1
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Gupta MP, Tandalam S, Ostrager S, Lever AS, Fung AR, Hurley DD, Alegre GB, Espinal JE, Remmel HL, Mukherjee S, Levine BM, Robins RP, Molina H, Dill BD, Kenific CM, Tuschl T, Lyden D, D'Amico DJ, Pena JTG. Non-reversible tissue fixation retains extracellular vesicles for in situ imaging. Nat Methods 2019; 16:1269-1273. [PMID: 31712780 DOI: 10.1038/s41592-019-0623-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 09/27/2019] [Indexed: 12/30/2022]
Abstract
Extracellular vesicles (EVs) are secreted nanosized particles with many biological functions and pathological associations. The inability to image EVs in fixed tissues has been a major limitation to understanding their role in healthy and diseased tissue microenvironments. Here, we show that crosslinking mammalian tissues with formaldehyde results in significant EV loss, which can be prevented by additional fixation with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) for visualization of EVs in a range of normal and cancer tissues.
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Affiliation(s)
- Mrinali P Gupta
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Sangeetha Tandalam
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Shariss Ostrager
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Alexander S Lever
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Angus R Fung
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - David D Hurley
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Gemstonn B Alegre
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Jasmin E Espinal
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - H Lawrence Remmel
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA.,Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sushmita Mukherjee
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin M Levine
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Russell P Robins
- Freeman School of Business, Tulane University, New Orleans, LA, USA
| | - Henrik Molina
- The Rockefeller University, Proteomics Resource Center, New York, NY, USA
| | - Brian D Dill
- The Rockefeller University, Proteomics Resource Center, New York, NY, USA
| | - Candia M Kenific
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - David Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Donald J D'Amico
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - John T G Pena
- Department of Ophthalmology and Margaret M. Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY, USA.
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2
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Fish L, Navickas A, Culbertson B, Xu Y, Nguyen HCB, Zhang S, Hochman M, Okimoto R, Dill BD, Molina H, Najafabadi HS, Alarcón C, Ruggero D, Goodarzi H. Nuclear TARBP2 Drives Oncogenic Dysregulation of RNA Splicing and Decay. Mol Cell 2019; 75:967-981.e9. [PMID: 31300274 DOI: 10.1016/j.molcel.2019.06.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [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: 03/08/2018] [Revised: 02/18/2019] [Accepted: 05/30/2019] [Indexed: 12/31/2022]
Abstract
Post-transcriptional regulation of RNA stability is a key step in gene expression control. We describe a regulatory program, mediated by the RNA binding protein TARBP2, that controls RNA stability in the nucleus. TARBP2 binding to pre-mRNAs results in increased intron retention, subsequently leading to targeted degradation of TARBP2-bound transcripts. This is mediated by TARBP2 recruitment of the m6A RNA methylation machinery to its target transcripts, where deposition of m6A marks influences the recruitment of splicing regulators, inhibiting efficient splicing. Interactions between TARBP2 and the nucleoprotein TPR then promote degradation of these TARBP2-bound transcripts by the nuclear exosome. Additionally, analysis of clinical gene expression datasets revealed a functional role for TARBP2 in lung cancer. Using xenograft mouse models, we find that TARBP2 affects tumor growth in the lung and that this is dependent on TARBP2-mediated destabilization of ABCA3 and FOXN3. Finally, we establish ZNF143 as an upstream regulator of TARBP2 expression.
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Affiliation(s)
- Lisa Fish
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bruce Culbertson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yichen Xu
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hoang C B Nguyen
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Steven Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Myles Hochman
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ross Okimoto
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian D Dill
- Proteome Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteome Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Claudio Alarcón
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
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3
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Guo M, Härtlova A, Gierliński M, Prescott A, Castellvi J, Losa JH, Petersen SK, Wenzel UA, Dill BD, Emmerich CH, Ramon Y Cajal S, Russell DG, Trost M. Triggering MSR1 promotes JNK-mediated inflammation in IL-4-activated macrophages. EMBO J 2019; 38:embj.2018100299. [PMID: 31028084 PMCID: PMC6545745 DOI: 10.15252/embj.2018100299] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/14/2022] Open
Abstract
Alternatively activated M2 macrophages play an important role in maintenance of tissue homeostasis by scavenging dead cells, cell debris and lipoprotein aggregates via phagocytosis. Using proteomics, we investigated how alternative activation, driven by IL‐4, modulated the phagosomal proteome to control macrophage function. Our data indicate that alternative activation enhances homeostatic functions such as proteolysis, lipolysis and nutrient transport. Intriguingly, we identified the enhanced recruitment of the TAK1/MKK7/JNK signalling complex to phagosomes of IL‐4‐activated macrophages. The recruitment of this signalling complex was mediated through K63 polyubiquitylation of the macrophage scavenger receptor 1 (MSR1). Triggering of MSR1 in IL‐4‐activated macrophages leads to enhanced JNK activation, thereby promoting a phenotypic switch from an anti‐inflammatory to a pro‐inflammatory state, which was abolished upon MSR1 deletion or JNK inhibition. Moreover, MSR1 K63 polyubiquitylation correlated with the activation of JNK signalling in ovarian cancer tissue from human patients, suggesting that it may be relevant for macrophage phenotypic shift in vivo. Altogether, we identified that MSR1 signals through JNK via K63 polyubiquitylation and provides evidence for the receptor's involvement in macrophage polarization.
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Affiliation(s)
- Manman Guo
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Anetta Härtlova
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK .,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marek Gierliński
- Data Analysis Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alan Prescott
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Josep Castellvi
- Department of Pathology, Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | - Javier Hernandez Losa
- Department of Pathology, Hospital Universitario Vall d'Hebron, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Sine K Petersen
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ulf A Wenzel
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Brian D Dill
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Christoph H Emmerich
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Santiago Ramon Y Cajal
- Department of Pathology, Hospital Universitario Vall d'Hebron, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - David G Russell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK .,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
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4
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Dallner OS, Marinis JM, Lu YH, Birsoy K, Werner E, Fayzikhodjaeva G, Dill BD, Molina H, Moscati A, Kutalik Z, Marques-Vidal P, Kilpeläinen TO, Grarup N, Linneberg A, Zhang Y, Vaughan R, Loos RJF, Lazar MA, Friedman JM. Dysregulation of a long noncoding RNA reduces leptin leading to a leptin-responsive form of obesity. Nat Med 2019; 25:507-516. [PMID: 30842678 DOI: 10.1038/s41591-019-0370-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 01/18/2019] [Indexed: 12/31/2022]
Abstract
Quantitative changes in leptin concentration lead to alterations in food intake and body weight, but the regulatory mechanisms that control leptin gene expression are poorly understood. Here we report that fat-specific and quantitative leptin expression is controlled by redundant cis elements and trans factors interacting with the proximal promoter together with a long noncoding RNA (lncOb). Diet-induced obese mice lacking lncOb show increased fat mass with reduced plasma leptin levels and lose weight after leptin treatment, whereas control mice do not. Consistent with this finding, large-scale genetic studies of humans reveal a significant association of single-nucleotide polymorphisms (SNPs) in the region of human lncOb with lower plasma leptin levels and obesity. These results show that reduced leptin gene expression can lead to a hypoleptinemic, leptin-responsive form of obesity and provide a framework for elucidating the pathogenic mechanism in the subset of obese patients with low endogenous leptin levels.
