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Zhang X, Ling T, Jin Z, Xu S, Gao Z, Sun B, Qiu Z, Wei J, Dong N, Wang G, Wang G, Li L, Abdul-Mageed M, Lakshmanan LVS, He F, Ouyang W, Chang C, Sun S. π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing. Nat Commun 2025; 16:267. [PMID: 39747823 PMCID: PMC11695716 DOI: 10.1038/s41467-024-55021-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 11/28/2024] [Indexed: 01/04/2025] Open
Abstract
Peptide sequencing via tandem mass spectrometry (MS/MS) is essential in proteomics. Unlike traditional database searches, deep learning excels at de novo peptide sequencing, even for peptides missing from existing databases. Current deep learning models often rely on autoregressive generation, which suffers from error accumulation and slow inference speeds. In this work, we introduce π-PrimeNovo, a non-autoregressive Transformer-based model for peptide sequencing. With our architecture design and a CUDA-enhanced decoding module for precise mass control, π-PrimeNovo achieves significantly higher accuracy and up to 89x faster inference than state-of-the-art methods, making it ideal for large-scale applications like metaproteomics. Additionally, it excels in phosphopeptide mining and detecting low-abundance post-translational modifications (PTMs), marking a substantial advance in peptide sequencing with broad potential in biological research.
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Affiliation(s)
- Xiang Zhang
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
- University of British Columbia, Vancouver, BC, Canada
| | - Tianze Ling
- Tsinghua University, Beijing, China
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhi Jin
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Sheng Xu
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China
| | - Zhiqiang Gao
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Boyan Sun
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zijie Qiu
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China
| | - Jiaqi Wei
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
- Zhejiang University, Zhejiang, China
| | - Nanqing Dong
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Guangshuai Wang
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China
| | - Guibin Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Leyuan Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Muhammad Abdul-Mageed
- University of British Columbia, Vancouver, BC, Canada
- MBZUAI, Abu Dhabi, United Arab Emirates
| | | | - Fuchu He
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
- International Academy of Phronesis Medicine (Guangdong), Guangdong, Guangzhou, China
| | - Wanli Ouyang
- Shanghai Artificial Intelligence Laboratory, Shanghai, China.
| | - Cheng Chang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| | - Siqi Sun
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.
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2
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Bergeron JJM. Proteomics Impact on Cell Biology to Resolve Cell Structure and Function. Mol Cell Proteomics 2024; 23:100758. [PMID: 38574860 PMCID: PMC11070594 DOI: 10.1016/j.mcpro.2024.100758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
The acceleration of advances in proteomics has enabled integration with imaging at the EM and light microscopy levels, cryo-EM of protein structures, and artificial intelligence with proteins comprehensively and accurately resolved for cell structures at nanometer to subnanometer resolution. Proteomics continues to outpace experimentally based structural imaging, but their ultimate integration is a path toward the goal of a compendium of all proteins to understand mechanistically cell structure and function.
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Affiliation(s)
- John J M Bergeron
- Department of Medicine, McGill University Hospital Research Institute, Montreal, Quebec, Canada.
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3
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Swenson CS, Pillai KS, Carlos AJ, Moellering RE. Spatial Chemoproteomics for Mapping the Active Proteome. Isr J Chem 2023; 63:e202200104. [PMID: 38046285 PMCID: PMC10688764 DOI: 10.1002/ijch.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Indexed: 01/06/2023]
Abstract
Functional regulation of cell signaling through dynamic changes in protein activity state as well as spatial organization represent two dynamic, complex, and conserved phenomena in biology. Seemingly separate areas of -omics method development have focused on building tools that can detect and quantify protein activity states, as well as map sub-cellular and intercellular protein organization. Integration of these efforts, through the development of chemical tools and platforms that enable detection and quantification of protein functional states with spatial resolution provide opportunities to better understand heterogeneity in the proteome within cell organelles, multi-cellular tissues, and whole organisms. This review provides an overview of and considerations for major classes of chemical proteomic probes and technologies that enable protein activity mapping from sub-cellular compartments to live animals.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Kavya Smitha Pillai
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Anthony J Carlos
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
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4
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Wynne ME, Lane AR, Singleton KS, Zlatic SA, Gokhale A, Werner E, Duong D, Kwong JQ, Crocker AJ, Faundez V. Heterogeneous Expression of Nuclear Encoded Mitochondrial Genes Distinguishes Inhibitory and Excitatory Neurons. eNeuro 2021; 8:ENEURO.0232-21.2021. [PMID: 34312306 PMCID: PMC8387155 DOI: 10.1523/eneuro.0232-21.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/25/2021] [Accepted: 07/17/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial composition varies by organ and their constituent cell types. This mitochondrial diversity likely determines variations in mitochondrial function. However, the heterogeneity of mitochondria in the brain remains underexplored despite the large diversity of cell types in neuronal tissue. Here, we used molecular systems biology tools to address whether mitochondrial composition varies by brain region and neuronal cell type in mice. We reasoned that proteomics and transcriptomics of microdissected brain regions combined with analysis of single-cell mRNA sequencing (scRNAseq) could reveal the extent of mitochondrial compositional diversity. We selected nuclear encoded gene products forming complexes of fixed stoichiometry, such as the respiratory chain complexes and the mitochondrial ribosome, as well as molecules likely to perform their function as monomers, such as the family of SLC25 transporters. We found that the proteome encompassing these nuclear-encoded mitochondrial genes and obtained from microdissected brain tissue segregated the hippocampus, striatum, and cortex from each other. Nuclear-encoded mitochondrial transcripts could only segregate cell types and brain regions when the analysis was performed at the single-cell level. In fact, single-cell mitochondrial transcriptomes were able to distinguish glutamatergic and distinct types of GABAergic neurons from one another. Within these cell categories, unique SLC25A transporters were able to identify distinct cell subpopulations. Our results demonstrate heterogeneous mitochondrial composition across brain regions and cell types. We postulate that mitochondrial heterogeneity influences regional and cell type-specific mechanisms in health and disease.
