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Gassaway BM, Huttlin EL, Huntsman EM, Yaron-Barir TM, Johnson JL, Kurmi K, Cantley LC, Paulo JA, Ringel AE, Gygi SP, Haigis MC. Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay. Mol Cell Proteomics 2024:100801. [PMID: 38880243 DOI: 10.1016/j.mcpro.2024.100801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
T cell activation is a complex biological process of naïve cells maturing into effector cells. Proteomic and phospho-proteomic approaches have provided critical insights into this process, yet it is not always clear how changes in individual proteins or phosphorylation sites have functional significance. Here, we developed the Phosphorylation Integrated Thermal Shift Assay (PITSA) that combines the measurement of protein or phosphorylation site abundance and thermal stability into a single TMT experiment and apply this method to study T cell activation. We quantified the abundance and thermal stability of over 7,500 proteins and 5,000 phosphorylation sites, and identified significant differences in chromatin-related, TCR signaling, DNA repair, and proliferative phosphoproteins. PITSA may be applied to a wide range of biological contexts to generate hypotheses as to which proteins or phosphorylation sites are functionally regulated in a given system, as well as the mechanisms by which this regulation may occur.
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Affiliation(s)
- Brandon M Gassaway
- Department of Cell Biology, Harvard Medical School; Boston, MA; Department of Chemistry and Biochemistry, Brigham Young University; Provo, UT
| | | | - Emily M Huntsman
- Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine; New York, NY
| | - Tomer M Yaron-Barir
- Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine; New York, NY; Columbia University Vagelos College of Physicians and Surgeons; New York, NY
| | - Jared L Johnson
- Department of Cell Biology, Harvard Medical School; Boston, MA; Dana Farber Cancer Institute; Boston, MA
| | - Kiran Kurmi
- Department of Cell Biology, Harvard Medical School; Boston, MA
| | - Lewis C Cantley
- Department of Cell Biology, Harvard Medical School; Boston, MA; Dana Farber Cancer Institute; Boston, MA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School; Boston, MA
| | - Alison E Ringel
- Department of Cell Biology, Harvard Medical School; Boston, MA; Ragon Institute of Mass General, MIT, and Harvard; Cambridge, MA; Department of Biology, Massachusetts Institute of Technology; Cambridge, MA; Koch Institute for Integrative Cancer Research; Cambridge, MA.
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School; Boston, MA.
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School; Boston, MA.
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2
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Manzoor Y, Aouida M, Ramadoss R, Moovarkumudalvan B, Ahmed N, Sulaiman AA, Mohanty A, Ali R, Mifsud B, Ramotar D. Loss of the yeast transporter Agp2 upregulates the pleiotropic drug-resistant pump Pdr5 and confers resistance to the protein synthesis inhibitor cycloheximide. PLoS One 2024; 19:e0303747. [PMID: 38776347 PMCID: PMC11111045 DOI: 10.1371/journal.pone.0303747] [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: 02/09/2024] [Accepted: 04/30/2024] [Indexed: 05/24/2024] Open
Abstract
The transmembrane protein Agp2, initially shown as a transporter of L-carnitine, mediates the high-affinity transport of polyamines and the anticancer drug bleomycin-A5. Cells lacking Agp2 are hyper-resistant to polyamine and bleomycin-A5. In these earlier studies, we showed that the protein synthesis inhibitor cycloheximide blocked the uptake of bleomycin-A5 into the cells suggesting that the drug uptake system may require de novo synthesis. However, our recent findings demonstrated that cycloheximide, instead, induced rapid degradation of Agp2, and in the absence of Agp2 cells are resistant to cycloheximide. These observations raised the possibility that the degradation of Agp2 may allow the cell to alter its drug resistance network to combat the toxic effects of cycloheximide. In this study, we show that membrane extracts from agp2Δ mutants accentuated several proteins that were differentially expressed in comparison to the parent. Mass spectrometry analysis of the membrane extracts uncovered the pleiotropic drug efflux pump, Pdr5, involved in the efflux of cycloheximide, as a key protein upregulated in the agp2Δ mutant. Moreover, a global gene expression analysis revealed that 322 genes were differentially affected in the agp2Δ mutant versus the parent, including the prominent PDR5 gene and genes required for mitochondrial function. We further show that Agp2 is associated with the upstream region of the PDR5 gene, leading to the hypothesis that cycloheximide resistance displayed by the agp2Δ mutant is due to the derepression of the PDR5 gene.
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Affiliation(s)
- Yusra Manzoor
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Ramya Ramadoss
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, India
| | - Balasubramanian Moovarkumudalvan
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, India
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Nisar Ahmed
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Abdallah Alhaj Sulaiman
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Ashima Mohanty
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Reem Ali
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Borbala Mifsud
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Dindial Ramotar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
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3
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Nguyen V, Li Y, Lu T. Emergence of Orchestrated and Dynamic Metabolism of Saccharomyces cerevisiae. ACS Synth Biol 2024; 13:1442-1453. [PMID: 38657170 PMCID: PMC11103795 DOI: 10.1021/acssynbio.3c00542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Microbial metabolism is a fundamental cellular process that involves many biochemical events and is distinguished by its emergent properties. While the molecular details of individual reactions have been increasingly elucidated, it is not well understood how these reactions are quantitatively orchestrated to produce collective cellular behaviors. Here we developed a coarse-grained, systems, and dynamic mathematical framework, which integrates metabolic reactions with signal transduction and gene regulation to dissect the emergent metabolic traits of Saccharomyces cerevisiae. Our framework mechanistically captures a set of characteristic cellular behaviors, including the Crabtree effect, diauxic shift, diauxic lag time, and differential growth under nutrient-altered environments. It also allows modular expansion for zooming in on specific pathways for detailed metabolic profiles. This study provides a systems mathematical framework for yeast metabolic behaviors, providing insights into yeast physiology and metabolic engineering.
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Affiliation(s)
- Viviana Nguyen
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yifei Li
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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4
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Dilmetz BA, Desire CT, Meneses J, Klingler-Hoffmann M, Young C, Hoffmann P. Impact of propagation time on yeast physiology during bottle conditioning of beer on an industrial scale. Food Chem 2024; 435:137655. [PMID: 37806202 DOI: 10.1016/j.foodchem.2023.137655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/27/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023]
Abstract
Bottle conditioning occurs when yeast and a fermentable extract are added to beer prior to packaging. Aside from ethanol and carbon dioxide production, this process can minimize the production of off-flavors and increase the shelf-life of beer. The advantages of bottle conditioning rely on the yeast being able to quickly referment the beer and maintain viability during storage. In this study, a commercial ale yeast was propagated in wort on a large scale (30 hL) for 24 h or 72 h and seeded into pale ale beer for bottle conditioning. We found that yeast propagated until the post-diauxic shift (72 h) provided better longevity in the bottle and improved foam stability compared to the 24 h propagated yeast. At the time of seeding, yeast propagated for 72 h showed an upregulation of proteins involved in cellular respiration and general stress pathways that may indicate responses toward mitigating cellular stress levels.
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Affiliation(s)
- Brooke A Dilmetz
- Clinical & Health Sciences, University of South Australia, Adelaide 5000, Australia.
| | - Christopher T Desire
- Future Industries Institute, University of South Australia, Mawson Lakes 5095, Australia.
| | - Jon Meneses
- Coopers Brewery Ltd, Regency Park, 5010, Australia.
| | | | - Clifford Young
- Clinical & Health Sciences, University of South Australia, Adelaide 5000, Australia.
| | - Peter Hoffmann
- Clinical & Health Sciences, University of South Australia, Adelaide 5000, Australia.
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5
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Niphadkar S, Karinje L, Laxman S. The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and enables adaptation to glucose depletion. PLoS Genet 2024; 20:e1011202. [PMID: 38452140 PMCID: PMC10950219 DOI: 10.1371/journal.pgen.1011202] [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: 10/31/2023] [Revised: 03/19/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
To sustain growth in changing nutrient conditions, cells reorganize outputs of metabolic networks and appropriately reallocate resources. Signaling by reversible protein phosphorylation can control such metabolic adaptations. In contrast to kinases, the functions of phosphatases that enable metabolic adaptation as glucose depletes are poorly studied. Using a Saccharomyces cerevisiae deletion screen, we identified the PP2A-like phosphatase Ppg1 as required for appropriate carbon allocations towards gluconeogenic outputs-trehalose, glycogen, UDP-glucose, UDP-GlcNAc-after glucose depletion. This Ppg1 function is mediated via regulation of the assembly of the Far complex-a multi-subunit complex that tethers to the ER and mitochondrial outer membranes forming localized signaling hubs. The Far complex assembly is Ppg1 catalytic activity-dependent. Ppg1 regulates the phosphorylation status of multiple ser/thr residues on Far11 to enable the proper assembly of the Far complex. The assembled Far complex is required to maintain gluconeogenic outputs after glucose depletion. Glucose in turn regulates Far complex amounts. This Ppg1-mediated Far complex assembly, and Ppg1-Far complex dependent control of gluconeogenic outputs enables adaptive growth under glucose depletion. Our study illustrates how protein dephosphorylation is required for the assembly of a multi-protein scaffold present in localized cytosolic pools, to thereby alter gluconeogenic flux and enable cells to metabolically adapt to nutrient fluctuations.
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Affiliation(s)
- Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lavanya Karinje
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
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6
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Solari CA, Ortolá Martínez MC, Fernandez JM, Bates C, Cueto G, Valacco MP, Morales-Polanco F, Moreno S, Rossi S, Ashe MP, Portela P. Riboproteome remodeling during quiescence exit in Saccharomyces cerevisiae. iScience 2024; 27:108727. [PMID: 38235324 PMCID: PMC10792236 DOI: 10.1016/j.isci.2023.108727] [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: 02/02/2023] [Revised: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
The quiescent state is the prevalent mode of cellular life in most cells. Saccharomyces cerevisiae is a useful model for studying the molecular basis of the cell cycle, quiescence, and aging. Previous studies indicate that heterogeneous ribosomes show a specialized translation function to adjust the cellular proteome upon a specific stimulus. Using nano LC-MS/MS, we identified 69 of the 79 ribosomal proteins (RPs) that constitute the eukaryotic 80S ribosome during quiescence. Our study shows that the riboproteome is composed of 444 accessory proteins comprising cellular functions such as translation, protein folding, amino acid and glucose metabolism, cellular responses to oxidative stress, and protein degradation. Furthermore, the stoichiometry of both RPs and accessory proteins on ribosome particles is different depending on growth conditions and among monosome and polysome fractions. Deficiency of different RPs resulted in defects of translational capacity, suggesting that ribosome composition can result in changes in translational activity during quiescence.
