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Wang H, Tarsio M, Kane PM, Rubinstein JL. Structure of yeast RAVE bound to a partial V 1 complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604153. [PMID: 39071316 PMCID: PMC11275763 DOI: 10.1101/2024.07.18.604153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multi-subunit enzymes consist of a soluble catalytic V 1 subcomplex and a membrane-embedded proton-translocating V O subcomplex. The V 1 and V O subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V 1 and V O requiring the protein complex known as RAVE (regulator of the A TPase of v acuoles and e ndosomes). In the yeast Saccharomyces cerevisiae , RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V 1 . In the structure, RAVE is a L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V 1 . Only Rav1p interacts with V 1 , binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V 1 is in a rotational state suitable for binding the free V O complex, but it is partially disrupted in the structure, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V 1 complex with RAVE appears poised for reassembly with V O .
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2
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Plank M, Carmiol N, Mitri B, Lipinski AA, Langlais PR, Capaldi AP. Systems level analysis of time and stimuli specific signaling through PKA. Mol Biol Cell 2024; 35:ar60. [PMID: 38446618 PMCID: PMC11064662 DOI: 10.1091/mbc.e23-02-0066] [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: 02/23/2023] [Revised: 02/13/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
It is well known that eukaryotic cells create gradients of cAMP across space and time to regulate the cAMP dependent protein kinase (PKA) and, in turn, growth and metabolism. However, it is unclear how PKA responds to different concentrations of cAMP. Here, to address this question, we examine PKA signaling in Saccharomyces cerevisiae in different conditions, timepoints, and concentrations of the chemical inhibitor 1-NM-PP1, using phosphoproteomics. These experiments show that there are numerous proteins that are only phosphorylated when cAMP and PKA activity are at/near their maximum level, while other proteins are phosphorylated even when cAMP levels and PKA activity are low. The data also show that PKA drives cells into distinct growth states by acting on proteins with different thresholds for phosphorylation in different conditions. Analysis of the sequences surrounding the 118 PKA-dependent phosphosites suggests that the phosphorylation thresholds are set, at least in part, by the affinity of PKA for each site.
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Affiliation(s)
- Michael Plank
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Nicole Carmiol
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | - Bassam Mitri
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | | | - Paul R. Langlais
- The Department of Medicine, University of Arizona, Tucson, AZ 85721
| | - Andrew P. Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
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3
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Reinhard J, Starke L, Klose C, Haberkant P, Hammarén H, Stein F, Klein O, Berhorst C, Stumpf H, Sáenz JP, Hub J, Schuldiner M, Ernst R. MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress. EMBO J 2024; 43:1653-1685. [PMID: 38491296 PMCID: PMC11021466 DOI: 10.1038/s44318-024-00063-y] [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: 09/14/2022] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
Biological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work has provided insights into the subcellular distribution of lipids in the yeast Saccharomyces cerevisiae, but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remains insufficiently characterized. Here, we describe a method for purifying organelle membranes from yeast, MemPrep. We demonstrate the purity of our ER membrane preparations by proteomics, and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings provide a baseline for studying membrane protein biogenesis and have important implications for understanding the role of lipids in regulating the unfolded protein response (UPR). The combined preparative and analytical MemPrep approach uncovers dynamic remodeling of ER membranes in stressed cells and establishes distinct molecular fingerprints of lipid bilayer stress.
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Affiliation(s)
- John Reinhard
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Leonhard Starke
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | | | - Per Haberkant
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | | | - Frank Stein
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | - Ofir Klein
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Charlotte Berhorst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Heike Stumpf
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - James P Sáenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Jochen Hub
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | - Maya Schuldiner
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Robert Ernst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany.
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany.
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4
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Ferreira MJ, Rodrigues TA, Pedrosa AG, Silva AR, Vilarinho BG, Francisco T, Azevedo JE. Glutathione and peroxisome redox homeostasis. Redox Biol 2023; 67:102917. [PMID: 37804696 PMCID: PMC10565873 DOI: 10.1016/j.redox.2023.102917] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023] Open
Abstract
Despite intensive research on peroxisome biochemistry, the role of glutathione in peroxisomal redox homeostasis has remained a matter of speculation for many years, and only recently has this issue started to be experimentally addressed. Here, we summarize and compare data from several organisms on the peroxisome-glutathione topic. It is clear from this comparison that the repertoire of glutathione-utilizing enzymes in peroxisomes of different organisms varies widely. In addition, the available data suggest that the kinetic connectivity between the cytosolic and peroxisomal pools of glutathione may also be different in different organisms, with some possessing a peroxisomal membrane that is promptly permeable to glutathione whereas in others this may not be the case. However, regardless of the differences, the picture that emerges from all these data is that glutathione is a crucial component of the antioxidative system that operates inside peroxisomes in all organisms.
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Affiliation(s)
- Maria J Ferreira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Ana R Silva
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Beatriz G Vilarinho
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
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5
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Gu Y, Alam S, Oliferenko S. Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size. Nat Commun 2023; 14:5544. [PMID: 37684233 PMCID: PMC10491753 DOI: 10.1038/s41467-023-41347-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD+ dependent reactions together with a dedicated NADH/NAD+ recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. Our reengineering and physiological experiments indicate that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.
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Affiliation(s)
- Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
| | - Sara Alam
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
- Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
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6
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Mark M, Klein O, Zhang Y, Das K, Elbaz A, Hazan RN, Lichtenstein M, Lehming N, Schuldiner M, Pines O. Systematic Approaches to Study Eclipsed Targeting of Proteins Uncover a New Family of Mitochondrial Proteins. Cells 2023; 12:1550. [PMID: 37296670 PMCID: PMC10252432 DOI: 10.3390/cells12111550] [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: 05/03/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Dual localization or dual targeting refers to the phenomenon by which identical, or almost identical, proteins are localized to two (or more) separate compartments of the cell. From previous work in the field, we had estimated that a third of the mitochondrial proteome is dual-targeted to extra-mitochondrial locations and suggested that this abundant dual targeting presents an evolutionary advantage. Here, we set out to study how many additional proteins whose main activity is outside mitochondria are also localized, albeit at low levels, to mitochondria (eclipsed). To do this, we employed two complementary approaches utilizing the α-complementation assay in yeast to uncover the extent of such an eclipsed distribution: one systematic and unbiased and the other based on mitochondrial targeting signal (MTS) predictions. Using these approaches, we suggest 280 new eclipsed distributed protein candidates. Interestingly, these proteins are enriched for distinctive properties compared to their exclusively mitochondrial-targeted counterparts. We focus on one unexpected eclipsed protein family of the Triose-phosphate DeHydrogenases (TDH) and prove that, indeed, their eclipsed distribution in mitochondria is important for mitochondrial activity. Our work provides a paradigm of deliberate eclipsed mitochondrial localization, targeting and function, and should expand our understanding of mitochondrial function in health and disease.
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Affiliation(s)
- Maayan Mark
- Department of Molecular Genetics and Microbiology, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 9112102, Israel; (M.M.); (K.D.); (A.E.); (R.N.H.)
| | - Ofir Klein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; (O.K.); (M.S.)
| | - Yu Zhang
- CREATE-NUS-HUJ Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138602, Singapore; (Y.Z.); (N.L.)
| | - Koyeli Das
- Department of Molecular Genetics and Microbiology, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 9112102, Israel; (M.M.); (K.D.); (A.E.); (R.N.H.)
| | - Adi Elbaz
- Department of Molecular Genetics and Microbiology, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 9112102, Israel; (M.M.); (K.D.); (A.E.); (R.N.H.)
| | - Reut Noa Hazan
- Department of Molecular Genetics and Microbiology, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 9112102, Israel; (M.M.); (K.D.); (A.E.); (R.N.H.)
| | - Michal Lichtenstein
- Department of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 9112102, Israel;
| | - Norbert Lehming
- CREATE-NUS-HUJ Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138602, Singapore; (Y.Z.); (N.L.)
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; (O.K.); (M.S.)
| | - Ophry Pines
- Department of Molecular Genetics and Microbiology, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 9112102, Israel; (M.M.); (K.D.); (A.E.); (R.N.H.)
- CREATE-NUS-HUJ Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138602, Singapore; (Y.Z.); (N.L.)
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7
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Tsirkas I, Zur T, Dovrat D, Paleiov Z, Ravkaie L, Aharoni A. Enhanced fluorescent imaging of proteins in live yeast cells using fluorescently labeled scFv. STAR Protoc 2023; 4:102299. [PMID: 37270779 DOI: 10.1016/j.xpro.2023.102299] [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: 01/05/2023] [Revised: 03/25/2023] [Accepted: 04/20/2023] [Indexed: 06/06/2023] Open
Abstract
Fluorescent labeling of proteins is a widespread approach for the microscopic examination of protein function, expression, and localization in the cell. Here, we present a protocol for the labeling of hemagglutinin (HA)-tagged protein of interest (POI) with the single-chain antibody (scFv) 2E2 fused to different fluorescent proteins (FPs) in Saccharomyces cerevisiae. We describe steps for expressing 2E2-FP, and HA tagging and labeling of POI. We detail in vivo fluorescent imaging of proteins at different cellular compartments and with diverse expression levels. For complete details on the use and execution of this protocol, please refer to Tsirkas et al. (2022).1.
