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Hamid MHBA, Cespedes PF, Jin C, Chen JL, Gileadi U, Antoun E, Liang Z, Gao F, Teague R, Manoharan N, Maldonado-Perez D, Khalid-Alham N, Cerundolo L, Ciaoca R, Hester SS, Pinto-Fernández A, Draganov SD, Vendrell I, Liu G, Yao X, Kvalvaag A, Dominey-Foy DCC, Nanayakkara C, Kanellakis N, Chen YL, Waugh C, Clark SA, Clark K, Sopp P, Rahman NM, Verrill C, Kessler BM, Ogg G, Fernandes RA, Fisher R, Peng Y, Dustin ML, Dong T. Unconventional human CD61 pairing with CD103 promotes TCR signaling and antigen-specific T cell cytotoxicity. Nat Immunol 2024; 25:834-846. [PMID: 38561495 PMCID: PMC11065694 DOI: 10.1038/s41590-024-01802-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
Cancer remains one of the leading causes of mortality worldwide, leading to increased interest in utilizing immunotherapy strategies for better cancer treatments. In the past decade, CD103+ T cells have been associated with better clinical prognosis in patients with cancer. However, the specific immune mechanisms contributing toward CD103-mediated protective immunity remain unclear. Here, we show an unexpected and transient CD61 expression, which is paired with CD103 at the synaptic microclusters of T cells. CD61 colocalization with the T cell antigen receptor further modulates downstream T cell antigen receptor signaling, improving antitumor cytotoxicity and promoting physiological control of tumor growth. Clinically, the presence of CD61+ tumor-infiltrating T lymphocytes is associated with improved clinical outcomes, mediated through enhanced effector functions and phenotype with limited evidence of cellular exhaustion. In conclusion, this study identified an unconventional and transient CD61 expression and pairing with CD103 on human immune cells, which potentiates a new target for immune-based cellular therapies.
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MESH Headings
- Humans
- Antigens, CD/metabolism
- Antigens, CD/immunology
- Integrin alpha Chains/metabolism
- Signal Transduction/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/immunology
- Animals
- Mice
- Cytotoxicity, Immunologic
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Cell Line, Tumor
- T-Lymphocytes, Cytotoxic/immunology
- Neoplasms/immunology
- Neoplasms/therapy
- Apyrase
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Affiliation(s)
- Megat H B A Hamid
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Pablo F Cespedes
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Chen Jin
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ji-Li Chen
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Uzi Gileadi
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Elie Antoun
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zhu Liang
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Fei Gao
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Renuka Teague
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Nikita Manoharan
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Maldonado-Perez
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Nasullah Khalid-Alham
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Lucia Cerundolo
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Raul Ciaoca
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Svenja S Hester
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Adán Pinto-Fernández
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Simeon D Draganov
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Iolanda Vendrell
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Guihai Liu
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Audun Kvalvaag
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Department of Molecular Cell Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Charunya Nanayakkara
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos Kanellakis
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Laboratory of Pleural and Lung Cancer Translational Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Respiratory Medicine, Churchill Hospital, Oxford University Hospitals, Oxford, UK
| | - Yi-Ling Chen
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Craig Waugh
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sally-Ann Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Najib M Rahman
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Laboratory of Pleural and Lung Cancer Translational Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Respiratory Medicine, Churchill Hospital, Oxford University Hospitals, Oxford, UK
| | - Clare Verrill
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Benedikt M Kessler
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Graham Ogg
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ricardo A Fernandes
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fisher
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Yanchun Peng
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Michael L Dustin
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Tao Dong
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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2
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John T, Saffoon N, Walsby-Tickle J, Hester SS, Dingler FA, Millington CL, McCullagh JSO, Patel KJ, Hopkinson RJ, Schofield CJ. Aldehyde-mediated inhibition of asparagine biosynthesis has implications for diabetes and alcoholism. Chem Sci 2024; 15:2509-2517. [PMID: 38362406 PMCID: PMC10866355 DOI: 10.1039/d3sc06551k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/01/2024] [Indexed: 02/17/2024] Open
Abstract
Patients with alcoholism and type 2 diabetes manifest altered metabolism, including elevated aldehyde levels and unusually low asparagine levels. We show that asparagine synthetase B (ASNS), the only human asparagine-forming enzyme, is inhibited by disease-relevant reactive aldehydes, including formaldehyde and acetaldehyde. Cellular studies show non-cytotoxic amounts of reactive aldehydes induce a decrease in asparagine levels. Biochemical analyses reveal inhibition results from reaction of the aldehydes with the catalytically important N-terminal cysteine of ASNS. The combined cellular and biochemical results suggest a possible mechanism underlying the low asparagine levels in alcoholism and diabetes. The results will stimulate research on the biological consequences of the reactions of aldehydes with nucleophilic residues.
