Takeshi Noda
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Graduate School of Dentistry, Osaka University, Osaka, Japan
- * E-mail: (TN); (YA)
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Saliba E, Evangelinos M, Gournas C, Corrillon F, Georis I, André B. The yeast H +-ATPase Pma1 promotes Rag/Gtr-dependent TORC1 activation in response to H +-coupled nutrient uptake. eLife 2018; 7:31981. [PMID: 29570051 PMCID: PMC5915174 DOI: 10.7554/elife.31981] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/22/2018] [Indexed: 11/25/2022] Open
Abstract
The yeast Target of Rapamycin Complex 1 (TORC1) plays a central role in controlling growth. How amino acids and other nutrients stimulate its activity via the Rag/Gtr GTPases remains poorly understood. We here report that the signal triggering Rag/Gtr-dependent TORC1 activation upon amino-acid uptake is the coupled H+ influx catalyzed by amino-acid/H+ symporters. H+-dependent uptake of other nutrients, ionophore-mediated H+ diffusion, and inhibition of the vacuolar V-ATPase also activate TORC1. As the increase in cytosolic H+ elicited by these processes stimulates the compensating H+-export activity of the plasma membrane H+-ATPase (Pma1), we have examined whether this major ATP-consuming enzyme might be involved in TORC1 control. We find that when the endogenous Pma1 is replaced with a plant H+-ATPase, H+ influx or increase fails to activate TORC1. Our results show that H+ influx coupled to nutrient uptake stimulates TORC1 activity and that Pma1 is a key actor in this mechanism. Cells adapt their growth rate depending on the amount of nutrients available. The protein complex called TORC1 plays a central role in this. When nutrients are abundant, TORC1 is very active and stimulates the production of proteins and other molecules needed for the cell to grow. However, when nutrients such as amino acids become scarce, TORC1 reduces its activity and allows the cells to adapt to starvation. This TORC1-mediated control of the metabolism is crucial for the cell to survive, and faulty TORC1 proteins have been associated with several diseases including cancers. TORC1 was originally discovered in yeast, which provides a powerful model to study this control system. However, until now, it was not known how TORC1 is reactivated when amino acids are added to cells that have been starved of these molecules. Knowing the answer to this question would allow us to better understand how the availability of nutrients controls the activity of TORC1. Now, Saliba et al. have discovered that TORC1 is not reactivated by the amino acids themselves, but by protons, which are positively charged hydrogen ions that travel into the cell together with the amino acids. This influx of protons is the driving force behind the active transport of amino acids and other nutrients into the cell, and potentially serves as a general signal to activate TORC1 in response to the uptake of nutrients, especially when cells have been starved. Furthermore, the results showed that a specific enzyme in the cell membrane plays an essential role in activating TORC1. This enzyme pumps the protons out of the cell to compensate for their influx and to maintain the proton gradient in the membrane that drives the absorption of nutrients. When this enzyme was replaced with an equivalent plant enzyme, the proton-coupled nutrient uptake did not activate TORC1 in the yeast cells. These findings may help scientists who are interested in how TORC1 is regulated in organisms other than mammals, such as plants or fungi. A next step will be to find out how exactly the proton pump in the cell membrane helps to activate TORC1.
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Affiliation(s)
- Elie Saliba
- Molecular Physiology of the Cell, Université Libre de Bruxelles, Biopark, Gosselies, Belgium
| | - Minoas Evangelinos
- Molecular Physiology of the Cell, Université Libre de Bruxelles, Biopark, Gosselies, Belgium
| | - Christos Gournas
- Molecular Physiology of the Cell, Université Libre de Bruxelles, Biopark, Gosselies, Belgium
| | - Florent Corrillon
- Molecular Physiology of the Cell, Université Libre de Bruxelles, Biopark, Gosselies, Belgium
| | - Isabelle Georis
- Institut de Recherches Microbiologiques J.-M. Wiame, Brussels, Belgium
| | - Bruno André
- Molecular Physiology of the Cell, Université Libre de Bruxelles, Biopark, Gosselies, Belgium
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Hao F, Kondo K, Itoh T, Ikari S, Nada S, Okada M, Noda T. Rheb localized on the Golgi membrane activates lysosome-localized mTORC1 at the Golgi-lysosome contact site. J Cell Sci 2018; 131:jcs.208017. [PMID: 29222112 DOI: 10.1242/jcs.208017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/26/2017] [Indexed: 12/31/2022] Open
Abstract
In response to amino acid supply, mTORC1, a master regulator of cell growth, is recruited to the lysosome and activated by the small GTPase Rheb. However, the intracellular localization of Rheb is controversial. In this study, we showed that a significant portion of Rheb is localized on the Golgi but not on the lysosome. GFP-Rheb could activate mTORC1, even when forced to exclusively localize to the Golgi. Likewise, artificial recruitment of mTORC1 to the Golgi allowed its activation. Accordingly, the Golgi was in contact with the lysosome at an newly discovered area of the cell that we term the Golgi-lysosome contact site (GLCS). The number of GLCSs increased in response to amino acid supply, whereas GLCS perturbation suppressed mTORC1 activation. These results suggest that inter-organelle communication between the Golgi and lysosome is important for mTORC1 regulation and the Golgi-localized Rheb may activate mTORC1 at GLCSs.
