1
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Masanta S, Wiesyk A, Panja C, Pilch S, Ciesla J, Sipko M, De A, Enkhbaatar T, Maslanka R, Skoneczna A, Kucharczyk R. Fmp40 ampylase regulates cell survival upon oxidative stress by controlling Prx1 and Trx3 oxidation. Redox Biol 2024; 73:103201. [PMID: 38795545 PMCID: PMC11140801 DOI: 10.1016/j.redox.2024.103201] [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: 04/21/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024] Open
Abstract
Reactive oxygen species (ROS), play important roles in cellular signaling, nonetheless are toxic at higher concentrations. Cells have many interconnected, overlapped or backup systems to neutralize ROS, but their regulatory mechanisms remain poorly understood. Here, we reveal an essential role for mitochondrial AMPylase Fmp40 from budding yeast in regulating the redox states of the mitochondrial 1-Cys peroxiredoxin Prx1, which is the only protein shown to neutralize H2O2 with the oxidation of the mitochondrial glutathione and the thioredoxin Trx3, directly involved in the reduction of Prx1. Deletion of FMP40 impacts a cellular response to H2O2 treatment that leads to programmed cell death (PCD) induction and an adaptive response involving up or down regulation of genes encoding, among others the catalase Cta1, PCD inducing factor Aif1, and mitochondrial redoxins Trx3 and Grx2. This ultimately perturbs the reduced glutathione and NADPH cellular pools. We further demonstrated that Fmp40 AMPylates Prx1, Trx3, and Grx2 in vitro and interacts with Trx3 in vivo. AMPylation of the threonine residue 66 in Trx3 is essential for this protein's proper endogenous level and its precursor forms' maturation under oxidative stress conditions. Additionally, we showed the Grx2 involvement in the reduction of Trx3 in vivo. Taken together, Fmp40, through control of the reduction of mitochondrial redoxins, regulates the hydrogen peroxide, GSH and NADPH signaling influencing the yeast cell survival.
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Affiliation(s)
- Suchismita Masanta
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Aneta Wiesyk
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Chiranjit Panja
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Sylwia Pilch
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Jaroslaw Ciesla
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Marta Sipko
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Abhipsita De
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Roman Maslanka
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland.
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2
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Wettstein R, Hugener J, Gillet L, Hernández-Armenta Y, Henggeler A, Xu J, van Gerwen J, Wollweber F, Arter M, Aebersold R, Beltrao P, Pilhofer M, Matos J. Waves of regulated protein expression and phosphorylation rewire the proteome to drive gametogenesis in budding yeast. Dev Cell 2024:S1534-5807(24)00343-5. [PMID: 38906138 DOI: 10.1016/j.devcel.2024.05.025] [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: 09/24/2023] [Revised: 02/25/2024] [Accepted: 05/20/2024] [Indexed: 06/23/2024]
Abstract
Sexually reproducing eukaryotes employ a developmentally regulated cell division program-meiosis-to generate haploid gametes from diploid germ cells. To understand how gametes arise, we generated a proteomic census encompassing the entire meiotic program of budding yeast. We found that concerted waves of protein expression and phosphorylation modify nearly all cellular pathways to support meiotic entry, meiotic progression, and gamete morphogenesis. Leveraging this comprehensive resource, we pinpointed dynamic changes in mitochondrial components and showed that phosphorylation of the FoF1-ATP synthase complex is required for efficient gametogenesis. Furthermore, using cryoET as an orthogonal approach to visualize mitochondria, we uncovered highly ordered filament arrays of Ald4ALDH2, a conserved aldehyde dehydrogenase that is highly expressed and phosphorylated during meiosis. Notably, phosphorylation-resistant mutants failed to accumulate filaments, suggesting that phosphorylation regulates context-specific Ald4ALDH2 polymerization. Overall, this proteomic census constitutes a broad resource to guide the exploration of the unique sequence of events underpinning gametogenesis.
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Affiliation(s)
- Rahel Wettstein
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Jannik Hugener
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Ludovic Gillet
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Yi Hernández-Armenta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Adrian Henggeler
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Jingwei Xu
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Julian van Gerwen
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Florian Wollweber
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Meret Arter
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
| | - Joao Matos
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland.
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3
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Li BZ, Kolodner RD, Putnam CD. Identification of different classes of genome instability suppressor genes through analysis of DNA damage response markers. G3 (BETHESDA, MD.) 2024; 14:jkae064. [PMID: 38526099 PMCID: PMC11152081 DOI: 10.1093/g3journal/jkae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024]
Abstract
Cellular pathways that detect DNA damage are useful for identifying genes that suppress DNA damage, which can cause genome instability and cancer predisposition syndromes when mutated. We identified 199 high-confidence and 530 low-confidence DNA damage-suppressing (DDS) genes in Saccharomyces cerevisiae through a whole-genome screen for mutations inducing Hug1 expression, a focused screen for mutations inducing Ddc2 foci, and data from previous screens for mutations causing Rad52 foci accumulation and Rnr3 induction. We also identified 286 high-confidence and 394 low-confidence diverse genome instability-suppressing (DGIS) genes through a whole-genome screen for mutations resulting in increased gross chromosomal rearrangements and data from previous screens for mutations causing increased genome instability as assessed in a diversity of genome instability assays. Genes that suppress both pathways (DDS+ DGIS+) prevent or repair DNA replication damage and likely include genes preventing collisions between the replication and transcription machineries. DDS+ DGIS- genes, including many transcription-related genes, likely suppress damage that is normally repaired properly or prevent inappropriate signaling, whereas DDS- DGIS+ genes, like PIF1, do not suppress damage but likely promote its proper, nonmutagenic repair. Thus, induction of DNA damage markers is not a reliable indicator of increased genome instability, and the DDS and DGIS categories define mechanistically distinct groups of genes.
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Affiliation(s)
- Bin-Zhong Li
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093-0669, USA
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093-0669, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0669, USA
- Moores-UCSD Cancer Center, University of California San Diego, La Jolla, CA 92093-0669, USA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093-0669, USA
| | - Christopher D Putnam
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093-0669, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92093-0669, USA
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4
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Xiao J, Turner JJ, Kõivomägi M, Skotheim JM. Whi5 hypo- and hyper-phosphorylation dynamics control cell-cycle entry and progression. Curr Biol 2024; 34:2434-2447.e5. [PMID: 38749424 DOI: 10.1016/j.cub.2024.04.052] [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: 09/13/2023] [Revised: 03/18/2024] [Accepted: 04/23/2024] [Indexed: 05/28/2024]
Abstract
Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the Swi4/Swi6 (SBF) complex that promotes transcription of the cyclins CLN1 and CLN2. In late G1, Whi5 is rapidly hyper-phosphorylated by Cln1 and Cln2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5's multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on "priming" sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.
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Affiliation(s)
- Jordan Xiao
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA
| | - Jonathan J Turner
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA
| | - Mardo Kõivomägi
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA; Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD 20892, USA.
| | - Jan M Skotheim
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA; Chan Zuckerberg Biohub, 499 Illinois St., San Francisco, CA 94158, USA.
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5
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Zbieralski K, Staszewski J, Konczak J, Lazarewicz N, Nowicka-Kazmierczak M, Wawrzycka D, Maciaszczyk-Dziubinska E. Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast. Int J Mol Sci 2024; 25:4450. [PMID: 38674035 PMCID: PMC11050377 DOI: 10.3390/ijms25084450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
In the face of flourishing industrialization and global trade, heavy metal and metalloid contamination of the environment is a growing concern throughout the world. The widespread presence of highly toxic compounds of arsenic, antimony, and cadmium in nature poses a particular threat to human health. Prolonged exposure to these toxins has been associated with severe human diseases, including cancer, diabetes, and neurodegenerative disorders. These toxins are known to induce analogous cellular stresses, such as DNA damage, disturbance of redox homeostasis, and proteotoxicity. To overcome these threats and improve or devise treatment methods, it is crucial to understand the mechanisms of cellular detoxification in metal and metalloid stress. Membrane proteins are key cellular components involved in the uptake, vacuolar/lysosomal sequestration, and efflux of these compounds; thus, deciphering the multilevel regulation of these proteins is of the utmost importance. In this review, we summarize data on the mechanisms of arsenic, antimony, and cadmium detoxification in the context of membrane proteome. We used yeast Saccharomyces cerevisiae as a eukaryotic model to elucidate the complex mechanisms of the production, regulation, and degradation of selected membrane transporters under metal(loid)-induced stress conditions. Additionally, we present data on orthologues membrane proteins involved in metal(loid)-associated diseases in humans.
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Affiliation(s)
| | | | | | | | | | | | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland; (K.Z.); (J.S.); (J.K.); (N.L.); (M.N.-K.); (D.W.)
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6
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Fan J, Dhingra N, Yang T, Yang V, Zhao X. Srs2 binding to PCNA and its sumoylation contribute to RPA antagonism during the DNA damage response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587206. [PMID: 38586001 PMCID: PMC10996639 DOI: 10.1101/2024.03.28.587206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Activation of the DNA damage checkpoint upon genotoxin treatment induces a multitude of cellular changes, such as cell cycle arrest, to cope with genome stress. After prolonged genotoxin treatment, the checkpoint can be downregulated to allow cell cycle and growth resumption. In yeast, downregulation of the DNA damage checkpoint requires the Srs2 DNA helicase, which removes the ssDNA binding complex RPA and the associated Mec1 checkpoint kinase from DNA, thus dampening Mec1 activation. However, it is unclear whether the 'anti-checkpoint' role of Srs2 is temporally and spatially regulated to both allow timely checkpoint termination and to prevent superfluous RPA removal. Here we address this question by examining regulatory elements of Srs2, including its phosphorylation, sumoylation, and protein-interaction sites. Our genetic analyses and checkpoint level assessment suggest that the RPA countering role of Srs2 is promoted by Srs2 binding to PCNA, which is known to recruit Srs2 to subsets of ssDNA regions. RPA antagonism is further fostered by Srs2 sumoylation, which we found depends on the Srs2-PCNA interaction. Srs2 sumoylation is additionally reliant on Mec1 and peaks after Mec1 activity reaches maximal levels. Collectively, our data provide evidence for a two-step model wherein checkpoint downregulation is facilitated by PCNA-mediated Srs2 recruitment to ssDNA-RPA filaments and the subsequent Srs2 sumoylation stimulated upon Mec1 hyperactivation. We propose that this mechanism allows Mec1 hyperactivation to trigger checkpoint recovery.