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Affiliation(s)
- Meghan E Wynne
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | - Alicia R Lane
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | | | | | - Avanti Gokhale
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | - Erica Werner
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | - Duc Duong
- Department of Biochemistry, Emory University, Atlanta, GA 30322
| | | | - Amanda J Crocker
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753
| | - Victor Faundez
- Department of Cell Biology, Emory University, Atlanta, GA 30322
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5
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SPP1 derived from silica-exposed macrophage exosomes triggers fibroblast transdifferentiation. Toxicol Appl Pharmacol 2021; 422:115559. [PMID: 33961903 DOI: 10.1016/j.taap.2021.115559] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 01/16/2023]
Abstract
The occurrence and development of silicosis is related to the interaction of multiple cells through signal transmission caused by silica dust. Including inflammatory changes reduced by macrophages and phenotypic transdifferentiation reduced by lung fibroblasts. As a communication medium between cells, exosomes have become a hot research topic. To explore the role of exosomal proteins in the occurrence and development of silicosis and the possible intervention targets, this study conducted proteomic analysis of macrophage-derived exosomes induced by silica, to identify specific proteins for intervention. In this study, we used proteomic analysis to screen exosomal protein profiles from the RAW264.7 macrophages exposed to silica. A total of 291 proteins were differentially expressed, of which 178 were upregulated and 113 were downregulated. By performing functional annotation and analysis of the differentially expressed proteins, we identified proteins SPP1, HMGB3, and HNRNPAB, which were consistent with the proteomics analysis. The involvement of SPP1 protein in fibrosis was studied further. Knocking down the expression of SPP1 in exosomes resulted in a decrease in fibrosis-related indicators. These results help to understand that exosomal protein can mediate cell communication and play a key role in the transition from fibroblasts to myofibroblasts. Further, this study also provided strategies and scientific basis for future studies on the intervention of silicosis.
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6
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Varikuti S, Jha BK, Holcomb EA, McDaniel JC, Karpurapu M, Srivastava N, McGwire BS, Satoskar AR, Parinandi NL. The role of vascular endothelium and exosomes in human protozoan parasitic diseases. ACTA ACUST UNITED AC 2020; 4. [PMID: 33089078 PMCID: PMC7575144 DOI: 10.20517/2574-1209.2020.27] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The vascular endothelium is a vital component in maintaining the structure and function of blood vessels. The endothelial cells (ECs) mediate vital regulatory functions such as the proliferation of cells, permeability of various tissue membranes, and exchange of gases, thrombolysis, blood flow, and homeostasis. The vascular endothelium also regulates inflammation and immune cell trafficking, and ECs serve as a replicative niche for many bacterial, viral, and protozoan infectious diseases. Endothelial dysfunction can lead to vasodilation and pro-inflammation, which are the hallmarks of many severe diseases. Exosomes are nanoscale membrane-bound vesicles that emerge from cells and serve as important extracellular components, which facilitate communication between cells and maintain homeostasis during normal and pathophysiological states. Exosomes are also involved in gene transfer, inflammation and antigen presentation, and mediation of the immune response during pathogenic states. Protozoa are a diverse group of unicellular organisms that cause many infectious diseases in humans. In this regard, it is becoming increasingly evident that many protozoan parasites (such as Plasmodium, Trypanosoma, Leishmania, and Toxoplasma) utilize exosomes for the transfer of their virulence factors and effector molecules into the host cells, which manipulate the host gene expression, immune responses, and other biological activities to establish and modulate infection. In this review, we discuss the role of the vascular endothelium and exosomes in and their contribution to pathogenesis in malaria, African sleeping sickness, Chagas disease, and leishmaniasis and toxoplasmosis with an emphasis on their actions on the innate and adaptive immune mechanisms of resistance.
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Affiliation(s)
- Sanjay Varikuti
- Department of Pathology, The Ohio State University Medical Center, Columbus, OH 43201, USA.,Department of Bioscience & Biotechnology, Banasthali University, Banasthali 304022, India
| | - Bijay Kumar Jha
- Division of Infectious Diseases, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH 43201, USA
| | - Erin A Holcomb
- Department of Pathology, The Ohio State University Medical Center, Columbus, OH 43201, USA
| | - Jodi C McDaniel
- College of Nursing, The Ohio State University, Columbus, OH 43201, USA
| | - Manjula Karpurapu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH 43201, USA
| | - Nidhi Srivastava
- Department of Bioscience & Biotechnology, Banasthali University, Banasthali 304022, India
| | - Bradford S McGwire
- Division of Infectious Diseases, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH 43201, USA
| | - Abhay R Satoskar
- Department of Pathology, The Ohio State University Medical Center, Columbus, OH 43201, USA
| | - Narasimham L Parinandi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH 43201, USA
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7
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Danielsson F, Mahdessian D, Axelsson U, Sullivan D, Uhlén M, Andersen JS, Thul PJ, Lundberg E. Spatial Characterization of the Human Centrosome Proteome Opens Up New Horizons for a Small but Versatile Organelle. Proteomics 2020; 20:e1900361. [PMID: 32558245 DOI: 10.1002/pmic.201900361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/29/2020] [Indexed: 12/27/2022]
Abstract
After a century of research, the human centrosome continues to fascinate. Based on immunofluorescence and confocal microscopy, an extensive inventory of the protein components of the human centrosome, and the centriolar satellites, with the important contribution of over 300 novel proteins localizing to these compartments is presented. A network of candidate centrosome proteins involved in ubiquitination, including six interaction partners of the Kelch-like protein 21, and an additional network of protein phosphatases, together supporting the suggested role of the centrosome as an interactive hub for cell signaling, is identified. Analysis of multi-localization across cellular organelles analyzed within the Human Protein Atlas (HPA) project shows how multi-localizing proteins are particularly overrepresented in centriolar satellites, supporting the dynamic nature and wide range of functions for this compartment. In summary, the spatial dissection of the human centrosome and centriolar satellites described here provides a comprehensive knowledgebase for further exploration of their proteomes.