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Affiliation(s)
- Ioannis Tsirkas
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel.
| | - Tomer Zur
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Zohar Paleiov
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Lior Ravkaie
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel.
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8
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Sec61 channel subunit Sbh1/Sec61β promotes ER translocation of proteins with suboptimal targeting sequences and is fine-tuned by phosphorylation. J Biol Chem 2023; 299:102895. [PMID: 36639027 PMCID: PMC9947333 DOI: 10.1016/j.jbc.2023.102895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
The highly conserved endoplasmic reticulum (ER) protein translocation channel contains one nonessential subunit, Sec61β/Sbh1, whose function is poorly understood so far. Its intrinsically unstructured cytosolic domain makes transient contact with ER-targeting sequences in the cytosolic channel vestibule and contains multiple phosphorylation sites suggesting a potential for regulating ER protein import. In a microscopic screen, we show that 12% of a GFP-tagged secretory protein library depends on Sbh1 for translocation into the ER. Sbh1-dependent proteins had targeting sequences with less pronounced hydrophobicity and often no charge bias or an inverse charge bias which reduces their insertion efficiency into the Sec61 channel. We determined that mutating two N-terminal, proline-flanked phosphorylation sites in the Sbh1 cytosolic domain to alanine phenocopied the temperature-sensitivity of a yeast strain lacking SBH1 and its ortholog SBH2. The phosphorylation site mutations reduced translocation into the ER of a subset of Sbh1-dependent proteins, including enzymes whose concentration in the ER lumen is critical for ER proteostasis. In addition, we found that ER import of these proteins depended on the activity of the phospho-S/T-specific proline isomerase Ess1 (PIN1 in mammals). We conclude that Sbh1 promotes ER translocation of substrates with suboptimal targeting sequences and that its activity can be regulated by a conformational change induced by N-terminal phosphorylation.
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9
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Tsirkas I, Zur T, Dovrat D, Cohen A, Ravkaie L, Aharoni A. Protein fluorescent labeling in live yeast cells using scFv-based probes. CELL REPORTS METHODS 2022; 2:100357. [PMID: 36590693 PMCID: PMC9795370 DOI: 10.1016/j.crmeth.2022.100357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/19/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022]
Abstract
The fusion of fluorescent proteins (FPs) to endogenous proteins is a widespread approach for microscopic examination of protein function, expression, and localization in the cell. However, proteins that are sensitive to FP fusion or expressed at low levels are difficult to monitor using this approach. Here, we develop a single-chain fragment variable (scFv)-FP approach to efficiently label Saccharomyces cerevisiae proteins that are tagged with repeats of hemagglutinin (HA)-tag sequences. We demonstrate the successful labeling of DNA-binding proteins and proteins localized to different cellular organelles including the nuclear membrane, peroxisome, Golgi apparatus, and mitochondria. This approach can lead to a significant increase in fluorescence intensity of the labeled protein, allows C'-terminal labeling of difficult-to-tag proteins and increased detection sensitivity of DNA-damage foci. Overall, the development of a scFv-FP labeling approach in yeast provides a general and simple tool for the function and localization analysis of the yeast proteome.
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Affiliation(s)
- Ioannis Tsirkas
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Tomer Zur
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Amit Cohen
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Lior Ravkaie
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
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10
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Mou M, Pan Z, Lu M, Sun H, Wang Y, Luo Y, Zhu F. Application of Machine Learning in Spatial Proteomics. J Chem Inf Model 2022; 62:5875-5895. [PMID: 36378082 DOI: 10.1021/acs.jcim.2c01161] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics of proteins, and it has gained extensive attention in recent years, especially the subcellular proteomics. Numerous evidence indicate that the subcellular localization of proteins is associated with various cellular processes and disease progression. Mass spectrometry (MS)-based and imaging-based experimental approaches have been developed to acquire large-scale spatial proteomic data. To allow the reliable analysis of increasingly complex spatial proteomics data, machine learning (ML) methods have been widely used in both MS-based and imaging-based spatial proteomic data analysis pipelines. Here, we comprehensively survey the applications of ML in spatial proteomics from following aspects: (1) data resources for spatial proteome are comprehensively introduced; (2) the roles of different ML algorithms in data analysis pipelines are elaborated; (3) successful applications of spatial proteomics and several analytical tools integrating ML methods are presented; (4) challenges existing in modern ML-based spatial proteomics studies are discussed. This review provides guidelines for researchers seeking to apply ML methods to analyze spatial proteomic data and can facilitate insightful understanding of cell biology as well as the future research in medical and drug discovery communities.
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Affiliation(s)
- Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huaicheng Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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11
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Pham T, Walden E, Huard S, Pezacki J, Fullerton MD, Baetz K. Fine tuning Acetyl-CoA Carboxylase 1 activity through localization: Functional genomics reveal a role for the lysine acetyltransferase NuA4 and sphingolipid metabolism in regulating Acc1 activity and localization. Genetics 2022; 221:6591204. [PMID: 35608294 PMCID: PMC9339284 DOI: 10.1093/genetics/iyac086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Acetyl-CoA Carboxylase 1 catalyzes the conversion of acetyl-CoA to malonyl-CoA, the committed step of de novo fatty acid synthesis. As a master regulator of lipid synthesis, acetyl-CoA carboxylase 1 has been proposed to be a therapeutic target for numerous metabolic diseases. We have shown that acetyl-CoA carboxylase 1 activity is reduced in the absence of the lysine acetyltransferase NuA4 in Saccharomyces cerevisiae. This change in acetyl-CoA carboxylase 1 activity is correlated with a change in localization. In wild-type cells, acetyl-CoA carboxylase 1 is localized throughout the cytoplasm in small punctate and rod-like structures. However, in NuA4 mutants, acetyl-CoA carboxylase 1 localization becomes diffuse. To uncover mechanisms regulating acetyl-CoA carboxylase 1 localization, we performed a microscopy screen to identify other deletion mutants that impact acetyl-CoA carboxylase 1 localization and then measured acetyl-CoA carboxylase 1 activity in these mutants through chemical genetics and biochemical assays. Three phenotypes were identified. Mutants with hyper-active acetyl-CoA carboxylase 1 form 1 or 2 rod-like structures centrally within the cytoplasm, mutants with mid-low acetyl-CoA carboxylase 1 activity displayed diffuse acetyl-CoA carboxylase 1, while the mutants with the lowest acetyl-CoA carboxylase 1 activity (hypomorphs) formed thick rod-like acetyl-CoA carboxylase 1 structures at the periphery of the cell. All the acetyl-CoA carboxylase 1 hypomorphic mutants were implicated in sphingolipid metabolism or very long-chain fatty acid elongation and in common, their deletion causes an accumulation of palmitoyl-CoA. Through exogenous lipid treatments, enzyme inhibitors, and genetics, we determined that increasing palmitoyl-CoA levels inhibits acetyl-CoA carboxylase 1 activity and remodels acetyl-CoA carboxylase 1 localization. Together this study suggests yeast cells have developed a dynamic feed-back mechanism in which downstream products of acetyl-CoA carboxylase 1 can fine-tune the rate of fatty acid synthesis.
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Affiliation(s)
- Trang Pham
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Elizabeth Walden
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Sylvain Huard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - John Pezacki
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa K1N6N5 Canada
| | - Morgan D Fullerton
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary T2N 1N4, Canada
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12
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Cohen N, Kahana A, Schuldiner M. A Similarity-Based Method for Predicting Enzymatic Functions in Yeast Uncovers a New AMP Hydrolase. J Mol Biol 2022; 434:167478. [PMID: 35123996 PMCID: PMC9005783 DOI: 10.1016/j.jmb.2022.167478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/01/2022]
Abstract
Despite decades of research and the availability of the full genomic sequence of the baker's yeast Saccharomyces cerevisiae, still a large fraction of its genome is not functionally annotated. This hinders our ability to fully understand cellular activity and suggests that many additional processes await discovery. The recent years have shown an explosion of high-quality genomic and structural data from multiple organisms, ranging from bacteria to mammals. New computational methods now allow us to integrate these data and extract meaningful insights into the functional identity of uncharacterized proteins in yeast. Here, we created a database of sensitive sequence similarity predictions for all yeast proteins. We use this information to identify candidate enzymes for known biochemical reactions whose enzymes are unidentified, and show how this provides a powerful basis for experimental validation. Using one pathway as a test case we pair a new function for the previously uncharacterized enzyme Yhr202w, as an extra-cellular AMP hydrolase in the NAD degradation pathway. Yhr202w, which we now term Smn1 for Scavenger MonoNucleotidase 1, is a highly conserved protein that is similar to the human protein E5NT/CD73, which is associated with multiple cancers. Hence, our new methodology provides a paradigm, that can be adopted to other organisms, for uncovering new enzymatic functions of uncharacterized proteins.