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Affiliation(s)
- Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Nadia Saffoon
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Svenja S Hester
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford Oxford UK
| | - Felix A Dingler
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital/Headley Way Oxford OX3 9DS UK
| | - Christopher L Millington
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital/Headley Way Oxford OX3 9DS UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Ketan J Patel
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital/Headley Way Oxford OX3 9DS UK
| | - Richard J Hopkinson
- Leicester Institute for Structural and Chemical Biology and School of Chemistry, University of Leicester, Henry Wellcome Building Lancaster Road Leicester LE1 7RH UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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3
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Zhang Q, Charles PD, Bendif EM, Hester SS, Mohammad S, Rickaby REM. Stimulating and toxic effect of chromium on growth and photosynthesis of a marine chlorophyte. New Phytol 2024; 241:676-686. [PMID: 37974482 DOI: 10.1111/nph.19376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
Marine phytoplankton can interchange trace metals in various biochemical functions, particularly under metal-limiting conditions. Here, we investigate the stimulating and toxicity effect of chromium (Cr) on a marine Chlorophyceae Osetreococcus tauri under Fe-replete and Fe-deficient conditions. We determined the growth, photosynthesis, and proteome expressions of Osetreococcus tauri cultured under different Cr and Fe concentrations. In Fe-replete conditions, the presence of Cr(VI) stimulated significantly the growth rate and the maximum yield of photochemistry of photosystem II (Fv /Fm ) of the phytoplankton, while the functional absorption cross-section of photosystem II (σPSII ) did not change. Minor additions of Cr(VI) partially rescued phytoplankton growth under Fe-limited conditions. Proteomic analysis of this alga grown in Fe-replete normal and Fe-replete with Cr addition media (10 μM Cr) showed that the presence of Cr significantly decreased the expression of phosphate-transporting proteins and photosynthetic proteins, while increasing the expression of proteins related to carbon assimilation. Cr can stimulate the growth and photosynthesis of O. tauri, but the effects are dependent on both the Cr(VI) concentration and the availability of Fe. The proteomic results further suggest that Cr(VI) addition might significantly increase starch production and carbon fixation.
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Affiliation(s)
- Qiong Zhang
- Department of Ocean Science and Center for Ocean Research in Hong Kong and Macau (CORE), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, 999077, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Tang Qi Road, Zhuhai, 519000, China
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
| | - Philip D Charles
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - El Mahdi Bendif
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski, Rimouski, G5L 3A1, QC, Canada
| | - Svenja S Hester
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Shabaz Mohammad
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
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4
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Kliszczak M, Moralli D, Jankowska JD, Bryjka P, Subha Meem L, Goncalves T, Hester SS, Fischer R, Clynes D, Green CM. Loss of FAM111B protease mutated in hereditary fibrosing poikiloderma negatively regulates telomere length. Front Cell Dev Biol 2023; 11:1175069. [PMID: 37342232 PMCID: PMC10277729 DOI: 10.3389/fcell.2023.1175069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/02/2023] [Indexed: 06/22/2023] Open
Abstract
Hereditary fibrosing poikiloderma (HFP) is a rare human dominant negative disorder caused by mutations in the FAM111B gene that encodes a nuclear trypsin-like serine protease. HFP patients present with symptoms including skin abnormalities, tendon contractures, myopathy and lung fibrosis. We characterized the cellular roles of human FAM111B using U2OS and MCF7 cell lines and report here that the protease interacts with components of the nuclear pore complex. Loss of FAM111B expression resulted in abnormal nuclear shape and reduced telomeric DNA content suggesting that FAM111B protease is required for normal telomere length; we show that this function is independent of telomerase or recombination driven telomere extension. Even though FAM111B-deficient cells were proficient in DNA repair, they showed hallmarks of genomic instability such as increased levels of micronuclei and ultra-fine DNA bridges. When mutated as in HFP, FAM111B was more frequently localized to the nuclear envelope, suggesting that accumulation of the mutated protease at the nuclear periphery may drive the disease pathology.