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Affiliation(s)
- Frida Danielsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Solna, 17121, Sweden
| | - Diana Mahdessian
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Solna, 17121, Sweden
| | - Ulrika Axelsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Solna, 17121, Sweden
| | - Devin Sullivan
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Solna, 17121, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Solna, 17121, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, 106 91, Sweden
| | - Jens S Andersen
- Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, 5230, Denmark
| | - Peter J Thul
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Solna, 17121, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Solna, 17121, Sweden
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8
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Zhu H, Tamura T, Hamachi I. Chemical proteomics for subcellular proteome analysis. Curr Opin Chem Biol 2019; 48:1-7. [DOI: 10.1016/j.cbpa.2018.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 11/17/2022]
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9
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Geladaki A, Kočevar Britovšek N, Breckels LM, Smith TS, Vennard OL, Mulvey CM, Crook OM, Gatto L, Lilley KS. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nat Commun 2019; 10:331. [PMID: 30659192 PMCID: PMC6338729 DOI: 10.1038/s41467-018-08191-w] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/18/2018] [Indexed: 01/09/2023] Open
Abstract
The study of protein localisation has greatly benefited from high-throughput methods utilising cellular fractionation and proteomic profiling. Hyperplexed Localisation of Organelle Proteins by Isotope Tagging (hyperLOPIT) is a well-established method in this area. It achieves high-resolution separation of organelles and subcellular compartments but is relatively time- and resource-intensive. As a simpler alternative, we here develop Localisation of Organelle Proteins by Isotope Tagging after Differential ultraCentrifugation (LOPIT-DC) and compare this method to the density gradient-based hyperLOPIT approach. We confirm that high-resolution maps can be obtained using differential centrifugation down to the suborganellar and protein complex level. HyperLOPIT and LOPIT-DC yield highly similar results, facilitating the identification of isoform-specific localisations and high-confidence localisation assignment for proteins in suborganellar structures, protein complexes and signalling pathways. By combining both approaches, we present a comprehensive high-resolution dataset of human protein localisations and deliver a flexible set of protocols for subcellular proteomics.
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Affiliation(s)
- Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Genetics, University of Cambridge, 20 Downing Place, Cambridge, CB2 3EJ, UK
| | - Nina Kočevar Britovšek
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Tom S Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Owen L Vennard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Claire M Mulvey
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- MRC Biostatistics Unit, Cambridge Institute for Public Health, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- de Duve Institute, UC Louvain, Avenue Hippocrate 75, Brussels, 1200, Belgium
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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10
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Mass Spectrometry Based Comparative Proteomics Using One Dimensional and Two Dimensional SDS-PAGE of Rat Atria Induced with Obstructive Sleep Apnea. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:541-561. [DOI: 10.1007/978-3-030-15950-4_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Teo CSH, O’Hare P. A bimodal switch in global protein translation coupled to eIF4H relocalisation during advancing cell-cell transmission of herpes simplex virus. PLoS Pathog 2018; 14:e1007196. [PMID: 30028874 PMCID: PMC6070287 DOI: 10.1371/journal.ppat.1007196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/01/2018] [Accepted: 07/02/2018] [Indexed: 12/28/2022] Open
Abstract
We used the bioorthogonal protein precursor, homopropargylglycine (HPG) and chemical ligation to fluorescent capture agents, to define spatiotemporal regulation of global translation during herpes simplex virus (HSV) cell-to-cell spread at single cell resolution. Translational activity was spatially stratified during advancing infection, with distal uninfected cells showing normal levels of translation, surrounding zones at the earliest stages of infection with profound global shutoff. These cells further surround previously infected cells with restored translation close to levels in uninfected cells, reflecting a very early biphasic switch in translational control. While this process was dependent on the virion host shutoff (vhs) function, in certain cell types we also observed temporally altered efficiency of shutoff whereby during early transmission, naïve cells initially exhibited resistance to shutoff but as infection advanced, naïve target cells succumbed to more extensive translational suppression. This may reflect spatiotemporal variation in the balance of oscillating suppression-recovery phases. Our results also strongly indicate that a single particle of HSV-2, can promote pronounced global shutoff. We also demonstrate that the vhs interacting factor, eIF4H, an RNA helicase accessory factor, switches from cytoplasmic to nuclear localisation precisely correlating with the initial shutdown of translation. However translational recovery occurs despite sustained eIF4H nuclear accumulation, indicating a qualitative change in the translational apparatus before and after suppression. Modelling simulations of high multiplicity infection reveal limitations in assessing translational activity due to sampling frequency in population studies and how analysis at the single cell level overcomes such limitations. The work reveals new insight and a revised model of translational manipulation during advancing infection which has important implications both mechanistically and with regards to the physiological role of translational control during virus propagation. The work also demonstrates the potential of bioorthogonal chemistry for single cell analysis of cellular metabolic processes during advancing infections in other virus systems.