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Affiliation(s)
- Jiayi Fan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Nalini Dhingra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Tammy Yang
- City University of New York Hunter College, New York, NY 10065
| | - Vicki Yang
- City University of New York Hunter College, New York, NY 10065
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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7
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Galanti L, Peritore M, Gnügge R, Cannavo E, Heipke J, Palumbieri MD, Steigenberger B, Symington LS, Cejka P, Pfander B. Dbf4-dependent kinase promotes cell cycle controlled resection of DNA double-strand breaks and repair by homologous recombination. Nat Commun 2024; 15:2890. [PMID: 38570537 PMCID: PMC10991553 DOI: 10.1038/s41467-024-46951-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired by several pathways. In eukaryotes, DSB repair pathway choice occurs at the level of DNA end resection and is controlled by the cell cycle. Upon cell cycle-dependent activation, cyclin-dependent kinases (CDKs) phosphorylate resection proteins and thereby stimulate end resection and repair by homologous recombination (HR). However, inability of CDK phospho-mimetic mutants to bypass this cell cycle regulation, suggests that additional cell cycle regulators may be important. Here, we identify Dbf4-dependent kinase (DDK) as a second major cell cycle regulator of DNA end resection. Using inducible genetic and chemical inhibition of DDK in budding yeast and human cells, we show that end resection and HR require activation by DDK. Mechanistically, DDK phosphorylates at least two resection nucleases in budding yeast: the Mre11 activator Sae2, which promotes resection initiation, as well as the Dna2 nuclease, which promotes resection elongation. Notably, synthetic activation of DDK allows limited resection and HR in G1 cells, suggesting that DDK is a key component of DSB repair pathway selection.
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Affiliation(s)
- Lorenzo Galanti
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Martina Peritore
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Robert Gnügge
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Elda Cannavo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Johannes Heipke
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Maria Dilia Palumbieri
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- Research Group of Proteomics and ADP-Ribosylation Signaling, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Boris Pfander
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany.
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany.
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8
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Diep DTV, Collado J, Hugenroth M, Fausten RM, Percifull L, Wälte M, Schuberth C, Schmidt O, Fernández-Busnadiego R, Bohnert M. A metabolically controlled contact site between vacuoles and lipid droplets in yeast. Dev Cell 2024; 59:740-758.e10. [PMID: 38367622 DOI: 10.1016/j.devcel.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/17/2023] [Accepted: 01/18/2024] [Indexed: 02/19/2024]
Abstract
The lipid droplet (LD) organization proteins Ldo16 and Ldo45 affect multiple aspects of LD biology in yeast. They are linked to the LD biogenesis machinery seipin, and their loss causes defects in LD positioning, protein targeting, and breakdown. However, their molecular roles remained enigmatic. Here, we report that Ldo16/45 form a tether complex with Vac8 to create vacuole lipid droplet (vCLIP) contact sites, which can form in the absence of seipin. The phosphatidylinositol transfer protein (PITP) Pdr16 is a further vCLIP-resident recruited specifically by Ldo45. While only an LD subpopulation is engaged in vCLIPs at glucose-replete conditions, nutrient deprivation results in vCLIP expansion, and vCLIP defects impair lipophagy upon prolonged starvation. In summary, Ldo16/45 are multifunctional proteins that control the formation of a metabolically regulated contact site. Our studies suggest a link between LD biogenesis and breakdown and contribute to a deeper understanding of how lipid homeostasis is maintained during metabolic challenges.
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Affiliation(s)
- Duy Trong Vien Diep
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Javier Collado
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Marie Hugenroth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Rebecca Martina Fausten
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Louis Percifull
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Mike Wälte
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany
| | - Christian Schuberth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter Innsbruck, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rubén Fernández-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany; Cluster of Excellence "Multiscale Imaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Faculty of Physics, University of Göttingen, Göttingen 37077, Germany
| | - Maria Bohnert
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany.
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9
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Litsios A, Grys BT, Kraus OZ, Friesen H, Ross C, Masinas MPD, Forster DT, Couvillion MT, Timmermann S, Billmann M, Myers C, Johnsson N, Churchman LS, Boone C, Andrews BJ. Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle. Cell 2024; 187:1490-1507.e21. [PMID: 38452761 PMCID: PMC10947830 DOI: 10.1016/j.cell.2024.02.014] [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: 09/12/2023] [Revised: 12/01/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024]
Abstract
Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ∼20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control and changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level.
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Affiliation(s)
- Athanasios Litsios
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Benjamin T Grys
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Oren Z Kraus
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Helena Friesen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Catherine Ross
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Myra Paz David Masinas
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Duncan T Forster
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mary T Couvillion
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stefanie Timmermann
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm 89081, Germany
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Chad Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nils Johnsson
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm 89081, Germany
| | | | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; RIKEN Center for Sustainable Resource Science, Wako 351-0198 Saitama, Japan.
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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10
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Sousa AD, Costa AL, Costa V, Pereira C. Prediction and biological analysis of yeast VDAC1 phosphorylation. Arch Biochem Biophys 2024; 753:109914. [PMID: 38290597 DOI: 10.1016/j.abb.2024.109914] [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: 10/30/2023] [Revised: 01/02/2024] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
The mitochondrial outer membrane protein porin 1 (Por1), the yeast orthologue of mammalian voltage-dependent anion channel (VDAC), is the major permeability pathway for the flux of metabolites and ions between cytosol and mitochondria. In yeast, several Por1 phosphorylation sites have been identified. Protein phosphorylation is a major modification regulating a variety of biological activities, but the potential biological roles of Por1 phosphorylation remains unaddressed. In this work, we analysed 10 experimentally observed phosphorylation sites in yeast Por1 using bioinformatics tools. Two of the residues, T100 and S133, predicted to reduce and increase pore permeability, respectively, were validated using biological assays. In accordance, Por1T100D reduced mitochondrial respiration, while Por1S133E phosphomimetic mutant increased it. Por1T100A expression also improved respiratory growth, while Por1S133A caused defects in all growth conditions tested, notably in fermenting media. In conclusion, we found phosphorylation has the potential to modulate Por1, causing a marked effect on mitochondrial function. It can also impact on cell morphology and growth both in respiratory and, unpredictably, also in fermenting conditions, expanding our knowledge on the role of Por1 in cell physiology.
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Affiliation(s)
- André D Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal
| | - Ana Luisa Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal
| | - Vítor Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Clara Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal.
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11
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Jiang L, Li Y, Gu Y, Zheng J, Wei L, Wei M, Zou J, Wei C, Mo B, Pan L, Zhao L, Wang D. Identification of the Beta Subunit Fas1p of Fatty Acid Synthetase as an Interacting Partner of Yeast Calcium/Calmodulin-Dependent Protein Kinase Cmk2p Through Mass Spectrometry Analysis. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04891-w. [PMID: 38411936 DOI: 10.1007/s12010-024-04891-w] [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] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
The calcium/calmodulin-dependent protein kinase II (CaMKII) is a mediator of calcium signals and regulates fatty acid metabolism in mammalian cells. Cmk2p is a yeast homolog of CaMKII and functions as a negative regulator of calcium signaling. However, its substrates remain to be identified. Combination of immunoprecipitation (IP) and mass spectrometry has been proven to be very useful for identification of interacting partner proteins and interactome. In this study, through these approaches, we have identified 65 and 110 potential Cmk2p-interacting proteins in yeast cells in the absence or presence of calcium stress, respectively. In yeast cells expressing both CMK2-HA and FAS1-GFP fusion proteins, in the absence or presence of calcium stress, less amounts of FAS1-GFP proteins are present in cell lysates after IP with anti-HA antibody than cell lysates before IP, while FAS1-GFP proteins are detected on both types of IP beads. However, as an internal control, similar amounts of Pgk1p proteins were detected in both after-IP and before-IP cell lysates but not on the IP beads. Therefore, our biochemical analysis demonstrates that the β subunit Fas1p of fatty acid synthetase interacts with Cmk2p in yeast cells independent of calcium stress. It is also interesting to note that, in addition to the expected 52-kDa CMK2-HA band, a faster-moving 48-kDa CMK2-HA band is present in the calcium-stressed cell lysate but not in the cell lysate without calcium stress. Our data would provide important clues for understanding the functions of CaMKII in the regulation of fatty acid metabolism as well as related diseases such as cancers, diabetes, and obesity.
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Affiliation(s)
- Linghuo Jiang
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China.
| | - Yiwu Li
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Yiying Gu
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China
| | - Jiashi Zheng
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Liudan Wei
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China
| | - Min Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Jie Zou
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Chunyu Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Bei Mo
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Lingxin Pan
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Lijiao Zhao
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Dan Wang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
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12
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Sunder S, Bauman JS, Decker SJ, Lifton AR, Kumar A. The yeast AMP-activated protein kinase Snf1 phosphorylates the inositol polyphosphate kinase Kcs1. J Biol Chem 2024; 300:105657. [PMID: 38224949 PMCID: PMC10851228 DOI: 10.1016/j.jbc.2024.105657] [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: 11/03/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
The yeast Snf1/AMP-activated kinase (AMPK) maintains energy homeostasis, controlling metabolic processes and glucose derepression in response to nutrient levels and environmental cues. Under conditions of nitrogen or glucose limitation, Snf1 regulates pseudohyphal growth, a morphological transition characterized by the formation of extended multicellular filaments. During pseudohyphal growth, Snf1 is required for wild-type levels of inositol polyphosphate (InsP), soluble phosphorylated species of the six-carbon cyclitol inositol that function as conserved metabolic second messengers. InsP levels are established through the activity of a family of inositol kinases, including the yeast inositol polyphosphate kinase Kcs1, which principally generates pyrophosphorylated InsP7. Here, we report that Snf1 regulates Kcs1, affecting Kcs1 phosphorylation and inositol kinase activity. A snf1 kinase-defective mutant exhibits decreased Kcs1 phosphorylation, and Kcs1 is phosphorylated in vivo at Ser residues 537 and 646 during pseudohyphal growth. By in vitro analysis, Snf1 directly phosphorylates Kcs1, predominantly at amino acids 537 and 646. A yeast strain carrying kcs1 encoding Ser-to-Ala point mutations at these residues (kcs1-S537A,S646A) shows elevated levels of pyrophosphorylated InsP7, comparable to InsP7 levels observed upon deletion of SNF1. The kcs1-S537A,S646A mutant exhibits decreased pseudohyphal growth, invasive growth, and cell elongation. Transcriptional profiling indicates extensive perturbation of metabolic pathways in kcs1-S537A,S646A. Growth of kcs1-S537A,S646A is affected on medium containing sucrose and antimycin A, consistent with decreased Snf1p signaling. This work identifies Snf1 phosphorylation of Kcs1, collectively highlighting the interconnectedness of AMPK activity and InsP signaling in coordinating nutrient availability, energy homoeostasis, and cell growth.