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Affiliation(s)
- Clara A. Solari
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - María Clara Ortolá Martínez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Juan M. Fernandez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Christian Bates
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Gerardo Cueto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (CONICET-UBA), Buenos Aires, Argentina
| | - María Pía Valacco
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Fabián Morales-Polanco
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Silvia Moreno
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Mark P. Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
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7
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Reuter C, Hauf L, Imdahl F, Sen R, Vafadarnejad E, Fey P, Finger T, Jones NG, Walles H, Barquist L, Saliba AE, Groeber-Becker F, Engstler M. Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms. Nat Commun 2023; 14:7660. [PMID: 37996412 PMCID: PMC10667367 DOI: 10.1038/s41467-023-43437-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Transmission of Trypanosoma brucei by tsetse flies involves the deposition of the cell cycle-arrested metacyclic life cycle stage into mammalian skin at the site of the fly's bite. We introduce an advanced human skin equivalent and use tsetse flies to naturally infect the skin with trypanosomes. We detail the chronological order of the parasites' development in the skin by single-cell RNA sequencing and find a rapid activation of metacyclic trypanosomes and differentiation to proliferative parasites. Here we show that after the establishment of a proliferative population, the parasites enter a reversible quiescent state characterized by slow replication and a strongly reduced metabolism. We term these quiescent trypanosomes skin tissue forms, a parasite population that may play an important role in maintaining the infection over long time periods and in asymptomatic infected individuals.
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Affiliation(s)
- Christian Reuter
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, Wuerzburg, Germany
| | - Laura Hauf
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Fabian Imdahl
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
- Core Unit Systems Medicine, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Rituparno Sen
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Ehsan Vafadarnejad
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Philipp Fey
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Tamara Finger
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Nicola G Jones
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Heike Walles
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
- Core Facility Tissue Engineering, Otto-von-Guericke University, Magdeburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
- Institute of Molecular Infection Biology (IMIB), Faculty of Medicine, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Florian Groeber-Becker
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, Wuerzburg, Germany
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany.
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8
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Nguyen V, Xue P, Li Y, Zhao H, Lu T. Controlling circuitry underlies the growth optimization of Saccharomyces cerevisiae. Metab Eng 2023; 80:173-183. [PMID: 37739159 PMCID: PMC11089650 DOI: 10.1016/j.ymben.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Microbial growth emerges from coordinated synthesis of various cellular components from limited resources. In Saccharomyces cerevisiae, cyclic AMP (cAMP)-mediated signaling is shown to orchestrate cellular metabolism; however, it remains unclear quantitatively how the controlling circuit drives resource partition and subsequently shapes biomass growth. Here we combined experiment with mathematical modeling to dissect the signaling-mediated growth optimization of S. cerevisiae. We showed that, through cAMP-mediated control, the organism achieves maximal or nearly maximal steady-state growth during the utilization of multiple tested substrates as well as under perturbations impairing glucose uptake. However, the optimal cAMP concentration varies across cases, suggesting that different modes of resource allocation are adopted for varied conditions. Under settings with nutrient alterations, S. cerevisiae tunes its cAMP level to dynamically reprogram itself to realize rapid adaptation. Moreover, to achieve growth maximization, cells employ additional regulatory systems such as the GCN2-mediated amino acid control. This study establishes a systematic understanding of global resource allocation in S. cerevisiae, providing insights into quantitative yeast physiology as well as metabolic strain engineering for biotechnological applications.
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Affiliation(s)
- Viviana Nguyen
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pu Xue
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yifei Li
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ting Lu
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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9
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Lanz MC, Zhang S, Swaffer MP, Hernández Götz L, McCarty F, Ziv I, Jarosz DF, Elias JE, Skotheim JM. Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562558. [PMID: 37905015 PMCID: PMC10614910 DOI: 10.1101/2023.10.16.562558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how size influences cell physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be biochemically different. Here, we corroborate these results in mouse hepatocytes and extend our analysis using yeast. We find that size-dependent proteome changes are highly conserved and mostly independent of metabolic state. As eukaryotic cells grow larger, the dilution of the genome elicits a starvation-like proteome phenotype, suggesting that growth in large cells is limited by the genome in a manner analogous to a limiting nutrient. We also demonstrate that the proteomes of replicatively-aged yeast are primarily determined by their large size. Overall, our data suggest that genome concentration is a universal determinant of proteome content in growing cells.
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10
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Rossio V, Liu X, Paulo JA. Comparative Proteomic Analysis of Two Commonly Used Laboratory Yeast Strains: W303 and BY4742. Proteomes 2023; 11:30. [PMID: 37873872 PMCID: PMC10594481 DOI: 10.3390/proteomes11040030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a powerful model system that is often used to expand our understanding of cellular processes and biological functions. Although many genetically well-characterized laboratory strains of S. cerevisiae are available, they may have different genetic backgrounds which can confound data interpretation. Here, we report a comparative whole-proteome analysis of two common laboratory yeast background strains, W303 and BY4742, in both exponential and stationary growth phases using isobaric-tag-based mass spectrometry to highlight differences in proteome complexity. We quantified over 4400 proteins, hundreds of which showed differences in abundance between strains and/or growth phases. Moreover, we used proteome-wide protein abundance to profile the mating type of the strains used in the experiment, the auxotrophic markers, and associated metabolic pathways, as well as to investigate differences in particular classes of proteins, such as the pleiotropic drug resistance (PDR) proteins. This study is a valuable resource that offers insight into mechanistic differences between two common yeast background strains and can be used as a guide to select a background that is best suited for addressing a particular biological question.
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Affiliation(s)
- Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA;
| | | | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA;
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11
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Knöringer K, Groh C, Krämer L, Stein KC, Hansen KG, Zimmermann J, Morgan B, Herrmann JM, Frydman J, Boos F. The unfolded protein response of the endoplasmic reticulum supports mitochondrial biogenesis by buffering nonimported proteins. Mol Biol Cell 2023; 34:ar95. [PMID: 37379206 PMCID: PMC10551703 DOI: 10.1091/mbc.e23-05-0205] [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: 06/01/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
Almost all mitochondrial proteins are synthesized in the cytosol and subsequently targeted to mitochondria. The accumulation of nonimported precursor proteins occurring upon mitochondrial dysfunction can challenge cellular protein homeostasis. Here we show that blocking protein translocation into mitochondria results in the accumulation of mitochondrial membrane proteins at the endoplasmic reticulum, thereby triggering the unfolded protein response (UPRER). Moreover, we find that mitochondrial membrane proteins are also routed to the ER under physiological conditions. The level of ER-resident mitochondrial precursors is enhanced by import defects as well as metabolic stimuli that increase the expression of mitochondrial proteins. Under such conditions, the UPRER is crucial to maintain protein homeostasis and cellular fitness. We propose the ER serves as a physiological buffer zone for those mitochondrial precursors that cannot be immediately imported into mitochondria while engaging the UPRER to adjust the ER proteostasis capacity to the extent of precursor accumulation.
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Affiliation(s)
| | - Carina Groh
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Lena Krämer
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Kevin C. Stein
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Katja G. Hansen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Jannik Zimmermann
- Institute of Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, 66123 Saarbrücken, Germany
| | - Bruce Morgan
- Institute of Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, 66123 Saarbrücken, Germany
| | | | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Felix Boos
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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12
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Ridder MD, van den Brandeler W, Altiner M, Daran-Lapujade P, Pabst M. Proteome dynamics during transition from exponential to stationary phase under aerobic and anaerobic conditions in yeast. Mol Cell Proteomics 2023; 22:100552. [PMID: 37076048 DOI: 10.1016/j.mcpro.2023.100552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/23/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used eukaryotic model organism and a promising cell factory for industry. However, despite decades of research, the regulation of its metabolism is not yet fully understood, and its complexity represents a major challenge for engineering and optimising biosynthetic routes. Recent studies have demonstrated the potential of resource and proteomic allocation data in enhancing models for metabolic processes. However, comprehensive and accurate proteome dynamics data that can be used for such approaches are still very limited. Therefore, we performed a quantitative proteome dynamics study to comprehensively cover the transition from exponential to stationary phase for both aerobically and anaerobically grown yeast cells. The combination of highly controlled reactor experiments, biological replicates and standardised sample preparation procedures ensured reproducibility and accuracy. Additionally, we selected the CEN.PK lineage for our experiments because of its relevance for both fundamental and applied research. Together with the prototrophic, standard haploid strain CEN.PK113-7D, we also investigated an engineered strain with genetic minimisation of the glycolytic pathway, resulting in the quantitative assessment of 54 proteomes. The anaerobic cultures showed remarkably less proteome-level changes compared to the aerobic cultures, during transition from the exponential to the stationary phase as a consequence of the lack of the diauxic shift in the absence of oxygen. These results support the notion that anaerobically growing cells lack resources to adequately adapt to starvation. This proteome dynamics study constitutes an important step towards better understanding of the impact of glucose exhaustion and oxygen on the complex proteome allocation process in yeast. Finally, the established proteome dynamics data provide a valuable resource for the development of resource allocation models as well as for metabolic engineering efforts.