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Affiliation(s)
- Maciej Kliszczak
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Daniela Moralli
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Julia D. Jankowska
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paulina Bryjka
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lamia Subha Meem
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tomas Goncalves
- Oncology Department, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Svenja S. Hester
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, Oxford, United Kingdom
| | - David Clynes
- Oncology Department, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Catherine M. Green
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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5
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John T, Pires E, Hester SS, Salah E, Hopkinson RJ, Schofield CJ. Formaldehyde reacts with N-terminal proline residues to give bicyclic aminals. Commun Chem 2023; 6:12. [PMID: 36698022 PMCID: PMC9839752 DOI: 10.1038/s42004-022-00801-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
Formaldehyde (HCHO) is a potent electrophile that is toxic above threshold levels, but which is also produced in the nuclei of eukaryotic cells by demethylases. We report studies with the four canonical human histones revealing that histone H2B reacts with HCHO, including as generated by a histone demethylase, to give a stable product. NMR studies show that HCHO reacts with the N-terminal proline and associated amide of H2B to give a 5,5-bicyclic aminal that is relatively stable to competition with HCHO scavengers. While the roles of histone modification by this reaction require further investigation, we demonstrated the potential of N-terminal aminal formation to modulate protein function by conducting biochemical and cellular studies on the effects of HCHO on catalysis by 4-oxalocrotonate tautomerase, which employs a nucleophilic N-terminal proline. The results suggest that reactions of N-terminal residues with HCHO and other aldehydes have potential to alter protein function.
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Affiliation(s)
- Tobias John
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Elisabete Pires
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Svenja S Hester
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Richard J Hopkinson
- Leicester Institute for Structural and Chemical Biology and School of Chemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH, UK.
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6
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Munshaw S, Bruche S, Redpath AN, Jones A, Patel J, Dubé KN, Lee R, Hester SS, Davies R, Neal G, Handa A, Sattler M, Fischer R, Channon KM, Smart N. Thymosin β4 protects against aortic aneurysm via endocytic regulation of growth factor signaling. J Clin Invest 2021; 131:127884. [PMID: 33784254 PMCID: PMC8121525 DOI: 10.1172/jci127884] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/23/2021] [Indexed: 01/06/2023] Open
Abstract
Vascular stability and tone are maintained by contractile smooth muscle cells (VSMCs). However, injury-induced growth factors stimulate a contractile-synthetic phenotypic modulation which increases susceptibility to abdominal aortic aneurysm (AAA). As a regulator of embryonic VSMC differentiation, we hypothesized that Thymosin β4 (Tβ4) may function to maintain healthy vasculature throughout postnatal life. This was supported by the identification of an interaction with low density lipoprotein receptor related protein 1 (LRP1), an endocytic regulator of platelet-derived growth factor BB (PDGF-BB) signaling and VSMC proliferation. LRP1 variants have been implicated by genome-wide association studies with risk of AAA and other arterial diseases. Tβ4-null mice displayed aortic VSMC and elastin defects that phenocopy those of LRP1 mutants, and their compromised vascular integrity predisposed them to Angiotensin II-induced aneurysm formation. Aneurysmal vessels were characterized by enhanced VSMC phenotypic modulation and augmented PDGFR-β signaling. In vitro, enhanced sensitivity to PDGF-BB upon loss of Tβ4 was associated with dysregulated endocytosis, with increased recycling and reduced lysosomal targeting of LRP1-PDGFR-β. Accordingly, the exacerbated aneurysmal phenotype in Tβ4-null mice was rescued upon treatment with the PDGFR-β antagonist Imatinib. Our study identifies Tβ4 as a key regulator of LRP1 for maintaining vascular health, and provides insights into the mechanisms of growth factor-controlled VSMC phenotypic modulation underlying aortic disease progression.