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Affiliation(s)
- Catherine Su Hui Teo
- Section of Virology, Faculty of Medicine, Imperial College London, St Mary’s Medical School, London, United Kingdom
| | - Peter O’Hare
- Section of Virology, Faculty of Medicine, Imperial College London, St Mary’s Medical School, London, United Kingdom
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12
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Li N, Han Z, Li L, Zhang B, Liu Z, Li J. The anti-cataract molecular mechanism study in selenium cataract rats for baicalin ophthalmic nanoparticles. Drug Des Devel Ther 2018; 12:1399-1411. [PMID: 29872263 PMCID: PMC5973426 DOI: 10.2147/dddt.s160524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE The objective of this study was to investigate the effects of the solid lipid nanoparticles of baicalin (BA-SLNs) on an experimental cataract model and explore the molecular mechanism combined with bioinformatics analysis. MATERIALS AND METHODS The transparency of lens was observed daily by slit-lamp and photography. Lenticular opacity was graded. Two-dimensional gel electrophoresis (2-DE) was employed to analyze the differential protein expression modes in each group. Proteins of interest were subjected to protein identification by nano-liquid chromatography tandem mass spectrometry (LC-MS/MS). Bioinformatics analysis was performed using the Ingenuity Pathway Analysis (IPA) online software to comprehend the biological implications of the proteins identified by proteomics. RESULTS At the end of the sodium selenite-induced cataract progression, almost all lenses from the model group developed partial nuclear opacity; however, all lenses were clear and normal in the blank group. There was no significant difference between the BA-SLNs group and the blank group. Many protein spots were differently expressed in 2-DE patterns of total proteins of lenses from each group, and 65 highly different protein spots were selected to be identified between the BA-SLNs group and the model group. A total of 23 proteins were identified, and 12 of which were crystalline proteins. CONCLUSION We considered crystalline proteins to play important roles in preserving the normal expression levels of proteins and the transparency of lenses. The general trend in the BA-SLN-treated lenses' data showed that BA-SLNs regulated the protein expression mode of cataract lenses to normal lenses. Our findings suggest that BA-SLNs may be a potential therapeutic agent in treating cataract by regulating protein expression and may also be a strong candidate for future clinical research.
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Affiliation(s)
- Nan Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Engineering Research Center of Modern Chinese Medicine Discovery and Preparation Technique, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
| | - Zhenzhen Han
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Baokang Hospital, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
| | - Lin Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
| | - Bing Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Engineering Research Center of Modern Chinese Medicine Discovery and Preparation Technique, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
| | - Zhidong Liu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Engineering Research Center of Modern Chinese Medicine Discovery and Preparation Technique, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
| | - Jiawei Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
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13
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Abstract
Peroxisomes are single-membrane bound intracellular organelles that can be found in organisms across the tree of eukaryotes, and thus are likely to derive from an ancestral peroxisome in the last eukaryotic common ancestor (LECA). Yet, peroxisomes in different lineages can present a large diversity in terms of their metabolic capabilities, which reflects a highly variable proteomic content. Theories on the evolutionary origin of peroxisomes have shifted in the last decades from scenarios involving an endosymbiotic origin, similar to those of mitochondria and plastids, towards hypotheses purporting an endogenous origin from within the endomembrane system. The peroxisomal proteome is highly dynamic in evolutionary terms, and can evolve via differential loss and gain of proteins, as well as via relocalization of proteins from and to other sub-cellular compartments. Here, I review current knowledge and discussions on the diversity, origin, and evolution of the peroxisomal proteome.
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14
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Kunze M. Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals. Subcell Biochem 2018; 89:157-199. [PMID: 30378023 DOI: 10.1007/978-981-13-2233-4_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxisomes harbor a plethora of proteins, but the peroxisomal proteome as the entirety of all peroxisomal proteins is still unknown for mammalian species. Computational algorithms can be used to predict the subcellular localization of proteins based on their amino acid sequence and this method has been amply used to forecast the intracellular fate of individual proteins. However, when applying such algorithms systematically to all proteins of an organism the prediction of its peroxisomal proteome in silico should be possible. Therefore, a reliable detection of peroxisomal targeting signals (PTS ) acting as postal codes for the intracellular distribution of the encoding protein is crucial. Peroxisomal proteins can utilize different routes to reach their destination depending on the type of PTS. Accordingly, independent prediction algorithms have been developed for each type of PTS, but only those for type-1 motifs (PTS1) have so far reached a satisfying predictive performance. This is partially due to the low number of peroxisomal proteins limiting the power of statistical analyses and partially due to specific properties of peroxisomal protein import, which render functional PTS motifs inactive in specific contexts. Moreover, the prediction of the peroxisomal proteome is limited by the high number of proteins encoded in mammalian genomes, which causes numerous false positive predictions even when using reliable algorithms and buries the few yet unidentified peroxisomal proteins. Thus, the application of prediction algorithms to identify all peroxisomal proteins is currently ineffective as stand-alone method, but can display its full potential when combined with other methods.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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15
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Tharkeshwar AK, Gevaert K, Annaert W. Organellar Omics-A Reviving Strategy to Untangle the Biomolecular Complexity of the Cell. Proteomics 2017; 18:e1700113. [PMID: 29125683 DOI: 10.1002/pmic.201700113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022]
Abstract
A eukaryotic cell encompasses many membrane-enclosed organelles, each of these holding several types of biomolecules that exhibit tremendous diversity in terms of their localization and expression. Despite the development of increasingly sensitive analytical tools, the enormous biomolecular complexity that exists within a cell cannot yet be fully resolved as low abundant molecules often remain unrecognized. Moreover, a drawback of whole cell analysis is that it does not provide spatial information and therefore it is not capable of assigning distinct biomolecules to specific compartments or analyzing changes in the composition of these compartments. Reduction of the biomolecular complexity of a sample helps to identify low abundant molecules, but such a reductionist approach requires methods that enable proper isolation and purification of individual cellular organelles. Decades of research have led to the development of a plethora of isolation methods for a broad range of subcellular organelles; yet, in particular, intrinsically dynamic compartments belonging to the endocytic machinery, including the plasma membrane, remain difficult to isolate in a sufficiently pure fraction. In this review, we discuss various methods that are commonly used to isolate subcellular organelles from cells and evaluate their advantages and disadvantages.