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Affiliation(s)
- Nir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amit Kahana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel. https://twitter.com/AmitKahana
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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13
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Huang H, Parker M, Karbstein K. The modifying enzyme Tsr3 establishes the hierarchy of Rio kinase binding in 40S ribosome assembly. RNA (NEW YORK, N.Y.) 2022; 28:568-582. [PMID: 35031584 PMCID: PMC8925970 DOI: 10.1261/rna.078994.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Ribosome assembly is an intricate process, which in eukaryotes is promoted by a large machinery comprised of over 200 assembly factors (AFs) that enable the modification, folding, and processing of the ribosomal RNA (rRNA) and the binding of the 79 ribosomal proteins. While some early assembly steps occur via parallel pathways, the process overall is highly hierarchical, which allows for the integration of maturation steps with quality control processes that ensure only fully and correctly assembled subunits are released into the translating pool. How exactly this hierarchy is established, in particular given that there are many instances of RNA substrate "handover" from one highly related AF to another, remains to be determined. Here we have investigated the role of Tsr3, which installs a universally conserved modification in the P-site of the small ribosomal subunit late in assembly. Our data demonstrate that Tsr3 separates the binding of the Rio kinases, Rio2 and Rio1, with whom it shares a binding site. By binding after Rio2 dissociation, Tsr3 prevents rebinding of Rio2, promoting forward assembly. After rRNA modification is complete, Tsr3 dissociates, thereby allowing for recruitment of Rio1 into its functional site. Inactive Tsr3 blocks Rio1 function, which can be rescued using mutants that bypass the requirement for Rio1 activity. Finally, yeast strains lacking Tsr3 randomize the binding of the two kinases, leading to the release of immature ribosomes into the translating pool. These data demonstrate a role for Tsr3 and its modification activity in establishing a hierarchy for the function of the Rio kinases.
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Affiliation(s)
- Haina Huang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, Jupiter, Florida 33458, USA
| | - Melissa Parker
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, Jupiter, Florida 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, Jupiter, Florida 33458, USA
- HHMI Faculty Scholar, Chevy Chase, Maryland 20815, USA
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14
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Sahoo A, Pechmann S. Functional network motifs defined through integration of protein-protein and genetic interactions. PeerJ 2022; 10:e13016. [PMID: 35223214 PMCID: PMC8877332 DOI: 10.7717/peerj.13016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/06/2022] [Indexed: 01/11/2023] Open
Abstract
Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.
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Affiliation(s)
- Amruta Sahoo
- Département de Biochimie, Université de Montréal, Montréal, QC, Canada
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15
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Mochida K, Otani T, Katsumata Y, Kirisako H, Kakuta C, Kotani T, Nakatogawa H. Atg39 links and deforms the outer and inner nuclear membranes in selective autophagy of the nucleus. J Cell Biol 2022; 221:212974. [PMID: 35061008 PMCID: PMC8789198 DOI: 10.1083/jcb.202103178] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 11/12/2021] [Accepted: 12/10/2021] [Indexed: 01/07/2023] Open
Abstract
In selective autophagy of the nucleus (hereafter nucleophagy), nucleus-derived double-membrane vesicles (NDVs) are formed, sequestered within autophagosomes, and delivered to lysosomes or vacuoles for degradation. In Saccharomyces cerevisiae, the nuclear envelope (NE) protein Atg39 acts as a nucleophagy receptor, which interacts with Atg8 to target NDVs to the forming autophagosomal membranes. In this study, we revealed that Atg39 is anchored to the outer nuclear membrane via its transmembrane domain and also associated with the inner nuclear membrane via membrane-binding amphipathic helices (APHs) in its perinuclear space region, thereby linking these membranes. We also revealed that autophagosome formation-coupled Atg39 crowding causes the NE to protrude toward the cytoplasm, and the tips of the protrusions are pinched off to generate NDVs. The APHs of Atg39 are crucial for Atg39 crowding in the NE and subsequent NE protrusion. These findings suggest that the nucleophagy receptor Atg39 plays pivotal roles in NE deformation during the generation of NDVs to be degraded by nucleophagy.
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Affiliation(s)
- Keisuke Mochida
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Toshifumi Otani
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuto Katsumata
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiromi Kirisako
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Chika Kakuta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Kotani
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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16
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Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. SUBCELLULAR TRANSCRIPTOMICS & PROTEOMICS: A COMPARATIVE METHODS REVIEW. Mol Cell Proteomics 2021; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics. Subcellular information of protein and RNA give insights into molecular function. This review discusses strategies available to measure subcellular information. Hybridization of methods shows promise for exploring the composition of organelles. Advances are aiding understanding of the organisation and dynamics of cells.
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Affiliation(s)
- Josie A Christopher
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Department of Genetics, University of Cambridge, 20 Downing Place, Cambridge, CB2 3EJ, UK
| | - Charlotte S Dawson
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Owen L Vennard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
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17
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Amoiradaki K, Bunting KR, Paine KM, Ayre JE, Hogg K, Laidlaw KME, MacDonald C. The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast. Int J Mol Sci 2021; 22:12477. [PMID: 34830359 PMCID: PMC8617818 DOI: 10.3390/ijms222212477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
Intracellular trafficking pathways control residency and bioactivity of integral membrane proteins at the cell surface. Upon internalisation, surface cargo proteins can be delivered back to the plasma membrane via endosomal recycling pathways. Recycling is thought to be controlled at the metabolic and transcriptional level, but such mechanisms are not fully understood. In yeast, recycling of surface proteins can be triggered by cargo deubiquitination and a series of molecular factors have been implicated in this trafficking. In this study, we follow up on the observation that many subunits of the Rpd3 lysine deacetylase complex are required for recycling. We validate ten Rpd3-complex subunits in recycling using two distinct assays and developed tools to quantify both. Fluorescently labelled Rpd3 localises to the nucleus and complements recycling defects, which we hypothesised were mediated by modulated expression of Rpd3 target gene(s). Bioinformatics implicated 32 candidates that function downstream of Rpd3, which were over-expressed and assessed for capacity to suppress recycling defects of rpd3∆ cells. This effort yielded three hits: Sit4, Dit1 and Ldb7, which were validated with a lipid dye recycling assay. Additionally, the essential phosphatidylinositol-4-kinase Pik1 was shown to have a role in recycling. We propose recycling is governed by Rpd3 at the transcriptional level via multiple downstream target genes.
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Affiliation(s)
- Konstantina Amoiradaki
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Kate R. Bunting
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Katherine M. Paine
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Josephine E. Ayre
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Karen Hogg
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, University of York, York YO10 5DD, UK;
| | - Kamilla M. E. Laidlaw
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Chris MacDonald
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
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18
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Eisenberg-Bord M, Zung N, Collado J, Drwesh L, Fenech EJ, Fadel A, Dezorella N, Bykov YS, Rapaport D, Fernandez-Busnadiego R, Schuldiner M. Cnm1 mediates nucleus-mitochondria contact site formation in response to phospholipid levels. J Cell Biol 2021; 220:212719. [PMID: 34694322 PMCID: PMC8548916 DOI: 10.1083/jcb.202104100] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/12/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial functions are tightly regulated by nuclear activity, requiring extensive communication between these organelles. One way by which organelles can communicate is through contact sites, areas of close apposition held together by tethering molecules. While many contacts have been characterized in yeast, the contact between the nucleus and mitochondria was not previously identified. Using fluorescence and electron microscopy in S. cerevisiae, we demonstrate specific areas of contact between the two organelles. Using a high-throughput screen, we uncover a role for the uncharacterized protein Ybr063c, which we have named Cnm1 (contact nucleus mitochondria 1), as a molecular tether on the nuclear membrane. We show that Cnm1 mediates contact by interacting with Tom70 on mitochondria. Moreover, Cnm1 abundance is regulated by phosphatidylcholine, enabling the coupling of phospholipid homeostasis with contact extent. The discovery of a molecular mechanism that allows mitochondrial crosstalk with the nucleus sets the ground for better understanding of mitochondrial functions in health and disease.