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Affiliation(s)
- Olof S Dallner
- Laboratory of Molecular Genetics, The Rockefeller University, New York, NY, USA
| | - Jill M Marinis
- Division of Endocrinology, Diabetes, and Metabolism and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Yi-Hsueh Lu
- Laboratory of Molecular Genetics, The Rockefeller University, New York, NY, USA
| | - Kivanc Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Emory Werner
- Laboratory of Molecular Genetics, The Rockefeller University, New York, NY, USA
| | | | - Brian D Dill
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pedro Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Linneberg
- Centre for Clinical Research and Prevention, Frederiksberg-Bispebjerg Hospital, Copenhagen, Denmark.,Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yinxin Zhang
- Laboratory of Molecular Genetics, The Rockefeller University, New York, NY, USA
| | - Roger Vaughan
- Department of Biostatistics, The Rockefeller University, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Mindich Childhood and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffrey M Friedman
- Laboratory of Molecular Genetics, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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5
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Trunk K, Peltier J, Liu YC, Dill BD, Walker L, Gow NAR, Stark MJR, Quinn J, Strahl H, Trost M, Coulthurst SJ. The type VI secretion system deploys antifungal effectors against microbial competitors. Nat Microbiol 2018; 3:920-931. [PMID: 30038307 PMCID: PMC6071859 DOI: 10.1038/s41564-018-0191-x] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [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: 07/22/2017] [Accepted: 06/07/2018] [Indexed: 12/28/2022]
Abstract
Interactions between bacterial and fungal cells shape many polymicrobial communities. Bacteria elaborate diverse strategies to interact and compete with other organisms, including the deployment of protein secretion systems. The type VI secretion system (T6SS) delivers toxic effector proteins into host eukaryotic cells and competitor bacterial cells, but, surprisingly, T6SS-delivered effectors targeting fungal cells have not been reported. Here we show that the 'antibacterial' T6SS of Serratia marcescens can act against fungal cells, including pathogenic Candida species, and identify the previously undescribed effector proteins responsible. These antifungal effectors, Tfe1 and Tfe2, have distinct impacts on the target cell, but both can ultimately cause fungal cell death. 'In competition' proteomics analysis revealed that T6SS-mediated delivery of Tfe2 disrupts nutrient uptake and amino acid metabolism in fungal cells, and leads to the induction of autophagy. Intoxication by Tfe1, in contrast, causes a loss of plasma membrane potential. Our findings extend the repertoire of the T6SS and suggest that antifungal T6SSs represent widespread and important determinants of the outcome of bacterial-fungal interactions.
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Affiliation(s)
- Katharina Trunk
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Julien Peltier
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Yi-Chia Liu
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Brian D Dill
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Louise Walker
- Aberdeen Fungal Group, Institute of Medical Sciences, MRC Centre for Medical Mycology at the University of Aberdeen, Aberdeen, UK
| | - Neil A R Gow
- Aberdeen Fungal Group, Institute of Medical Sciences, MRC Centre for Medical Mycology at the University of Aberdeen, Aberdeen, UK
| | - Michael J R Stark
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Janet Quinn
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle-upon-Tyne, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK.
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
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6
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Härtlova A, Herbst S, Peltier J, Rodgers A, Bilkei-Gorzo O, Fearns A, Dill BD, Lee H, Flynn R, Cowley SA, Davies P, Lewis PA, Ganley IG, Martinez J, Alessi DR, Reith AD, Trost M, Gutierrez MG. LRRK2 is a negative regulator of Mycobacterium tuberculosis phagosome maturation in macrophages. EMBO J 2018; 37:e98694. [PMID: 29789389 PMCID: PMC6003659 DOI: 10.15252/embj.201798694] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [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: 11/21/2017] [Revised: 04/05/2018] [Accepted: 04/24/2018] [Indexed: 12/18/2022] Open
Abstract
Mutations in the leucine-rich repeat kinase 2 (LRRK2) are associated with Parkinson's disease, chronic inflammation and mycobacterial infections. Although there is evidence supporting the idea that LRRK2 has an immune function, the cellular function of this kinase is still largely unknown. By using genetic, pharmacological and proteomics approaches, we show that LRRK2 kinase activity negatively regulates phagosome maturation via the recruitment of the Class III phosphatidylinositol-3 kinase complex and Rubicon to the phagosome in macrophages. Moreover, inhibition of LRRK2 kinase activity in mouse and human macrophages enhanced Mycobacterium tuberculosis phagosome maturation and mycobacterial control independently of autophagy. In vivo, LRRK2 deficiency in mice resulted in a significant decrease in M. tuberculosis burdens early during the infection. Collectively, our findings provide a molecular mechanism explaining genetic evidence linking LRRK2 to mycobacterial diseases and establish an LRRK2-dependent cellular pathway that controls M. tuberculosis replication by regulating phagosome maturation.