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Affiliation(s)
- Sham Sunder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Joshua S Bauman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stuart J Decker
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandra R Lifton
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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13
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Ros-Carrero C, Spiridon-Bodi M, Igual JC, Gomar-Alba M. The CDK Pho85 inhibits Whi7 Start repressor to promote cell cycle entry in budding yeast. EMBO Rep 2024; 25:745-769. [PMID: 38233717 PMCID: PMC10897450 DOI: 10.1038/s44319-023-00049-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/19/2024] Open
Abstract
Pho85 is a multifunctional CDK that signals to the cell when environmental conditions are favorable. It has been connected to cell cycle control, mainly in Start where it promotes the G1/S transition. Here we describe that the Start repressor Whi7 is a key target of Pho85 in the regulation of cell cycle entry. The phosphorylation of Whi7 by Pho85 inhibits the repressor and explains most of the contribution of the CDK in the activation of Start. Mechanistically, Pho85 downregulates Whi7 protein levels through the control of Whi7 protein stability and WHI7 gene transcription. Whi7 phosphorylation by Pho85 also restrains the intrinsic ability of Whi7 to associate with promoters. Furthermore, although Whi5 is the main Start repressor in normal cycling cells, in the absence of Pho85, Whi7 becomes the major repressor leading to G1 arrest. Overall, our results reveal a novel mechanism by which Pho85 promotes Start through the regulation of the Whi7 repressor at multiple levels, which may confer to Whi7 a functional specialization to connect the response to adverse conditions with the cell cycle control.
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Affiliation(s)
- Cristina Ros-Carrero
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100, Burjassot, Spain
| | - Mihai Spiridon-Bodi
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100, Burjassot, Spain
| | - J Carlos Igual
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100, Burjassot, Spain.
| | - Mercè Gomar-Alba
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100, Burjassot, Spain.
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14
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Banerjee R, Mukherjee A, Adhikary A, Sharma S, Hussain MS, Ali ME, Nagotu S. Insights into the role of the conserved GTPase domain residues T62 and S277 in yeast Dnm1. Int J Biol Macromol 2023; 253:127381. [PMID: 37838106 DOI: 10.1016/j.ijbiomac.2023.127381] [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: 06/08/2023] [Revised: 09/10/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
Mitochondrial division is a highly regulated process. The master regulator of this process is the multi-domain, conserved protein called Dnm1 in yeast. In this study, we systematically analyzed two residues, T62 and S277, reported to be putatively phosphorylated in the GTPase domain of the protein. These residues lie in the G2 and G5 motifs of the GTPase domain. Both residues are important for the function of the protein, as evident from in vivo and in vitro analysis of the non-phosphorylatable and phosphomimetic variants. Dnm1T62A/D and Dnm1S277A/D showed differences with respect to the protein localization and puncta dynamics in vivo, albeit both were non-functional as assessed by mitochondrial morphology and GTPase activity. Overall, the secondary structure of the protein variants was unaltered, but local conformational changes were observed. Interestingly, both Dnm1T62A/D and Dnm1S277A/D exhibited dominant-negative behavior when expressed in cells containing endogenous Dnm1. To our knowledge, we report for the first time a single residue (S277) change that does not alter the localization of Dnm1 but makes it non-functional in a dominant-negative manner. Intriguingly, the two residues analyzed in this study are present in the same domain but exhibit variable effects when mutated to alanine or aspartic acid.
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Affiliation(s)
- Riddhi Banerjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Agradeep Mukherjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ankita Adhikary
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shikha Sharma
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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15
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Blank HM, Griffith WP, Polymenis M. Targeting APEX2 to the mRNA encoding fatty acid synthase β in yeast identifies interacting proteins that control its abundance in the cell cycle. Mol Biol Cell 2023; 34:br20. [PMID: 37792491 PMCID: PMC10848943 DOI: 10.1091/mbc.e23-05-0166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/06/2023] Open
Abstract
Profiling the repertoire of proteins associated with a given mRNA during the cell cycle is unstudied. Furthermore, it is easier to ask and answer what mRNAs a specific protein might bind to than the other way around. Here, we implemented an RNA-centric proximity labeling technology at different points in the cell cycle in highly synchronous yeast cultures. To understand how the abundance of FAS1, encoding fatty acid synthase, peaks late in the cell cycle, we identified proteins that interact with the FAS1 transcript in a cell cycle-dependent manner. We used dCas13d-APEX2 fusions to target FAS1 and label nearby proteins, which were then identified by mass spectrometry. The glycolytic enzyme Tdh3p, a known RNA-binding protein, interacted with the FAS1 mRNA, and it was necessary for the periodic abundance of Fas1p in the cell cycle. These results point to unexpected connections between major metabolic pathways. They also underscore the role of mRNA-protein interactions for gene expression during cell division.
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Affiliation(s)
- Heidi M. Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Wendell P. Griffith
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
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16
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Hu J, Ferlez B, Dau J, Crickard JB. Rad53 regulates the lifetime of Rdh54 at homologous recombination intermediates. Nucleic Acids Res 2023; 51:11688-11705. [PMID: 37850655 PMCID: PMC10681728 DOI: 10.1093/nar/gkad848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023] Open
Abstract
Rdh54 is a conserved DNA translocase that participates in homologous recombination (HR), DNA checkpoint adaptation, and chromosome segregation. Saccharomyces cerevisiae Rdh54 is a known target of the Mec1/Rad53 signaling axis, which globally protects genome integrity during DNA metabolism. While phosphorylation of DNA repair proteins by Mec1/Rad53 is critical for HR progression little is known about how specific post translational modifications alter HR reactions. Phosphorylation of Rdh54 is linked to protection of genomic integrity but the consequences of modification remain poorly understood. Here, we demonstrate that phosphorylation of the Rdh54 C-terminus by the effector kinase Rad53 regulates Rdh54 clustering activity as revealed by single molecule imaging. This stems from phosphorylation dependent and independent interactions between Rdh54 and Rad53. Genetic assays reveal that loss of phosphorylation leads to phenotypic changes resulting in loss-of-heterozygosity (LOH) outcomes. Our data highlight Rad53 as a key regulator of HR intermediates through activation and attenuation of Rdh54 motor function.
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Affiliation(s)
- Jingyi Hu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bryan Ferlez
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer Dau
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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17
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Xiao J, Turner JJ, Kõivomägi M, Skotheim JM. Whi5 hypo- and hyper-phosphorylation dynamics control cell cycle entry and progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565392. [PMID: 37961465 PMCID: PMC10635099 DOI: 10.1101/2023.11.02.565392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates the G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the SBF complex that promotes transcription of the cyclins CLN1 and CLN2 . In late-G1, Whi5 is rapidly hyper-phosphorylated by Cln1,2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5's multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on 'priming' sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.
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18
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Leutert M, Barente AS, Fukuda NK, Rodriguez-Mias RA, Villén J. The regulatory landscape of the yeast phosphoproteome. Nat Struct Mol Biol 2023; 30:1761-1773. [PMID: 37845410 PMCID: PMC10841839 DOI: 10.1038/s41594-023-01115-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023]
Abstract
The cellular ability to react to environmental fluctuations depends on signaling networks that are controlled by the dynamic activities of kinases and phosphatases. Here, to gain insight into these stress-responsive phosphorylation networks, we generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses in Saccharomyces cerevisiae exposed to 101 environmental and chemical perturbations. We report phosphosites on 59% of the yeast proteome, with 18% of the proteome harboring a phosphosite that is regulated within 5 min of stress exposure. We identify shared and perturbation-specific stress response programs, uncover loss of phosphorylation as an integral early event, and dissect the interconnected regulatory landscape of kinase-substrate networks, as we exemplify with target of rapamycin signaling. We further reveal functional organization principles of the stress-responsive phosphoproteome based on phosphorylation site motifs, kinase activities, subcellular localizations, shared functions and pathway intersections. This information-rich map of 25,000 regulated phosphosites advances our understanding of signaling networks.
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Affiliation(s)
- Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Anthony S Barente
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Noelle K Fukuda
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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19
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Abeliovich H. Mitophagy in yeast: known unknowns and unknown unknowns. Biochem J 2023; 480:1639-1657. [PMID: 37850532 PMCID: PMC10586778 DOI: 10.1042/bcj20230279] [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: 07/12/2023] [Revised: 09/06/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
Mitophagy, the autophagic breakdown of mitochondria, is observed in eukaryotic cells under various different physiological circumstances. These can be broadly categorized into two types: mitophagy related to quality control events and mitophagy induced during developmental transitions. Quality control mitophagy involves the lysosomal or vacuolar degradation of malfunctioning or superfluous mitochondria within lysosomes or vacuoles, and this is thought to serve as a vital maintenance function in respiring eukaryotic cells. It plays a crucial role in maintaining physiological balance, and its disruption has been associated with the progression of late-onset diseases. Developmentally induced mitophagy has been reported in the differentiation of metazoan tissues which undergo metabolic shifts upon developmental transitions, such as in the differentiation of red blood cells and muscle cells. Although the mechanistic studies of mitophagy in mammalian cells were initiated after the initial mechanistic findings in Saccharomyces cerevisiae, our current understanding of the physiological role of mitophagy in yeast remains more limited, despite the presence of better-defined assays and tools. In this review, I present my perspective on our present knowledge of mitophagy in yeast, focusing on physiological and mechanistic aspects. I aim to focus on areas where our understanding is still incomplete, such as the role of mitochondrial dynamics and the phenomenon of protein-level selectivity.
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Affiliation(s)
- Hagai Abeliovich
- Institute of Biochemistry, Food Science and Nutrition, Hebrew University of Jerusalem, 1 Hankin St, Rehovot 7610001, Israel
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20
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Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561337. [PMID: 37873463 PMCID: PMC10592693 DOI: 10.1101/2023.10.08.561337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
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Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
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21
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Ahmadpour D, Kumar N, Fischbach A, Chawla S, Widlund PO, Nyström T. Syntaxin 5-dependent phosphorylation of the small heat shock protein Hsp42 and its role in protein quality control. FEBS J 2023; 290:4744-4761. [PMID: 37306264 DOI: 10.1111/febs.16886] [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: 06/13/2022] [Revised: 05/11/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023]
Abstract
The small heat shock protein Hsp42 and the t-SNARE protein Sed5 have central roles in the sequestration of misfolded proteins into insoluble protein deposits in the yeast Saccharomyces cerevisiae. However, whether these proteins/processes interact in protein quality control (PQC) is not known. Here, we show that Sed5 and anterograde trafficking modulate phosphorylation of Hsp42 partially via the MAPK kinase Hog1. Such phosphorylation, specifically at residue S215, abrogated the co-localization of Hsp42 with the Hsp104 disaggregase, aggregate clearance, chaperone activity, and sequestration of aggregates to IPOD and mitochondria. Furthermore, we found that Hsp42 is hyperphosphorylated in old cells leading to a drastic failure in disaggregation. Old cells also displayed a retarded anterograde trafficking, which, together with slow aggregate clearance and hyperphosphorylation of Hsp42, could be counteracted by Sed5 overproduction. We hypothesize that the breakdown of proper PQC during yeast aging may, in part, be due to a retarded anterograde trafficking leading to hyperphosphorylation of Hsp42.