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Affiliation(s)
| | - Naama Zung
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Javier Collado
- Institute for Neuropathology, Georg August Universität Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Layla Drwesh
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nili Dezorella
- Electron Microscopy Unit, Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Yury S Bykov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Ruben Fernandez-Busnadiego
- Institute for Neuropathology, Georg August Universität Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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19
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Mercurio K, Singh D, Walden E, Baetz K. Global analysis of Saccharomyces cerevisiae growth in mucin. G3 (BETHESDA, MD.) 2021; 11:jkab294. [PMID: 34849793 PMCID: PMC8527512 DOI: 10.1093/g3journal/jkab294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/03/2021] [Indexed: 11/12/2022]
Abstract
Metagenomic profiling of the human gut microbiome has discovered DNA from dietary yeasts like Saccharomyces cerevisiae. However, it is unknown if the S. cerevisiae detected by common metagenomic methods are from dead dietary sources, or from live S. cerevisiae colonizing the gut similar to their close relative Candida albicans. While S. cerevisiae can adapt to minimal oxygen and acidic environments, it has not been explored whether this yeast can metabolize mucin, the large, gel-forming, highly glycosylated proteins representing a major source of carbon in the gut mucosa. We reveal that S. cerevisiae can utilize mucin as their main carbon source, as well as perform both a transcriptome analysis and a chemogenomic screen to identify biological pathways required for this yeast to grow optimally in mucin. In total, 739 genes demonstrate significant differential expression in mucin culture, and deletion of 21 genes impact growth in mucin. Both screens suggest that mitochondrial function is required for proper growth in mucin, and through secondary assays we determine that mucin exposure induces mitogenesis and cellular respiration. We further show that deletion of an uncharacterized ORF, YCR095W-A, led to dysfunction in mitochondrial morphology and oxygen consumption in mucin. Finally, we demonstrate that Yps7, an aspartyl protease and homolog to mucin-degrading proteins in C. albicans, is important for growth on mucin. Collectively, our work serves as the initial step toward establishing how this common dietary fungus can survive in the mucus environment of the human gut.
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Affiliation(s)
- Kevin Mercurio
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Dylan Singh
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Elizabeth Walden
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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20
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UbiB proteins regulate cellular CoQ distribution in Saccharomyces cerevisiae. Nat Commun 2021; 12:4769. [PMID: 34362905 PMCID: PMC8346625 DOI: 10.1038/s41467-021-25084-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
Beyond its role in mitochondrial bioenergetics, Coenzyme Q (CoQ, ubiquinone) serves as a key membrane-embedded antioxidant throughout the cell. However, how CoQ is mobilized from its site of synthesis on the inner mitochondrial membrane to other sites of action remains a longstanding mystery. Here, using a combination of Saccharomyces cerevisiae genetics, biochemical fractionation, and lipid profiling, we identify two highly conserved but poorly characterized mitochondrial proteins, Ypl109c (Cqd1) and Ylr253w (Cqd2), that reciprocally affect this process. Loss of Cqd1 skews cellular CoQ distribution away from mitochondria, resulting in markedly enhanced resistance to oxidative stress caused by exogenous polyunsaturated fatty acids, whereas loss of Cqd2 promotes the opposite effects. The activities of both proteins rely on their atypical kinase/ATPase domains, which they share with Coq8-an essential auxiliary protein for CoQ biosynthesis. Overall, our results reveal protein machinery central to CoQ trafficking in yeast and lend insights into the broader interplay between mitochondria and the rest of the cell.
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21
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Matia-González AM, Jabre I, Laing EE, Gerber AP. Oxidative stress induces coordinated remodeling of RNA-enzyme interactions. iScience 2021; 24:102753. [PMID: 34278261 PMCID: PMC8261671 DOI: 10.1016/j.isci.2021.102753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/01/2021] [Accepted: 06/16/2021] [Indexed: 11/28/2022] Open
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators that play a substantial role during stress adaptation. Recent proteome-wide surveys have uncovered a large number of new and “unconventional” RBPs such as metabolic enzymes, yet little is known about the reconfiguration of the RNA-binding proteome (RBPome) and RNA-enzyme interactions in response to cellular stress. Here, we applied RNA-interactome capture to monitor the dynamics of the mRBPome upon mild oxidative stress in the yeast Saccharomyces cerevisiae. Among the 257 proteins that significantly changed RNA associations, we observed the coordinated remodeling of RNA-binding enzymes — particularly of the central carbon metabolism — that complemented known metabolic responses. Furthermore, we recognized the propensity for paralogous specific alterations of enzyme-RNA interactions. Our results suggest coordinated cross talk between RNA-enzyme interactions and intermediary metabolism to maintain the physiological and molecular balance upon oxidative stress, perhaps through specialization of paralogous during evolution. Oxidative stress induces the rearrangement of 257 proteins on polyadenylated RNAs Coordinated response of RNA-enzyme interactions and metabolism Yeast RNA-binding enzymes are paralog specific Integration of three different mass spectrometry analysis tools
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Affiliation(s)
- Ana M Matia-González
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK.,Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Avda Fuentenueva s/n, Granada 18071, Spain
| | - Ibtissam Jabre
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Emma E Laing
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - André P Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
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22
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Fenech EJ, Ben-Dor S, Schuldiner M. Double the Fun, Double the Trouble: Paralogs and Homologs Functioning in the Endoplasmic Reticulum. Annu Rev Biochem 2021; 89:637-666. [PMID: 32569522 DOI: 10.1146/annurev-biochem-011520-104831] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of eukaryotic genomes has been propelled by a series of gene duplication events, leading to an expansion in new functions and pathways. While duplicate genes may retain some functional redundancy, it is clear that to survive selection they cannot simply serve as a backup but rather must acquire distinct functions required for cellular processes to work accurately and efficiently. Understanding these differences and characterizing gene-specific functions is complex. Here we explore different gene pairs and families within the context of the endoplasmic reticulum (ER), the main cellular hub of lipid biosynthesis and the entry site for the secretory pathway. Focusing on each of the ER functions, we highlight specificities of related proteins and the capabilities conferred to cells through their conservation. More generally, these examples suggest why related genes have been maintained by evolutionary forces and provide a conceptual framework to experimentally determine why they have survived selection.
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Affiliation(s)
- Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
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23
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Jaskolka MC, Tarsio M, Smardon AM, Khan MM, Kane PM. Defining steps in RAVE-catalyzed V-ATPase assembly using purified RAVE and V-ATPase subcomplexes. J Biol Chem 2021; 296:100703. [PMID: 33895134 PMCID: PMC8138766 DOI: 10.1016/j.jbc.2021.100703] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/30/2022] Open
Abstract
The vacuolar H+-ATPase (V-ATPase) is a highly conserved proton pump responsible for the acidification of intracellular organelles in virtually all eukaryotic cells. V-ATPases are regulated by the rapid and reversible disassembly of the peripheral V1 domain from the integral membrane Vo domain, accompanied by release of the V1 C subunit from both domains. Efficient reassembly of V-ATPases requires the Regulator of the H+-ATPase of Vacuoles and Endosomes (RAVE) complex in yeast. Although a number of pairwise interactions between RAVE and V-ATPase subunits have been mapped, the low endogenous levels of the RAVE complex and lethality of constitutive RAV1 overexpression have hindered biochemical characterization of the intact RAVE complex. We describe a novel inducible overexpression system that allows purification of native RAVE and RAVE–V1 complexes. Both purified RAVE and RAVE–V1 contain substoichiometric levels of subunit C. RAVE–V1 binds tightly to expressed subunit C in vitro, but binding of subunit C to RAVE alone is weak. Neither RAVE nor RAVE–V1 interacts with the N-terminal domain of Vo subunit Vph1 in vitro. RAVE–V1 complexes, like isolated V1, have no MgATPase activity, suggesting that RAVE cannot reverse V1 inhibition generated by rotation of subunit H and entrapment of MgADP that occur upon disassembly. However, purified RAVE can accelerate reassembly of V1 carrying a mutant subunit H incapable of inhibition with Vo complexes reconstituted into lipid nanodiscs, consistent with its catalytic activity in vivo. These results provide new insights into the possible order of events in V-ATPase reassembly and the roles of the RAVE complex in each event.
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Affiliation(s)
- Michael C Jaskolka
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Maureen Tarsio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anne M Smardon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Md Murad Khan
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA.
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Zarin T, Strome B, Peng G, Pritišanac I, Forman-Kay JD, Moses AM. Identifying molecular features that are associated with biological function of intrinsically disordered protein regions. eLife 2021; 10:e60220. [PMID: 33616531 PMCID: PMC7932695 DOI: 10.7554/elife.60220] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
In previous work, we showed that intrinsically disordered regions (IDRs) of proteins contain sequence-distributed molecular features that are conserved over evolution, despite little sequence similarity that can be detected in alignments (Zarin et al., 2019). Here, we aim to use these molecular features to predict specific biological functions for individual IDRs and identify the molecular features within them that are associated with these functions. We find that the predictable functions are diverse. Examining the associated molecular features, we note some that are consistent with previous reports and identify others that were previously unknown. We experimentally confirm that elevated isoelectric point and hydrophobicity, features that are positively associated with mitochondrial localization, are necessary for mitochondrial targeting function. Remarkably, increasing isoelectric point in a synthetic IDR restores weak mitochondrial targeting. We believe feature analysis represents a new systematic approach to understand how biological functions of IDRs are specified by their protein sequences.