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Affiliation(s)
- Anetta Härtlova
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Newcastle University, Newcastle-upon-Tyne, UK
| | - Susanne Herbst
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline Pharmaceuticals R&D, Stevenage, UK
| | - Julien Peltier
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Newcastle University, Newcastle-upon-Tyne, UK
| | - Angela Rodgers
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Orsolya Bilkei-Gorzo
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Antony Fearns
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Brian D Dill
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Heyne Lee
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rowan Flynn
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sally A Cowley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Patrick A Lewis
- University of Reading, Reading, UK
- UCL Institute of Neurology, Queen Square, London, UK
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | | | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Alastair D Reith
- Neurodegeneration Discovery Performance Unit, RD Neurosciences, GlaxoSmithKline Pharmaceuticals R&D, Stevenage, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Newcastle University, Newcastle-upon-Tyne, UK
| | - Maximiliano G Gutierrez
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
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7
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Blachère NE, Parveen S, Frank MO, Dill BD, Molina H, Orange DE. High-Titer Rheumatoid Arthritis Antibodies Preferentially Bind Fibrinogen Citrullinated by Peptidylarginine Deiminase 4. Arthritis Rheumatol 2017; 69:986-995. [PMID: 28029744 DOI: 10.1002/art.40035] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 12/22/2016] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Most patients with rheumatoid arthritis (RA) harbor antibodies to citrullinated autoantigens such as citrullinated fibrinogen. Two isoforms of peptidylarginine deiminase (PAD), PAD type 2 (PAD2) and PAD4, which catalyze citrullination with different substrate specificities, can be detected in the synovium of RA patients. This study was undertaken to determine whether RA antibodies preferentially bind PAD2- or PAD4-citrullinated fibrinogen. METHODS RA patient and normal donor plasma specimens were tested for binding to PAD2- or PAD4-citrullinated fibrinogen, native fibrinogen, or citrullinated fibrinogen peptides in various dilutions by enzyme-linked immunosorbent assay (ELISA) and Western blotting. Bands corresponding to masses demonstrating RA antibody reactivity by Western blotting were excised and analyzed by mass spectrometry. RESULTS At low antibody titers (1:40 and 1:100), there was no significant difference between RA antibody reactivity to PAD2- and PAD4-citrullinated fibrinogen. When plasma was further diluted to 1:250 and 1:1,000, RA patient plasma bound PAD4-citrullinated fibrinogen significantly more than PAD2-citrullinated fibrinogen, as measured by ELISA and Western blotting. An increased antibody titer was associated with increased avidity for both PAD2- and PAD4-citrullinated fibrinogen. Both enzymes hypercitrullinated fibrinogen, but PAD4 citrullinated arginines more intermittently, generating a mix of citrullinated and noncitrullinated arginines. Peptide ELISA and preadsorption assays confirmed that the region of intermittent citrullination accounts for the majority of RA antibody binding to the β-chain of citrullinated fibrinogen. CONCLUSION At high titers, RA antibodies preferentially bind fibrinogen modified by PAD4, because intermittent citrullination offers a more diverse assortment of citrullinated epitopes.
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Affiliation(s)
- Nathalie E Blachère
- Rockefeller University and Howard Hughes Medical Institute, New York, New York
| | | | - Mayu O Frank
- Rockefeller University and New York Genome Center, New York, New York
| | | | | | - Dana E Orange
- Rockefeller University, Hospital for Special Surgery, and New York Genome Center, New York, New York
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8
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Sendoel A, Dunn JG, Rodriguez EH, Naik S, Gomez NC, Hurwitz B, Levorse J, Dill BD, Schramek D, Molina H, Weissman JS, Fuchs E. Abstract 4766: Translation from unconventional 5' start sites drives tumor initiation. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
How translational control impacts tumor-initiation and malignancy is just beginning to unfold. Here, we devise an epidermis-specific, in vivo ribosome profiling strategy to interrogate the translational landscape during the transition from normal homeostasis to malignancy. Inducing SOX2, broadly expressed in oncogenic RAS-associated cancers, we find that despite widespread reductions in translation and protein synthesis, certain oncogenic mRNAs are spared. Seeking mechanism, we find that during tumor-initiation, the translational apparatus is redirected towards unconventional upstream initiation sites, enhancing translational efficiency of oncogenic mRNAs. An in vivo RNAi screen of translational regulators revealed that dampening conventional EIF2 complexes has dire consequences for normal but not oncogenic growth. Conversely, we identify alternative initiation factors essential for cancer progression, where they mediate initiation at these upstream sites, differentially skewing translation and protein expression. Our findings unveil a hitherto unappreciated role of 5’UTR translation in cancer, and expose new targets for therapeutic intervention.
Citation Format: Ataman Sendoel, Joshua G. Dunn, Edwin H. Rodriguez, Shruti Naik, Nicholas C. Gomez, Brian Hurwitz, John Levorse, Brian D. Dill, Daniel Schramek, Henrik Molina, Jonathan S. Weissman, Elaine Fuchs. Translation from unconventional 5' start sites drives tumor initiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4766. doi:10.1158/1538-7445.AM2017-4766
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9
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Goodarzi H, Nguyen HCB, Zhang S, Dill BD, Molina H, Tavazoie SF. Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression. Cell 2016; 165:1416-1427. [PMID: 27259150 DOI: 10.1016/j.cell.2016.05.046] [Citation(s) in RCA: 295] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/04/2016] [Accepted: 05/13/2016] [Indexed: 01/01/2023]
Abstract
Transfer RNAs (tRNAs) are primarily viewed as static contributors to gene expression. By developing a high-throughput tRNA profiling method, we find that specific tRNAs are upregulated in human breast cancer cells as they gain metastatic activity. Through loss-of-function, gain-of-function, and clinical-association studies, we implicate tRNAGluUUC and tRNAArgCCG as promoters of breast cancer metastasis. Upregulation of these tRNAs enhances stability and ribosome occupancy of transcripts enriched for their cognate codons. Specifically, tRNAGluUUC promotes metastatic progression by directly enhancing EXOSC2 expression and enhancing GRIPAP1-constituting an "inducible" pathway driven by a tRNA. The cellular proteomic shift toward a pro-metastatic state mirrors global tRNA shifts, allowing for cell-state and cell-type transgene expression optimization through codon content quantification. TRNA modulation represents a mechanism by which cells achieve altered expression of specific transcripts and proteins. TRNAs are thus dynamic regulators of gene expression and the tRNA codon landscape can causally and specifically impact disease progression.
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Affiliation(s)
- Hani Goodarzi
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Hoang C B Nguyen
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Steven Zhang
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Brian D Dill
- Proteome Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteome Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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10
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Josefowicz SZ, Shimada M, Armache A, Li CH, Miller RM, Lin S, Yang A, Dill BD, Molina H, Park HS, Garcia BA, Taunton J, Roeder RG, Allis CD. Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription. Mol Cell 2016; 64:347-361. [PMID: 27768872 PMCID: PMC5081221 DOI: 10.1016/j.molcel.2016.09.026] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [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: 02/16/2016] [Revised: 05/12/2016] [Accepted: 09/20/2016] [Indexed: 02/05/2023]
Abstract
The inflammatory response requires coordinated activation of both transcription factors and chromatin to induce transcription for defense against pathogens and environmental insults. We sought to elucidate the connections between inflammatory signaling pathways and chromatin through genomic footprinting of kinase activity and unbiased identification of prominent histone phosphorylation events. We identified H3 serine 28 phosphorylation (H3S28ph) as the principal stimulation-dependent histone modification and observed its enrichment at induced genes in mouse macrophages stimulated with bacterial lipopolysaccharide. Using pharmacological and genetic approaches, we identified mitogen- and stress-activated protein kinases (MSKs) as primary mediators of H3S28ph in macrophages. Cell-free transcription assays demonstrated that H3S28ph directly promotes p300/CBP-dependent transcription. Further, MSKs can activate both signal-responsive transcription factors and the chromatin template with additive effects on transcription. Specific inhibition of MSKs in macrophages selectively reduced transcription of stimulation-induced genes. Our results suggest that MSKs incorporate upstream signaling inputs and control multiple downstream regulators of inducible transcription.