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Affiliation(s)
- Arun Kumar Tharkeshwar
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium.,Department of Cell Biology, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Ghent University, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium
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16
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Charting organellar importomes by quantitative mass spectrometry. Nat Commun 2017; 8:15272. [PMID: 28485388 PMCID: PMC5436138 DOI: 10.1038/ncomms15272] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/15/2017] [Indexed: 11/08/2022] Open
Abstract
Protein import into organelles is essential for all eukaryotes and facilitated by multi-protein translocation machineries. Analysing whether a protein is transported into an organelle is largely restricted to single constituents. This renders knowledge about imported proteins incomplete, limiting our understanding of organellar biogenesis and function. Here we introduce a method that enables charting an organelle's importome. The approach relies on inducible RNAi-mediated knockdown of an essential subunit of a translocase to impair import and quantitative mass spectrometry. To highlight its potential, we established the mitochondrial importome of Trypanosoma brucei, comprising 1,120 proteins including 331 new candidates. Furthermore, the method allows for the identification of proteins with dual or multiple locations and the substrates of distinct protein import pathways. We demonstrate the specificity and versatility of this ImportOmics method by targeting import factors in mitochondria and glycosomes, which demonstrates its potential for globally studying protein import and inventories of organelles. Knowing the specific protein content of individual organelles is necessary for an integrated understanding of cellular physiology. Here the authors describe a mass spectrometry-based approach to identify the substrates of distinct protein import pathways and define organellar proteomes.
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17
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A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics: the case of NPC1 deficiency. Sci Rep 2017; 7:41408. [PMID: 28134274 PMCID: PMC5278418 DOI: 10.1038/srep41408] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) have mainly been used as cellular carriers for genes and therapeutic products, while their use in subcellular organelle isolation remains underexploited. We engineered SPIONs targeting distinct subcellular compartments. Dimercaptosuccinic acid-coated SPIONs are internalized and accumulate in late endosomes/lysosomes, while aminolipid-SPIONs reside at the plasma membrane. These features allowed us to establish standardized magnetic isolation procedures for these membrane compartments with a yield and purity permitting proteomic and lipidomic profiling. We validated our approach by comparing the biomolecular compositions of lysosomes and plasma membranes isolated from wild-type and Niemann-Pick disease type C1 (NPC1) deficient cells. While the accumulation of cholesterol and glycosphingolipids is seen as a primary hallmark of NPC1 deficiency, our lipidomics analysis revealed the buildup of several species of glycerophospholipids and other storage lipids in selectively late endosomes/lysosomes of NPC1-KO cells. While the plasma membrane proteome remained largely invariable, we observed pronounced alterations in several proteins linked to autophagy and lysosomal catabolism reflecting vesicular transport obstruction and defective lysosomal turnover resulting from NPC1 deficiency. Thus the use of SPIONs provides a major advancement in fingerprinting subcellular compartments, with an increased potential to identify disease-related alterations in their biomolecular compositions.