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Affiliation(s)
- Taraneh Zarin
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Bob Strome
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Gang Peng
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Iva Pritišanac
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
- Program in Molecular Medicine, Hospital for Sick ChildrenTorontoCanada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, Hospital for Sick ChildrenTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - Alan M Moses
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
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25
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Kang JY, Kim S, Kim J, Kang NG, Yang CS, Min SJ, Kim JW. Cell-penetrating peptide-conjugated lipid/polymer hybrid nanovesicles for endoplasmic reticulum-targeting intracellular delivery. J Mater Chem B 2021; 9:464-470. [DOI: 10.1039/d0tb01940b] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An ER-targeting, intracellular delivery approach that utilizes cell-penetrating peptide-conjugated lipid/polymer hybrid nanovehicles is proposed.
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Affiliation(s)
- Jeong Yi Kang
- School of Chemical Engineering
- Sungkyunkwan University
- Suwon 16419
- Republic of Korea
| | - Seulgi Kim
- School of Chemical Engineering
- Sungkyunkwan University
- Suwon 16419
- Republic of Korea
| | - Juhyeon Kim
- Department of Chemistry
- Korea University
- Seoul 02841
- Republic of Korea
| | - Nae-Gyu Kang
- R&D Campus
- LG Household & Health Care
- Seoul 07795
- Republic of Korea
| | - Chul-Su Yang
- Department of Molecular & Life Science
- Hanyang University
- Ansan 15588
- Republic of Korea
| | - Sun-Joon Min
- Department of Chemical & Molecular Engineering/Applied Chemistry, Center for Bionano Intelligence Education and Research
- Hanyang University
- Ansan 15588
- Republic of Korea
| | - Jin Woong Kim
- School of Chemical Engineering
- Sungkyunkwan University
- Suwon 16419
- Republic of Korea
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26
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Pechmann S. Programmed Trade-offs in Protein Folding Networks. Structure 2020; 28:1361-1375.e4. [PMID: 33053320 DOI: 10.1016/j.str.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/25/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
Molecular chaperones as specialized protein quality control enzymes form the core of cellular protein homeostasis. How chaperones selectively interact with their substrate proteins thus allocate their overall limited capacity remains poorly understood. Here, I present an integrated analysis of sequence and structural determinants that define interactions of protein domains as the basic protein folding unit with the Saccharomyces cerevisiae Hsp70 Ssb. Structural homologs of single-domain proteins that differentially interact with Ssb for de novo folding were found to systematically differ in complexity of their folding landscapes, selective use of nonoptimal codons, and presence of short discriminative sequences, thus highlighting pervasive trade-offs in chaperone-assisted protein folding landscapes. However, short discriminative sequences were found to contribute by far the strongest signal toward explaining Ssb interactions. This observation suggested that some chaperone interactions may be directly programmed in the amino acid sequences rather than responding to folding challenges, possibly for regulatory advantages.
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Affiliation(s)
- Sebastian Pechmann
- Département de biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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27
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TheCellVision.org: A Database for Visualizing and Mining High-Content Cell Imaging Projects. G3-GENES GENOMES GENETICS 2020; 10:3969-3976. [PMID: 32934016 PMCID: PMC7642925 DOI: 10.1534/g3.120.401570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Advances in genome engineering and high throughput imaging technologies have enabled genome-scale screens of single cells for a variety of phenotypes, including subcellular morphology and protein localization. We constructed TheCellVision.org, a freely available and web-accessible image visualization and data browsing tool that serves as a central repository for fluorescence microscopy images and associated quantitative data produced by high-content screening experiments. Currently, TheCellVision.org hosts ∼575,590 images and associated analysis results from two published high-content screening (HCS) projects focused on the budding yeast Saccharomyces cerevisiae TheCellVision.org allows users to access, visualize and explore fluorescence microscopy images, and to search, compare, and extract data related to subcellular compartment morphology, protein abundance, and localization. Each dataset can be queried independently or as part of a search across multiple datasets using the advanced search option. The website also hosts computational tools associated with the available datasets, which can be applied to other projects and cell systems, a feature we demonstrate using published images of mammalian cells. Providing access to HCS data through websites such as TheCelllVision.org enables new discovery and independent re-analyses of imaging data.
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Mallik S, Tawfik DS. Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PLoS Comput Biol 2020; 16:e1008145. [PMID: 32853212 PMCID: PMC7480870 DOI: 10.1371/journal.pcbi.1008145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/09/2020] [Accepted: 07/12/2020] [Indexed: 12/16/2022] Open
Abstract
Oligomeric proteins are central to life. Duplication and divergence of their genes is a key evolutionary driver, also because duplications can yield very different outcomes. Given a homomeric ancestor, duplication can yield two paralogs that form two distinct homomeric complexes, or a heteromeric complex comprising both paralogs. Alternatively, one paralog remains a homomer while the other acquires a new partner. However, so far, conflicting trends have been noted with respect to which fate dominates, primarily because different methods and criteria are being used to assign the interaction status of paralogs. Here, we systematically analyzed all Saccharomyces cerevisiae and Escherichia coli oligomeric complexes that include paralogous proteins. We found that the proportions of homo-hetero duplication fates strongly depend on a variety of factors, yet that nonetheless, rigorous filtering gives a consistent picture. In E. coli about 50%, of the paralogous pairs appear to have retained the ancestral homomeric interaction, whereas in S. cerevisiae only ~10% retained a homomeric state. This difference was also observed when unique complexes were counted instead of paralogous gene pairs. We further show that this difference is accounted for by multiple cases of heteromeric yeast complexes that share common ancestry with homomeric bacterial complexes. Our analysis settles contradicting trends and conflicting previous analyses, and provides a systematic and rigorous pipeline for delineating the fate of duplicated oligomers in any organism for which protein-protein interaction data are available. About half of all proteins assemble as oligomers, either by self-interaction (homomers) or via interaction with another protein (heteromers). The latter can be unrelated, yet, quite commonly, the interacting proteins are paralogs, namely two genes that arose by gene duplication. Indeed, while a homomer is encoded by a single gene, heteromers demand two genes as a minimum. Duplication can therefore yield two discrete homomeric complexes or a single heteromer. Do paralogs tend to retain the ancestral homomeric interaction, or do they mostly diverge into heteromeric complexes? Despite several studies addressing this question, to date, we lack a systematic, rigorous approach for delineating the oligomeric fates of paralogs on an organism scale. To this end, we developed a new pipeline for analysis of molecular interaction databases that includes various filtering steps and unambiguous definitions of all possible oligomeric fates. Applying this method to Escherichia coli and Saccharomyces cerevisiae we noted that paralogous pairs tend to remain homomeric in the former while in the latter heteromeric complexes dominate. We consequently note a systematic trend of homomeric bacterial proteins diverging into heteromeric complexes in eukaryotes.
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Affiliation(s)
- Saurav Mallik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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29
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Ivashov V, Zimmer J, Schwabl S, Kahlhofer J, Weys S, Gstir R, Jakschitz T, Kremser L, Bonn GK, Lindner H, Huber LA, Leon S, Schmidt O, Teis D. Complementary α-arrestin-ubiquitin ligase complexes control nutrient transporter endocytosis in response to amino acids. eLife 2020; 9:e58246. [PMID: 32744498 PMCID: PMC7449699 DOI: 10.7554/elife.58246] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/01/2020] [Indexed: 12/12/2022] Open
Abstract
How cells adjust nutrient transport across their membranes is incompletely understood. Previously, we have shown that S. cerevisiae broadly re-configures the nutrient transporters at the plasma membrane in response to amino acid availability, through endocytosis of sugar- and amino acid transporters (AATs) (Müller et al., 2015). A genome-wide screen now revealed that the selective endocytosis of four AATs during starvation required the α-arrestin family protein Art2/Ecm21, an adaptor for the ubiquitin ligase Rsp5, and its induction through the general amino acid control pathway. Art2 uses a basic patch to recognize C-terminal acidic sorting motifs in AATs and thereby instructs Rsp5 to ubiquitinate proximal lysine residues. When amino acids are in excess, Rsp5 instead uses TORC1-activated Art1 to detect N-terminal acidic sorting motifs within the same AATs, which initiates exclusive substrate-induced endocytosis. Thus, amino acid excess or starvation activate complementary α-arrestin-Rsp5-complexes to control selective endocytosis and adapt nutrient acquisition.