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Affiliation(s)
- Steven Z Josefowicz
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Anja Armache
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Charles H Li
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Rand M Miller
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shu Lin
- Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aerin Yang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Brian D Dill
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
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11
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Farrelly LA, Dill BD, Molina H, Birtwistle MR, Maze I. Current Proteomic Methods to Investigate the Dynamics of Histone Turnover in the Central Nervous System. Methods Enzymol 2016; 574:331-354. [PMID: 27423867 DOI: 10.1016/bs.mie.2016.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Characterizing the dynamic behavior of nucleosomes in the central nervous system is vital to our understanding of brain-specific chromatin-templated processes and their roles in transcriptional plasticity. Histone turnover-the complete loss of old, and replacement by new, nucleosomal histones-is one such phenomenon that has recently been shown to be critical for cell-type-specific transcription in brain, synaptic plasticity, and cognition. Such revelations that histones, long believed to static proteins in postmitotic cells, are highly dynamic in neurons were only possible owing to significant advances in analytical chemistry-based techniques, which now provide a platform for investigations of histone dynamics in both healthy and diseased tissues. Here, we discuss both past and present proteomic methods (eg, mass spectrometry, human "bomb pulse labeling") for investigating histone turnover in brain with the hope that such information may stimulate future investigations of both adaptive and aberrant forms of "neuroepigenetic" plasticity.
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Affiliation(s)
- L A Farrelly
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - B D Dill
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, United States
| | - H Molina
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, United States
| | - M R Birtwistle
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - I Maze
- Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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12
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Naujoks J, Tabeling C, Dill BD, Hoffmann C, Brown AS, Kunze M, Kempa S, Peter A, Mollenkopf HJ, Dorhoi A, Kershaw O, Gruber AD, Sander LE, Witzenrath M, Herold S, Nerlich A, Hocke AC, van Driel I, Suttorp N, Bedoui S, Hilbi H, Trost M, Opitz B. IFNs Modify the Proteome of Legionella-Containing Vacuoles and Restrict Infection Via IRG1-Derived Itaconic Acid. PLoS Pathog 2016; 12:e1005408. [PMID: 26829557 PMCID: PMC4734697 DOI: 10.1371/journal.ppat.1005408] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [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: 08/13/2015] [Accepted: 12/30/2015] [Indexed: 11/21/2022] Open
Abstract
Macrophages can be niches for bacterial pathogens or antibacterial effector cells depending on the pathogen and signals from the immune system. Here we show that type I and II IFNs are master regulators of gene expression during Legionella pneumophila infection, and activators of an alveolar macrophage-intrinsic immune response that restricts bacterial growth during pneumonia. Quantitative mass spectrometry revealed that both IFNs substantially modify Legionella-containing vacuoles, and comparative analyses reveal distinct subsets of transcriptionally and spatially IFN-regulated proteins. Immune-responsive gene (IRG)1 is induced by IFNs in mitochondria that closely associate with Legionella-containing vacuoles, and mediates production of itaconic acid. This metabolite is bactericidal against intravacuolar L. pneumophila as well as extracellular multidrug-resistant Gram-positive and -negative bacteria. Our study explores the overall role IFNs play in inducing substantial remodeling of bacterial vacuoles and in stimulating production of IRG1-derived itaconic acid which targets intravacuolar pathogens. IRG1 or its product itaconic acid might be therapeutically targetable to fight intracellular and drug-resistant bacteria. Numerous intracellular bacterial pathogens replicate in specialized vacuoles within macrophages. We systematically study the molecular mechanism and the impact of macrophage-intrinsic antibacterial defense. Using L. pneumophila, an important cause of pneumonia and model organism for intracellular bacteria, we found that type I and II interferons critically modify the proteome of bacterial vacuoles to restrict infection. We identify IRG1 and demonstrate a bactericidal activity of its metabolite itaconic acid on bacteria in their vacuole. Moreover, our study provides evidence for the impact of this cell-autonomous defense pathway in alveolar macrophages to restrict lung infection. We speculate that vacuolar IRG1 or its product itaconic acid could serve as future therapeutic targets to fight intracellular and drug-resistant bacteria.
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Affiliation(s)
- Jan Naujoks
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Christoph Tabeling
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Brian D. Dill
- MRC Protein Phosphorylation Unit, University of Dundee, Dundee, United Kingdom
| | - Christine Hoffmann
- Max-von-Pettenkofer Institute, Ludwig Maximilian University, Munich, Germany
| | - Andrew S. Brown
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia
| | - Mareike Kunze
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Stefan Kempa
- Integrative Metabolomics and Proteomics, Institute of Medical Systems Biology/Max-Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Andrea Peter
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
| | | | - Anca Dorhoi
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Olivia Kershaw
- Department of Veterinary Pathology, Free University Berlin, Berlin, Germany
| | - Achim D. Gruber
- Department of Veterinary Pathology, Free University Berlin, Berlin, Germany
| | - Leif E. Sander
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Martin Witzenrath
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Susanne Herold
- Medizinische Klinik II, University Giessen and Marburg Lung Center, Justus-Liebig-University Giessen, Giessen, Germany
| | - Andreas Nerlich
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Andreas C. Hocke
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Ian van Driel
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia
| | - Norbert Suttorp
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Sammy Bedoui
- The Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Australia
| | - Hubert Hilbi
- Max-von-Pettenkofer Institute, Ludwig Maximilian University, Munich, Germany
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Matthias Trost
- MRC Protein Phosphorylation Unit, University of Dundee, Dundee, United Kingdom
| | - Bastian Opitz
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine Berlin, Berlin, Germany
- * E-mail:
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13
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Lai YC, Kondapalli C, Lehneck R, Procter JB, Dill BD, Woodroof HI, Gourlay R, Peggie M, Macartney TJ, Corti O, Corvol JC, Campbell DG, Itzen A, Trost M, Muqit MM. Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1. EMBO J 2015; 34:2840-61. [PMID: 26471730 PMCID: PMC4654935 DOI: 10.15252/embj.201591593] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 09/18/2015] [Indexed: 12/21/2022] Open
Abstract
Mutations in the PTEN‐induced kinase 1 (PINK1) are causative of autosomal recessive Parkinson's disease (PD). We have previously reported that PINK1 is activated by mitochondrial depolarisation and phosphorylates serine 65 (Ser65) of the ubiquitin ligase Parkin and ubiquitin to stimulate Parkin E3 ligase activity. Here, we have employed quantitative phosphoproteomics to search for novel PINK1‐dependent phosphorylation targets in HEK (human embryonic kidney) 293 cells stimulated by mitochondrial depolarisation. This led to the identification of 14,213 phosphosites from 4,499 gene products. Whilst most phosphosites were unaffected, we strikingly observed three members of a sub‐family of Rab GTPases namely Rab8A, 8B and 13 that are all phosphorylated at the highly conserved residue of serine 111 (Ser111) in response to PINK1 activation. Using phospho‐specific antibodies raised against Ser111 of each of the Rabs, we demonstrate that Rab Ser111 phosphorylation occurs specifically in response to PINK1 activation and is abolished in HeLa PINK1 knockout cells and mutant PINK1 PD patient‐derived fibroblasts stimulated by mitochondrial depolarisation. We provide evidence that Rab8A GTPase Ser111 phosphorylation is not directly regulated by PINK1 in vitro and demonstrate in cells the time course of Ser111 phosphorylation of Rab8A, 8B and 13 is markedly delayed compared to phosphorylation of Parkin at Ser65. We further show mechanistically that phosphorylation at Ser111 significantly impairs Rab8A activation by its cognate guanine nucleotide exchange factor (GEF), Rabin8 (by using the Ser111Glu phosphorylation mimic). These findings provide the first evidence that PINK1 is able to regulate the phosphorylation of Rab GTPases and indicate that monitoring phosphorylation of Rab8A/8B/13 at Ser111 may represent novel biomarkers of PINK1 activity in vivo. Our findings also suggest that disruption of Rab GTPase‐mediated signalling may represent a major mechanism in the neurodegenerative cascade of Parkinson's disease.