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Affiliation(s)
- Doryaneh Ahmadpour
- Institute for Biomedicine, Sahlgrenska Academy, Center for Aging and Health-AgeCap, University of Gothenburg, Sweden
- Center for Bionics and Pain Research, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Navinder Kumar
- Institute for Biomedicine, Sahlgrenska Academy, Center for Aging and Health-AgeCap, University of Gothenburg, Sweden
| | - Arthur Fischbach
- Institute for Biomedicine, Sahlgrenska Academy, Center for Aging and Health-AgeCap, University of Gothenburg, Sweden
| | - Srishti Chawla
- Institute for Biomedicine, Sahlgrenska Academy, Center for Aging and Health-AgeCap, University of Gothenburg, Sweden
| | - Per O Widlund
- Institute for Biomedicine, Sahlgrenska Academy, Center for Aging and Health-AgeCap, University of Gothenburg, Sweden
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Center for Aging and Health-AgeCap, University of Gothenburg, Sweden
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22
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Somashekara SC, Dhyani KM, Thakur M, Muniyappa K. SUMOylation of yeast Pso2 enhances its translocation and accumulation in the mitochondria and suppresses methyl methanesulfonate-induced mitochondrial DNA damage. Mol Microbiol 2023; 120:587-607. [PMID: 37649278 DOI: 10.1111/mmi.15145] [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: 03/27/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
Saccharomyces cerevisiae Pso2/SNM1 is essential for DNA interstrand crosslink (ICL) repair; however, its mechanism of action remains incompletely understood. While recent work has revealed that Pso2/Snm1 is dual-localized in the nucleus and mitochondria, it remains unclear whether cell-intrinsic and -extrinsic factors regulate its subcellular localization and function. Herein, we show that Pso2 undergoes ubiquitination and phosphorylation, but not SUMOylation, in unstressed cells. Unexpectedly, we found that methyl methanesulfonate (MMS), rather than ICL-forming agents, induced robust SUMOylation of Pso2 on two conserved residues, K97 and K575, and that SUMOylation markedly increased its abundance in the mitochondria. Reciprocally, SUMOylation had no discernible impact on Pso2 translocation to the nucleus, despite the presence of steady-state levels of SUMOylated Pso2 across the cell cycle. Furthermore, substitution of the invariant residues K97 and K575 by arginine in the Pso2 SUMO consensus motifs severely impaired SUMOylation and abolished its translocation to the mitochondria of MMS-treated wild type cells, but not in unstressed cells. We demonstrate that whilst Siz1 and Siz2 SUMO E3 ligases catalyze Pso2 SUMOylation, the former plays a dominant role. Notably, we found that the phenotypic characteristics of the SUMOylation-defective mutant Pso2K97R/K575R closely mirrored those observed in the Pso2Δ petite mutant. Additionally, leveraging next-generation sequencing analysis, we demonstrate that Pso2 mitigates MMS-induced damage to mitochondrial DNA (mtDNA). Viewed together, our work offers previously unknown insights into the link between genotoxic stress-induced SUMOylation of Pso2 and its preferential targeting to the mitochondria, as well as its role in attenuating MMS-induced mtDNA damage.
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Affiliation(s)
| | - Kshitiza M Dhyani
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Manoj Thakur
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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23
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Lai CC, Chiu WY, Chen YT, Wu CL, Lee FJS. The SNARE-associated protein Sft2 functions in Imh1-mediated SNARE recycling transport upon ER stress. Mol Biol Cell 2023; 34:ar112. [PMID: 37610835 PMCID: PMC10559307 DOI: 10.1091/mbc.e23-01-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Vesicular trafficking involving SNARE proteins play a crucial role in the delivery of cargo to the target membrane. Arf-like protein 1 (Arl1) is an important regulator of the endosomal trans-Golgi network (TGN) and secretory trafficking. In yeast, ER stress-enhances Arl1 activation and Golgin Imh1 recruitment to the late-Golgi. Although Arl1 and Imh1 are critical for GARP-mediated endosomal SNARE-recycling transport in response to ER stress, their downstream effectors are unknown. Here, we report that the SNARE-associated protein Sft2 acts downstream of the Arl1-Imh1 axis to regulate SNARE recycling upon ER stress. We first demonstrated that Sft2 is required for Tlg1/Snc1 SNARE-recycling transport under tunicamycin-induced ER stress. Interestingly, we found that Imh1 regulates Tlg2 retrograde transport to the late-Golgi under ER stress, which in turn is required for Sft2 targeting to the late-Golgi. We further showed that Sft2 with 40 amino acids deleted from the N-terminus exhibits defective mediation of SNARE recycling and decreased association with Tlg1 under ER stress. Finally, we demonstrated that Sft2 is required for GARP-dependent endosome-to-Golgi transport in the absence of Rab protein Ypt6. This study highlights Sft2 as a critical downstream effector of the Arl1-Imh1 axis, mediating the endosome-to-Golgi transport of SNAREs.
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Affiliation(s)
- Chun-Chi Lai
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Wan-Yun Chiu
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Yan-Ting Chen
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Chia-Lu Wu
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Fang-Jen S. Lee
- Institute of Molecular Medicine, National Taiwan University, Taipei 10002, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei 100, Taiwan
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24
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Blank HM, Reuse C, Schmidt‐Hohagen K, Hammer SE, Hiller K, Polymenis M. Branched-chain amino acid synthesis is coupled to TOR activation early in the cell cycle in yeast. EMBO Rep 2023; 24:e57372. [PMID: 37497662 PMCID: PMC10481666 DOI: 10.15252/embr.202357372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
How cells coordinate their metabolism with division determines the rate of cell proliferation. Dynamic patterns of metabolite synthesis during the cell cycle are unexplored. We report the first isotope tracing analysis in synchronous, growing budding yeast cells. Synthesis of leucine, a branched-chain amino acid (BCAA), increases through the G1 phase of the cell cycle, peaking later during DNA replication. Cells lacking Bat1, a mitochondrial aminotransferase that synthesizes BCAAs, grow slower, are smaller, and are delayed in the G1 phase, phenocopying cells in which the growth-promoting kinase complex TORC1 is moderately inhibited. Loss of Bat1 lowers the levels of BCAAs and reduces TORC1 activity. Exogenous provision of valine and, to a lesser extent, leucine to cells lacking Bat1 promotes cell division. Valine addition also increases TORC1 activity. In wild-type cells, TORC1 activity is dynamic in the cell cycle, starting low in early G1 but increasing later in the cell cycle. These results suggest a link between BCAA synthesis from glucose to TORC1 activation in the G1 phase of the cell cycle.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Carsten Reuse
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Kerstin Schmidt‐Hohagen
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Staci E Hammer
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Michael Polymenis
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
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25
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Lee Y, Kim B, Jang HS, Huh WK. Atg1-dependent phosphorylation of Vps34 is required for dynamic regulation of the phagophore assembly site and autophagy in Saccharomyces cerevisiae. Autophagy 2023; 19:2428-2442. [PMID: 36803233 PMCID: PMC10392759 DOI: 10.1080/15548627.2023.2182478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Macroautophagy/autophagy is a key catabolic pathway in which double-membrane autophagosomes sequester various substrates destined for degradation, enabling cells to maintain homeostasis and survive under stressful conditions. Several autophagy-related (Atg) proteins are recruited to the phagophore assembly site (PAS) and cooperatively function to generate autophagosomes. Vps34 is a class III phosphatidylinositol 3-kinase, and Atg14-containing Vps34 complex I plays essential roles in autophagosome formation. However, the regulatory mechanisms of yeast Vps34 complex I are still poorly understood. Here, we demonstrate that Atg1-dependent phosphorylation of Vps34 is required for robust autophagy activity in Saccharomyces cerevisiae. Following nitrogen starvation, Vps34 in complex I is selectively phosphorylated on multiple serine/threonine residues in its helical domain. This phosphorylation is important for full autophagy activation and cell survival. The absence of Atg1 or its kinase activity leads to complete loss of Vps34 phosphorylation in vivo, and Atg1 directly phosphorylates Vps34 in vitro, regardless of its complex association type. We also demonstrate that the localization of Vps34 complex I to the PAS provides a molecular basis for the complex I-specific phosphorylation of Vps34. This phosphorylation is required for the normal dynamics of Atg18 and Atg8 at the PAS. Together, our results reveal a novel regulatory mechanism of yeast Vps34 complex I and provide new insights into the Atg1-dependent dynamic regulation of the PAS.Abbreviations: ATG: autophagy-related; BARA: the repeated, autophagy-specific Co-IP: co-immunoprecipitation; GFP: green fluorescent protein; IP-MS: immunoprecipitation followed by tandem mass spectrometry; NTD: the N-terminal domain; PAS: phagophore assembly site; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns3K: phosphatidylinositol 3-kinase; SUR: structurally uncharacterized region; Vps34[KD]: Vps34D731N.
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Affiliation(s)
- Yongook Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Bongkeun Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hae-Soo Jang
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Won-Ki Huh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
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26
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Yates LA, Zhang X. Phosphoregulation of the checkpoint kinase Mec1 ATR. DNA Repair (Amst) 2023; 129:103543. [PMID: 37480741 DOI: 10.1016/j.dnarep.2023.103543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Yeast Mec1, and its mammalian ortholog, Ataxia-Telangiectasia and Rad3-related, are giant protein kinases central to replication stress and double strand DNA break repair. Mec1ATR, in complex with Ddc2ATRIP, is a 'sensor' of single stranded DNA, and phosphorylates numerous cell cycle and DNA repair factors to enforce cell cycle arrest and facilitate repair. Over the last several years, new techniques - particularly in structural biology - have provided molecular mechanisms for Mec1ATR function. It is becoming increasingly clear how post-translational modification of Mec1ATR and its interaction partners modulates the DNA damage checkpoint. In this review, we summarise the most recent work unravelling Mec1ATR function in the DNA damage checkpoint and provide a molecular context for its regulation by phosphorylation.