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Affiliation(s)
- Vasyl Ivashov
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Johannes Zimmer
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Sinead Schwabl
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Jennifer Kahlhofer
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Sabine Weys
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Ronald Gstir
- ADSI – Austrian Drug Screening Institute GmbHInnsbruckAustria
| | | | - Leopold Kremser
- Division of Clinical Biochemistry, ProteinMicroAnalysis Facility, Medical University of InnsbruckInnsbruckAustria
| | - Günther K Bonn
- ADSI – Austrian Drug Screening Institute GmbHInnsbruckAustria
| | - Herbert Lindner
- Division of Clinical Biochemistry, ProteinMicroAnalysis Facility, Medical University of InnsbruckInnsbruckAustria
| | - Lukas A Huber
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
- ADSI – Austrian Drug Screening Institute GmbHInnsbruckAustria
| | - Sebastien Leon
- Université de Paris, CNRS, Institut Jacques MonodParisFrance
| | - Oliver Schmidt
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - David Teis
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
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30
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A Genome-Wide Screen for Genes Affecting Spontaneous Direct-Repeat Recombination in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2020; 10:1853-1867. [PMID: 32265288 PMCID: PMC7263696 DOI: 10.1534/g3.120.401137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Homologous recombination is an important mechanism for genome integrity maintenance, and several homologous recombination genes are mutated in various cancers and cancer-prone syndromes. However, since in some cases homologous recombination can lead to mutagenic outcomes, this pathway must be tightly regulated, and mitotic hyper-recombination is a hallmark of genomic instability. We performed two screens in Saccharomyces cerevisiae for genes that, when deleted, cause hyper-recombination between direct repeats. One was performed with the classical patch and replica-plating method. The other was performed with a high-throughput replica-pinning technique that was designed to detect low-frequency events. This approach allowed us to validate the high-throughput replica-pinning methodology independently of the replicative aging context in which it was developed. Furthermore, by combining the two approaches, we were able to identify and validate 35 genes whose deletion causes elevated spontaneous direct-repeat recombination. Among these are mismatch repair genes, the Sgs1-Top3-Rmi1 complex, the RNase H2 complex, genes involved in the oxidative stress response, and a number of other DNA replication, repair and recombination genes. Since several of our hits are evolutionarily conserved, and repeated elements constitute a significant fraction of mammalian genomes, our work might be relevant for understanding genome integrity maintenance in humans.
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31
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Dubreuil B, Sass E, Nadav Y, Heidenreich M, Georgeson JM, Weill U, Duan Y, Meurer M, Schuldiner M, Knop M, Levy ED. YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries. Nucleic Acids Res 2020; 47:D1245-D1249. [PMID: 30357397 PMCID: PMC6324022 DOI: 10.1093/nar/gky941] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/18/2018] [Indexed: 01/06/2023] Open
Abstract
The ability to measure the abundance and visualize the localization of proteins across the yeast proteome has stimulated hypotheses on gene function and fueled discoveries. While the classic C’ tagged GFP yeast library has been the only resource for over a decade, the recent development of the SWAT technology has led to the creation of multiple novel yeast libraries where new-generation fluorescent reporters are fused at the N’ and C’ of open reading frames. Efficient access to these data requires a user interface to visualize and compare protein abundance, localization and co-localization across cells, strains, and libraries. YeastRGB (www.yeastRGB.org) was designed to address such a need, through a user-friendly interface that maximizes informative content. It employs a compact display where cells are cropped and tiled together into a ‘cell-grid.’ This representation enables viewing dozens of cells for a particular strain within a display unit, and up to 30 display units can be arrayed on a standard high-definition screen. Additionally, the display unit allows users to control zoom-level and overlay of images acquired using different color channels. Thus, YeastRGB makes comparing abundance and localization efficient, across thousands of cells from different strains and libraries.
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Affiliation(s)
- Benjamin Dubreuil
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ehud Sass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yotam Nadav
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Meta Heidenreich
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joseph M Georgeson
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yuanqiang Duan
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Matthias Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,Cell Morphogenesis and Signal Transduction, DKFZ-ZMBH Alliance and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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32
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Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H. Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition. Nucleic Acids Res 2020; 47:10942-10955. [PMID: 31586407 PMCID: PMC6847430 DOI: 10.1093/nar/gkz856] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/20/2019] [Accepted: 10/02/2019] [Indexed: 12/18/2022] Open
Abstract
The complex between Trm7 and Trm734 (Trm7–Trm734) from Saccharomyces cerevisiae catalyzes 2′-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7–Trm734 complex. Purified recombinant Trm7–Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7–Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7–Trm734. Small angle X-ray scattering reveals that Trm7–Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 β-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7–Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.
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Affiliation(s)
- Akira Hirata
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Keisuke Okada
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Kazuaki Yoshii
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Shiraishi
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Shinya Saijo
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kento Yonezawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
- To whom correspondence should be addressed. Tel: +81 89 927 8548; Fax: +81 89 927 9941;
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Lundberg E, Borner GHH. Spatial proteomics: a powerful discovery tool for cell biology. Nat Rev Mol Cell Biol 2020; 20:285-302. [PMID: 30659282 DOI: 10.1038/s41580-018-0094-y] [Citation(s) in RCA: 264] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein subcellular localization is tightly controlled and intimately linked to protein function in health and disease. Capturing the spatial proteome - that is, the localizations of proteins and their dynamics at the subcellular level - is therefore essential for a complete understanding of cell biology. Owing to substantial advances in microscopy, mass spectrometry and machine learning applications for data analysis, the field is now mature for proteome-wide investigations of spatial cellular regulation. Studies of the human proteome have begun to reveal a complex architecture, including single-cell variations, dynamic protein translocations, changing interaction networks and proteins localizing to multiple compartments. Furthermore, several studies have successfully harnessed the power of comparative spatial proteomics as a discovery tool to unravel disease mechanisms. We are at the beginning of an era in which spatial proteomics finally integrates with cell biology and medical research, thereby paving the way for unbiased systems-level insights into cellular processes. Here, we discuss current methods for spatial proteomics using imaging or mass spectrometry and specifically highlight global comparative applications. The aim of this Review is to survey the state of the field and also to encourage more cell biologists to apply spatial proteomics approaches.
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Affiliation(s)
- Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden. .,Department of Genetics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Georg H H Borner
- Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany.
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Chapal M, Mintzer S, Brodsky S, Carmi M, Barkai N. Resolving noise-control conflict by gene duplication. PLoS Biol 2019; 17:e3000289. [PMID: 31756183 PMCID: PMC6874299 DOI: 10.1371/journal.pbio.3000289] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/21/2019] [Indexed: 12/15/2022] Open
Abstract
Gene duplication promotes adaptive evolution in two main ways: allowing one duplicate to evolve a new function and splitting ancestral functions between the duplicates. The second scenario may resolve adaptive conflicts that can rise when one gene performs different functions. In an apparent departure from both scenarios, low-expressing transcription factor (TF) duplicates commonly bind to the same DNA motifs and act in overlapping conditions. To examine for possible benefits of this apparent redundancy, we examined the Msn2 and Msn4 duplicates in budding yeast. We show that Msn2,4 function as one unit by inducing the same set of target genes in overlapping conditions. Yet, the two-factor composition allows this unit's expression to be both environmentally responsive and with low noise, resolving an adaptive conflict that limits expression of single genes. We propose that duplication can provide adaptive benefit through cooperation rather than functional divergence, allowing two-factor dynamics with beneficial properties that cannot be achieved by a single gene.
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Affiliation(s)
- Michal Chapal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sefi Mintzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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35
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Slee JA, Levine TP. Systematic prediction of FFAT motifs across eukaryote proteomes identifies nucleolar and eisosome proteins with the predicted capacity to form bridges to the endoplasmic reticulum. ACTA ACUST UNITED AC 2019; 2:1-21. [PMID: 31777772 DOI: 10.1177/2515256419883136] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The endoplasmic reticulum (ER), the most pervasive organelle, exchanges information and material with many other organelles, but the extent of its inter-organelle connections and the proteins that form bridges are not well known. The integral ER membrane protein VAMP-associated protein (VAP) is found in multiple bridges, interacting with many proteins that contain a short linear motif consisting of "two phenylalanines in an acidic tract" (FFAT). The VAP-FFAT interaction is the most common mechanism by which cytoplasmic proteins, particularly inter-organelle bridges, target the ER. Therefore, predicting new FFAT motifs may both find new individual peripheral ER proteins and identify new routes of communication involving the ER. Here we searched for FFAT motifs across whole proteomes. The excess of eukaryotic proteins with FFAT motifs over background was ≥0.8%, suggesting this is the minimum number of peripheral ER proteins. In yeast, where VAP was previously known to bind 4 proteins with FFAT motifs, a detailed analysis of a subset of proteins predicted 20 FFAT motifs. Extrapolating these findings to the whole proteome estimated the number of FFAT motifs in yeast at approximately 50-55 (0.9% of proteome). Among these previously unstudied FFAT motifs, most have known functions outside the ER, so could be involved in inter-organelle communication. Many of these can target well-characterised membrane contact sites, however some are in nucleoli and eisosomes, organelles previously unknown to have molecular bridges to the ER. We speculate that the nucleolar and eisosomal proteins with predicted motifs may function while bridging to the ER, indicating novel ER-nucleolus and ER-eisosome routes of inter-organelle communication.