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Affiliation(s)
- Feike Hao
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan
| | - Kazuhiko Kondo
- Graduate School of Frontier Bioscience, Osaka University, Osaka 565-0871, Japan
| | - Takashi Itoh
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan
| | - Sumiko Ikari
- Graduate School of Frontier Bioscience, Osaka University, Osaka 565-0871, Japan
| | - Shigeyuki Nada
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Masato Okada
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Takeshi Noda
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan .,Graduate School of Frontier Bioscience, Osaka University, Osaka 565-0871, Japan
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45
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Deprez MA, Eskes E, Wilms T, Ludovico P, Winderickx J. pH homeostasis links the nutrient sensing PKA/TORC1/Sch9 ménage-à-trois to stress tolerance and longevity. MICROBIAL CELL 2018; 5:119-136. [PMID: 29487859 PMCID: PMC5826700 DOI: 10.15698/mic2018.03.618] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The plasma membrane H+-ATPase Pma1 and the vacuolar V-ATPase act in close harmony to tightly control pH homeostasis, which is essential for a vast number of physiological processes. As these main two regulators of pH are responsive to the nutritional status of the cell, it seems evident that pH homeostasis acts in conjunction with nutrient-induced signalling pathways. Indeed, both PKA and the TORC1-Sch9 axis influence the proton pumping activity of the V-ATPase and possibly also of Pma1. In addition, it recently became clear that the proton acts as a second messenger to signal glucose availability via the V-ATPase to PKA and TORC1-Sch9. Given the prominent role of nutrient signalling in longevity, it is not surprising that pH homeostasis has been linked to ageing and longevity as well. A first indication is provided by acetic acid, whose uptake by the cell induces toxicity and affects longevity. Secondly, vacuolar acidity has been linked to autophagic processes, including mitophagy. In agreement with this, a decline in vacuolar acidity was shown to induce mitochondrial dysfunction and shorten lifespan. In addition, the asymmetric inheritance of Pma1 has been associated with replicative ageing and this again links to repercussions on vacuolar pH. Taken together, accumulating evidence indicates that pH homeostasis plays a prominent role in the determination of ageing and longevity, thereby providing new perspectives and avenues to explore the underlying molecular mechanisms.
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Affiliation(s)
| | - Elja Eskes
- Functional Biology, KU Leuven, Leuven, Belgium
| | | | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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Abstract
The mammalian target of rapamycin (mTOR) senses nutrients and growth factors to coordinate cell growth, metabolism and autophagy. Extensive research has mapped the signaling pathways regulated by mTOR that are involved in human diseases, such as cancer, and in diabetes and ageing. Recently, however, new studies have demonstrated important roles for mTOR in promoting the differentiation of adult stem cells, driving the growth and proliferation of stem and progenitor cells, and dictating the differentiation program of multipotent stem cell populations. Here, we review these advances, providing an overview of mTOR signaling and its role in murine and human stem and progenitor cells.
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Affiliation(s)
- Delong Meng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anderson R Frank
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jenna L Jewell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA .,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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47
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Takeda E, Jin N, Itakura E, Kira S, Kamada Y, Weisman LS, Noda T, Matsuura A. Vacuole-mediated selective regulation of TORC1-Sch9 signaling following oxidative stress. Mol Biol Cell 2017; 29:510-522. [PMID: 29237820 PMCID: PMC6014174 DOI: 10.1091/mbc.e17-09-0553] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 12/22/2022] Open
Abstract
TORC1 modulates proteosynthesis, nitrogen metabolism, stress responses, and autophagy. Here it is shown that the Sch9 branch of TORC1 signaling depends specifically on vacuolar membranes and that this specificity allows the cells to regulate selectively the outputs of divergent downstream pathways in response to oxidative stress. Target of rapamycin complex 1 (TORC1) is a central cellular signaling coordinator that allows eukaryotic cells to adapt to the environment. In the budding yeast, Saccharomyces cerevisiae, TORC1 senses nitrogen and various stressors and modulates proteosynthesis, nitrogen uptake and metabolism, stress responses, and autophagy. There is some indication that TORC1 may regulate these downstream pathways individually. However, the potential mechanisms for such differential regulation are unknown. Here we show that the serine/threonine protein kinase Sch9 branch of TORC1 signaling depends specifically on the integrity of the vacuolar membrane, and this dependency originates in changes in Sch9 localization reflected by phosphatidylinositol 3,5-bisphosphate. Moreover, oxidative stress induces the delocalization of Sch9 from vacuoles, contributing to the persistent inhibition of the Sch9 branch after stress. Thus, our results establish that regulation of the vacuolar localization of Sch9 serves as a selective switch for the Sch9 branch in divergent TORC1 signaling. We propose that the Sch9 branch integrates the intrinsic activity of TORC1 kinase and vacuolar status, which is monitored by the phospholipids of the vacuolar membrane, into the regulation of macromolecular synthesis.