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Affiliation(s)
- Luke A Yates
- Section of Structural, Department of Infectious Disease, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK; DNA processing machines laboratory, Francis Crick Institute, London NW1 1AT, UK.
| | - Xiaodong Zhang
- Section of Structural, Department of Infectious Disease, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK; DNA processing machines laboratory, Francis Crick Institute, London NW1 1AT, UK.
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27
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Panessa GM, Tassoni-Tsuchida E, Pires MR, Felix RR, Jekabson R, de Souza-Pinto NC, da Cunha FM, Brandman O, Cussiol JRR. Opi1-mediated transcriptional modulation orchestrates genotoxic stress response in budding yeast. Genetics 2023; 225:iyad130. [PMID: 37440469 PMCID: PMC10691878 DOI: 10.1093/genetics/iyad130] [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: 06/05/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
In budding yeast, the transcriptional repressor Opi1 regulates phospholipid biosynthesis by repressing expression of genes containing inositol-sensitive upstream activation sequences. Upon genotoxic stress, cells activate the DNA damage response to coordinate a complex network of signaling pathways aimed at preserving genomic integrity. Here, we reveal that Opi1 is important to modulate transcription in response to genotoxic stress. We find that cells lacking Opi1 exhibit hypersensitivity to genotoxins, along with a delayed G1-to-S-phase transition and decreased gamma-H2A levels. Transcriptome analysis using RNA sequencing reveals that Opi1 plays a central role in modulating essential biological processes during methyl methanesulfonate (MMS)-associated stress, including repression of phospholipid biosynthesis and transduction of mating signaling. Moreover, Opi1 induces sulfate assimilation and amino acid metabolic processes, such as arginine and histidine biosynthesis and glycine catabolism. Furthermore, we observe increased mitochondrial DNA instability in opi1Δ cells upon MMS treatment. Notably, we show that constitutive activation of the transcription factor Ino2-Ino4 is responsible for genotoxin sensitivity in Opi1-deficient cells, and the production of inositol pyrophosphates by Kcs1 counteracts Opi1 function specifically during MMS-induced stress. Overall, our findings highlight Opi1 as a critical sensor of genotoxic stress in budding yeast, orchestrating gene expression to facilitate appropriate stress responses.
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Affiliation(s)
- Giovanna Marques Panessa
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Eduardo Tassoni-Tsuchida
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Marina Rodrigues Pires
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Rodrigo Rodrigues Felix
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Rafaella Jekabson
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | | | - Fernanda Marques da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - José Renato Rosa Cussiol
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
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28
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Farajzadeh N, Shahbabian K, Bouaziz Y, Querido E, Chartrand P. Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast. RNA (NEW YORK, N.Y.) 2023; 29:745-755. [PMID: 36921931 PMCID: PMC10187671 DOI: 10.1261/rna.079555.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/24/2023] [Indexed: 05/18/2023]
Abstract
Messenger RNA (mRNA) localization is an important mechanism controlling local protein synthesis. In budding yeast, asymmetric localization of transcripts such as ASH1 mRNA to the bud tip depends on the She2 RNA-binding protein. She2 assembles as a tetramer to bind RNA, but the regulation of this process as part of the mRNA locasome is still unclear. Here, we performed a phosphoproteomic analysis of She2 in vivo and identified new phosphosites, several of which are located at the dimerization or tetramerization interfaces of She2. Remarkably, phosphomimetic mutations at these residues disrupt the capacity of She2 to promote Ash1 asymmetric accumulation. A detailed analysis of one of these residues, T109, shows that a T109D mutation inhibits She2 oligomerization and its interaction with She3 and the importin-α Srp1. She2 proteins harboring the T109D mutation also display reduced expression. More importantly, this phosphomimetic mutation strongly impairs the capacity of She2 to bind RNA and disrupts ASH1 mRNA localization. These results demonstrate that the control of She2 oligomerization by phosphorylation constitutes an important regulatory step in the mRNA localization pathway.
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Affiliation(s)
- Nastaran Farajzadeh
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Karen Shahbabian
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Yani Bouaziz
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Emmanuelle Querido
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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29
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Pipercevic J, Kohl B, Gerasimaite R, Comte-Miserez V, Hostachy S, Müntener T, Agustoni E, Jessen HJ, Fiedler D, Mayer A, Hiller S. Inositol pyrophosphates activate the vacuolar transport chaperone complex in yeast by disrupting a homotypic SPX domain interaction. Nat Commun 2023; 14:2645. [PMID: 37156835 PMCID: PMC10167327 DOI: 10.1038/s41467-023-38315-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
Many proteins involved in eukaryotic phosphate homeostasis are regulated by SPX domains. In yeast, the vacuolar transporter chaperone (VTC) complex contains two such domains, but mechanistic details of its regulation are not well understood. Here, we show at the atomic level how inositol pyrophosphates interact with SPX domains of subunits Vtc2 and Vtc3 to control the activity of the VTC complex. Vtc2 inhibits the catalytically active VTC subunit Vtc4 by homotypic SPX-SPX interactions via the conserved helix α1 and the previously undescribed helix α7. Binding of inositol pyrophosphates to Vtc2 abrogates this interaction, thus activating the VTC complex. Accordingly, VTC activation is also achieved by site-specific point mutations that disrupt the SPX-SPX interface. Structural data suggest that ligand binding induces reorientation of helix α1 and exposes the modifiable helix α7, which might facilitate its post-translational modification in vivo. The variable composition of these regions within the SPX domain family might contribute to the diversified SPX functions in eukaryotic phosphate homeostasis.
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Affiliation(s)
- Joka Pipercevic
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Bastian Kohl
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Ruta Gerasimaite
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
- Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Véronique Comte-Miserez
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
| | - Sarah Hostachy
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Elia Agustoni
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Henning Jacob Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Dorothea Fiedler
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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30
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Lesko MA, Chandrashekarappa DG, Jordahl EM, Oppenheimer KG, Bowman RW, Shang C, Durrant JD, Schmidt MC, O’Donnell AF. Changing course: Glucose starvation drives nuclear accumulation of Hexokinase 2 in S. cerevisiae. PLoS Genet 2023; 19:e1010745. [PMID: 37196001 PMCID: PMC10228819 DOI: 10.1371/journal.pgen.1010745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/30/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Glucose is the preferred carbon source for most eukaryotes, and the first step in its metabolism is phosphorylation to glucose-6-phosphate. This reaction is catalyzed by hexokinases or glucokinases. The yeast Saccharomyces cerevisiae encodes three such enzymes, Hxk1, Hxk2, and Glk1. In yeast and mammals, some isoforms of this enzyme are found in the nucleus, suggesting a possible moonlighting function beyond glucose phosphorylation. In contrast to mammalian hexokinases, yeast Hxk2 has been proposed to shuttle into the nucleus in glucose-replete conditions, where it reportedly moonlights as part of a glucose-repressive transcriptional complex. To achieve its role in glucose repression, Hxk2 reportedly binds the Mig1 transcriptional repressor, is dephosphorylated at serine 15 and requires an N-terminal nuclear localization sequence (NLS). We used high-resolution, quantitative, fluorescent microscopy of live cells to determine the conditions, residues, and regulatory proteins required for Hxk2 nuclear localization. Countering previous yeast studies, we find that Hxk2 is largely excluded from the nucleus under glucose-replete conditions but is retained in the nucleus under glucose-limiting conditions. We find that the Hxk2 N-terminus does not contain an NLS but instead is necessary for nuclear exclusion and regulating multimerization. Amino acid substitutions of the phosphorylated residue, serine 15, disrupt Hxk2 dimerization but have no effect on its glucose-regulated nuclear localization. Alanine substation at nearby lysine 13 affects dimerization and maintenance of nuclear exclusion in glucose-replete conditions. Modeling and simulation provide insight into the molecular mechanisms of this regulation. In contrast to earlier studies, we find that the transcriptional repressor Mig1 and the protein kinase Snf1 have little effect on Hxk2 localization. Instead, the protein kinase Tda1 regulates Hxk2 localization. RNAseq analyses of the yeast transcriptome dispels the idea that Hxk2 moonlights as a transcriptional regulator of glucose repression, demonstrating that Hxk2 has a negligible role in transcriptional regulation in both glucose-replete and limiting conditions. Our studies define a new model of cis- and trans-acting regulators of Hxk2 dimerization and nuclear localization. Based on our data, the nuclear translocation of Hxk2 in yeast occurs in glucose starvation conditions, which aligns well with the nuclear regulation of mammalian orthologs. Our results lay the foundation for future studies of Hxk2 nuclear activity.
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Affiliation(s)
- Mitchell A. Lesko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dakshayini G. Chandrashekarappa
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Eric M. Jordahl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Katherine G. Oppenheimer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ray W. Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chaowei Shang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Martin C. Schmidt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Allyson F. O’Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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31
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Yates L, Tannous E, Morgan R, Burgers P, Zhang X. A DNA damage-induced phosphorylation circuit enhances Mec1 ATR Ddc2 ATRIP recruitment to Replication Protein A. Proc Natl Acad Sci U S A 2023; 120:e2300150120. [PMID: 36996117 PMCID: PMC10083555 DOI: 10.1073/pnas.2300150120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 03/31/2023] Open
Abstract
The cell cycle checkpoint kinase Mec1ATR and its integral partner Ddc2ATRIP are vital for the DNA damage and replication stress response. Mec1-Ddc2 "senses" single-stranded DNA (ssDNA) by being recruited to the ssDNA binding Replication Protein A (RPA) via Ddc2. In this study, we show that a DNA damage-induced phosphorylation circuit modulates checkpoint recruitment and function. We demonstrate that Ddc2-RPA interactions modulate the association between RPA and ssDNA and that Rfa1-phosphorylation aids in the further recruitment of Mec1-Ddc2. We also uncover an underappreciated role for Ddc2 phosphorylation that enhances its recruitment to RPA-ssDNA that is important for the DNA damage checkpoint in yeast. The crystal structure of a phosphorylated Ddc2 peptide in complex with its RPA interaction domain provides molecular details of how checkpoint recruitment is enhanced, which involves Zn2+. Using electron microscopy and structural modeling approaches, we propose that Mec1-Ddc2 complexes can form higher order assemblies with RPA when Ddc2 is phosphorylated. Together, our results provide insight into Mec1 recruitment and suggest that formation of supramolecular complexes of RPA and Mec1-Ddc2, modulated by phosphorylation, would allow for rapid clustering of damage foci to promote checkpoint signaling.