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Affiliation(s)
- Maxime den Ridder
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wiebeke van den Brandeler
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Meryem Altiner
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Martin Pabst
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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13
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Peng G, Hu K, Shang X, Li W, Dou F. The phosphorylation status of Hsp82 regulates mitochondrial homeostasis during glucose sensing in Saccharomyces cerevisiae. J Mol Biol 2023; 435:168106. [PMID: 37068581 DOI: 10.1016/j.jmb.2023.168106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/19/2023]
Abstract
Sensing extracellular glucose, budding yeast switches from aerobic glycolysis to oxidative phosphorylation to adapt to environmental changes. During the conversion of metabolic mode, mitochondrial function and morphology change significantly. Mitochondria are the main supply factories of energy for various life activities in cells. However, the research on the signal pathways from glucose sensing to changes in mitochondrial function and morphology is still scarce and worthy of further exploration. In this study, we found that in addition to the known involvement of molecular chaperone Hsp82 in stress response during the conversion of metabolic mode, the phosphorylation status of Hsp82 at S485 residue regulates mitochondrial function and morphology to maintain mitochondrial homeostasis. The Hsp82S485A mutant that mimics dephosphorylation at S485 residue showed abnormal growth phenotypes related to mitochondrial defects, such as the petite phenotype, slow growth rates, and inability to use non-fermentable carbon sources. Further exploring the causes of growth defects, we found that the Hsp82S485A mutant caused mitochondrial dysfunction, including a decrease in cellular oxygen consumption rate, defects in mitochondrial electron transport chain, decreased mitochondrial membrane potential and complete loss of mtDNA. Furthermore, the Hsp82S485A mutant displayed fragmented or globular mitochondria, which may be responsible for its mitochondrial dysfunction. Our findings suggested that the phosphorylation status of Hsp82 at S485 residue might regulate mitochondrial function and morphology by affecting the stability of mitochondrial fission and fusion-related proteins. Thus, Hsp82 might be a key molecule in the signal pathway from glucose sensing to changes in mitochondrial function and morphology.
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Affiliation(s)
- Guanzu Peng
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Kaiyu Hu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xuan Shang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wanjie Li
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Fei Dou
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China.
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14
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Liu X, Rossio V, Gygi SP, Paulo JA. Enriching Cysteine-Containing Peptides Using a Sulfhydryl-Reactive Alkylating Reagent with a Phosphonic Acid Group and Immobilized Metal Affinity Chromatography. J Proteome Res 2023; 22:1270-1279. [PMID: 36971515 PMCID: PMC10311885 DOI: 10.1021/acs.jproteome.2c00806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The reduction of disulfide bonds and their subsequent alkylation are commonplace in typical proteomics workflows. Here, we highlight a sulfhydryl-reactive alkylating reagent with a phosphonic acid group (iodoacetamido-LC-phosphonic acid, 6C-CysPAT) that facilitates the enrichment of cysteine-containing peptides for isobaric tag-based proteome abundance profiling. Specifically, we profile the proteome of the SH-SY5Y human cell line following 24 h treatments with two proteasome inhibitors (bortezomib and MG-132) in a tandem mass tag (TMT)pro9-plex experiment. We acquire three datasets─(1) Cys-peptide enriched, (2) the unbound complement, and (3) the non-depleted control─and compare the peptides and proteins quantified in each dataset, with emphasis on Cys-containing peptides. The data show that enrichment using 6C-Cys phosphonate adaptable tag (6C-CysPAT) can quantify over 38,000 Cys-containing peptides in 5 h with >90% specificity. In addition, our combined dataset provides the research community with a resource of over 9900 protein abundance profiles exhibiting the effects of two different proteasome inhibitors. Overall, the seamless incorporation of alkylation by 6C-CysPAT into a current TMT-based workflow permits the enrichment of a Cys-containing peptide subproteome. The acquisition of this "mini-Cys" dataset can be used to preview and assess the quality of a deep, fractionated dataset.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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15
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Kamrad S, Correia-Melo C, Szyrwiel L, Aulakh SK, Bähler J, Demichev V, Mülleder M, Ralser M. Metabolic heterogeneity and cross-feeding within isogenic yeast populations captured by DILAC. Nat Microbiol 2023; 8:441-454. [PMID: 36797484 PMCID: PMC9981460 DOI: 10.1038/s41564-022-01304-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/13/2022] [Indexed: 02/18/2023]
Abstract
Genetically identical cells are known to differ in many physiological parameters such as growth rate and drug tolerance. Metabolic specialization is believed to be a cause of such phenotypic heterogeneity, but detection of metabolically divergent subpopulations remains technically challenging. We developed a proteomics-based technology, termed differential isotope labelling by amino acids (DILAC), that can detect producer and consumer subpopulations of a particular amino acid within an isogenic cell population by monitoring peptides with multiple occurrences of the amino acid. We reveal that young, morphologically undifferentiated yeast colonies contain subpopulations of lysine producers and consumers that emerge due to nutrient gradients. Deconvoluting their proteomes using DILAC, we find evidence for in situ cross-feeding where rapidly growing cells ferment and provide the more slowly growing, respiring cells with ethanol. Finally, by combining DILAC with fluorescence-activated cell sorting, we show that the metabolic subpopulations diverge phenotypically, as exemplified by a different tolerance to the antifungal drug amphotericin B. Overall, DILAC captures previously unnoticed metabolic heterogeneity and provides experimental evidence for the role of metabolic specialization and cross-feeding interactions as a source of phenotypic heterogeneity in isogenic cell populations.
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Affiliation(s)
- Stephan Kamrad
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Clara Correia-Melo
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Lukasz Szyrwiel
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Vadim Demichev
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Michael Mülleder
- Core Facility-High-Throughput Mass Spectrometry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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16
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Holay N, Kennedy BE, Murphy JP, Konda P, Giacomantonio M, Brauer-Chapin T, Paulo JA, Kumar V, Kim Y, Elaghil M, Sisson G, Clements D, Richardson C, Gygi SP, Gujar S. After virus exposure, early bystander naïve CD8 T cell activation relies on NAD + salvage metabolism. Front Immunol 2023; 13:1047661. [PMID: 36818473 PMCID: PMC9932030 DOI: 10.3389/fimmu.2022.1047661] [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: 09/18/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023] Open
Abstract
CD8 T cells play a central role in antiviral immunity. Type I interferons are among the earliest responders after virus exposure and can cause extensive reprogramming and antigen-independent bystander activation of CD8 T cells. Although bystander activation of pre-existing memory CD8 T cells is known to play an important role in host defense and immunopathology, its impact on naïve CD8 T cells remains underappreciated. Here we report that exposure to reovirus, both in vitro or in vivo, promotes bystander activation of naïve CD8 T cells within 24 hours and that this distinct subtype of CD8 T cell displays an innate, antiviral, type I interferon sensitized signature. The induction of bystander naïve CD8 T cells is STAT1 dependent and regulated through nicotinamide phosphoribosyl transferase (NAMPT)-mediated enzymatic actions within NAD+ salvage metabolic biosynthesis. These findings identify a novel aspect of CD8 T cell activation following virus infection with implications for human health and physiology.
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Affiliation(s)
- Namit Holay
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Barry E. Kennedy
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- IMV Inc, Halifax, NS, Canada
| | - J. Patrick Murphy
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Biology, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - Prathyusha Konda
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | | | - Tatjana Brauer-Chapin
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, United States
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, United States
| | | | - Youra Kim
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Mariam Elaghil
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- IMV Inc, Halifax, NS, Canada
| | - Gary Sisson
- Department of Biology, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - Derek Clements
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Christopher Richardson
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Canadian Centre for Vaccinology, IWK Health Centre, Goldbloom Pavilion, Halifax, NS, Canada
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, United States
| | - Shashi Gujar
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
- Cancer Immunotherapy: Innovation & Global Partnerships, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
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17
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Protocol for CAROM: A machine learning tool to predict post-translational regulation from metabolic signatures. STAR Protoc 2022; 3:101799. [PMID: 36340881 PMCID: PMC9630780 DOI: 10.1016/j.xpro.2022.101799] [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] [Indexed: 11/06/2022] Open
Abstract
This protocol describes CAROM, a computational tool that combines genome-scale metabolic networks (GEMs) and machine learning to identify enzyme targets of post-translational modifications (PTMs). Condition-specific enzyme and reaction properties are used to predict targets of phosphorylation and acetylation in multiple organisms. CAROM is influenced by the accuracy of GEMs and associated flux-balance analysis (FBA), which generate the inputs of the model. We demonstrate the protocol using multi-omics data from E. coli. For complete details on the use and execution of this protocol, please refer to Smith et al. (2022).
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18
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Abstract
Most cells live in environments that are permissive for proliferation only a small fraction of the time. Entering quiescence enables cells to survive long periods of nondivision and reenter the cell cycle when signaled to do so. Here, we describe what is known about the molecular basis for quiescence in Saccharomyces cerevisiae, with emphasis on the progress made in the last decade. Quiescence is triggered by depletion of an essential nutrient. It begins well before nutrient exhaustion, and there is extensive crosstalk between signaling pathways to ensure that all proliferation-specific activities are stopped when any one essential nutrient is limiting. Every aspect of gene expression is modified to redirect and conserve resources. Chromatin structure and composition change on a global scale, from histone modifications to three-dimensional chromatin structure. Thousands of proteins and RNAs aggregate, forming unique structures with unique fates, and the cytoplasm transitions to a glass-like state.
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Affiliation(s)
- Linda L Breeden
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
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19
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Schubert OT, Bloom JS, Sadhu MJ, Kruglyak L. Genome-wide base editor screen identifies regulators of protein abundance in yeast. eLife 2022; 11:e79525. [PMID: 36326816 PMCID: PMC9633064 DOI: 10.7554/elife.79525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
Proteins are key molecular players in a cell, and their abundance is extensively regulated not just at the level of gene expression but also post-transcriptionally. Here, we describe a genetic screen in yeast that enables systematic characterization of how protein abundance regulation is encoded in the genome. The screen combines a CRISPR/Cas9 base editor to introduce point mutations with fluorescent tagging of endogenous proteins to facilitate a flow-cytometric readout. We first benchmarked base editor performance in yeast with individual gRNAs as well as in positive and negative selection screens. We then examined the effects of 16,452 genetic perturbations on the abundance of eleven proteins representing a variety of cellular functions. We uncovered hundreds of regulatory relationships, including a novel link between the GAPDH isoenzymes Tdh1/2/3 and the Ras/PKA pathway. Many of the identified regulators are specific to one of the eleven proteins, but we also found genes that, upon perturbation, affected the abundance of most of the tested proteins. While the more specific regulators usually act transcriptionally, broad regulators often have roles in protein translation. Overall, our novel screening approach provides unprecedented insights into the components, scale and connectedness of the protein regulatory network.
