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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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Klössel S, Zhu Y, Amado L, Bisinski DD, Ruta J, Liu F, González Montoro A. Yeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase. EMBO J 2024; 43:1870-1897. [PMID: 38589611 PMCID: PMC11066047 DOI: 10.1038/s44318-024-00097-2] [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: 01/18/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 04/10/2024] Open
Abstract
Yeast vacuoles perform crucial cellular functions as acidic degradative organelles, storage compartments, and signaling hubs. These functions are mediated by important protein complexes, including the vacuolar-type H+-ATPase (V-ATPase), responsible for organelle acidification. To gain a more detailed understanding of vacuole function, we performed cross-linking mass spectrometry on isolated vacuoles, detecting many known as well as novel protein-protein interactions. Among these, we identified the uncharacterized TLDc-domain-containing protein Rtc5 as a novel interactor of the V-ATPase. We further analyzed the influence of Rtc5 and of Oxr1, the only other yeast TLDc-domain-containing protein, on V-ATPase function. We find that both Rtc5 and Oxr1 promote the disassembly of the vacuolar V-ATPase in vivo, counteracting the role of the RAVE complex, a V-ATPase assembly chaperone. Furthermore, Oxr1 is necessary for the retention of a Golgi-specific subunit of the V-ATPase in this compartment. Collectively, our results shed light on the in vivo roles of yeast TLDc-domain proteins as regulators of the V-ATPase, highlighting the multifaceted regulation of this crucial protein complex.
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Affiliation(s)
- Samira Klössel
- Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Ying Zhu
- Department of Structural Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin, 13125, Germany
| | - Lucia Amado
- Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Daniel D Bisinski
- Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Julia Ruta
- Department of Structural Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin, 13125, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin, 13125, Germany
- Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117, Berlin, Germany
| | - Ayelén González Montoro
- Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076, Osnabrück, Germany.
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076, Osnabrück, Germany.
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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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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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Attfield PV. Crucial aspects of metabolism and cell biology relating to industrial production and processing of Saccharomyces biomass. Crit Rev Biotechnol 2023; 43:920-937. [PMID: 35731243 DOI: 10.1080/07388551.2022.2072268] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
The multitude of applications to which Saccharomyces spp. are put makes these yeasts the most prolific of industrial microorganisms. This review considers biological aspects pertaining to the manufacture of industrial yeast biomass. It is proposed that the production of yeast biomass can be considered in two distinct but interdependent phases. Firstly, there is a cell replication phase that involves reproduction of cells by their transitions through multiple budding and metabolic cycles. Secondly, there needs to be a cell conditioning phase that enables the accrued biomass to withstand the physicochemical challenges associated with downstream processing and storage. The production of yeast biomass is not simply a case of providing sugar, nutrients, and other growth conditions to enable multiple budding cycles to occur. In the latter stages of culturing, it is important that all cells are induced to complete their current budding cycle and subsequently enter into a quiescent state engendering robustness. Both the cell replication and conditioning phases need to be optimized and considered in concert to ensure good biomass production economics, and optimum performance of industrial yeasts in food and fermentation applications. Key features of metabolism and cell biology affecting replication and conditioning of industrial Saccharomyces are presented. Alternatives for growth substrates are discussed, along with the challenges and prospects associated with defining the genetic bases of industrially important phenotypes, and the generation of new yeast strains."I must be cruel only to be kind: Thus bad begins, and worse remains behind." William Shakespeare: Hamlet, Act 3, Scene 4.
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Druseikis M, Mottola A, Berman J. The Metabolism of Susceptibility: Clearing the FoG Between Tolerance and Resistance in Candida albicans. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023; 10:36-46. [DOI: 10.1007/s40588-023-00189-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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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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The NPR/Hal family of protein kinases in yeasts: biological role, phylogeny and regulation under environmental challenges. Comput Struct Biotechnol J 2022; 20:5698-5712. [PMID: 36320937 PMCID: PMC9596735 DOI: 10.1016/j.csbj.2022.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 11/30/2022] Open
Abstract
Protein phosphorylation is the most common and versatile post-translational modification occurring in eukaryotes. In yeast, protein phosphorylation is fundamental for maintaining cell growth and adapting to sudden changes in environmental conditions by regulating cellular processes and activating signal transduction pathways. Protein kinases catalyze the reversible addition of phosphate groups to target proteins, thereby regulating their activity. In Saccharomyces cerevisiae, kinases are classified into six major groups based on structural and functional similarities. The NPR/Hal family of kinases comprises nine fungal-specific kinases that, due to lack of similarity with the remaining kinases, were classified to the “Other” group. These kinases are primarily implicated in regulating fundamental cellular processes such as maintaining ion homeostasis and controlling nutrient transporters’ concentration at the plasma membrane. Despite their biological relevance, these kinases remain poorly characterized and explored. This review provides an overview of the information available regarding each of the kinases from the NPR/Hal family, including their known biological functions, mechanisms of regulation, and integration in signaling pathways in S. cerevisiae. Information gathered for non-Saccharomyces species of biotechnological or clinical relevance is also included.
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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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