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Affiliation(s)
- Luke A. Yates
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, South Kensington, LondonSW7 2AZ, United Kingdom
| | - Elias A. Tannous
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO63110
| | - R. Marc Morgan
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, South Kensington, LondonSW7 2AZ, United Kingdom
| | - Peter M. Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO63110
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, South Kensington, LondonSW7 2AZ, United Kingdom
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32
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Luther CH, Brandt P, Vylkova S, Dandekar T, Müller T, Dittrich M. Integrated analysis of SR-like protein kinases Sky1 and Sky2 links signaling networks with transcriptional regulation in Candida albicans. Front Cell Infect Microbiol 2023; 13:1108235. [PMID: 37082713 PMCID: PMC10111165 DOI: 10.3389/fcimb.2023.1108235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
Fungal infections are a major global health burden where Candida albicans is among the most common fungal pathogen in humans and is a common cause of invasive candidiasis. Fungal phenotypes, such as those related to morphology, proliferation and virulence are mainly driven by gene expression, which is primarily regulated by kinase signaling cascades. Serine-arginine (SR) protein kinases are highly conserved among eukaryotes and are involved in major transcriptional processes in human and S. cerevisiae. Candida albicans harbors two SR protein kinases, while Sky2 is important for metabolic adaptation, Sky1 has similar functions as in S. cerevisiae. To investigate the role of these SR kinases for the regulation of transcriptional responses in C. albicans, we performed RNA sequencing of sky1Δ and sky2Δ and integrated a comprehensive phosphoproteome dataset of these mutants. Using a Systems Biology approach, we study transcriptional regulation in the context of kinase signaling networks. Transcriptomic enrichment analysis indicates that pathways involved in the regulation of gene expression are downregulated and mitochondrial processes are upregulated in sky1Δ. In sky2Δ, primarily metabolic processes are affected, especially for arginine, and we observed that arginine-induced hyphae formation is impaired in sky2Δ. In addition, our analysis identifies several transcription factors as potential drivers of the transcriptional response. Among these, a core set is shared between both kinase knockouts, but it appears to regulate different subsets of target genes. To elucidate these diverse regulatory patterns, we created network modules by integrating the data of site-specific protein phosphorylation and gene expression with kinase-substrate predictions and protein-protein interactions. These integrated signaling modules reveal shared parts but also highlight specific patterns characteristic for each kinase. Interestingly, the modules contain many proteins involved in fungal morphogenesis and stress response. Accordingly, experimental phenotyping shows a higher resistance to Hygromycin B for sky1Δ. Thus, our study demonstrates that a combination of computational approaches with integration of experimental data can offer a new systems biological perspective on the complex network of signaling and transcription. With that, the investigation of the interface between signaling and transcriptional regulation in C. albicans provides a deeper insight into how cellular mechanisms can shape the phenotype.
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Affiliation(s)
- Christian H. Luther
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Philipp Brandt
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Slavena Vylkova
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Thomas Dandekar
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Tobias Müller
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Marcus Dittrich
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
- University of Würzburg, Institut of Human Genetics, Biocenter/Am Hubland 97074, Würzburg, Germany
- *Correspondence: Marcus Dittrich,
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33
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Agrotis A, Lamoliatte F, Williams TD, Black A, Horberry R, Rousseau A. Multiple phosphorylation of the Cdc48/p97 cofactor protein Shp1/p47 occurs upon cell stress in budding yeast. Life Sci Alliance 2023; 6:e202201642. [PMID: 36693698 PMCID: PMC9874129 DOI: 10.26508/lsa.202201642] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
The homohexameric p97 complex, composed of Cdc48 subunits in yeast, is a crucial component of protein quality control pathways including ER-associated degradation. The complex acts to segregate protein complexes in an ATP-dependent manner, requiring the engagement of cofactor proteins that determine substrate specificity. The function of different Cdc48 cofactors and how they are regulated remains relatively poorly understood. In this study, we assess the phosphorylation of Cdc48 adaptor proteins, revealing a unique and distinctive phosphorylation pattern of Shp1/p47 that changed in response to TORC1 inhibition. Site-directed mutagenesis confirmed that this pattern corresponded to phosphorylation at residues S108 and S315 of Shp1, with the double-phosphorylated form becoming predominant upon TORC1 inhibition, ER-stress, and oxidative stress. Finally, we assessed candidate kinases and phosphatases responsible for Shp1 phosphorylation and identified two regulators. We found that cells lacking the kinase Mpk1/Slt2 show reduced Shp1 phosphorylation, whereas impaired PP1 phosphatase catalytic subunit (Glc7) activity resulted in increased Shp1 phosphorylation. Overall, these findings identify a phosphoregulation of Shp1 at multiple sites by Mpk1 kinase and PP1 phosphatase upon various stresses.
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Affiliation(s)
- Alexander Agrotis
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas D Williams
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ailsa Black
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Rhuari Horberry
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Adrien Rousseau
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
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34
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Evolutionary conservation of sequence motifs at sites of protein modification. J Biol Chem 2023; 299:104617. [PMID: 36933807 PMCID: PMC10139944 DOI: 10.1016/j.jbc.2023.104617] [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: 01/12/2023] [Revised: 02/20/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
Gene duplications are common in biology and are likely to be an important source of functional diversification and specialization. The yeast Saccharomyces cerevisiae underwent a whole genome duplication event early in evolution, and a substantial number of duplicated genes have been retained. We identified more than 3,500 instances where only one of two paralogous proteins undergoes post-translational modification despite having retained the same amino acid residue in both. We also developed a web-based search algorithm (CoSMoS.c.) that scores conservation of amino acid sequences based on 1011 wild and domesticated yeast isolates and used it to compare differentially-modified pairs of paralogous proteins. We found that the most common modifications - phosphorylation, ubiquitylation and acylation but not N-glycosylation - occur in regions of high sequence conservation. Such conservation is evident even for ubiquitylation and succinylation, where there is no established 'consensus site' for modification. Differences in phosphorylation were not associated with predicted secondary structure or solvent accessibility, but did mirror known differences in kinase-substrate interactions. Thus, differences in post-translational modification likely result from differences in adjoining amino acids and their interactions with modifying enzymes. By integrating data from large scale proteomics and genomics analysis, in a system with such substantial genetic diversity, we obtained a more comprehensive understanding of the functional basis for genetic redundancies that have persisted for 100 million years.
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35
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Post-Transcriptional and Post-Translational Modifications in Telomerase Biogenesis and Recruitment to Telomeres. Int J Mol Sci 2023; 24:ijms24055027. [PMID: 36902458 PMCID: PMC10003056 DOI: 10.3390/ijms24055027] [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: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Telomere length is associated with the proliferative potential of cells. Telomerase is an enzyme that elongates telomeres throughout the entire lifespan of an organism in stem cells, germ cells, and cells of constantly renewed tissues. It is activated during cellular division, including regeneration and immune responses. The biogenesis of telomerase components and their assembly and functional localization to the telomere is a complex system regulated at multiple levels, where each step must be tuned to the cellular requirements. Any defect in the function or localization of the components of the telomerase biogenesis and functional system will affect the maintenance of telomere length, which is critical to the processes of regeneration, immune response, embryonic development, and cancer progression. An understanding of the regulatory mechanisms of telomerase biogenesis and activity is necessary for the development of approaches toward manipulating telomerase to influence these processes. The present review focuses on the molecular mechanisms involved in the major steps of telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates.
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36
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Elliff J, Biswas A, Roshan P, Kuppa S, Patterson A, Mattice J, Chinnaraj M, Burd R, Walker SE, Pozzi N, Antony E, Bothner B, Origanti S. Dynamic states of eIF6 and SDS variants modulate interactions with uL14 of the 60S ribosomal subunit. Nucleic Acids Res 2023; 51:1803-1822. [PMID: 36651285 PMCID: PMC9976893 DOI: 10.1093/nar/gkac1266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023] Open
Abstract
Assembly of ribosomal subunits into active ribosomal complexes is integral to protein synthesis. Release of eIF6 from the 60S ribosomal subunit primes 60S to associate with the 40S subunit and engage in translation. The dynamics of eIF6 interaction with the uL14 (RPL23) interface of 60S and its perturbation by somatic mutations acquired in Shwachman-Diamond Syndrome (SDS) is yet to be clearly understood. Here, by using a modified strategy to obtain high yields of recombinant human eIF6 we have uncovered the critical interface entailing eight key residues in the C-tail of uL14 that is essential for physical interactions between 60S and eIF6. Disruption of the complementary binding interface by conformational changes in eIF6 disease variants provide a mechanism for weakened interactions of variants with the 60S. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) analyses uncovered dynamic configurational rearrangements in eIF6 induced by binding to uL14 and exposed an allosteric interface regulated by the C-tail of eIF6. Disrupting key residues in the eIF6-60S binding interface markedly limits proliferation of cancer cells, which highlights the significance of therapeutically targeting this interface. Establishing these key interfaces thus provide a therapeutic framework for targeting eIF6 in cancers and SDS.
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Affiliation(s)
- Jonah Elliff
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
- Department of Immunology, The University of Iowa, Iowa City, IA 52242, USA
| | - Aparna Biswas
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Poonam Roshan
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, MO 63104, USA
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Jenna Mattice
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Mathivanan Chinnaraj
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, MO 63104, USA
| | - Ryan Burd
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Sarah E Walker
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA
| | - Nicola Pozzi
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, MO 63104, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, MO 63104, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Sofia Origanti
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
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37
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Liu L, Ansari RU, Vang-Smith M, Hittinger CT, Sato TK. A role for ion homeostasis in yeast ionic liquid tolerance. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000718. [PMID: 36820393 PMCID: PMC9938406 DOI: 10.17912/micropub.biology.000718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/24/2023]
Abstract
The model yeast Saccharomyces cerevisiae is being developed as a biocatalyst for the conversion of renewable lignocellulosic biomass into biofuels. The ionic liquid 1-ethyl-3-methylimidazolium chloride (EMIMCl) solubilizes lignocellulose for deconstruction into fermentable sugars, but it inhibits yeast fermentation. EMIMCl tolerance is mediated by the efflux pump Sge1p and uncharacterized protein Ilt1p. Through genetic investigation, we found that disruption of ion homeostasis through mutations in genes encoding the Trk1p potassium transporter and its protein kinase regulators, Sat4p and Hal5p, causes EMIMCl sensitivity. These results suggest that maintenance of ion homeostasis is important for tolerance to EMIMCl.