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Affiliation(s)
- Olga T Schubert
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
- Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH)ZürichSwitzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
| | - Meru J Sadhu
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
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20
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Schlossarek D, Luzarowski M, Sokołowska EM, Thirumalaikumar VP, Dengler L, Willmitzer L, Ewald JC, Skirycz A. Rewiring of the protein-protein-metabolite interactome during the diauxic shift in yeast. Cell Mol Life Sci 2022; 79:550. [PMID: 36242648 PMCID: PMC9569316 DOI: 10.1007/s00018-022-04569-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/02/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022]
Abstract
In budding yeast Saccharomyces cerevisiae, the switch from aerobic fermentation to respiratory growth is separated by a period of growth arrest, known as the diauxic shift, accompanied by a significant metabolic rewiring, including the derepression of gluconeogenesis and the establishment of mitochondrial respiration. Previous studies reported hundreds of proteins and tens of metabolites accumulating differentially across the diauxic shift transition. To assess the differences in the protein-protein (PPIs) and protein-metabolite interactions (PMIs) yeast samples harvested in the glucose-utilizing, fermentative phase, ethanol-utilizing and early stationary respiratory phases were analysed using isothermal shift assay (iTSA) and a co-fractionation mass spectrometry approach, PROMIS. Whereas iTSA monitors changes in protein stability and is informative towards protein interaction status, PROMIS uses co-elution to delineate putative PPIs and PMIs. The resulting dataset comprises 1627 proteins and 247 metabolites, hundreds of proteins and tens of metabolites characterized by differential thermal stability and/or fractionation profile, constituting a novel resource to be mined for the regulatory PPIs and PMIs. The examples discussed here include (i) dissociation of the core and regulatory particle of the proteasome in the early stationary phase, (ii) the differential binding of a co-factor pyridoxal phosphate to the enzymes of amino acid metabolism and (iii) the putative, phase-specific interactions between proline-containing dipeptides and enzymes of central carbon metabolism.
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Affiliation(s)
- Dennis Schlossarek
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marcin Luzarowski
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
- Core Facility for Mass Spectrometry and Proteomics, ZMBH, Universität Heidelberg, 69120, Heidelberg, Germany.
| | - Ewelina M Sokołowska
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | | | - Lisa Dengler
- Interfaculty Institute of Cell Biology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Lothar Willmitzer
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Jennifer C Ewald
- Interfaculty Institute of Cell Biology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Aleksandra Skirycz
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
- Boyce Thompson Institute, Cornell University, Ithaca, 14850, USA.
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21
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Sultonova M, Blackmore B, Du R, Philips O, Paulo JA, Murphy JP. Integrated changes in thermal stability and proteome abundance during altered nutrient states in Escherichia coli and human cells. Proteomics 2022; 22:e2100254. [PMID: 36082775 PMCID: PMC10782824 DOI: 10.1002/pmic.202100254] [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: 02/22/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/11/2022]
Abstract
Altered thermal solubility measurement techniques are emerging as powerful tools to assess ligand binding, post-translational modification, protein-protein interactions, and many other cellular processes that affect protein state under various cellular conditions. Thermal solubility or stability profiling techniques are enabled on a global proteomic scale by employing isobaric tagging reagents that facilitate multiplexing capacity required to measure changes in the proteome across thermal gradients. Key among these is thermal proteomic profiling (TPP), which requires 8-10 isobaric tags per gradient and generation of multiple proteomic datasets to measure different replicates and conditions. Furthermore, using TPP to measure protein thermal stability state across different conditions may also require measurements of differential protein abundance. Here, we use the proteome integral stability alteration (PISA) assay, a higher throughput version of TPP, to measure global changes in protein thermal stability normalized to their protein abundance. We explore the use of this approach to determine changes in protein state between logarithmic and stationary phase Escherichia coli as well as glucose-starved human Hek293T cells. We observed protein intensity-corrected PISA changes in 290 and 350 proteins due to stationary phase transition in E. coli and glucose starvation, respectively. These data reveal several examples of proteins that were not previously associated with nutrient states by abundance alone. These include E. coli proteins such as putative acyl-CoA dehydrogenase (aidB) and chaperedoxin (cnoX) as well as human RAB vesicle trafficking proteins and many others which may indicate their involvement in metabolic diseases such as cancer.
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Affiliation(s)
- Mukhayyo Sultonova
- Department of Biology, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Beau Blackmore
- Department of Biology, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Ronnie Du
- Department of Biology, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Olivier Philips
- Department of Biology, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - John Patrick Murphy
- Department of Biology, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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22
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Galeota-Sprung B, Fernandez A, Sniegowski P. Changes to the mtDNA copy number during yeast culture growth. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211842. [PMID: 35814911 PMCID: PMC9257595 DOI: 10.1098/rsos.211842] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
We show that the mitochondrial DNA (mtDNA) copy number in growing cultures of the yeast Saccharomyces cerevisiae increases by a factor of up to 4, being lowest (approx. 10 per haploid genome) and stable during rapid fermentative growth, and highest at the end of the respiratory phase. When yeast are grown on glucose, the onset of the mtDNA copy number increase coincides with the early stages of the diauxic shift, and the increase continues through respiration. A lesser yet still substantial copy number increase occurs when yeast are grown on a nonfermentable carbon source, i.e. when there is no diauxic shift. The mtDNA copy number increase during and for some time after the diauxic shift is not driven by an increase in cell size. The copy number increase occurs in both haploid and diploid strains but is markedly attenuated in a diploid wild isolate that is a ready sporulator. Strain-to-strain differences in mtDNA copy number are least apparent in fermentation and most apparent in late respiration or stationary phase. While changes in mitochondrial morphology and function were previously known to accompany changes in physiological state, it had not been previously shown that the mtDNA copy number changes substantially over time in a clonal growing culture. The mtDNA copy number in yeast is therefore a highly dynamic phenotype.
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Affiliation(s)
- Ben Galeota-Sprung
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy Fernandez
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Sniegowski
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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23
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Kennedy BE, Giacomantonio M, Murphy JP, Cutler S, Sadek M, Konda P, Paulo JA, Pathak GP, Renkens SH, Grieve S, Pol J, Gygi SP, Richardson C, Gaston D, Reiman A, Kroemer G, Elnenaei MO, Gujar SA. NAD+ depletion enhances reovirus-induced oncolysis in multiple myeloma. Mol Ther Oncolytics 2022; 24:695-706. [PMID: 35284625 PMCID: PMC8904403 DOI: 10.1016/j.omto.2022.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/17/2022] [Indexed: 11/26/2022] Open
Abstract
Cancer cell energy metabolism plays an important role in dictating the efficacy of oncolysis by oncolytic viruses. To understand the role of multiple myeloma metabolism in reovirus oncolysis, we performed semi-targeted mass spectrometry-based metabolomics on 12 multiple myeloma cell lines and revealed a negative correlation between NAD+ levels and susceptibility to oncolysis. Likewise, a negative correlation was observed between the activity of the rate-limiting NAD+ synthesis enzyme NAMPT and oncolysis. Indeed, depletion of NAD+ levels by pharmacological inhibition of NAMPT using FK866 sensitized several myeloma cell lines to reovirus-induced killing. The myelomas that were most sensitive to this combination therapy expressed a functional p53 and had a metabolic and transcriptomic profile favoring mitochondrial metabolism over glycolysis, with the highest synergistic effect in KMS12 cells. Mechanistically, U-13C-labeled glucose flux, extracellular flux analysis, multiplex proteomics, and cell death assays revealed that the reovirus + FK866 combination caused mitochondrial dysfunction and energy depletion, leading to enhanced autophagic cell death in KMS12 cells. Finally, the combination of reovirus and NAD+ depletion achieved greater antitumor effects in KMS12 tumors in vivo and patient-derived CD138+ multiple myeloma cells. These findings identify NAD+ depletion as a potential combinatorial strategy to enhance the efficacy of oncolytic virus-based therapies in multiple myeloma.
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24
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Smith K, Shen F, Lee HJ, Chandrasekaran S. Metabolic signatures of regulation by phosphorylation and acetylation. iScience 2022; 25:103730. [PMID: 35072016 PMCID: PMC8762462 DOI: 10.1016/j.isci.2021.103730] [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: 06/04/2021] [Revised: 12/15/2021] [Accepted: 12/30/2021] [Indexed: 10/31/2022] Open
Abstract
Acetylation and phosphorylation are highly conserved posttranslational modifications (PTMs) that regulate cellular metabolism, yet how metabolic control is shared between these PTMs is unknown. Here we analyze transcriptome, proteome, acetylome, and phosphoproteome datasets in E. coli, S. cerevisiae, and mammalian cells across diverse conditions using CAROM, a new approach that uses genome-scale metabolic networks and machine learning to classify targets of PTMs. We built a single machine learning model that predicted targets of each PTM in a condition across all three organisms based on reaction attributes (AUC>0.8). Our model predicted phosphorylated enzymes during a mammalian cell-cycle, which we validate using phosphoproteomics. Interpreting the machine learning model using game theory uncovered enzyme properties including network connectivity, essentiality, and condition-specific factors such as maximum flux that differentiate targets of phosphorylation from acetylation. The conserved and predictable partitioning of metabolic regulation identified here between these PTMs may enable rational rewiring of regulatory circuits.