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Affiliation(s)
- Yu-Chiang Lai
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Chandana Kondapalli
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Ronny Lehneck
- Centre for Integrated Protein Science Munich, Department Chemistry Technische Universität München, Garching, Germany
| | - James B Procter
- Division of Computational Biology, College of Life Sciences University of Dundee, Dundee, UK
| | - Brian D Dill
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Helen I Woodroof
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Robert Gourlay
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Mark Peggie
- Division of Signal Transduction Therapy, College of Life Sciences University of Dundee, Dundee, UK
| | - Thomas J Macartney
- Division of Signal Transduction Therapy, College of Life Sciences University of Dundee, Dundee, UK
| | - Olga Corti
- Inserm U 1127, Paris, France CNRS UMR 7225, Paris, France Sorbonne Universités UPMC Paris 06 UMR S 1127, Paris, France Institut du Cerveau et de la Moelle épinière ICM, Paris, France
| | - Jean-Christophe Corvol
- Inserm U 1127, Paris, France CNRS UMR 7225, Paris, France Sorbonne Universités UPMC Paris 06 UMR S 1127, Paris, France Institut du Cerveau et de la Moelle épinière ICM, Paris, France Inserm Centre d'Investigation Clinique (CIC), Paris, France AP-HP, Département des maladies du système nerveux, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - David G Campbell
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Aymelt Itzen
- Centre for Integrated Protein Science Munich, Department Chemistry Technische Universität München, Garching, Germany
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Miratul Mk Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK College of Medicine, Dentistry & Nursing, University of Dundee, Dundee, UK
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14
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Dill BD, Gierlinski M, Härtlova A, Arandilla AG, Guo M, Clarke RG, Trost M. Quantitative proteome analysis of temporally resolved phagosomes following uptake via key phagocytic receptors. Mol Cell Proteomics 2015; 14:1334-49. [PMID: 25755298 PMCID: PMC4424403 DOI: 10.1074/mcp.m114.044594] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [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: 09/12/2014] [Revised: 02/26/2015] [Indexed: 12/31/2022] Open
Abstract
Macrophages operate at the forefront of innate immunity and their discrimination of foreign versus "self" particles is critical for a number of responses including efficient pathogen killing, antigen presentation, and cytokine induction. In order to efficiently destroy the particles and detect potential threats, macrophages express an array of receptors to sense and phagocytose prey particles. In this study, we accurately quantified a proteomic time-course of isolated phagosomes from murine bone marrow-derived macrophages induced by particles conjugated to seven different ligands representing pathogen-associated molecular patterns, immune opsonins or apoptotic cell markers. We identified a clear functional differentiation over the three timepoints and detected subtle differences between certain ligand-phagosomes, indicating that triggering of receptors through a single ligand type has mild, but distinct, effects on phagosome proteome and function. Moreover, our data shows that uptake of phosphatidylserine-coated beads induces an active repression of NF-κB immune responses upon Toll-like receptor (TLR)-activation by recruitment of anti-inflammatory regulators to the phagosome. This data shows for the first time a systematic time-course analysis of bone marrow-derived macrophages phagosomes and how phagosome fate is regulated by the receptors triggered for phagocytosis.
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Affiliation(s)
- Brian D Dill
- From the ‡MRC Protein Phosphorylation and Ubiquitylation Unit
| | | | - Anetta Härtlova
- From the ‡MRC Protein Phosphorylation and Ubiquitylation Unit
| | | | - Manman Guo
- From the ‡MRC Protein Phosphorylation and Ubiquitylation Unit
| | - Rosemary G Clarke
- ¶Division of Cell Signalling and Immunology, University of Dundee, Scotland, DD1 5EH, United Kingdom
| | - Matthias Trost
- From the ‡MRC Protein Phosphorylation and Ubiquitylation Unit,
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15
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Guo M, Härtlova A, Dill BD, Prescott AR, Gierliński M, Trost M. High-resolution quantitative proteome analysis reveals substantial differences between phagosomes of RAW 264.7 and bone marrow derived macrophages. Proteomics 2015; 15:3169-74. [PMID: 25504905 PMCID: PMC4833182 DOI: 10.1002/pmic.201400431] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 09/08/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022]
Abstract
Macrophages are important immune cells operating at the forefront of innate immunity by taking up foreign particles and microbes through phagocytosis. The RAW 264.7 cell line is commonly used for experiments in the macrophage and phagocytosis field. However, little is known how its functions compare to primary macrophages. Here, we have performed an in‐depth proteomics characterization of phagosomes from RAW 264.7 and bone marrow derived macrophages by quantifying more than 2500 phagosomal proteins. Our data indicate that there are significant differences for a large number of proteins including important receptors such as mannose receptor 1 and Siglec‐1. Moreover, bone marrow derived macrophages phagosomes mature considerably faster by fusion with endosomes and the lysosome which we validated using fluorogenic phagocytic assays. We provide a valuable resource for researcher in the field and recommend careful use of the RAW 264.7 cell line when studying phagosome functions. All MS data have been deposited in the ProteomeXchange with identifier PXD001293 (http://proteomecentral.proteomexchange.org/dataset/PXD001293).