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Affiliation(s)
| | - Timothy P Levine
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
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36
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mRNA structure determines modification by pseudouridine synthase 1. Nat Chem Biol 2019; 15:966-974. [PMID: 31477916 PMCID: PMC6764900 DOI: 10.1038/s41589-019-0353-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/22/2019] [Indexed: 01/28/2023]
Abstract
Pseudouridine (Ψ) is a post-transcriptional RNA modification that alters RNA-RNA and RNA-protein interactions that affect gene expression. mRNA pseudouridylation was recently discovered as a widespread and conserved phenomenon, but the mechanisms responsible for selective, regulated pseudouridylation of specific sequences within mRNAs were unknown. Here, we have revealed new mRNA targets for five pseudouridine synthases and probed the determinants of mRNA target recognition by the predominant mRNA pseudouridylating enzyme, Pus1, by developing high-throughput kinetic analysis of pseudouridylation in vitro. Combining computational prediction and rational mutational analysis revealed an RNA structural motif that is both necessary and sufficient for mRNA pseudouridylation. Applying this structural context information predicted hundreds of additional mRNA targets, that we showed were pseudouridylated in vivo. These results demonstrate a structure-dependent mode of mRNA target recognition by a conserved pseudouridine synthase and implicate modulation of RNA structure as the likely mechanism to regulate mRNA pseudouridylation.
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Louzoun‐Zada S, Jaber QZ, Fridman M. Guiding Drugs to Target‐Harboring Organelles: Stretching Drug‐Delivery to a Higher Level of Resolution. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sivan Louzoun‐Zada
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Qais Z. Jaber
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Micha Fridman
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv 6997801 Israel
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Louzoun-Zada S, Jaber QZ, Fridman M. Guiding Drugs to Target-Harboring Organelles: Stretching Drug-Delivery to a Higher Level of Resolution. Angew Chem Int Ed Engl 2019; 58:15584-15594. [PMID: 31237741 DOI: 10.1002/anie.201906284] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Indexed: 01/04/2023]
Abstract
The ratio between the dose of drug required for optimal efficacy and the dose that causes toxicity is referred to as the therapeutic window. This ratio can be increased by directing the drug to the diseased tissue or pathogenic cell. For drugs targeting fungi and malignant cells, the therapeutic window can be further improved by increasing the resolution of drug delivery to the specific organelle that harbors the drug's target. Organelle targeting is challenging and is, therefore, an under-exploited strategy. Here we provide an overview of recent advances in control of the subcellular distribution of small molecules with the focus on chemical modifications. Highlighted are recent examples of active and passive organelle-specific targeting by incorporation of organelle-directing molecular determinants or by chemical modifications of the pharmacophore. The outstanding potential that lies in the development of organelle-specific drugs is becoming increasingly apparent.
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Affiliation(s)
- Sivan Louzoun-Zada
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Qais Z Jaber
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
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Bykov YS, Cohen N, Gabrielli N, Manenschijn H, Welsch S, Chlanda P, Kukulski W, Patil KR, Schuldiner M, Briggs JAG. High-throughput ultrastructure screening using electron microscopy and fluorescent barcoding. J Cell Biol 2019; 218:2797-2811. [PMID: 31289126 PMCID: PMC6683748 DOI: 10.1083/jcb.201812081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/28/2019] [Accepted: 06/11/2019] [Indexed: 01/24/2023] Open
Abstract
Genetic screens using high-throughput fluorescent microscopes have generated large datasets, contributing many cell biological insights. Such approaches cannot tackle questions requiring knowledge of ultrastructure below the resolution limit of fluorescent microscopy. Electron microscopy (EM) reveals detailed cellular ultrastructure but requires time-consuming sample preparation, limiting throughput. Here we describe a robust method for screening by high-throughput EM. Our approach uses combinations of fluorophores as barcodes to uniquely mark each cell type in mixed populations and correlative light and EM (CLEM) to read the barcode of each cell before it is imaged by EM. Coupled with an easy-to-use software workflow for correlation, segmentation, and computer image analysis, our method, called "MultiCLEM," allows us to extract and analyze multiple cell populations from each EM sample preparation. We demonstrate several uses for MultiCLEM with 15 different yeast variants. The methodology is not restricted to yeast, can be scaled to higher throughput, and can be used in multiple ways to enable EM to become a powerful screening technique.
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Affiliation(s)
- Yury S Bykov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Nir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Natalia Gabrielli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hetty Manenschijn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sonja Welsch
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Petr Chlanda
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wanda Kukulski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kiran R Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany .,Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Fukuoka H, Kawase T, Oku M, Yurimoto H, Sakai Y, Hayakawa T, Nakagawa T. Peroxisomal Fba2p and Tal2p complementally function in the rearrangement pathway for xylulose 5-phosphate in the methylotrophic yeast Pichia pastoris. J Biosci Bioeng 2019; 128:33-38. [DOI: 10.1016/j.jbiosc.2019.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/08/2019] [Accepted: 01/14/2019] [Indexed: 10/27/2022]
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41
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Serrano-Bueno G, Madroñal JM, Manzano-López J, Muñiz M, Pérez-Castiñeira JR, Hernández A, Serrano A. Nuclear proteasomal degradation of Saccharomyces cerevisiae inorganic pyrophosphatase Ipp1p, a nucleocytoplasmic protein whose stability depends on its subcellular localization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1019-1033. [DOI: 10.1016/j.bbamcr.2019.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/13/2019] [Accepted: 02/26/2019] [Indexed: 12/29/2022]
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Ledesma L, Sandoval E, Cruz-Martínez U, Escalante AM, Mejía S, Moreno-Álvarez P, Ávila E, García E, Coello G, Torres-Quiroz F. YAAM: Yeast Amino Acid Modifications Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4797096. [PMID: 29688347 PMCID: PMC7206644 DOI: 10.1093/database/bax099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 12/06/2017] [Indexed: 01/29/2023]
Abstract
Proteins are dynamic molecules that regulate a myriad of cellular functions; these functions may be regulated by protein post-translational modifications (PTMs) that mediate the activity, localization and interaction partners of proteins. Thus, understanding the meaning of a single PTM or the combination of several of them is essential to unravel the mechanisms of protein regulation. Yeast Amino Acid Modification (YAAM) (http://yaam.ifc.unam.mx) is a comprehensive database that contains information from 121 921 residues of proteins, which are post-translationally modified in the yeast model Saccharomyces cerevisiae. All the PTMs contained in YAAM have been confirmed experimentally. YAAM database maps PTM residues in a 3D canvas for 680 proteins with a known 3D structure. The structure can be visualized and manipulated using the most common web browsers without the need for any additional plugin. The aim of our database is to retrieve and organize data about the location of modified amino acids providing information in a concise but comprehensive and user-friendly way, enabling users to find relevant information on PTMs. Given that PTMs influence almost all aspects of the biology of both healthy and diseased cells, identifying and understanding PTMs is critical in the study of molecular and cell biology. YAAM allows users to perform multiple searches, up to three modifications at the same residue, giving the possibility to explore possible regulatory mechanism for some proteins. Using YAAM search engine, we found three different PTMs of lysine residues involved in protein translation. This suggests an important regulatory mechanism for protein translation that needs to be further studied. Database URL: http://yaam.ifc.unam.mx/
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Affiliation(s)
- Leonardo Ledesma
- Unidad de Cómputo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Eduardo Sandoval
- Unidad de Cómputo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Uriel Cruz-Martínez
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Ana María Escalante
- Unidad de Cómputo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Selene Mejía
- Coordinación de Difusión y Divulgación, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Paola Moreno-Álvarez
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Emiliano Ávila
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Erik García
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Gerardo Coello
- Unidad de Cómputo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Francisco Torres-Quiroz
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
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Benhamou RI, Bibi M, Berman J, Fridman M. Localizing Antifungal Drugs to the Correct Organelle Can Markedly Enhance their Efficacy. Angew Chem Int Ed Engl 2018; 57:6230-6235. [PMID: 29575397 PMCID: PMC7035955 DOI: 10.1002/anie.201802509] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 11/06/2022]
Abstract
A critical aspect of drug design is optimal target inhibition by specifically delivering the drug molecule not only to the target tissue or cell but also to its therapeutically active site within the cell. This study demonstrates, as a proof of principle, that drug efficacy can be increased considerably by a structural modification that targets it to the relevant organelle. Specifically, by varying the fluorescent dye segment an antifungal azole was directed from the fungal cell mitochondria to the endoplasmic reticulum (ER), the organelle that harbors the drug target. The ER-localized azole displayed up to two orders of magnitude improved antifungal activity and also dramatically reduced the growth of drug-tolerant fungal subpopulations in a panel of Candida species, which are the most prevalent causes of serious human fungal infections. The principle underlying the "target organelle localization" approach provides a new paradigm to improve drug potency and replenish the limited pipeline of antifungal drugs.