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MESH Headings
- Angiotensin II/adverse effects
- Angiotensin II/pharmacology
- Animals
- Aortic Aneurysm, Abdominal/chemically induced
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/metabolism
- Aortic Aneurysm, Abdominal/prevention & control
- Becaplermin/genetics
- Becaplermin/metabolism
- Low Density Lipoprotein Receptor-Related Protein-1/genetics
- Low Density Lipoprotein Receptor-Related Protein-1/metabolism
- Male
- Mice
- Mice, Knockout
- Muscle, Smooth, Vascular/metabolism
- Myocytes, Smooth Muscle/metabolism
- Receptor, Platelet-Derived Growth Factor beta/genetics
- Receptor, Platelet-Derived Growth Factor beta/metabolism
- Signal Transduction/drug effects
- Signal Transduction/genetics
- Thymosin/genetics
- Thymosin/metabolism
- Thymosin/pharmacology
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Affiliation(s)
- Sonali Munshaw
- Burdon Sanderson Cardiac Science Centre, Department of Physiology, Anatomy & Genetics, University of Oxford, Sherrington Building, Oxford, United Kingdom
| | - Susann Bruche
- Burdon Sanderson Cardiac Science Centre, Department of Physiology, Anatomy & Genetics, University of Oxford, Sherrington Building, Oxford, United Kingdom
| | - Andia N. Redpath
- Burdon Sanderson Cardiac Science Centre, Department of Physiology, Anatomy & Genetics, University of Oxford, Sherrington Building, Oxford, United Kingdom
| | - Alisha Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Munich, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Chemistry Department, Technical University of Munich, Garching, Munich, Germany
| | - Jyoti Patel
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | | | - Regent Lee
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Svenja S. Hester
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Rachel Davies
- Burdon Sanderson Cardiac Science Centre, Department of Physiology, Anatomy & Genetics, University of Oxford, Sherrington Building, Oxford, United Kingdom
| | - Giles Neal
- Burdon Sanderson Cardiac Science Centre, Department of Physiology, Anatomy & Genetics, University of Oxford, Sherrington Building, Oxford, United Kingdom
| | - Ashok Handa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Munich, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Chemistry Department, Technical University of Munich, Garching, Munich, Germany
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Keith M. Channon
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Nicola Smart
- Burdon Sanderson Cardiac Science Centre, Department of Physiology, Anatomy & Genetics, University of Oxford, Sherrington Building, Oxford, United Kingdom
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7
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Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS, Dominguez D, Rhodes D, Humphrey TC, Shirahige K, Esashi F. MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress. Proc Natl Acad Sci U S A 2017; 114:7671-7676. [PMID: 28673974 PMCID: PMC5530651 DOI: 10.1073/pnas.1620208114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The partner and localiser of BRCA2 (PALB2) plays important roles in the maintenance of genome integrity and protection against cancer. Although PALB2 is commonly described as a repair factor recruited to sites of DNA breaks, recent studies provide evidence that PALB2 also associates with unperturbed chromatin. Here, we investigated the previously poorly described role of chromatin-associated PALB2 in undamaged cells. We found that PALB2 associates with active genes through its major binding partner, MRG15, which recognizes histone H3 trimethylated at lysine 36 (H3K36me3) by the SETD2 methyltransferase. Missense mutations that ablate PALB2 binding to MRG15 confer elevated sensitivity to the topoisomerase inhibitor camptothecin (CPT) and increased levels of aberrant metaphase chromosomes and DNA stress in gene bodies, which were suppressed by preventing DNA replication. Remarkably, the level of PALB2 at genic regions was frequently decreased, rather than increased, upon CPT treatment. We propose that the steady-state presence of PALB2 at active genes, mediated through the SETD2/H3K36me3/MRG15 axis, ensures an immediate response to DNA stress and therefore effective protection of these regions during DNA replication. This study provides a conceptual advance in demonstrating that the constitutive chromatin association of repair factors plays a key role in the maintenance of genome stability and furthers our understanding of why PALB2 defects lead to human genome instability syndromes.