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Affiliation(s)
- Manman Guo
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Science, University of Dundee, Scotland, UK
| | - Anetta Härtlova
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Science, University of Dundee, Scotland, UK
| | - Brian D Dill
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Science, University of Dundee, Scotland, UK
| | - Alan R Prescott
- Division of Cell Signalling and Immunology, College of Life Science, University of Dundee, Scotland, UK
| | - Marek Gierliński
- Division of Computational Biology, College of Life Sciences, University of Dundee, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Science, University of Dundee, Scotland, UK
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16
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Steffen MM, Dearth SP, Dill BD, Li Z, Larsen KM, Campagna SR, Wilhelm SW. Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis. ISME J 2014; 8:2080-92. [PMID: 24858783 PMCID: PMC4184021 DOI: 10.1038/ismej.2014.78] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/02/2014] [Accepted: 04/08/2014] [Indexed: 11/09/2022]
Abstract
The cyanobacterium Microcystis aeruginosa is a globally distributed bloom-forming organism that degrades freshwater systems around the world. Factors that drive its dispersion, diversification and success remain, however, poorly understood. To develop insight into cellular-level responses to nutrient drivers of eutrophication, RNA sequencing was coupled to a comprehensive metabolomics survey of M. aeruginosa sp. NIES 843 grown in various nutrient-reduced conditions. Transcriptomes were generated for cultures grown in nutrient-replete (with nitrate as the nitrogen (N) source), nitrogen-reduced (with nitrate, urea or ammonium acting as the N sources) and phosphate-reduced conditions. Extensive expression differences (up to 696 genes for urea-grown cells) relative to the control treatment were observed, demonstrating that the chemical variant of nitrogen available to cells affected transcriptional activity. Of particular note, a high number of transposase genes (up to 81) were significantly and reproducibly up-regulated relative to the control when grown on urea. Conversely, phosphorus (P) reduction resulted in a significant cessation in transcription of transposase genes, indicating that variation in nutrient chemistry may influence transcription of transposases and may impact the highly mosaic genomic architecture of M. aeruginosa. Corresponding metabolomes showed comparably few differences between treatments, suggesting broad changes to gene transcription are required to maintain metabolic homeostasis under nutrient reduction. The combined observations provide novel and extensive insight into the complex cellular interactions that take place in this important bloom-forming organism during variable nutrient conditions and highlight a potential unknown molecular mechanism that may drive Microcystis blooms and evolution.
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Affiliation(s)
- Morgan M Steffen
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Stephen P Dearth
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Brian D Dill
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zhou Li
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Kristen M Larsen
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
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17
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Gawden-Bone C, West MA, Morrison VL, Edgar AJ, McMillan SJ, Dill BD, Trost M, Prescott A, Fagerholm SC, Watts C. A crucial role for β2 integrins in podosome formation, dynamics and Toll-like-receptor-signaled disassembly in dendritic cells. J Cell Sci 2014; 127:4213-24. [PMID: 25086067 PMCID: PMC4179490 DOI: 10.1242/jcs.151167] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The dynamic properties of podosomes, their ability to degrade the underlying matrix and their modulation by Toll-like receptor (TLR) signaling in dendritic cells (DCs) suggests they have an important role in migration. Integrins are thought to participate in formation and dynamics of podosomes but the multiplicity of integrins in podosomes has made this difficult to assess. We report that murine DCs that lack β2 integrins fail to form podosomes. Re-expression of β2 integrins restored podosomes but not when the membrane proximal or distal NPxF motifs, or when an intervening triplet of threonine residues were mutated. We show that β2 integrins are remarkably long-lived in podosome clusters and form a persistent framework that hosts multiple actin-core-formation events at the same or adjacent sites. When β2 integrin amino acid residues 745 or 756 were mutated from Ser to Ala, podosomes became resistant to dissolution mediated through TLR signaling. TLR signaling did not detectably modulate phosphorylation at these sites but mutation of either residue to phospho-mimetic Asp increased β2 integrin turnover in podosomes, indicating that phosphorylation at one or both sites establishes permissive conditions for TLR-signaled podosome disassembly.
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Affiliation(s)
- Christian Gawden-Bone
- Division of Cell Biology and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Michele A West
- Division of Cell Biology and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Vicky L Morrison
- University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Alexander J Edgar
- Division of Cell Biology and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Sarah J McMillan
- Division of Cell Biology and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Brian D Dill
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alan Prescott
- Division of Cell Biology and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Susanna C Fagerholm
- University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Colin Watts
- Division of Cell Biology and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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18
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Sharma R, Dill BD, Chourey K, Shah M, VerBerkmoes NC, Hettich RL. Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization. J Proteome Res 2012; 11:6008-18. [PMID: 23126408 DOI: 10.1021/pr300709k] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The expanding use of surfactants for proteome sample preparations has prompted the need to systematically optimize the application and removal of these MS-deleterious agents prior to proteome measurements. Here we compare four detergent cleanup methods (trichloroacetic acid (TCA) precipitation, chloroform/methanol/water (CMW) extraction, a commercial detergent removal spin column method (DRS) and filter-aided sample preparation (FASP)) to provide efficiency benchmarks with respect to protein, peptide, and spectral identifications in each case. Our results show that for protein-limited samples, FASP outperforms the other three cleanup methods, while at high protein amounts, all the methods are comparable. This information was used to investigate and contrast molecular weight-based fractionated with unfractionated lysates from three increasingly complex samples ( Escherichia coli K-12, a five microbial isolate mixture, and a natural microbial community groundwater sample), all of which were prepared with an SDS-FASP approach. The additional fractionation step enhanced the number of protein identifications by 8% to 25% over the unfractionated approach across the three samples.
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Affiliation(s)
- Ritin Sharma
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville-Tennessee 37996, United States
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19
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Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, Fremaux C, Horvath P, Barrangou R, VerBerkmoes NC. Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PLoS One 2012; 7:e38077. [PMID: 22666452 PMCID: PMC3364186 DOI: 10.1371/journal.pone.0038077] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/30/2012] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas system, comprised of clustered regularly interspaced short palindromic repeats along with their associated (Cas) proteins, protects bacteria and archaea from viral predation and invading nucleic acids. While the mechanism of action for this acquired immunity is currently under investigation, the response of Cas protein expression to phage infection has yet to be elucidated. In this study, we employed shotgun proteomics to measure the global proteome expression in a model system for studying the CRISPR/Cas response in S. thermophilus DGCC7710 infected with phage 2972. Host and viral proteins were simultaneously measured following inoculation at two different multiplicities of infection and across various time points using two-dimensional liquid chromatography tandem mass spectrometry. Thirty-seven out of forty predicted viral proteins were detected, including all proteins of the structural virome and viral effector proteins. In total, 1,013 of 2,079 predicted S. thermophilus proteins were detected, facilitating the monitoring of host protein synthesis changes in response to virus infection. Importantly, Cas proteins from all four CRISPR loci in the S. thermophilus DGCC7710 genome were detected, including loci previously thought to be inactive. Many Cas proteins were found to be constitutively expressed, but several demonstrated increased abundance following infection, including the signature Cas9 proteins from the CRISPR1 and CRISPR3 loci, which are key players in the interference phase of the CRISPR/Cas response. Altogether, these results provide novel insights into the proteomic response of S. thermophilus, specifically CRISPR-associated proteins, upon phage 2972 infection.