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18
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Mathieu AA, Ohl-Séguy E, Dubois ML, Jean D, Jones C, Boudreau F, Boisvert FM. Subcellular proteomics analysis of different stages of colorectal cancer cell lines. Proteomics 2016; 16:3009-3018. [DOI: 10.1002/pmic.201600314] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/20/2016] [Accepted: 09/29/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Alex-Ane Mathieu
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - Emma Ohl-Séguy
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - Marie-Line Dubois
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - Dominique Jean
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - Christine Jones
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - François Boudreau
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
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Su Hui Teo C, Serwa RA, O’Hare P. Spatial and Temporal Resolution of Global Protein Synthesis during HSV Infection Using Bioorthogonal Precursors and Click Chemistry. PLoS Pathog 2016; 12:e1005927. [PMID: 27706239 PMCID: PMC5051704 DOI: 10.1371/journal.ppat.1005927] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/12/2016] [Indexed: 12/04/2022] Open
Abstract
We used pulse-labeling with the methionine analogue homopropargylglycine (HPG) to investigate spatiotemporal aspects of protein synthesis during herpes simplex virus (HSV) infection. In vivo incorporation of HPG enables subsequent selective coupling of fluorochrome-capture reagents to newly synthesised proteins. We demonstrate that HPG labeling had no effect on cell viability, on accumulation of test early or late viral proteins, or on overall virus yields. HPG pulse-labeling followed by SDS-PAGE analysis confirmed incorporation into newly synthesised proteins, while parallel processing by in situ cycloaddition revealed new insight into spatiotemporal aspects of protein localisation during infection. A striking feature was the rapid accumulation of newly synthesised proteins not only in a general nuclear pattern but additionally in newly forming sub-compartments represented by small discrete foci. These newly synthesised protein domains (NPDs) were similar in size and morphology to PML domains but were more numerous, and whereas PML domains were progressively disrupted, NPDs were progressively induced and persisted. Immediate-early proteins ICP4 and ICP0 were excluded from NPDs, but using an ICP0 mutant defective in PML disruption, we show a clear spatial relationship between NPDs and PML domains with NPDs frequently forming immediately adjacent and co-joining persisting PML domains. Further analysis of location of the chaperone Hsc70 demonstrated that while NPDs formed early in infection without overt Hsc70 recruitment, later in infection Hsc70 showed pronounced recruitment frequently in a coat-like fashion around NPDs. Moreover, while ICP4 and ICP0 were excluded from NPDs, ICP22 showed selective recruitment. Our data indicate that NPDs represent early recruitment of host and viral de novo translated protein to distinct structural entities which are precursors to the previously described VICE domains involved in protein quality control in the nucleus, and reveal new features from which we propose spatially linked platforms of newly synthesised protein processing after nuclear import.
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Affiliation(s)
- Catherine Su Hui Teo
- Section of Virology, Faculty of Medicine, Imperial College London, St Mary’s Medical School, Norfolk Place, London, United Kingdom
| | - Remigiusz A. Serwa
- Department of Chemistry, Imperial College London, London, United Kingdom
| | - Peter O’Hare
- Section of Virology, Faculty of Medicine, Imperial College London, St Mary’s Medical School, Norfolk Place, London, United Kingdom
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Santos BMD, Balbuena TS. Carbon assimilation in Eucalyptus urophylla grown under high atmospheric CO 2 concentrations: A proteomics perspective. J Proteomics 2016; 150:252-257. [PMID: 27677843 DOI: 10.1016/j.jprot.2016.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/16/2016] [Accepted: 09/21/2016] [Indexed: 11/26/2022]
Abstract
Photosynthetic organisms may be drastically affected by the future climate projections of a considerable increase in CO2 concentrations. Growth under a high concentration of CO2 could stimulate carbon assimilation-especially in C3-type plants. We used a proteomics approach to test the hypothesis of an increase in the abundance of the enzymes involved in carbon assimilation in Eucalyptus urophylla plants grown under conditions of high atmospheric CO2. Our strategy allowed the profiling of all Calvin-Benson cycle enzymes and associated protein species. Among the 816 isolated proteins, those involved in carbon fixation were found to be the most abundant ones. An increase in the abundance of six key enzymes out of the eleven core enzymes involved in carbon fixation was detected in plants grown at a high CO2 concentration. Proteome changes were corroborated by the detection of a decrease in the stomatal aperture and in the vascular bundle area in Eucalyptus urophylla plantlets grown in an environment of high atmospheric CO2. Our proteomics approach indicates a positive metabolic response regarding carbon fixation in a CO2-enriched atmosphere. The slight but significant increase in the abundance of the Calvin enzymes suggests that stomatal closure did not prevent an increase in the carbon assimilation rates. BIOLOGICAL SIGNIFICANCE The sample enrichment strategy and data analysis used here enabled the identification of all enzymes and most protein isoforms involved in the Calvin-Benson-Bessham cycle in Eucalyptus urophylla. Upon growth in CO2-enriched chambers, Eucalyptus urophylla plantlets responded by reducing the vascular bundle area and stomatal aperture size and by increasing the abundance of six of the eleven core enzymes involved in carbon fixation. Our proteome approach provides an estimate on how a commercially important C3-type plant would respond to an increase in CO2 concentrations. Additionally, confirmation at the protein level of the predicted genes involved in carbon assimilation may be used in plant transformation strategies aiming to increase plant adaptability to climate changes or to increase plant productivity.
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Affiliation(s)
- Bruna Marques Dos Santos
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Tiago Santana Balbuena
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil.
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21
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Häupl B, Ihling CH, Sinz A. Protein Interaction Network of Human Protein Kinase D2 Revealed by Chemical Cross-Linking/Mass Spectrometry. J Proteome Res 2016; 15:3686-3699. [PMID: 27559607 DOI: 10.1021/acs.jproteome.6b00513] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the interaction network of human PKD2 in the cytosol and in Golgi-enriched subcellular protein fractions by an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins in the cytosolic and Golgi fractions. The covalent fixation of transient or weak interactors by chemical cross-linking allowed capturing interaction partners that might otherwise disappear during conventional pull-down experiments. In total, 31 interaction partners were identified for PKD2, including glycogen synthase kinase-3 beta (GSK3B), 14-3-3 protein gamma (YWHAG), and the alpha isoform of 55 kDa regulatory subunit B of protein phosphatase 2A (PPP2R2A). Remarkably, the entire seven-subunit Arp2/3 complex (ARPC1B, ARPC2, ARPC3, ARPC4, ARPC5, ACTR3, ACTR2) as well as ARPC1A and ARPC5L, which are putative substitutes of ARPC1B and ARPC5, were identified. We provide evidence of a direct protein-protein interaction between PKD2 and Arp2/3. Our findings will pave the way for further structural and functional studies of PKD2 complexes, especially the PKD2/Arp2/3 interaction, to elucidate the role of PKD2 for transport processes at the trans-Golgi network. Data are available via ProteomeXchange with identifiers PXD003909 (enrichment from cytosolic fractions), PXD003913 (enrichment from Golgi fractions), and PXD003917 (subcellular fractionation).