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Affiliation(s)
- Jean-Yves Bleuyard
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Marjorie Fournier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Ryuichiro Nakato
- Research Center for Epigenetic Disease, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Anthony M Couturier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Yuki Katou
- Research Center for Epigenetic Disease, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Christine Ralf
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Svenja S Hester
- Advanced Proteomics Facility, Department of Biochemisty, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Daniel Dominguez
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139-4307
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Timothy C Humphrey
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom;
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8
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Howie D, Cobbold SP, Adams E, Ten Bokum A, Necula AS, Zhang W, Huang H, Roberts DJ, Thomas B, Hester SS, Vaux DJ, Betz AG, Waldmann H. Foxp3 drives oxidative phosphorylation and protection from lipotoxicity. JCI Insight 2017; 2:e89160. [PMID: 28194435 DOI: 10.1172/jci.insight.89160] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tregs can adopt a catabolic metabolic program with increased capacity for fatty acid oxidation-fueled oxidative phosphorylation (OXPHOS). It is unclear why this form of metabolism is favored in Tregs and, more specifically, whether this program represents an adaptation to the environment and developmental cues or is "hardwired" by Foxp3. Here we show, using metabolic analysis and an unbiased mass spectroscopy-based proteomics approach, that Foxp3 is both necessary and sufficient to program Treg-increased respiratory capacity and Tregs' increased ability to utilize fatty acids to fuel oxidative phosphorylation. Foxp3 drives upregulation of components of all the electron transport complexes, increasing their activity and ATP generation by oxidative phosphorylation. Increased fatty acid β-oxidation also results in selective protection of Foxp3+ cells from fatty acid-induced cell death. This observation may provide novel targets for modulating Treg function or selection therapeutically.
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Affiliation(s)
| | | | | | | | | | - Wei Zhang
- Nuffield Department of Obstetrics and Gynaecology, John Radcliffe Hospital
| | - Honglei Huang
- Radcliffe Department of Medicine, John Radcliffe Hospital
| | - David J Roberts
- Radcliffe Department of Medicine, John Radcliffe Hospital.,National Health Service Blood and Transplant, John Radcliffe Hospital, University of Oxford, Oxford, England, United Kingdom
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9
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Howie D, Cobbold SP, Adams E, Ten Bokum A, Necula AS, Zhang W, Huang H, Roberts DJ, Thomas B, Hester SS, Vaux DJ, Betz AG, Waldmann H. Foxp3 drives oxidative phosphorylation and protection from lipotoxicity. JCI Insight 2017. [PMID: 28194435 DOI: 10.1172/jci.insight.89160.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tregs can adopt a catabolic metabolic program with increased capacity for fatty acid oxidation-fueled oxidative phosphorylation (OXPHOS). It is unclear why this form of metabolism is favored in Tregs and, more specifically, whether this program represents an adaptation to the environment and developmental cues or is "hardwired" by Foxp3. Here we show, using metabolic analysis and an unbiased mass spectroscopy-based proteomics approach, that Foxp3 is both necessary and sufficient to program Treg-increased respiratory capacity and Tregs' increased ability to utilize fatty acids to fuel oxidative phosphorylation. Foxp3 drives upregulation of components of all the electron transport complexes, increasing their activity and ATP generation by oxidative phosphorylation. Increased fatty acid β-oxidation also results in selective protection of Foxp3+ cells from fatty acid-induced cell death. This observation may provide novel targets for modulating Treg function or selection therapeutically.
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Affiliation(s)
| | | | | | | | | | - Wei Zhang
- Nuffield Department of Obstetrics and Gynaecology, John Radcliffe Hospital
| | - Honglei Huang
- Radcliffe Department of Medicine, John Radcliffe Hospital
| | - David J Roberts
- Radcliffe Department of Medicine, John Radcliffe Hospital.,National Health Service Blood and Transplant, John Radcliffe Hospital, University of Oxford, Oxford, England, United Kingdom
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10
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Hutchinson EC, Charles PD, Hester SS, Thomas B, Trudgian D, Martínez-Alonso M, Fodor E. Erratum: Conserved and host-specific features of influenza virion architecture. Nat Commun 2015; 6:6446. [PMID: 25687574 DOI: 10.1038/ncomms7446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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11
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Hutchinson EC, Charles PD, Hester SS, Thomas B, Trudgian D, Martínez-Alonso M, Fodor E. Conserved and host-specific features of influenza virion architecture. Nat Commun 2014; 5:4816. [PMID: 25226414 PMCID: PMC4167602 DOI: 10.1038/ncomms5816] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/28/2014] [Indexed: 01/11/2023] Open
Abstract
Viruses use virions to spread between hosts, and virion composition is therefore the primary determinant of viral transmissibility and immunogenicity. However, the virions of many viruses are complex and pleomorphic, making them difficult to analyse in detail. Here we address this by identifying and quantifying virion proteins with mass spectrometry, producing a complete and quantified model of the hundreds of viral and host-encoded proteins that make up the pleomorphic virions of influenza viruses. We show that a conserved influenza virion architecture is maintained across diverse combinations of virus and host. This ‘core’ architecture, which includes substantial quantities of host proteins as well as the viral protein NS1, is elaborated with abundant host-dependent features. As a result, influenza virions produced by mammalian and avian hosts have distinct protein compositions. Finally we note that influenza virions share an underlying protein composition with exosomes, suggesting that influenza virions form by subverting microvesicle production.