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Affiliation(s)
- Jacque C. Young
- Graduate School for Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Brian D. Dill
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
| | - Manesh Shah
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | | | - Rodolphe Barrangou
- DuPont Nutrition and Health, Madison, Wisconsin, United States of America
| | - Nathan C. VerBerkmoes
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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20
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Campbell-Valois FX, Trost M, Chemali M, Dill BD, Laplante A, Duclos S, Sadeghi S, Rondeau C, Morrow IC, Bell C, Gagnon E, Hatsuzawa K, Thibault P, Desjardins M. Quantitative proteomics reveals that only a subset of the endoplasmic reticulum contributes to the phagosome. Mol Cell Proteomics 2012; 11:M111.016378. [PMID: 22427703 DOI: 10.1074/mcp.m111.016378] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phagosomes, by killing and degrading pathogens for antigen presentation, are organelles implicated in key aspects of innate and adaptive immunity. Although it has been well established that phagosomes consist of membranes from the plasma membrane, endosomes, and lysosomes, the notion that the endoplasmic reticulum (ER) membrane could play an important role in the formation of the phagosome is debated. However, a method to accurately estimate the contribution of potential source organelles and contaminants to the phagosome proteome has been lacking. Herein, we have developed a proteomic approach for objectively quantifying the contribution of various organelles to the early and late phagosomes by comparing these fractions to their total membrane and postnuclear supernatant of origin in the J774A.1 murine macrophage cell line. Using quantitative label-free mass spectrometry, the abundance of peptides corresponding to hundreds of proteins was estimated and attributed to one of five organelles (e.g. plasma membrane, endosomes/lysosomes, ER, Golgi, and mitochondria). These data in combination with a stable isotope labeling in cell culture method designed to detect potential contaminant sources revealed that the ER is part of the phagosomal membrane and contributes ≈ 20% of the early phagosome proteome. In addition, only a subset of ER proteins is recruited to the phagosome, suggesting that a specific subdomain(s) of the ER might be involved in phagocytosis. Western blotting and immunofluorescence substantially validated this conclusion; we were able to demonstrate that the fraction of the ER in which the ER marker GFP-KDEL accumulates is excluded from the phagosomes, whereas that containing the mVenus-Syntaxin 18 is recruited. These results highlight promising new avenues for the description of the pathogenic mechanisms used by Leishmania, Brucella, and Legionella spp., which thrive in ER-rich phagosomes.
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21
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Jiao Y, D'haeseleer P, Dill BD, Shah M, VerBerkmoes NC, Hettich RL, Banfield JF, Thelen MP. Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. Appl Environ Microbiol 2011; 77:5230-7. [PMID: 21685158 PMCID: PMC3147463 DOI: 10.1128/aem.03005-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 06/03/2011] [Indexed: 01/01/2023] Open
Abstract
In microbial communities, extracellular polymeric substances (EPS), also called the extracellular matrix, provide the spatial organization and structural stability during biofilm development. One of the major components of EPS is protein, but it is not clear what specific functions these proteins contribute to the extracellular matrix or to microbial physiology. To investigate this in biofilms from an extremely acidic environment, we used shotgun proteomics analyses to identify proteins associated with EPS in biofilms at two developmental stages, designated DS1 and DS2. The proteome composition of the EPS was significantly different from that of the cell fraction, with more than 80% of the cellular proteins underrepresented or undetectable in EPS. In contrast, predicted periplasmic, outer membrane, and extracellular proteins were overrepresented by 3- to 7-fold in EPS. Also, EPS proteins were more basic by ∼2 pH units on average and about half the length. When categorized by predicted function, proteins involved in motility, defense, cell envelope, and unknown functions were enriched in EPS. Chaperones, such as histone-like DNA binding protein and cold shock protein, were overrepresented in EPS. Enzymes, such as protein peptidases, disulfide-isomerases, and those associated with cell wall and polysaccharide metabolism, were also detected. Two of these enzymes, identified as β-N-acetylhexosaminidase and cellulase, were confirmed in the EPS fraction by enzymatic activity assays. Compared to the differences between EPS and cellular fractions, the relative differences in the EPS proteomes between DS1 and DS2 were smaller and consistent with expected physiological changes during biofilm development.
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Affiliation(s)
| | - Patrik D'haeseleer
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | | | - Manesh Shah
- Biosciences Divisions, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | | | | | - Jillian F. Banfield
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720
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22
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Hall JV, Schell M, Dessus-Babus S, Moore CG, Whittimore JD, Sal M, Dill BD, Wyrick PB. The multifaceted role of oestrogen in enhancing Chlamydia trachomatis infection in polarized human endometrial epithelial cells. Cell Microbiol 2011; 13:1183-99. [PMID: 21615662 DOI: 10.1111/j.1462-5822.2011.01608.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The oestrogen receptor (ER) α-β+ HEC-1B and the ERα+β+ Ishikawa (IK) cell lines were investigated to dissect the effects of oestrogen exposure on several parameters of Chlamydia trachomatis infection. Antibody blockage of ERα or ERβ alone or simultaneously significantly decreased C. trachomatis infectivity (45-68%). Addition of the ERβ antagonist, tamoxifen, to IK or HEC-1B prior to or after chlamydial infection caused a 30-90% decrease in infectivity, the latter due to disrupted eukaryotic organelles. In vivo, endometrial glandular epithelial cells are stimulated by hormonally influenced stromal signals. Accordingly, chlamydial infectivity was significantly increased by 27% and 21% in IK and HEC-1B cells co-cultured with SHT-290 stromal cells exposed to oestrogen. Endometrial stromal cell/epithelial cell co-culture revealed indirect effects of oestrogen on phosphorylation of extracellular signal-regulated kinase and calcium-dependant phospholipase A2 and significantly increased production of interleukin (IL)-8 and IL-6 in both uninfected and chlamydiae-infected epithelial cells. These results indicate that oestrogen and its receptors play multiple roles in chlamydial infection: (i) membrane oestrogen receptors (mERs) aid in chlamydial entry into host cells, and (ii) mER signalling may contribute to inclusion development during infection. Additionally, enhancement of chlamydial infection is affected by hormonally influenced stromal signals in conjunction with direct oestrogen stimulation of the human epithelia.