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Affiliation(s)
- Kirk Smith
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fangzhou Shen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ho Joon Lee
- Department of Genetics, Yale University, New Haven, CT 06510, USA.,Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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25
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Rampelt H, Wollweber F, Licheva M, de Boer R, Perschil I, Steidle L, Becker T, Bohnert M, van der Klei I, Kraft C, van der Laan M, Pfanner N. Dual role of Mic10 in mitochondrial cristae organization and ATP synthase-linked metabolic adaptation and respiratory growth. Cell Rep 2022; 38:110290. [PMID: 35081352 PMCID: PMC8810396 DOI: 10.1016/j.celrep.2021.110290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/01/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
Invaginations of the mitochondrial inner membrane, termed cristae, are hubs for oxidative phosphorylation. The mitochondrial contact site and cristae organizing system (MICOS) and the dimeric F1Fo-ATP synthase play important roles in controlling cristae architecture. A fraction of the MICOS core subunit Mic10 is found in association with the ATP synthase, yet it is unknown whether this interaction is of relevance for mitochondrial or cellular functions. Here, we established conditions to selectively study the role of Mic10 at the ATP synthase. Mic10 variants impaired in MICOS functions stimulate ATP synthase oligomerization like wild-type Mic10 and promote efficient inner membrane energization, adaptation to non-fermentable carbon sources, and respiratory growth. Mic10's functions in respiratory growth largely depend on Mic10ATPsynthase, not on Mic10MICOS. We conclude that Mic10 plays a dual role as core subunit of MICOS and as partner of the F1Fo-ATP synthase, serving distinct functions in cristae shaping and respiratory adaptation and growth. Dual role of Mic10 of mitochondrial contact site and cristae organizing system (MICOS) Mic10 binds to mitochondrial ATP synthase and stabilizes higher order assemblies Oligomerization of Mic10 is required for its function in MICOS, not at ATP synthase Mic10 binding to ATP synthase supports metabolic adaptation and respiratory growth
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Affiliation(s)
- Heike Rampelt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Florian Wollweber
- Medical Biochemistry & Molecular Biology, Center for Molecular Signaling, PZMS, Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Rinse de Boer
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700 Groningen, the Netherlands
| | - Inge Perschil
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Liesa Steidle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Maria Bohnert
- Institute of Cell Dynamics and Imaging, Cells in Motion Interfaculty Centre (CiM), University of Münster, 48149 Münster, Germany
| | - Ida van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700 Groningen, the Netherlands
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Martin van der Laan
- Medical Biochemistry & Molecular Biology, Center for Molecular Signaling, PZMS, Faculty of Medicine, Saarland University, 66421 Homburg, Germany.
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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26
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Mardones W, Villarroel CA, Abarca V, Urbina K, Peña TA, Molinet J, Nespolo RF, Cubillos FA. Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing conditions. Microb Biotechnol 2021; 15:967-984. [PMID: 33755311 PMCID: PMC8913853 DOI: 10.1111/1751-7915.13803] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 01/02/2023] Open
Abstract
Although the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multiple Saccharomyces eubayanus genotypes, one of the parents of lager yeast. Then, we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (6 months) and compared them with propagated controls exposed solely to glucose. Propagated populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time‐course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated that de novo genetic variants were produced in all propagated lines, including SNPs, aneuploidies, INDELs and translocations. In addition, the different propagated populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic off‐flavours and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in ‘fast motion’ in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.
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Affiliation(s)
- Wladimir Mardones
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Carlos A Villarroel
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Valentina Abarca
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Kamila Urbina
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Tomás A Peña
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Jennifer Molinet
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Roberto F Nespolo
- Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile.,Institute of Environmental and Evolutionary Science, Universidad Austral de Chile, Valdivia, 5110566, Chile.,Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco A Cubillos
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
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27
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Gassaway BM, Paulo JA, Gygi SP. Categorization of Phosphorylation Site Behavior during the Diauxic Shift in Saccharomyces cerevisiae. J Proteome Res 2021; 20:2487-2496. [PMID: 33630598 DOI: 10.1021/acs.jproteome.0c00943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation has long been recognized as an essential regulator of protein activity, structure, complex formation, and subcellular localization among other cellular mechanisms. However, interpretation of the changes in protein phosphorylation is difficult. To address this difficulty, we measured protein and phosphorylation site changes across 11 points of a time course and developed a method for categorizing phosphorylation site behavior relative to protein level changes using the diauxic shift in yeast as a model and TMT11 sample multiplexing. We classified quantified proteins into behavioral categories that reflected differences in kinase activity, protein complex structure, and growth and metabolic pathway regulation across different phases of the diauxic shift. These data also provide a valuable resource for the study of fermentative versus respiratory growth and set a new benchmark for temporal quantitative proteomics and phosphoproteomics for the diauxic shift in Saccharomyces cerevisiae. Data are available via ProteomeXchange with identifier PXD022741.
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Affiliation(s)
- Brandon M Gassaway
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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28
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Aponte-Ubillus JJ, Barajas D, Sterling H, Aghajanirefah A, Bardliving C, Peltier J, Shamlou P, Roy M, Gold D. Proteome profiling and vector yield optimization in a recombinant adeno-associated virus-producing yeast model. Microbiologyopen 2020; 9:e1136. [PMID: 33166081 PMCID: PMC7755776 DOI: 10.1002/mbo3.1136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/03/2022] Open
Abstract
Recent studies on recombinant adeno‐associated viral (rAAV) vector production demonstrated the generation of infectious viral particles in Saccharomyces cerevisiae. Proof‐of‐concept results showed low vector yields that correlated with low AAV DNA encapsidation rates. In an attempt to understand the host cell response to rAAV production, we profiled proteomic changes throughout the fermentation process by mass spectrometry. By comparing an rAAV‐producing yeast strain with a respective non‐producer control, we identified a subset of yeast host proteins with significantly different expression patterns during the rAAV induction period. Gene ontology enrichment and network interaction analyses identified changes in expression patterns associated mainly with protein folding, as well as amino acid metabolism, gluconeogenesis, and stress response. Specific fold change patterns of heat shock proteins and other stress protein markers suggested the occurrence of a cytosolic unfolded protein response during rAAV protein expression. Also, a correlative increase in proteins involved in response to oxidative stress suggested cellular activities to ameliorate the effects of reactive oxygen species or other oxidants. We tested the functional relevance of the identified host proteins by overexpressing selected protein leads using low‐ and high‐copy number plasmids. Increased vector yields up to threefold were observed in clones where proteins SSA1, SSE1, SSE2, CCP1, GTT1, and RVB2 were overexpressed. Recombinant expression of SSA1 and YDJ insect homologues (HSP40 and HSC70, respectively) in Sf9 cells led to a volumetric vector yield increase of 50% relative to control, which validated the importance of chaperone proteins in rAAV‐producing systems. Overall, these results highlight the utility of proteomic‐based tools for the understanding and optimization of rAAV‐producing recombinant strains.
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Affiliation(s)
- Juan Jose Aponte-Ubillus
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA.,Amgen Bioprocessing Center, Keck Graduate Institute, Claremont, CA, USA
| | - Daniel Barajas
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | - Harry Sterling
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | - Ali Aghajanirefah
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | | | - Joseph Peltier
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | - Parviz Shamlou
- Amgen Bioprocessing Center, Keck Graduate Institute, Claremont, CA, USA
| | - Mimi Roy
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | - Daniel Gold
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
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29
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Zhang T, Gygi SP, Paulo JA. Temporal Proteomic Profiling of SH-SY5Y Differentiation with Retinoic Acid Using FAIMS and Real-Time Searching. J Proteome Res 2020; 20:704-714. [PMID: 33054241 DOI: 10.1021/acs.jproteome.0c00614] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The SH-SY5Y cell line is often used as a surrogate for neurons in cell-based studies. This cell line is frequently differentiated with all-trans retinoic acid (ATRA) over a 7-day period, which confers neuron-like properties to the cells. However, no analysis of proteome remodeling has followed the progress of this transition. Here, we quantitatively profiled over 9400 proteins across a 7-day treatment with retinoic acid using state-of-the-art mass spectrometry-based proteomics technologies, including FAIMS, real-time database searching, and TMTpro16 sample multiplexing. Gene ontology analysis revealed that categories with the highest increases in protein abundance were related to the plasma membrane/extracellular space. To showcase our data set, we surveyed the protein abundance profiles linked to neurofilament bundle assembly, neuron projections, and neuronal cell body formation. These proteins exhibited increases in abundance level, yet we observed multiple patterns among the queried proteins. The data presented represent a rich resource for investigating temporal protein abundance changes in SH-SY5Y cells differentiated with retinoic acid. Moreover, the sample preparation and data acquisition strategies used here can be readily applied to any analogous cell line differentiation analysis.
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Affiliation(s)
- Tian Zhang
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, United States
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30
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Tsvetkov P, Eisen TJ, Heinrich SU, Brune Z, Hallacli E, Newby GA, Kayatekin C, Pincus D, Lindquist S. Persistent Activation of mRNA Translation by Transient Hsp90 Inhibition. Cell Rep 2020; 32:108001. [PMID: 32783929 PMCID: PMC10088179 DOI: 10.1016/j.celrep.2020.108001] [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: 08/09/2018] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022] Open
Abstract
The heat shock protein 90 (Hsp90) chaperone functions as a protein-folding buffer and plays a role promoting the evolution of new heritable traits. To better understand how Hsp90 can affect mRNA translation, we screen more than 1,600 factors involved in mRNA regulation for physical interactions with Hsp90 in human cells. The mRNA binding protein CPEB2 strongly binds Hsp90 via its prion domain. In a yeast model, transient inhibition of Hsp90 results in persistent activation of a CPEB translation reporter even in the absence of exogenous CPEB that persists for 30 generations after the inhibitor is removed. Ribosomal profiling reveals that some endogenous yeast mRNAs, including HAC1, show a persistent change in translation efficiency following transient Hsp90 inhibition. Thus, transient loss of Hsp90 function can promote a nongenetic inheritance of a translational state affecting specific mRNAs, introducing a mechanism by which Hsp90 can promote phenotypic variation.