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Affiliation(s)
- Edward C Hutchinson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Philip D Charles
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Svenja S Hester
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Benjamin Thomas
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - David Trudgian
- 1] Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK [2]
| | - Mónica Martínez-Alonso
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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12
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Hiemstra TF, Charles PD, Gracia T, Hester SS, Gatto L, Al-Lamki R, Floto RA, Su Y, Skepper JN, Lilley KS, Karet Frankl FE. Human urinary exosomes as innate immune effectors. J Am Soc Nephrol 2014; 25:2017-27. [PMID: 24700864 DOI: 10.1681/asn.2013101066] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Exosomes are small extracellular vesicles, approximately 50 nm in diameter, derived from the endocytic pathway and released by a variety of cell types. Recent data indicate a spectrum of exosomal functions, including RNA transfer, antigen presentation, modulation of apoptosis, and shedding of obsolete protein. Exosomes derived from all nephron segments are also present in human urine, where their function is unknown. Although one report suggested in vitro uptake of exosomes by renal cortical collecting duct cells, most studies of human urinary exosomes have focused on biomarker discovery rather than exosome function. Here, we report results from in-depth proteomic analyses and EM showing that normal human urinary exosomes are significantly enriched for innate immune proteins that include antimicrobial proteins and peptides and bacterial and viral receptors. Urinary exosomes, but not the prevalent soluble urinary protein uromodulin (Tamm-Horsfall protein), potently inhibited growth of pathogenic and commensal Escherichia coli and induced bacterial lysis. Bacterial killing depended on exosome structural integrity and occurred optimally at the acidic pH typical of urine from omnivorous humans. Thus, exosomes are innate immune effectors that contribute to host defense within the urinary tract.
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Affiliation(s)
- Thomas F Hiemstra
- Department of Medicine, Cambridge Centre for Proteome Research and Cambridge Systems Biology Centre, Department of Biochemistry
| | - Philip D Charles
- Cambridge Centre for Proteome Research and Cambridge Systems Biology Centre, Department of Biochemistry
| | | | - Svenja S Hester
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Laurent Gatto
- Cambridge Centre for Proteome Research and Cambridge Systems Biology Centre, Department of Biochemistry
| | | | | | - Ya Su
- Department of Medical Genetics, and
| | - Jeremy N Skepper
- Multi-Imaging Centre, Department of Anatomy, University of Cambridge, Cambridge, United Kingdom; and
| | - Kathryn S Lilley
- Cambridge Centre for Proteome Research and Cambridge Systems Biology Centre, Department of Biochemistry,
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13
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Hutchinson EC, Denham EM, Thomas B, Trudgian DC, Hester SS, Ridlova G, York A, Turrell L, Fodor E. Mapping the phosphoproteome of influenza A and B viruses by mass spectrometry. PLoS Pathog 2012; 8:e1002993. [PMID: 23144613 PMCID: PMC3493474 DOI: 10.1371/journal.ppat.1002993] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/29/2012] [Indexed: 01/06/2023] Open
Abstract
Protein phosphorylation is a common post-translational modification in eukaryotic cells and has a wide range of functional effects. Here, we used mass spectrometry to search for phosphorylated residues in all the proteins of influenza A and B viruses--to the best of our knowledge, the first time such a comprehensive approach has been applied to a virus. We identified 36 novel phosphorylation sites, as well as confirming 3 previously-identified sites. N-terminal processing and ubiquitination of viral proteins was also detected. Phosphorylation was detected in the polymerase proteins (PB2, PB1 and PA), glycoproteins (HA and NA), nucleoprotein (NP), matrix protein (M1), ion channel (M2), non-structural protein (NS1) and nuclear export protein (NEP). Many of the phosphorylation sites detected were conserved between influenza virus genera, indicating the fundamental importance of phosphorylation for all influenza viruses. Their structural context indicates roles for phosphorylation in regulating viral entry and exit (HA and NA); nuclear localisation (PB2, M1, NP, NS1 and, through NP and NEP, of the viral RNA genome); and protein multimerisation (NS1 dimers, M2 tetramers and NP oligomers). Using reverse genetics we show that for NP of influenza A viruses phosphorylation sites in the N-terminal NLS are important for viral growth, whereas mutating sites in the C-terminus has little or no effect. Mutating phosphorylation sites in the oligomerisation domains of NP inhibits viral growth and in some cases transcription and replication of the viral RNA genome. However, constitutive phosphorylation of these sites is not optimal. Taken together, the conservation, structural context and functional significance of phosphorylation sites implies a key role for phosphorylation in influenza biology. By identifying phosphorylation sites throughout the proteomes of influenza A and B viruses we provide a framework for further study of phosphorylation events in the viral life cycle and suggest a range of potential antiviral targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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14