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Affiliation(s)
- Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
,
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI
| | - Rahim U. Ansari
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Maikayeng Vang-Smith
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
,
Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
,
Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI
,
J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI
,
Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
,
Correspondence to: Chris Todd Hittinger (
)
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
,
Correspondence to: Trey K. Sato (
)
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38
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Cairo G, Greiwe C, Jung GI, Blengini C, Schindler K, Lacefield S. Distinct Aurora B pools at the inner centromere and kinetochore have different contributions to meiotic and mitotic chromosome segregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.05.527197. [PMID: 36778459 PMCID: PMC9915740 DOI: 10.1101/2023.02.05.527197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proper chromosome segregation depends on establishment of bioriented kinetochore-microtubule attachments, which often requires multiple rounds of release and reattachment. Aurora B and C kinases phosphorylate kinetochore proteins to release tensionless attachments. Multiple pathways recruit Aurora B/C to the centromere and kinetochore. We studied how these pathways contribute to anaphase onset timing and correction of kinetochore-microtubule attachments in budding yeast meiosis and mitosis. We find that the pool localized by the Bub1/Bub3 pathway sets the normal duration of meiosis and mitosis, in differing ways. Our meiosis data suggests that disruption of this pathway leads to PP1 kinetochore localization, which dephosphorylates Cdc20 for premature anaphase onset. For error correction, the Bub1/Bub3 and COMA pathways are individually important in meiosis but compensatory in mitosis. Finally, we find that the haspin and Bub1/3 pathways function together to ensure error correction in mouse oogenesis. Our results suggest that each recruitment pathway localizes spatially distinct kinetochore-localized Aurora B/C pools that function differently between meiosis and mitosis.
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Affiliation(s)
- Gisela Cairo
- Indiana University, Department of Biology, Bloomington, IN USA
- Geisel School of Medicine at Dartmouth, Department of Biochemistry and Cell Biology, Hanover, NH USA
| | - Cora Greiwe
- Indiana University, Department of Biology, Bloomington, IN USA
| | - Gyu Ik Jung
- Rutgers University, Department of Genetics, Piscataway, NJ USA
| | | | - Karen Schindler
- Rutgers University, Department of Genetics, Piscataway, NJ USA
| | - Soni Lacefield
- Indiana University, Department of Biology, Bloomington, IN USA
- Geisel School of Medicine at Dartmouth, Department of Biochemistry and Cell Biology, Hanover, NH USA
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39
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Chou KY, Lee JY, Kim KB, Kim E, Lee HS, Ryu HY. Histone modification in Saccharomyces cerevisiae: A review of the current status. Comput Struct Biotechnol J 2023; 21:1843-1850. [PMID: 36915383 PMCID: PMC10006725 DOI: 10.1016/j.csbj.2023.02.037] [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: 11/15/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a well-characterized and popular model system for investigating histone modifications and the inheritance of chromatin states. The data obtained from this model organism have provided essential and critical information for understanding the complexity of epigenetic interactions and regulation in eukaryotes. Recent advances in biotechnology have facilitated the detection and quantitation of protein post-translational modification (PTM), including acetylation, methylation, phosphorylation, ubiquitylation, sumoylation, and acylation, and led to the identification of several novel modification sites in histones. Determining the cellular function of these new histone markers is essential for understanding epigenetic mechanisms and their impact on various biological processes. In this review, we describe recent advances and current views on histone modifications and their effects on chromatin dynamics in S. cerevisiae.
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Key Words
- AdoMet, S-adenosylmethionine
- CAF-1, chromatin assembly factor-1
- CTD, C-terminal domain
- DSB, double-strand break
- E Glu, glutamic acid
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- Histone acetylation
- Histone acylation
- Histone methylation
- Histone phosphorylation
- Histone sumoylation
- Histone ubiquitylation
- JMJC, Jumonji C
- K Lys, lysine
- PTM, post-translational modification
- R Arg, arginine
- S, serine
- SAGA, Spt-Ada-Gcn5 acetyltransferase
- STUbL, SUMO-targeted ubiquitin ligase
- SUMO, small ubiquitin-like modifier
- T, threonine
- Y, tyrosine
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Affiliation(s)
- Kwon Young Chou
- School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jun-Yeong Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kee-Beom Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eunjeong Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyun-Shik Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hong-Yeoul Ryu
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
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40
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Reichling S, Doubleday PF, Germade T, Bergmann A, Loewith R, Sauer U, Holbrook-Smith D. Dynamic metabolome profiling uncovers potential TOR signaling genes. eLife 2023; 12:84295. [PMID: 36598488 PMCID: PMC9812406 DOI: 10.7554/elife.84295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 01/05/2023] Open
Abstract
Although the genetic code of the yeast Saccharomyces cerevisiae was sequenced 25 years ago, the characterization of the roles of genes within it is far from complete. The lack of a complete mapping of functions to genes hampers systematic understanding of the biology of the cell. The advent of high-throughput metabolomics offers a unique approach to uncovering gene function with an attractive combination of cost, robustness, and breadth of applicability. Here, we used flow-injection time-of-flight mass spectrometry to dynamically profile the metabolome of 164 loss-of-function mutants in TOR and receptor or receptor-like genes under a time course of rapamycin treatment, generating a dataset with >7000 metabolomics measurements. In order to provide a resource to the broader community, those data are made available for browsing through an interactive data visualization app hosted at https://rapamycin-yeast.ethz.ch. We demonstrate that dynamic metabolite responses to rapamycin are more informative than steady-state responses when recovering known regulators of TOR signaling, as well as identifying new ones. Deletion of a subset of the novel genes causes phenotypes and proteome responses to rapamycin that further implicate them in TOR signaling. We found that one of these genes, CFF1, was connected to the regulation of pyrimidine biosynthesis through URA10. These results demonstrate the efficacy of the approach for flagging novel potential TOR signaling-related genes and highlight the utility of dynamic perturbations when using functional metabolomics to deliver biological insight.
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Affiliation(s)
- Stella Reichling
- Institute of Molecular Systems Biology, ETH ZurichZurichSwitzerland
| | | | - Tomas Germade
- Institute of Molecular Systems Biology, ETH ZurichZurichSwitzerland
| | - Ariane Bergmann
- Department of Molecular Biology, University of GenevaGenevaSwitzerland
| | - Robbie Loewith
- Department of Molecular Biology, University of GenevaGenevaSwitzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH ZurichZurichSwitzerland
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41
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Castro IG, Shortill SP, Dziurdzik SK, Cadou A, Ganesan S, Valenti R, David Y, Davey M, Mattes C, Thomas FB, Avraham RE, Meyer H, Fadel A, Fenech EJ, Ernst R, Zaremberg V, Levine TP, Stefan C, Conibear E, Schuldiner M. Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution. eLife 2022; 11:74602. [DOI: 10.7554/elife.74602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Actively maintained close appositions between organelle membranes, also known as contact sites, enable the efficient transfer of biomolecules between cellular compartments. Several such sites have been described as well as their tethering machineries. Despite these advances we are still far from a comprehensive understanding of the function and regulation of most contact sites. To systematically characterize contact site proteomes, we established a high-throughput screening approach in Saccharomyces cerevisiae based on co-localization imaging. We imaged split fluorescence reporters for six different contact sites, several of which are poorly characterized, on the background of 1165 strains expressing a mCherry-tagged yeast protein that has a cellular punctate distribution (a hallmark of contact sites), under regulation of the strong TEF2 promoter. By scoring both co-localization events and effects on reporter size and abundance, we discovered over 100 new potential contact site residents and effectors in yeast. Focusing on several of the newly identified residents, we identified three homologs of Vps13 and Atg2 that are residents of multiple contact sites. These proteins share their lipid transport domain, thus expanding this family of lipid transporters. Analysis of another candidate, Ypr097w, which we now call Lec1 (Lipid-droplet Ergosterol Cortex 1), revealed that this previously uncharacterized protein dynamically shifts between lipid droplets and the cell cortex, and plays a role in regulation of ergosterol distribution in the cell. Overall, our analysis expands the universe of contact site residents and effectors and creates a rich database to mine for new functions, tethers, and regulators.
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Affiliation(s)
| | - Shawn P Shortill
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Samantha Katarzyna Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Angela Cadou
- Laboratory for Molecular Cell Biology, University College London
| | | | - Rosario Valenti
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Yotam David
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
| | - Carsten Mattes
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | - Ffion B Thomas
- Laboratory for Molecular Cell Biology, University College London
| | | | - Hadar Meyer
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | | | - Tim P Levine
- UCL Institute of Ophthalmology, University College London
| | | | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science
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42
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Collin A, González-Jiménez A, González-Jiménez MDC, Alfonso MJ, Calvo O. The Role of S. cerevisiae Sub1/PC4 in Transcription Elongation Depends on the C-Terminal Region and Is Independent of the ssDNA Binding Domain. Cells 2022; 11:cells11203320. [PMID: 36291192 PMCID: PMC9600219 DOI: 10.3390/cells11203320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Saccharomyces cerevisiae Sub1 (ScSub1) has been defined as a transcriptional stimulatory protein due to its homology to the ssDNA binding domain (ssDBD) of human PC4 (hPC4). Recently, PC4/Sub1 orthologues have been elucidated in eukaryotes, prokaryotes, and bacteriophages with functions related to DNA metabolism. Additionally, ScSub1 contains a unique carboxyl–terminal region (CT) of unknown function up to date. Specifically, it has been shown that Sub1 is required for transcription activation, as well as other processes, throughout the transcription cycle. Despite the progress that has been made in understanding the mechanism underlying Sub1′s functions, some questions remain unanswered. As a case in point: whether Sub1’s roles in initiation and elongation are differentially predicated on distinct regions of the protein or how Sub1′s functions are regulated. Here, we uncover some residues that are key for DNA–ScSub1 interaction in vivo, localized in the ssDBD, and required for Sub1 recruitment to promoters. Furthermore, using an array of genetic and molecular techniques, we demonstrate that the CT region is required for transcription elongation by RNA polymerase II (RNAPII). Altogether, our data indicate that Sub1 plays a dual role during transcription—in initiation through the ssDBD and in elongation through the CT region.