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Affiliation(s)
- Jennifer Vanover Hall
- Department of Microbiology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
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23
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Mueller RS, Dill BD, Pan C, Belnap CP, Thomas BC, VerBerkmoes NC, Hettich RL, Banfield JF. Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ Microbiol 2011; 13:2279-92. [PMID: 21518216 DOI: 10.1111/j.1462-2920.2011.02486.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Proteomes of acid mine drainage biofilms at different stages of ecological succession were examined to understand microbial responses to changing community membership. We evaluated the degree of reproducibility of the community proteomes between samples of the same growth stage and found stable and predictable protein abundance patterns across time and sampling space, allowing for a set of 50 classifier proteins to be identified for use in predicting growth stages of undefined communities. Additionally, physiological changes in the dominant species, Leptospirillum Group II, were analysed as biofilms mature. During early growth stages, this population responds to abiotic stresses related to growth on the acid mine drainage solution. Enzymes involved in protein synthesis, cell division and utilization of 1- and 2-carbon compounds were more abundant in early growth stages, suggesting rapid growth and a reorganization of metabolism during biofilm initiation. As biofilms thicken and diversify, external stresses arise from competition for dwindling resources, which may inhibit cell division of Leptospirillum Group II through the SOS response. This population also represses translation and synthesizes more complex carbohydrates and amino acids in mature biofilms. These findings provide unprecedented insight into the physiological changes that may result from competitive interactions within communities in natural environments.
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Affiliation(s)
- Ryan S Mueller
- University of California, Berkeley, California 94720, USA.
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24
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Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, VerBerkmoes NC, Hettich RL, Banfield JF. Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A 2010; 107:8806-11. [PMID: 20421484 PMCID: PMC2889320 DOI: 10.1073/pnas.0914470107] [Citation(s) in RCA: 204] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete approximately 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher coding density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3:159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.
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Affiliation(s)
| | - Luis R. Comolli
- Lawrence Berkeley National Laboratories, Berkeley, CA 94720; and
| | | | | | | | - Brian D. Dill
- Chemical Sciences Divisions, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | | | | | - Robert L. Hettich
- Chemical Sciences Divisions, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Jillian F. Banfield
- Department of Earth and Planetary Science and
- Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
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25
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Dill BD, Dessus-Babus S, Raulston JE. Identification of iron-responsive proteins expressed by Chlamydia trachomatis reticulate bodies during intracellular growth. Microbiology (Reading) 2009; 155:210-219. [DOI: 10.1099/mic.0.022731-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The obligate intracellular bacterium Chlamydia trachomatis serovar E is the most prevalent cause of bacterial sexually transmitted disease. With an established requirement for iron, the developmental cycle arrests at the intracellular reticulate body stage during iron restriction, resulting in a phenomenon termed persistence. Persistence has implications in natural infections for altered expression of virulence factors and antigens, in addition to a potential role in producing chronic infection. In this study, chlamydial proteins in iron-restricted, infected HEC-1B cells were radiolabelled during mid-developmental cycle growth, harvested, and separated using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Of ∼250 radiolabelled protein species visualized, densitometric analysis revealed 25 proteins that increased in expression under iron restriction compared to iron-sufficient control samples; ten protein species identified by mass spectrometry are involved in the oxidative damage response (alkyl hydroperoxide reductase, 6-phosphogluconolactonase and acyl carrier protein synthase), transcription (RNA polymerase subunit alpha and transcription anti-termination factors NusA and NusG), protein modification (peptide deformylase and trigger factor), and virulence (Chlamydia protein associating with death domains, CADD). Transcript-level expression patterns of ahpC, devB, cadd, fabF and ct538 were measured by quantitative RT-PCR throughout the developmental cycle, and each gene examined demonstrated a significant but small mid-cycle increase in transcript level in iron-restricted cultures compared to iron-replete controls. Taken together, these data suggest that the primary response of chlamydiae to reduced iron availability is to increase expression of proteins involved in protection against oxidative damage via iron-catalysed generation of reactive oxygen species and adaptation to stress by increasing expression of transcriptional machinery and other stress-responsive proteins.
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Affiliation(s)
- Brian D. Dill
- Department of Microbiology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614-1700, USA
| | - Sophie Dessus-Babus
- Department of Microbiology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614-1700, USA
| | - Jane E. Raulston
- Department of Microbiology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614-1700, USA
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26
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Dill BD, Raulston JE. Examination of an inducible expression system for limiting iron availability during Chlamydia trachomatis infection. Microbes Infect 2007; 9:947-53. [PMID: 17544798 PMCID: PMC2083192 DOI: 10.1016/j.micinf.2007.03.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 03/20/2007] [Accepted: 03/28/2007] [Indexed: 11/24/2022]
Abstract
The obligate intracellular bacterium Chlamydia trachomatis requires iron in order to complete its developmental cycle. Addition of an iron-chelating drug, Desferal (deferoxamine mesylate), to infected cell culture causes Chlamydia to enter persistence. Here, we explore the ability of a stably-transfected cell line with inducible over-expression of the eukaryotic iron efflux protein ferroportin to starve C. trachomatis serovar E for iron. Ferroportin-induced iron removal is perhaps a more direct method of removing iron from the intracellular compartment versus exposure to an exogenous chemical chelator. Following induction, ferroportin-green fluorescent protein (Fpn-GFP) was detected in the plasma membrane, and cells expressing Fpn-GFP remained viable throughout the timescale required for Chlamydia to complete its developmental cycle. Following Fpn-GFP induction in infected cells, chlamydial infectivity remained unchanged, indicating chlamydiae were not in persistence. Ferritin levels indicate only a small decrease in cellular iron following Fpn-GFP expression relative to cultures exposed to Desferal. These data indicate that expression of Fpn-GFP in chlamydiae-infected cells is not capable of reducing iron below the threshold concentration needed to cause chlamydiae to enter persistence.
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Affiliation(s)
- Brian D Dill
- Department of Microbiology, Box 70579, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614-0579, USA.
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27
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LaRue RW, Dill BD, Giles DK, Whittimore JD, Raulston JE. Chlamydial Hsp60-2 is iron responsive in Chlamydia trachomatis serovar E-infected human endometrial epithelial cells in vitro. Infect Immun 2007; 75:2374-80. [PMID: 17307941 PMCID: PMC1865735 DOI: 10.1128/iai.01465-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Chlamydial 60-kDa heat shock proteins (cHsp60s) are known to play a prominent role in the immunopathogenesis of disease. It is also known that several stress-inducing growth conditions, such as heat, iron deprivation, or exposure to gamma interferon, result in the development of persistent chlamydial forms that often exhibit enhanced expression of cHsp60. We have shown previously that the expression of cHsp60 is greatly enhanced in Chlamydia trachomatis serovar E propagated in an iron-deficient medium. The objective of this work was to determine which single cHsp60 or combination of the three cHsp60 homologs encoded by this organism responds to iron limitation. Using monospecific polyclonal peptide antisera that recognize only cHsp60-1, cHsp60-2, or cHsp60-3, we found that expression of cHsp60-2 is responsive to iron deprivation. Overall, our studies suggest that the expression of cHsp60 homologs differs among the mechanisms currently known to induce persistence.
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Affiliation(s)
- Richard W LaRue
- Department of Microbiology, James H. Quillen College of Medicine, East Tennessee State University, P.O. Box 70579, Johnson City, TN 37614-1708, USA
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