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Affiliation(s)
- Eigo Takeda
- Department of Nanobiology, Graduate School of Advanced Integration Science
| | | | - Eisuke Itakura
- Department of Nanobiology, Graduate School of Advanced Integration Science.,Molecular Chirality Research Center, Chiba University, Inage-ku, Chiba, 263-8522, Japan
| | - Shintaro Kira
- Department of Biology, Graduate School of Science, Chiba University, Inage-ku, Chiba, 263-8522, Japan
| | - Yoshiaki Kamada
- Laboratory of Biological Diversity, National Institute for Basic Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Lois S Weisman
- Life Sciences Institute and.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Takeshi Noda
- Center for Frontier Oral Science, Graduate School of Dentistry, and.,Graduate School of Frontier BioSciences, Osaka University, Osaka 565-0871, Japan
| | - Akira Matsuura
- Department of Nanobiology, Graduate School of Advanced Integration Science .,Life Sciences Institute and.,Molecular Chirality Research Center, Chiba University, Inage-ku, Chiba, 263-8522, Japan
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48
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Varlakhanova NV, Mihalevic MJ, Bernstein KA, Ford MGJ. Pib2 and the EGO complex are both required for activation of TORC1. J Cell Sci 2017; 130:3878-3890. [PMID: 28993463 DOI: 10.1242/jcs.207910] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/03/2017] [Indexed: 01/12/2023] Open
Abstract
The TORC1 complex is a key regulator of cell growth and metabolism in Saccharomyces cerevisiae The vacuole-associated EGO complex couples activation of TORC1 to the availability of amino acids, specifically glutamine and leucine. The EGO complex is also essential for reactivation of TORC1 following rapamycin-induced growth arrest and for its distribution on the vacuolar membrane. Pib2, a FYVE-containing phosphatidylinositol 3-phosphate (PI3P)-binding protein, is a newly discovered and poorly characterized activator of TORC1. Here, we show that Pib2 is required for reactivation of TORC1 following rapamycin-induced growth arrest. Pib2 is required for EGO complex-mediated activation of TORC1 by glutamine and leucine as well as for redistribution of Tor1 on the vacuolar membrane. Therefore, Pib2 and the EGO complex cooperate to activate TORC1 and connect phosphoinositide 3-kinase (PI3K) signaling and TORC1 activity.
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Affiliation(s)
- Natalia V Varlakhanova
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, 3500 Terrace Street, Pittsburgh, PA 15261, USA
| | - Michael J Mihalevic
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Marijn G J Ford
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, 3500 Terrace Street, Pittsburgh, PA 15261, USA
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49
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Nguyen TP, Frank AR, Jewell JL. Amino acid and small GTPase regulation of mTORC1. CELLULAR LOGISTICS 2017; 7:e1378794. [PMID: 29296509 PMCID: PMC5739091 DOI: 10.1080/21592799.2017.1378794] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 11/03/2022]
Abstract
The mammalian target of rapamycin (mTOR) is an evolutionarily conserved serine/threonine kinase that belongs to the phosphatidylinositol 3-kinase-related kinase (PIKK) family. mTOR is the catalytic subunit of mTOR complex 1 (mTORC1), which integrates multiple environmental signals to control cell growth and metabolism. Nutrients, specifically amino acids, are the most potent stimuli for mTORC1 activation. Multiple studies have focused on how leucine and arginine activate mTORC1 through the Rag GTPases, with mechanistic details slowly emerging. Recently, a Rag GTPase-independent glutamine signaling pathway to mTORC1 has been identified, suggesting that mTORC1 is differentially regulated through distinct pathways by specific amino acids. In this review, we summarize our current understanding of how amino acids modulate mTORC1, and the role of other small GTPases in the regulation of mTORC1 activity.
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Affiliation(s)
- Thu P Nguyen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Anderson R Frank
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Jenna L Jewell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX USA
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50
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The Architecture of the Rag GTPase Signaling Network. Biomolecules 2017; 7:biom7030048. [PMID: 28788436 PMCID: PMC5618229 DOI: 10.3390/biom7030048] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022] Open
Abstract
The evolutionarily conserved target of rapamycin complex 1 (TORC1) couples an array of intra- and extracellular stimuli to cell growth, proliferation and metabolism, and its deregulation is associated with various human pathologies such as immunodeficiency, epilepsy, and cancer. Among the diverse stimuli impinging on TORC1, amino acids represent essential input signals, but how they control TORC1 has long remained a mystery. The recent discovery of the Rag GTPases, which assemble as heterodimeric complexes on vacuolar/lysosomal membranes, as central elements of an amino acid signaling network upstream of TORC1 in yeast, flies, and mammalian cells represented a breakthrough in this field. Here, we review the architecture of the Rag GTPase signaling network with a special focus on structural aspects of the Rag GTPases and their regulators in yeast and highlight both the evolutionary conservation and divergence of the mechanisms that control Rag GTPases.
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