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Affiliation(s)
- Björn Häupl
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
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22
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Abstract
Apoptosis triggered by ricin toxin (RT) has previously been associated with certain cellular organellar compartments, but the diversity in the composition of the organellar proteins remains unclear. Here, we applied a shotgun proteomics strategy to examine the differential expression of proteins in the mitochondria, nuclei, and cytoplasm of HeLa cells treated and not treated with RT. Data were combined with a global bioinformatics analysis and experimental confirmations. A total of 3107 proteins were identified. Bioinformatics predictors (Proteome Analyst, WoLF PSORT, TargetP, MitoPred, Nucleo, MultiLoc, and k-nearest neighbor) and a Bayesian model that integrated these predictors were used to predict the locations of 1349 distinct organellar proteins. Our data indicate that the Bayesian model was more efficient than the individual implementation of these predictors. Additionally, a Biomolecular Interaction Network (BIN) analysis was used to identify 149 BIN subnetworks. Our experimental confirmations indicate that certain apoptosis-related proteins (e.g. cytochrome c, enolase, lamin B, Bax, and Drp1) were found to be translocated and had variable expression levels. These results provide new insights for the systematic understanding of RT-induced apoptosis responses.
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Affiliation(s)
- Peng Liao
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, People's Republic of China Institute of Military Veterinary Science, Academy of Military Medical Science, Changchun, Jilin Province, People's Republic of China
| | - Yunhu Li
- Hunan Biological and Electromechanical Polytechnic, The Party and Government Office, Changsha, Hunan Province, People's Republic of China
| | - Hongyang Li
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, People's Republic of China
| | - Wensen Liu
- Institute of Military Veterinary Science, Academy of Military Medical Science, Changchun, Jilin Province, People's Republic of China
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23
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Yasueda Y, Tamura T, Hamachi I. Nucleus-selective Chemical Proteomics Using Hoechst-tagged Reactive Molecules. CHEM LETT 2016. [DOI: 10.1246/cl.151083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yuki Yasueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency
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24
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Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nat Protoc 2016; 11:456-75. [PMID: 26866790 DOI: 10.1038/nprot.2016.018] [Citation(s) in RCA: 388] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This protocol describes a method to obtain spatially resolved proteomic maps of specific compartments within living mammalian cells. An engineered peroxidase, APEX2, is genetically targeted to a cellular region of interest. Upon the addition of hydrogen peroxide for 1 min to cells preloaded with a biotin-phenol substrate, APEX2 generates biotin-phenoxyl radicals that covalently tag proximal endogenous proteins. Cells are then lysed, and biotinylated proteins are enriched with streptavidin beads and identified by mass spectrometry. We describe the generation of an appropriate APEX2 fusion construct, proteomic sample preparation, and mass spectrometric data acquisition and analysis. A two-state stable isotope labeling by amino acids in cell culture (SILAC) protocol is used for proteomic mapping of membrane-enclosed cellular compartments from which APEX2-generated biotin-phenoxyl radicals cannot escape. For mapping of open cellular regions, we instead use a 'ratiometric' three-state SILAC protocol for high spatial specificity. Isotopic labeling of proteins takes 5-7 cell doublings. Generation of the biotinylated proteomic sample takes 1 d, acquiring the mass spectrometric data takes 2-5 d and analysis of the data to obtain the final proteomic list takes 1 week.
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25
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Albrethsen J, Goetze JP, Johnsen AH. Mining the granule proteome: a potential source of endocrine biomarkers. Biomark Med 2015; 9:259-65. [PMID: 25731211 DOI: 10.2217/bmm.14.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Proteomics of secretory granules is an emerging strategy for identifying secreted proteins, including potentially novel candidate biomarkers and peptide hormones. In addition, proteomics can provide information about the abundance, localization and structure (post-translational modification) of granule proteins and peptides. Analytical strategies within this research line include so-called 'subtractive proteomics', 'peptidomics' and granule purification by the use of multiple gradient centrifugations. Here we review the literature, and describe the challenges and opportunities in proteomics of secretory granules.