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Affiliation(s)
- Peter Tsvetkov
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Timothy J Eisen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sven U Heinrich
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Zarina Brune
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Erinc Hallacli
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Greg A Newby
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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31
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Factors affecting yeast ethanol tolerance and fermentation efficiency. World J Microbiol Biotechnol 2020; 36:114. [DOI: 10.1007/s11274-020-02881-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/27/2020] [Indexed: 01/01/2023]
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32
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Shin D, Park J, Han D, Moon JH, Ryu HS, Kim Y. Identification of TUBB2A by quantitative proteomic analysis as a novel biomarker for the prediction of distant metastatic breast cancer. Clin Proteomics 2020; 17:16. [PMID: 32489334 PMCID: PMC7247212 DOI: 10.1186/s12014-020-09280-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/15/2020] [Indexed: 12/20/2022] Open
Abstract
Background Metastasis of breast cancer to distal organs is fatal. However, few studies have identified biomarkers that are associated with distant metastatic breast cancer. Furthermore, the inability of current biomarkers, such as HER2, ER, and PR, to differentiate between distant and nondistant metastatic breast cancers accurately has necessitated the development of novel biomarker candidates. Methods An integrated proteomics approach that combined filter-aided sample preparation, tandem mass tag labeling (TMT), high pH fractionation, and high-resolution MS was applied to acquire in-depth proteomic data from FFPE distant metastatic breast cancer tissues. A bioinformatics analysis was performed with regard to gene ontology and signaling pathways using differentially expressed proteins (DEPs) to examine the molecular characteristics of distant metastatic breast cancer. In addition, real-time polymerase chain reaction (RT-PCR) and invasion/migration assays were performed to validate the differential regulation and function of our protein targets. Results A total of 9441 and 8746 proteins were identified from the pooled and individual sample sets, respectively. Based on our criteria, TUBB2A was selected as a novel biomarker candidate. The metastatic activities of TUBB2A were subsequently validated. In our bioinformatics analysis using DEPs, we characterized the overall molecular features of distant metastasis and measured differences in the molecular functions of distant metastatic breast cancer between breast cancer subtypes. Conclusions Our report is the first study to examine the distant metastatic breast cancer proteome using FFPE tissues. The depth of our dataset allowed us to discover a novel biomarker candidate and a proteomic characteristics of distant metastatic breast cancer. Distinct molecular features of various breast cancer subtypes were also established. Our proteomic data constitute a valuable resource for research on distant metastatic breast cancer.
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Affiliation(s)
- Dongyoon Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehakro, Seoul, 30380 Korea
| | - Joonho Park
- Interdisciplinary Program for Bioengineering, Seoul National University College of Engineering, Seoul, Korea
| | - Dohyun Han
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehakro, Seoul, Korea
| | - Ji Hye Moon
- Department of Pathology, Seoul National University Hospital, 101 Daehakro, Seoul, 03080 Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, 101 Daehakro, Seoul, 03080 Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehakro, Seoul, 30380 Korea.,Interdisciplinary Program for Bioengineering, Seoul National University College of Engineering, Seoul, Korea
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33
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Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. Proc Natl Acad Sci U S A 2020; 117:7524-7535. [PMID: 32184324 PMCID: PMC7132131 DOI: 10.1073/pnas.1918216117] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This work offers a unique portrayal of yeast mitochondria through the characterization of its absolute proteome. The study of biophysical changes in the mitochondrial network associated with proteome profiling, throughout yeast growth and the transition from fermentative to respiratory metabolism, lays out the crucial role this organelle has in balancing the overall metabolic status of the cell. Using proteomic mass spectrometry, state of the art fluorescence microscopy, and lipidomics analysis, these data provide a highly quantitative description of key mitochondrial processes across three states of metabolism. In particular, the work highlights the significant contribution of functional and structural remodeling occurring during the diauxic shift of this subcellular organelle. Saccharomyces cerevisiae constitutes a popular eukaryal model for research on mitochondrial physiology. Being Crabtree-positive, this yeast has evolved the ability to ferment glucose to ethanol and respire ethanol once glucose is consumed. Its transition phase from fermentative to respiratory metabolism, known as the diauxic shift, is reflected by dramatic rearrangements of mitochondrial function and structure. To date, the metabolic adaptations that occur during the diauxic shift have not been fully characterized at the organelle level. In this study, the absolute proteome of mitochondria was quantified alongside precise parametrization of biophysical properties associated with the mitochondrial network using state-of-the-art optical-imaging techniques. This allowed the determination of absolute protein abundances at a subcellular level. By tracking the transformation of mitochondrial mass and volume, alongside changes in the absolute mitochondrial proteome allocation, we could quantify how mitochondria balance their dual role as a biosynthetic hub as well as a center for cellular respiration. Furthermore, our findings suggest that in the transition from a fermentative to a respiratory metabolism, the diauxic shift represents the stage where major structural and functional reorganizations in mitochondrial metabolism occur. This metabolic transition, initiated at the mitochondria level, is then extended to the rest of the yeast cell.
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34
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Krapp A, Hamelin R, Armand F, Chiappe D, Krapp L, Cano E, Moniatte M, Simanis V. Analysis of the S. pombe Meiotic Proteome Reveals a Switch from Anabolic to Catabolic Processes and Extensive Post-transcriptional Regulation. Cell Rep 2020; 26:1044-1058.e5. [PMID: 30673600 DOI: 10.1016/j.celrep.2018.12.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/09/2018] [Accepted: 12/17/2018] [Indexed: 12/31/2022] Open
Abstract
Meiotic progression in S. pombe is regulated by stage-specific gene expression and translation, changes in RNA stability, expression of anti-sense transcripts, and targeted proteolysis of regulatory proteins. We have used SILAC labeling to examine the relative levels of proteins in diploid S. pombe cells during meiosis. Among the 3,268 proteins quantified at all time points, the levels of 880 proteins changed at least 2-fold; the majority of proteins showed stepwise increases or decreases during the meiotic divisions, while some changed transiently. Overall, we observed reductions in proteins involved in anabolism and increases in proteins involved in catabolism. We also observed increases in the levels of proteins of the ESCRT-III complex and revealed a role for ESCRT-III components in chromosome segregation and spore formation. Correlation with studies of meiotic gene expression and ribosome occupancy reveals that many of the changes in steady-state protein levels are post-transcriptional.
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Affiliation(s)
- Andrea Krapp
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, 1015 Lausanne, Switzerland
| | - Romain Hamelin
- EPFL Proteomics Core Facility, EPFL SV PTECH PTP, AI 0149, Station 15, 1015 Lausanne, Switzerland
| | - Florence Armand
- EPFL Proteomics Core Facility, EPFL SV PTECH PTP, AI 0149, Station 15, 1015 Lausanne, Switzerland
| | - Diego Chiappe
- EPFL Proteomics Core Facility, EPFL SV PTECH PTP, AI 0149, Station 15, 1015 Lausanne, Switzerland
| | - Lucien Krapp
- EPFL SV IBI-SV UPDALPE, AAB 1 17, Station 19, 1015 Lausanne, Switzerland
| | - Elena Cano
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, 1015 Lausanne, Switzerland
| | - Marc Moniatte
- EPFL Proteomics Core Facility, EPFL SV PTECH PTP, AI 0149, Station 15, 1015 Lausanne, Switzerland
| | - Viesturs Simanis
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, 1015 Lausanne, Switzerland.
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35
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Boos F, Labbadia J, Herrmann JM. How the Mitoprotein-Induced Stress Response Safeguards the Cytosol: A Unified View. Trends Cell Biol 2020; 30:241-254. [DOI: 10.1016/j.tcb.2019.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/09/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022]
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36
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Mmi1, the Yeast Ortholog of Mammalian Translationally Controlled Tumor Protein (TCTP), Negatively Affects Rapamycin-Induced Autophagy in Post-Diauxic Growth Phase. Cells 2020; 9:cells9010138. [PMID: 31936125 PMCID: PMC7017036 DOI: 10.3390/cells9010138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 12/16/2022] Open
Abstract
Translationally controlled tumor protein (TCTP) is a multifunctional and highly conserved protein from yeast to humans. Recently, its role in non-selective autophagy has been reported with controversial results in mammalian and human cells. Herein we examine the effect of Mmi1, the yeast ortholog of TCTP, on non-selective autophagy in budding yeast Saccharomyces cerevisiae, a well-established model system to monitor autophagy. We induced autophagy by nitrogen starvation or rapamycin addition and measured autophagy by using the Pho8Δ60 and GFP-Atg8 processing assays in WT, mmi1Δ, and in autophagy-deficient strains atg8Δ or atg1Δ. Our results demonstrate that Mmi1 does not affect basal or nitrogen starvation-induced autophagy. However, an increased rapamycin-induced autophagy is detected in mmi1Δ strain when the cells enter the post-diauxic growth phase, and this phenotype can be rescued by inserted wild-type MMI1 gene. Further, the mmi1Δ cells exhibit significantly lower amounts of reactive oxygen species (ROS) in the post-diauxic growth phase compared to WT cells. In summary, our study suggests that Mmi1 negatively affects rapamycin-induced autophagy in the post-diauxic growth phase and supports the role of Mmi1/TCTP as a negative autophagy regulator in eukaryotic cells.