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Hiemstra TF, Charles PD, Hester SS, Karet FE, Lilley KS. Uromodulin exclusion list improves urinary exosomal protein identification. J Biomol Tech 2011; 22:136-145. [PMID: 22131889 PMCID: PMC3221452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Advances in mass spectrometry (MS) have encouraged interest in its deployment in urine biomarker studies, but success has been limited. Urine exosomes have been proposed as an ideal source of biomarkers for renal disease. However, the abundant urinary protein, uromodulin, cofractionates with exosomes during isolation and represents a practical contaminant that limits MS sensitivity. Uromodulin depletion has been attempted but is labor- and time-intensive and may remove important protein biomarkers. We describe the application of an exclusion list (ExL) of uromodulin-related peptide ions, coupled with high-sensitivity mass spectrometric analysis, to increase the depth of coverage of the urinary exosomal proteome. Urine exosomal protein samples from healthy volunteers were subjected to tandem MS and abundant uromodulin peptides identified. Samples were run for a second time, while excluding these uromodulin peptides from fragmentation to allow identification of peptides from lower-abundance proteins. Uromodulin exclusion was performed in addition to dynamic exclusion. Results from these two procedures revealed 222 distinct proteins from conventional analysis, compared with 254 proteins after uromodulin exclusion, of which 188 were common to both methods. By unmasking a previously unidentified protein set, adding the ExL increased overall protein identifications by 29.7% to a total of 288 proteins. A fixed ExL, used in combination with conventional methods, effectively increases the depth of urinary exosomal proteins identified by MS, reducing the need for uromodulin depletion.
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Affiliation(s)
- Thomas F. Hiemstra
- Department of Medical Genetics and Division of Renal Medicine, and
- Centre for Proteomics, Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Philip D. Charles
- Centre for Proteomics, Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Svenja S. Hester
- Centre for Proteomics, Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Fiona E. Karet
- Department of Medical Genetics and Division of Renal Medicine, and
| | - Kathryn S. Lilley
- Centre for Proteomics, Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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15
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Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DCJ, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, O'Donoghue K, Hester SS, Dunkley TPJ, Hart SR, Swainston N, Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG. Growth control of the eukaryote cell: a systems biology study in yeast. J Biol 2007; 6:4. [PMID: 17439666 PMCID: PMC2373899 DOI: 10.1186/jbiol54] [Citation(s) in RCA: 215] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Revised: 11/20/2006] [Accepted: 02/07/2007] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. RESULTS Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. CONCLUSION This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.
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Affiliation(s)
- Juan I Castrillo
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Leo A Zeef
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David C Hoyle
- Northwest Institute for Bio-Health Informatics (NIBHI), School of Medicine, Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Nianshu Zhang
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Andrew Hayes
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David CJ Gardner
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Michael J Cornell
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - June Petty
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Luke Hakes
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Leanne Wardleworth
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Bharat Rash
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Marie Brown
- School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Warwick B Dunn
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - David Broadhurst
- School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Kerry O'Donoghue
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Svenja S Hester
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Tom PJ Dunkley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Sarah R Hart
- School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Neil Swainston
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Peter Li
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Simon J Gaskell
- School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Norman W Paton
- School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Douglas B Kell
- School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Stephen G Oliver
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
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