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Affiliation(s)
- Raphael I Benhamou
- School of Chemistry, Raymond&Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Maayan Bibi
- Dept. of Molecular Microbiology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Judith Berman
- Dept. of Molecular Microbiology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond&Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
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Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact. Nat Commun 2018; 9:1761. [PMID: 29720625 PMCID: PMC5932058 DOI: 10.1038/s41467-018-03957-8] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/22/2018] [Indexed: 12/15/2022] Open
Abstract
The understanding that organelles are not floating in the cytosol, but rather held in an organized yet dynamic interplay through membrane contact sites, is altering the way we grasp cell biological phenomena. However, we still have not identified the entire repertoire of contact sites, their tethering molecules and functions. To systematically characterize contact sites and their tethering molecules here we employ a proximity detection method based on split fluorophores and discover four potential new yeast contact sites. We then focus on a little-studied yet highly disease-relevant contact, the Peroxisome-Mitochondria (PerMit) proximity, and uncover and characterize two tether proteins: Fzo1 and Pex34. We genetically expand the PerMit contact site and demonstrate a physiological function in β-oxidation of fatty acids. Our work showcases how systematic analysis of contact site machinery and functions can deepen our understanding of these structures in health and disease.
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Benhamou RI, Bibi M, Berman J, Fridman M. Localizing Antifungal Drugs to the Correct Organelle Can Markedly Enhance their Efficacy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Raphael I. Benhamou
- School of Chemistry, Raymond&Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Maayan Bibi
- Dept. of Molecular Microbiology & Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Judith Berman
- Dept. of Molecular Microbiology & Biotechnology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Micha Fridman
- School of Chemistry, Raymond&Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv 6997801 Israel
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46
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Lu AX, Chong YT, Hsu IS, Strome B, Handfield LF, Kraus O, Andrews BJ, Moses AM. Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins. eLife 2018; 7:e31872. [PMID: 29620521 PMCID: PMC5935485 DOI: 10.7554/elife.31872] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/30/2018] [Indexed: 01/29/2023] Open
Abstract
The evaluation of protein localization changes on a systematic level is a powerful tool for understanding how cells respond to environmental, chemical, or genetic perturbations. To date, work in understanding these proteomic responses through high-throughput imaging has catalogued localization changes independently for each perturbation. To distinguish changes that are targeted responses to the specific perturbation or more generalized programs, we developed a scalable approach to visualize the localization behavior of proteins across multiple experiments as a quantitative pattern. By applying this approach to 24 experimental screens consisting of nearly 400,000 images, we differentiated specific responses from more generalized ones, discovered nuance in the localization behavior of stress-responsive proteins, and formed hypotheses by clustering proteins that have similar patterns. Previous approaches aim to capture all localization changes for a single screen as accurately as possible, whereas our work aims to integrate large amounts of imaging data to find unexpected new cell biology.
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Affiliation(s)
- Alex X Lu
- Department of Computer ScienceUniversity of TorontoTorontoCanada
| | - Yolanda T Chong
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
| | - Ian Shen Hsu
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Bob Strome
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | | | - Oren Kraus
- Department of Electrical and Computer EngineeringUniversity of TorontoTorontoCanada
| | - Brenda J Andrews
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
| | - Alan M Moses
- Department of Computer ScienceUniversity of TorontoTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
- Center for Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoCanada
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Cabral M, Cheng X, Singh S, Ivessa AS. Absence of Non-histone Protein Complexes at Natural Chromosomal Pause Sites Results in Reduced Replication Pausing in Aging Yeast Cells. Cell Rep 2017; 17:1747-1754. [PMID: 27829146 DOI: 10.1016/j.celrep.2016.10.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/08/2016] [Accepted: 10/14/2016] [Indexed: 11/26/2022] Open
Abstract
There is substantial evidence that genomic instability increases during aging. Replication pausing (and stalling) at difficult-to-replicate chromosomal sites may induce genomic instability. Interestingly, in aging yeast cells, we observed reduced replication pausing at various natural replication pause sites (RPSs) in ribosomal DNA (rDNA) and non-rDNA locations (e.g., silent replication origins and tRNA genes). The reduced pausing occurs independent of the DNA helicase Rrm3p, which facilitates replication past these non-histone protein-complex-bound RPSs, and is independent of the deacetylase Sir2p. Conditions of caloric restriction (CR), which extend life span, also cause reduced replication pausing at the 5S rDNA and at tRNA genes. In aged and CR cells, the RPSs are less occupied by their specific non-histone protein complexes (e.g., the preinitiation complex TFIIIC), likely because members of these complexes have primarily cytosolic localization. These conditions may lead to reduced replication pausing and may lower replication stress at these sites during aging.
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Affiliation(s)
- Marleny Cabral
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Xin Cheng
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Sukhwinder Singh
- Pathology and Laboratory Medicine/Flow Cytometry and Immunology Core Laboratory, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA.
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An Overview of data science uses in bioimage informatics. Methods 2017; 115:110-118. [DOI: 10.1016/j.ymeth.2016.12.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/09/2016] [Accepted: 12/30/2016] [Indexed: 01/17/2023] Open
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Kowalec P, Fronk J, Kurlandzka A. The Irr1/Scc3 protein implicated in chromosome segregation in Saccharomyces cerevisiae has a dual nuclear-cytoplasmic localization. Cell Div 2017; 12:1. [PMID: 28077952 PMCID: PMC5223379 DOI: 10.1186/s13008-016-0027-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/15/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Correct chromosome segregation depends on the sister chromatid cohesion complex. The essential, evolutionarily conserved regulatory protein Irr1/Scc3, is responsible for the complex loading onto DNA and for its removal. We found that, unexpectedly, Irr1 is present not only in the nucleus but also in the cytoplasm. RESULTS We show that Irr1 protein is enriched in the cytoplasm upon arrest of yeast cells in G1 phase following nitrogen starvation, diauxic shift or α-factor action, and also during normal cell cycle. Despite the presence of numerous Crm1-dependent export signals, the cytoplasmic pool of Irr1 is not derived through export from the nucleus but instead is simply retained in the cytoplasm. Cytoplasmic Irr1 interacts with the Imi1 protein implicated in glutathione homeostasis and mitochondrial integrity. CONCLUSIONS Besides regulation of the sister chromatid cohesion complex in the nucleus Irr1 appears to have an additional role in the cytoplasm, possibly through interaction with the cytoplasmic protein Imi1.
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Affiliation(s)
- Piotr Kowalec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Jan Fronk
- Department of Molecular Biology, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Kurlandzka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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50
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Bredeweg EL, Pomraning KR, Dai Z, Nielsen J, Kerkhoven EJ, Baker SE. A molecular genetic toolbox for Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:2. [PMID: 28066508 PMCID: PMC5210315 DOI: 10.1186/s13068-016-0687-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/13/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND Yarrowia lipolytica is an ascomycete yeast used in biotechnological research for its abilities to secrete high concentrations of proteins and accumulate lipids. Genetic tools have been made in a variety of backgrounds with varying similarity to a comprehensively sequenced strain. RESULTS We have developed a set of genetic and molecular tools in order to expand capabilities of Y. lipolytica for both biological research and industrial bioengineering applications. In this work, we generated a set of isogenic auxotrophic strains with decreased non-homologous end joining for targeted DNA incorporation. Genome sequencing, assembly, and annotation of this genetic background uncovers previously unidentified genes in Y. lipolytica. To complement these strains, we constructed plasmids with Y. lipolytica-optimized superfolder GFP for targeted overexpression and fluorescent tagging. We used these tools to build the "Yarrowia lipolytica Cell Atlas," a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells. CONCLUSIONS These molecular and isogenetic tools are useful for live assessment of organelle-specific protein expression, and for localization of lipid biosynthetic enzymes or other proteins in Y. lipolytica. This work provides the Yarrowia community with tools for cell biology and metabolism research in Y. lipolytica for further development of biofuels and natural products.
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Affiliation(s)
- Erin L. Bredeweg
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
| | - Kyle R. Pomraning
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Ziyu Dai
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
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