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37
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Thompson A, Wölmer N, Koncarevic S, Selzer S, Böhm G, Legner H, Schmid P, Kienle S, Penning P, Höhle C, Berfelde A, Martinez-Pinna R, Farztdinov V, Jung S, Kuhn K, Pike I. TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set. Anal Chem 2019; 91:15941-15950. [DOI: 10.1021/acs.analchem.9b04474] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andrew Thompson
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London WC1H 9BB, United Kingdom
| | - Nikolai Wölmer
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Sasa Koncarevic
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Stefan Selzer
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Gitte Böhm
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Harald Legner
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Peter Schmid
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Stefan Kienle
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Petra Penning
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Claudia Höhle
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Antje Berfelde
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Roxana Martinez-Pinna
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Vadim Farztdinov
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Stephan Jung
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Karsten Kuhn
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Ian Pike
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London WC1H 9BB, United Kingdom
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38
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Schwämmle V, Jensen ON. VSClust: feature-based variance-sensitive clustering of omics data. Bioinformatics 2019; 34:2965-2972. [PMID: 29635359 DOI: 10.1093/bioinformatics/bty224] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 04/06/2018] [Indexed: 12/25/2022] Open
Abstract
Motivation Data clustering is indispensable for identifying biologically relevant molecular features in large-scale omics experiments with thousands of measurements at multiple conditions. Optimal clustering results yield groups of functionally related features that may include genes, proteins and metabolites in biological processes and molecular networks. Omics experiments typically include replicated measurements of each feature within a given condition to statistically assess feature-specific variation. Current clustering approaches ignore this variation by averaging, which often leads to incorrect cluster assignments. Results We present VSClust that accounts for feature-specific variance. Based on an algorithm derived from fuzzy clustering, VSClust unifies statistical testing with pattern recognition to cluster the data into feature groups that more accurately reflect the underlying molecular and functional behavior. We apply VSClust to artificial and experimental datasets comprising hundreds to >80 000 features across 6-20 different conditions including genomics, transcriptomics, proteomics and metabolomics experiments. VSClust avoids arbitrary averaging methods, outperforms standard fuzzy c-means clustering and simplifies the data analysis workflow in large-scale omics studies. Availability and implementation Download VSClust at https://bitbucket.org/veitveit/vsclust or access it through computproteomics.bmb.sdu.dk/Apps/VSClust. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.,VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.,VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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39
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Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S. Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy. J Proteome Res 2019; 18:2666-2675. [PMID: 31095916 DOI: 10.1021/acs.jproteome.9b00173] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Oncolytic viruses (OVs), known for their cancer-killing characteristics, also overturn tumor-associated defects in antigen presentation through the MHC class I pathway and induce protective neo-antitumor CD8 T cell responses. Nonetheless, whether OVs shape the tumor MHC-I ligandome remains unknown. Here, we investigated if an OV induces the presentation of novel MHC I-bound tumor antigens (termed tumor MHC-I ligands). Using comparative mass spectrometry (MS)-based MHC-I ligandomics, we determined differential tumor MHC-I ligand expression following treatment with oncolytic reovirus in a murine ovarian cancer model. In vitro, we found that reovirus changes the tumor ligandome of cancer cells. Concurrent multiplexed quantitative proteomics revealed that the reovirus-induced changes in tumor MHC-I ligand presentation were mostly independent of their source proteins. In an in vivo model, tumor MHC-I ligands induced by reovirus were detectable not only in tumor tissues but also the spleens (a source of antigen-presenting cells) of tumor-bearing mice. Most importantly, therapy-induced MHC-I ligands stimulated antigen-specific IFNγ responses in antitumor CD8 T cells from mice treated with reovirus. These data show that therapy-induced MHC-I ligands may shape underlying neo-antitumor CD8 T cell responses. As such, they should be considered in strategies promoting the efficacy of OV-based cancer immunotherapies.
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Affiliation(s)
| | | | | | | | - Heiko Schuster
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72074 Tübingen , Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen , Germany
| | - Daniel J Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72074 Tübingen , Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen , Germany
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | | | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72074 Tübingen , Germany
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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40
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Kennedy BE, Murphy JP, Clements DR, Konda P, Holay N, Kim Y, Pathak GP, Giacomantonio MA, Hiani YE, Gujar S. Inhibition of Pyruvate Dehydrogenase Kinase Enhances the Antitumor Efficacy of Oncolytic Reovirus. Cancer Res 2019; 79:3824-3836. [PMID: 31088833 DOI: 10.1158/0008-5472.can-18-2414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/27/2019] [Accepted: 05/10/2019] [Indexed: 11/16/2022]
Abstract
Oncolytic viruses (OV) such as reovirus preferentially infect and kill cancer cells. Thus, the mechanisms that dictate the susceptibility of cancer cells to OV-induced cytotoxicity hold the key to their success in clinics. Here, we investigated whether cancer cell metabolism defines its susceptibility to OV and if OV-induced metabolic perturbations can be therapeutically targeted. Using mass spectrometry-based metabolomics and extracellular flux analysis on a panel of cancer cell lines with varying degrees of susceptibility to reovirus, we found that OV-induced changes in central energy metabolism, pyruvate metabolism, and oxidative stress correlate with their susceptibility to reovirus. In particular, reovirus infection accentuated Warburg-like metabolic perturbations in cell lines relatively resistant to oncolysis. These metabolic changes were facilitated by oxidative stress-induced inhibitory phosphorylation of pyruvate dehydrogenase (PDH) that impaired the routing of pyruvate into the tricarboxylic acid cycle and established a metabolic state unsupportive of OV replication. From the therapeutic perspective, reactivation of PDH in cancer cells that were weakly sensitive for reovirus, either through PDH kinase (PDK) inhibitors dichloroacetate and AZD7545 or short hairpin RNA-specific depletion of PDK1, enhanced the efficacy of reovirus-induced oncolysis in vitro and in vivo. These findings identify targeted metabolic reprogramming as a possible combination strategy to enhance the antitumor effects of OV in clinics. SIGNIFICANCE: This study proposes targeted metabolic reprogramming as a valid combinatorial strategy to enhance the translational efficacy of oncolytic virus-based cancer therapies.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/15/3824/F1.large.jpg.
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Affiliation(s)
- Barry E Kennedy
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Derek R Clements
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Prathyusha Konda
- Department Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Namit Holay
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Youra Kim
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gopal P Pathak
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Yassine El Hiani
- Department Physiology and Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shashi Gujar
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada. .,Department Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Innovative and Collaborative Health Systems Research, IWK Health Centre, Halifax, Nova Scotia, Canada
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41
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Sharif T, Martell E, Dai C, Ghassemi-Rad MS, Hanes MR, Murphy PJ, Margam NN, Parmar HB, Giacomantonio CA, Duncan R, Lee PW, Gujar S. HDAC6 differentially regulates autophagy in stem-like versus differentiated cancer cells. Autophagy 2019; 15:686-706. [PMID: 30444165 PMCID: PMC6526821 DOI: 10.1080/15548627.2018.1548547] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 10/05/2018] [Accepted: 10/31/2018] [Indexed: 12/19/2022] Open
Abstract
Cancer stem-like cells (CSCs), a small population of pluripotent cells residing within heterogeneous tumor mass, remain highly resistant to various chemotherapies as compared to the differentiated cancer cells. It is being postulated that CSCs possess unique molecular mechanisms, such as autophagic homeostasis, that allow CSCs to withstand the therapeutic assaults. Here we demonstrate that HDAC6 inhibition differentially modulates macroautophagy/autophagy in CSCs as compared to that of differentiated cancer cells. Using human and murine CSC models and differentiated cells, we show that the inhibition or knockdown (KD) of HDAC6 decreases CSC pluripotency by downregulating major pluripotency factors POU5F1, NANOG and SOX2. This decreased HDAC6 expression increases ACTB, TUBB3 and CSN2 expression and promotes differentiation in CSCs in an apoptosis-independent manner. Mechanistically, HDAC6 KD in CSCs decreases pluripotency by promoting autophagy, whereas the inhibition of pluripotency via retinoic acid treatment, POU5F1 or autophagy-related gene (ATG7 and ATG12) KD in CSCs decreases HDAC6 expression and promotes differentiation. Interestingly, HDAC6 KD-mediated CSC growth inhibition is further enhanced in the presence of autophagy inducers Tat-Beclin 1 peptide and rapamycin. In contrast to the results observed in CSCs, HDAC6 KD in differentiated breast cancer cells downregulates autophagy and increases apoptosis. Furthermore, the autophagy regulator p-MTOR, upstream negative regulators of p-MTOR (TSC1 and TSC2) and downstream effectors of p-MTOR (p-RPS6KB and p-EIF4EBP1) are differentially regulated in CSCs versus differentiated cancer cells following HDAC6 KD. Overall these data identify the differential regulation of autophagy as a molecular link behind the differing chemo-susceptibility of CSCs and differentiated cancer cells.
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Affiliation(s)
- Tanveer Sharif
- Deaprtment of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Emma Martell
- Deaprtment of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Cathleen Dai
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Mark Robert Hanes
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Patrick J. Murphy
- Deaprtment of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Nandini N. Margam
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Carman A. Giacomantonio
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Surgery, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Roy Duncan
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Patrick W.K. Lee
- Deaprtment of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shashi Gujar
- Deaprtment of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Innovative and Collaborative Health Systems Research, IWK Health Centre, Halifax, Nova Scotia, Canada
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42
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Badr KR, Parente‐Rocha JA, Baeza LC, Ficcadori FS, Souza M, Soares CM, Guissoni ACP, Almeida TN, Cardoso DD. Quantitative proteomic analysis of A549 cells infected with human adenovirus type 2. J Med Virol 2019; 91:1239-1249. [DOI: 10.1002/jmv.25439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Kareem R. Badr
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Juliana A. Parente‐Rocha
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Lilian C. Baeza
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Fabiola S. Ficcadori
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Menira Souza
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Célia M. Soares
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Ana Carla P. Guissoni
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Tâmera N. Almeida
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Divina D. Cardoso
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
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43
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Liu CW, Chi L, Tu P, Xue J, Ru H, Lu K. Quantitative proteomics reveals systematic dysregulations of liver protein metabolism in sucralose-treated mice. J Proteomics 2019; 196:1-10. [DOI: 10.1016/j.jprot.2019.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/26/2018] [Accepted: 01/13/2019] [Indexed: 12/19/2022]
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44
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Murphy JP, Yu Q, Konda P, Paulo JA, Jedrychowski MP, Kowalewski DJ, Schuster H, Kim Y, Clements D, Jain A, Stevanovic S, Gygi SP, Mancias JD, Gujar S. Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin. Anal Chem 2019; 91:5106-5115. [PMID: 30779550 DOI: 10.1021/acs.analchem.8b05616] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MHC-I peptides are intracellular-cleaved peptides, usually 8-11 amino acids in length, which are presented on the cell surface and facilitate CD8+ T cell responses. Despite the appreciation of CD8+ T-cell antitumor immune responses toward improvement in patient outcomes, the MHC-I peptide ligands that facilitate the response are poorly described. Along these same lines, although many therapies have been recognized for their ability to reinvigorate antitumor CD8+ T-cell responses, whether these therapies alter the MHC-I peptide repertoire has not been fully assessed due to the lack of quantitative strategies. We develop a multiplexing platform for screening therapy-induced MHC-I ligands by employing tandem mass tags (TMTs). We applied this approach to measuring responses to doxorubicin, which is known to promote antitumor CD8+ T-cell responses during its therapeutic administration in cancer patients. Using both in vitro and in vivo systems, we show successful relative quantitation of MHC-I ligands using TMT-based multiplexing and demonstrate that doxorubicin induces MHC-I peptide ligands that are largely derived from mitotic progression and cell-cycle proteins. This high-throughput MHC-I ligand discovery approach may enable further explorations to understand how small molecules and other therapies alter MHC-I ligand presentation that may be harnessed for CD8+ T-cell-based immunotherapies.