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Affiliation(s)
- Alejandro Collin
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas-INICSA, CONICET-Universidad Nacional de Córdoba, Haya de la Torre s/n, Pabellón Argentina, 2º piso. Ciudad Universitaria, Cordoba CP5000, Argentina
| | - Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | | | - Manuel J. Alfonso
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
- Correspondence:
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TOR complex 2 is a master regulator of plasma membrane homeostasis. Biochem J 2022; 479:1917-1940. [PMID: 36149412 PMCID: PMC9555796 DOI: 10.1042/bcj20220388] [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: 07/22/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
As first demonstrated in budding yeast (Saccharomyces cerevisiae), all eukaryotic cells contain two, distinct multi-component protein kinase complexes that each harbor the TOR (Target Of Rapamycin) polypeptide as the catalytic subunit. These ensembles, dubbed TORC1 and TORC2, function as universal, centrally important sensors, integrators, and controllers of eukaryotic cell growth and homeostasis. TORC1, activated on the cytosolic surface of the lysosome (or, in yeast, on the cytosolic surface of the vacuole), has emerged as a primary nutrient sensor that promotes cellular biosynthesis and suppresses autophagy. TORC2, located primarily at the plasma membrane, plays a major role in maintaining the proper levels and bilayer distribution of all plasma membrane components (sphingolipids, glycerophospholipids, sterols, and integral membrane proteins). This article surveys what we have learned about signaling via the TORC2 complex, largely through studies conducted in S. cerevisiae. In this yeast, conditions that challenge plasma membrane integrity can, depending on the nature of the stress, stimulate or inhibit TORC2, resulting in, respectively, up-regulation or down-regulation of the phosphorylation and thus the activity of its essential downstream effector the AGC family protein kinase Ypk1. Through the ensuing effect on the efficiency with which Ypk1 phosphorylates multiple substrates that control diverse processes, membrane homeostasis is maintained. Thus, the major focus here is on TORC2, Ypk1, and the multifarious targets of Ypk1 and how the functions of these substrates are regulated by their Ypk1-mediated phosphorylation, with emphasis on recent advances in our understanding of these processes.
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Kwiatek JM, Gutierrez B, Izgu EC, Han GS, Carman GM. Phosphatidic acid mediates the Nem1-Spo7/Pah1 phosphatase cascade in yeast lipid synthesis. J Lipid Res 2022; 63:100282. [DOI: 10.1016/j.jlr.2022.100282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 10/31/2022] Open
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Zahumenský J, Mota Fernandes C, Veselá P, Del Poeta M, Konopka JB, Malínský J. Microdomain Protein Nce102 Is a Local Sensor of Plasma Membrane Sphingolipid Balance. Microbiol Spectr 2022; 10:e0196122. [PMID: 35758748 PMCID: PMC9431316 DOI: 10.1128/spectrum.01961-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 01/17/2023] Open
Abstract
Sphingolipids are essential building blocks of eukaryotic membranes and important signaling molecules that are regulated tightly in response to environmental and physiological inputs. While their biosynthetic pathway has been well-described, the mechanisms that facilitate the perception of sphingolipid levels at the plasma membrane remain to be uncovered. In Saccharomyces cerevisiae, the Nce102 protein has been proposed to function as a sphingolipid sensor as it changes its plasma membrane distribution in response to sphingolipid biosynthesis inhibition. We show that Nce102 redistributes specifically in regions of increased sphingolipid demand, e.g., membranes of nascent buds. Furthermore, we report that the production of Nce102 increases following sphingolipid biosynthesis inhibition and that Nce102 is internalized when excess sphingolipid precursors are supplied. This finding suggests that the total amount of Nce102 in the plasma membrane is a measure of the current need for sphingolipids, whereas its local distribution marks sites of high sphingolipid demand. The physiological role of Nce102 in the regulation of sphingolipid synthesis is demonstrated by mass spectrometry analysis showing reduced levels of hydroxylated complex sphingolipids in response to heat stress in the nce102Δ deletion mutant. We also demonstrate that Nce102 behaves analogously in the widespread human fungal pathogen Candida albicans, suggesting a conserved principle of local sphingolipid control across species. IMPORTANCE Microorganisms are challenged constantly by their rapidly changing environment. To survive, they have developed diverse mechanisms to quickly perceive stressful situations and adapt to them appropriately. The primary site of both stress sensing and adaptation is the plasma membrane. We identified the yeast protein Nce102 as a marker of local sphingolipid levels and fluidity in the plasma membrane. Nce102 is an important structural and functional component of the membrane compartment Can1 (MCC), a plasma membrane microdomain stabilized by a large cytosolic hemitubular protein scaffold, the eisosome. The MCC/eisosomes are widely conserved among fungi and unicellular algae. To determine if Nce102 carries out similar functions in other organisms, we analyzed the human fungal pathogen Candida albicans and found that Nce102 responds to sphingolipid levels also in this organism, which has potential applications for the development of novel therapeutic approaches. The presented study represents a valuable model for how organisms regulate plasma membrane sphingolipids.
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Affiliation(s)
- Jakub Zahumenský
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Caroline Mota Fernandes
- Department of Microbiology and Immunology, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Petra Veselá
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Veterans Administration Medical Center, Northport, New York, USA
| | - James B. Konopka
- Department of Microbiology and Immunology, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Jan Malínský
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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A DNA Replication Fork-centric View of the Budding Yeast DNA Damage Response. DNA Repair (Amst) 2022; 119:103393. [DOI: 10.1016/j.dnarep.2022.103393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/23/2022]
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48
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He R, Zhang Z. Rad53 arrests leading and lagging strand DNA synthesis via distinct mechanisms in response to DNA replication stress. Bioessays 2022; 44:e2200061. [PMID: 35778827 DOI: 10.1002/bies.202200061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 12/18/2022]
Abstract
DNA replication stress threatens ordinary DNA synthesis. The evolutionarily conserved DNA replication stress response pathway involves sensor kinase Mec1/ATR, adaptor protein Mrc1/Claspin, and effector kinase Rad53/Chk1, which spurs a host of changes to stabilize replication forks and maintain genome integrity. DNA replication forks consist of largely distinct sets of proteins at leading and lagging strands that function autonomously in DNA synthesis in vitro. In this article, we discuss eSPAN and BrdU-IP-ssSeq, strand-specific sequencing technologies that permit analysis of protein localization and DNA synthesis at individual strands in budding yeast. Using these approaches, we show that under replication stress Rad53 stalls DNA synthesis on both leading and lagging strands. On lagging strands, it stimulates PCNA unloading, and on leading strands, it attenuates the replication function of Mrc1-Tof1. We propose that in doing so, Rad53 couples leading and lagging strand DNA synthesis during replication stress, thereby preventing the emergence of harmful ssDNA.
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Affiliation(s)
- Richard He
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA.,Department of Pediatrics, Columbia University Medical Center, New York, New York, USA.,Department of Genetics and Development, Columbia University Medical Center, New York, New York, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA.,Department of Pediatrics, Columbia University Medical Center, New York, New York, USA.,Department of Genetics and Development, Columbia University Medical Center, New York, New York, USA
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49
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Lahiri V, Metur SP, Hu Z, Song X, Mari M, Hawkins WD, Bhattarai J, Delorme-Axford E, Reggiori F, Tang D, Dengjel J, Klionsky DJ. Post-transcriptional regulation of ATG1 is a critical node that modulates autophagy during distinct nutrient stresses. Autophagy 2022; 18:1694-1714. [PMID: 34836487 PMCID: PMC9298455 DOI: 10.1080/15548627.2021.1997305] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023] Open
Abstract
Macroautophagy/autophagy is a highly conserved nutrient-recycling pathway that eukaryotes utilize to combat diverse stresses including nutrient depletion. Dysregulation of autophagy disrupts cellular homeostasis leading to starvation susceptibility in yeast and disease development in humans. In yeast, the robust autophagy response to starvation is controlled by the upregulation of ATG genes, via regulatory processes involving multiple levels of gene expression. Despite the identification of several regulators through genetic studies, the predominant mechanism of regulation modulating the autophagy response to subtle differences in nutrient status remains undefined. Here, we report the unexpected finding that subtle changes in nutrient availability can cause large differences in autophagy flux, governed by hitherto unknown post-transcriptional regulatory mechanisms affecting the expression of the key autophagyinducing kinase Atg1 (ULK1/ULK2 in mammals). We have identified two novel post-transcriptional regulators of ATG1 expression, the kinase Rad53 and the RNA-binding protein Ded1 (DDX3 in mammals). Furthermore, we show that DDX3 regulates ULK1 expression post-transcriptionally, establishing mechanistic conservation and highlighting the power of yeast biology in uncovering regulatory mechanisms that can inform therapeutic approaches.
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Affiliation(s)
- Vikramjit Lahiri
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shree Padma Metur
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zehan Hu
- Department of Biology, University of Fribourg, FribourgSwitzerland
| | - Xinxin Song
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, GroningenThe Netherlands
| | - Wayne D. Hawkins
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Janakraj Bhattarai
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, GroningenThe Netherlands
| | - Daolin Tang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joern Dengjel
- Department of Biology, University of Fribourg, FribourgSwitzerland
| | - Daniel J. Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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50
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Khondker S, Kwiatek JM, Han GS, Carman GM. Glycogen synthase kinase homolog Rim11 regulates lipid synthesis through the phosphorylation of Pah1 phosphatidate phosphatase in yeast. J Biol Chem 2022; 298:102221. [PMID: 35780834 PMCID: PMC9352556 DOI: 10.1016/j.jbc.2022.102221] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/24/2022] Open
Abstract
Pah1 phosphatidate (PA) phosphatase plays a major role in triacylglycerol synthesis in Saccharomyces cerevisiae by producing its precursor diacylglycerol and concurrently regulates de novo phospholipid synthesis by consuming its precursor PA. The function of Pah1 requires its membrane localization, which is controlled by its phosphorylation state. Pah1 is dephosphorylated by the Nem1-Spo7 protein phosphatase, whereas its phosphorylation occurs by multiple known and unknown protein kinases. In this work, we show that Rim11, a yeast homolog of mammalian glycogen synthase kinase-3β, is a protein kinase that phosphorylates Pah1 on serine (Ser12, Ser602, and Ser818) and threonine (Thr163, Thr164, Thr522) residues. Enzymological characterization of Rim11 showed that its Km for Pah1 (0.4 μM) is similar to those of other Pah1-phosphorylating protein kinases, but its Km for ATP (30 μM) is significantly higher than those of these same kinases. Furthermore, we demonstrate Rim11 phosphorylation of Pah1 does not require substrate prephosphorylation but was increased ∼2-fold upon its prephosphorylation by the Pho85-Pho80 protein kinase. In addition, we show Rim11-phosphorylated Pah1 was a substrate for dephosphorylation by Nem1-Spo7. Finally, we demonstrate the Rim11 phosphorylation of Pah1 exerted an inhibitory effect on its PA phosphatase activity by reduction of its catalytic efficiency. Mutational analysis of the major phosphorylation sites (Thr163, Thr164, and Ser602) indicated that Rim11-mediated phosphorylation at these sites was required to ensure Nem1-Spo7-dependent localization of the enzyme to the membrane. Overall, these findings advance our understanding of the phosphorylation-mediated regulation of Pah1 function in lipid synthesis.
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Affiliation(s)
- Shoily Khondker
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901
| | - Joanna M Kwiatek
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901.
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