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Affiliation(s)
- J Patrick Murphy
- Department of Pathology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Qijia Yu
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States
| | - Prathyusha Konda
- Department of Microbiology and Immunology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Mark P Jedrychowski
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States.,Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Daniel J Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72076 Tübingen , Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen , Germany
| | - Heiko Schuster
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72076 Tübingen , Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen , Germany
| | - Youra Kim
- Department of Pathology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Derek Clements
- Department of Pathology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Aditya Jain
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72076 Tübingen , Germany
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joseph D Mancias
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States
| | - Shashi Gujar
- Department of Pathology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada.,Department of Microbiology and Immunology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada.,Centre for Innovative and Collaborative Health Systems Research Quality and System Performance , IWK Health Centre , Halifax , Nova Scotia B3K 6R8 , Canada
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45
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Iwama R, Ohsumi Y. Analysis of autophagy activated during changes in carbon source availability in yeast cells. J Biol Chem 2019; 294:5590-5603. [PMID: 30755486 DOI: 10.1074/jbc.ra118.005698] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 02/05/2019] [Indexed: 11/06/2022] Open
Abstract
Autophagy is a conserved intracellular degradation system in eukaryotes. Recent studies have revealed that autophagy can be induced not only by nitrogen starvation but also by many other stimuli. However, questions persist regarding the types of conditions that induce autophagy, as well as the particular kinds of autophagy that are induced under these specific conditions. In experimental studies, abrupt nutrient changes are often used to induce autophagy. In this study, we investigated autophagy induction in batch culture on low-glucose medium, in which growth of yeast (Saccharomyces cerevisiae) cells is clearly reflected exclusively by carbon source state. In this medium, cells pass sequentially through three stages: glucose-utilizing, ethanol-utilizing, and ethanol-depleted phases. Using GFP cleavage assay by immunoblotting methods, fluorescence microscopy, and transmission electron microscopy ultrastructural analysis, we found that bulk autophagy and endoplasmic reticulum-phagy are induced starting at the ethanol-utilizing phase, and bulk autophagy is activated to a greater extent in the ethanol-depleted phase. Furthermore, we found that mitophagy is induced by ethanol depletion. Microautophagy occurred after glucose depletion and involved incorporation of cytosolic components and lipid droplets into the vacuolar lumen. Moreover, we observed that autophagy-deficient cells grow more slowly in the ethanol-utilizing phase and exhibit a delay in growth resumption when they are shifted to fresh medium from the ethanol-depleted phase. Our findings suggest that distinct types of autophagy are induced in yeast cells undergoing gradual changes in carbon source availability.
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Affiliation(s)
- Ryo Iwama
- From the Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-12 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yoshinori Ohsumi
- From the Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-12 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
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46
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Escalera-Fanjul X, Quezada H, Riego-Ruiz L, González A. Whole-Genome Duplication and Yeast’s Fruitful Way of Life. Trends Genet 2019; 35:42-54. [DOI: 10.1016/j.tig.2018.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/10/2018] [Accepted: 09/27/2018] [Indexed: 01/30/2023]
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47
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Sharif T, Dai C, Martell E, Ghassemi-Rad MS, Hanes MR, Murphy PJ, Kennedy BE, Venugopal C, Subapanditha M, Giacomantonio CA, Marcato P, Singh SK, Gujar S. TAp73 Modifies Metabolism and Positively Regulates Growth of Cancer Stem-Like Cells in a Redox-Sensitive Manner. Clin Cancer Res 2018; 25:2001-2017. [PMID: 30593514 DOI: 10.1158/1078-0432.ccr-17-3177] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/14/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022]
Abstract
PURPOSE Stem-like cancer cells, with characteristic self-renewal abilities, remain highly refractory to various clinical interventions. As such, stemness-inhibiting entities, such as tumor suppressor p53, are therapeutically pursued for their anticancer activities. Interestingly, similar implications for tumor suppressor TAp73 in regulating stemness features within stem-like cancer cells remain unknown.Experimental Design: This study utilizes various in vitro molecular biology techniques, including immunoblotting, qRT-PCR, and mass spectrometry-based proteomics, and metabolomics approaches to study the role of TAp73 in human and murine embryonal carcinoma stem-like cells (ECSLC) as well as human breast cancer stem-like cells (BCSLC). These findings were confirmed using patient-derived brain tumor-initiating cells (BTIC) and in vivo xenograft models. RESULTS TAp73 inhibition decreases the expression of stem cell transcription factors Oct4, Nanog, and Sox-2, as well as tumorsphere formation capacity in ECSLCs. In vivo, TAp73-deficient ECSLCs and BCSLCs demonstrate decreased tumorigenic potential when xenografted in mice. Mechanistically, TAp73 modifies the proline regulatory axis through regulation of enzymes GLS, OAT, and PYCR1 involved in the interconversion of proline-glutamine-ornithine. Further, TAp73 deficiency exacerbates glutamine dependency, enhances accumulation of reactive oxygen species through reduced superoxide dismutase 1 (SOD1) expression, and promotes differentiation by arresting cell cycle and elevating autophagy. Most importantly, the knockdown of TAp73 in CD133HI BTICs, separated from three different glioblastoma patients, strongly decreases the expression of prosurvival factors Sox-2, BMI-1, and SOD1, and profoundly decreases their self-renewal capacity as evidenced through their reduced tumorsphere formation ability. CONCLUSIONS Collectively, we reveal a clinically relevant aspect of cancer cell growth and stemness regulation through TAp73-mediated redox-sensitive metabolic reprogramming.
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Affiliation(s)
- Tanveer Sharif
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Cathleen Dai
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Emma Martell
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Mark Robert Hanes
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Patrick J Murphy
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Barry E Kennedy
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Chitra Venugopal
- McMaster Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Minomi Subapanditha
- McMaster Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Carman A Giacomantonio
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Surgery, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sheila K Singh
- McMaster Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada.,Department of Surgery, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Shashi Gujar
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada. .,Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Innovative and Collaborative Health Systems Research, IWK Health Centre, Halifax, Nova Scotia, Canada
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48
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Liu CW, Chi L, Tu P, Xue J, Ru H, Lu K. Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic. J Proteome Res 2018; 18:970-981. [DOI: 10.1021/acs.jproteome.8b00666] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jingchuan Xue
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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49
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Cerulus B, Jariani A, Perez-Samper G, Vermeersch L, Pietsch JMJ, Crane MM, New AM, Gallone B, Roncoroni M, Dzialo MC, Govers SK, Hendrickx JO, Galle E, Coomans M, Berden P, Verbandt S, Swain PS, Verstrepen KJ. Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources. eLife 2018; 7:e39234. [PMID: 30299256 PMCID: PMC6211830 DOI: 10.7554/elife.39234] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/05/2018] [Indexed: 01/24/2023] Open
Abstract
Cells constantly adapt to environmental fluctuations. These physiological changes require time and therefore cause a lag phase during which the cells do not function optimally. Interestingly, past exposure to an environmental condition can shorten the time needed to adapt when the condition re-occurs, even in daughter cells that never directly encountered the initial condition. Here, we use the molecular toolbox of Saccharomyces cerevisiae to systematically unravel the molecular mechanism underlying such history-dependent behavior in transitions between glucose and maltose. In contrast to previous hypotheses, the behavior does not depend on persistence of proteins involved in metabolism of a specific sugar. Instead, presence of glucose induces a gradual decline in the cells' ability to activate respiration, which is needed to metabolize alternative carbon sources. These results reveal how trans-generational transitions in central carbon metabolism generate history-dependent behavior in yeast, and provide a mechanistic framework for similar phenomena in other cell types.
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Affiliation(s)
- Bram Cerulus
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Abbas Jariani
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Gemma Perez-Samper
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Lieselotte Vermeersch
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Julian MJ Pietsch
- Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Matthew M Crane
- Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
- Department of PathologyUniversity of WashingtonWashingtonUnited States
| | - Aaron M New
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Brigida Gallone
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Miguel Roncoroni
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Maria C Dzialo
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Sander K Govers
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Jhana O Hendrickx
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Eva Galle
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Maarten Coomans
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Pieter Berden
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Sara Verbandt
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Peter S Swain
- Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Kevin J Verstrepen
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
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50
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Dannenmaier S, Stiller SB, Morgenstern M, Lübbert P, Oeljeklaus S, Wiedemann N, Warscheid B. Complete Native Stable Isotope Labeling by Amino Acids of Saccharomyces cerevisiae for Global Proteomic Analysis. Anal Chem 2018; 90:10501-10509. [PMID: 30102515 PMCID: PMC6300314 DOI: 10.1021/acs.analchem.8b02557] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Knowledge about the functions of individual proteins on a system-wide level is crucial to fully understand molecular mechanisms underlying cellular processes. A considerable part of the proteome across all organisms is still poorly characterized. Mass spectrometry is an efficient technology for the global study of proteins. One of the most prominent methods for accurate proteome-wide comparative quantification is stable isotope labeling by amino acids in cell culture (SILAC). However, application of SILAC to prototrophic organisms such as Saccharomyces cerevisiae, also known as baker's yeast, is compromised since they are able to synthesize all amino acids on their own. Here, we describe an advanced strategy, termed 2nSILAC, that allows for in vivo labeling of prototrophic baker's yeast using heavy arginine and lysine under fermentable and respiratory growth conditions, making it a suitable tool for the global study of protein functions. This generic 2nSILAC strategy allows for directly using and systematically screening yeast mutant strain collections available to the scientific community. We exemplarily demonstrate its high potential by analyzing the effects of mitochondrial gene deletions in mitochondrial fractions using quantitative mass spectrometry revealing the role of Coi1 for the assembly of cytochrome c oxidase (respiratory chain complex IV).
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