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Affiliation(s)
- Jakob Albrethsen
- Department of Clinical Biochemistry (KB3014), Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
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26
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Kunze M, Berger J. The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance. Front Physiol 2015; 6:259. [PMID: 26441678 PMCID: PMC4585086 DOI: 10.3389/fphys.2015.00259] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/04/2015] [Indexed: 12/04/2022] Open
Abstract
The proper distribution of proteins between the cytosol and various membrane-bound compartments is crucial for the functionality of eukaryotic cells. This requires the cooperation between protein transport machineries that translocate diverse proteins from the cytosol into these compartments and targeting signal(s) encoded within the primary sequence of these proteins that define their cellular destination. The mechanisms exerting protein translocation differ remarkably between the compartments, but the predominant targeting signals for mitochondria, chloroplasts and the ER share the N-terminal position, an α-helical structural element and the removal from the core protein by intraorganellar cleavage. Interestingly, similar properties have been described for the peroxisomal targeting signal type 2 mediating the import of a fraction of soluble peroxisomal proteins, whereas other peroxisomal matrix proteins encode the type 1 targeting signal residing at the extreme C-terminus. The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments. Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals. Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
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27
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Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:381-400. [PMID: 26306749 PMCID: PMC4679367 DOI: 10.1002/wsbm.1311] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/25/2015] [Accepted: 06/29/2015] [Indexed: 12/16/2022]
Abstract
Parasitic diseases caused by protozoan pathogens lead to hundreds of thousands of deaths per year in addition to substantial suffering and socioeconomic decline for millions of people worldwide. The lack of effective vaccines coupled with the widespread emergence of drug‐resistant parasites necessitates that the research community take an active role in understanding host–parasite infection biology in order to develop improved therapeutics. Recent advances in next‐generation sequencing and the rapid development of publicly accessible genomic databases for many human pathogens have facilitated the application of systems biology to the study of host–parasite interactions. Over the past decade, these technologies have led to the discovery of many important biological processes governing parasitic disease. The integration and interpretation of high‐throughput ‐omic data will undoubtedly generate extraordinary insight into host–parasite interaction networks essential to navigate the intricacies of these complex systems. As systems analysis continues to build the foundation for our understanding of host–parasite biology, this will provide the framework necessary to drive drug discovery research forward and accelerate the development of new antiparasitic therapies. WIREs Syst Biol Med 2015, 7:381–400. doi: 10.1002/wsbm.1311 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Justine Swann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Neema Jamshidi
- Department of Radiological Sciences, University of California, Los Angeles, Los Angeles, CA, USA.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Pediatrics and Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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28
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Hong WX, Huang A, Lin S, Yang X, Yang L, Zhou L, Huang H, Wu D, Huang X, Xu H, Liu J. Differential expression profile of membrane proteins in L-02 cells exposed to trichloroethylene. Toxicol Ind Health 2015; 32:1774-83. [PMID: 26045551 DOI: 10.1177/0748233715588438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Trichloroethylene (TCE), a halogenated organic solvent widely used in industries, is known to cause severe hepatotoxicity. However, the mechanisms underlying TCE hepatotoxicity are still not well understood. It is predicted that membrane proteins are responsible for key biological functions, and recent studies have revealed that TCE exposure can induce abnormal levels of membrane proteins in body fluids and cultured cells. The aim of this study is to investigate the TCE-induced alterations of membrane proteins profiles in human hepatic L-02 liver cells. A comparative membrane proteomics analysis was performed in combination with two-dimensional fluorescence difference gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry. A total of 15 proteins were identified as differentially expressed (4 upregulated and 11 downregulated) between TCE-treated cells and normal controls. Among this, 14 of them are suggested as membrane-associated proteins by their transmembrane domain and/or subcellular location. Furthermore, the differential expression of β subunit of adenosine triphosphate synthase (ATP5B) and prolyl 4-hydroxylase, β polypeptide (P4HB) were verified by Western blot analysis in TCE-treated L-02 cells. Our work not only reveals the association between TCE exposure and altered expression of membrane proteins but also provides a novel strategy to discover membrane biomarkers and elucidate the potential mechanisms involving with membrane proteins response to chemical-induced toxic effect.
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Affiliation(s)
- Wen-Xu Hong
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Aibo Huang
- Pharmacy College of Jinan University, Guangzhou, China
| | - Sheng Lin
- Shenzhen Research Institute of Population and Family Planning, Shenzhen, China
| | - Xifei Yang
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Linqing Yang
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Li Zhou
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Haiyan Huang
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Desheng Wu
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xinfeng Huang
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Hua Xu
- Pharmacy College of Jinan University, Guangzhou, China
| | - Jianjun Liu
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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Yan G, Yan X. Ribosomal proteomics: Strategies, approaches, and perspectives. Biochimie 2015; 113:69-77. [PMID: 25869001 DOI: 10.1016/j.biochi.2015.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 12/20/2022]
Abstract
Over the past few decades, proteomic research has seen unprecedented development due to technological advancement. However, whole-cell proteomics still has limitations with respect to sample complexity and the accuracy of determining protein locations. To deal with these limitations, several subcellular proteomic studies have been initiated. Nevertheless, compared to other subcellular proteomic fields, such as mitochondrial proteomics, ribosomal proteomics has lagged behind due to the long-held idea that the ribosome is just a translation machine. Recently, with the proposed ribosome filter hypothesis and subsequent studies of ribosome-specific regulatory capacity, ribosomal proteomics has become a promising chapter for both proteomic and ribosomal research. In this review, we discuss the current strategies and approaches in ribosomal proteomics and the efficacies as well as disadvantages of individual approaches for further improvement.
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Affiliation(s)
- Guokai Yan
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Xianghua Yan
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
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Gabaldón T, Pittis AA. Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes. Biochimie 2015; 119:262-8. [PMID: 25869000 PMCID: PMC4678951 DOI: 10.1016/j.biochi.2015.03.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/25/2015] [Indexed: 12/19/2022]
Abstract
A high level of subcellular compartmentalization is a hallmark of eukaryotic cells. This intricate internal organization was present already in the common ancestor of all extant eukaryotes, and the determination of the origins and early evolution of the different organelles remains largely elusive. Organellar proteomes are determined through regulated pathways that target proteins produced in the cytosol to their final subcellular destinations. This internal sorting of proteins can vary across different physiological conditions, cell types and lineages. Evolutionary retargeting - the alteration of a subcellular localization of a protein in the course of evolution - has been rampant in eukaryotes and involves any possible combination of organelles. This fact adds another layer of difficulty to the reconstruction of the origins and evolution of organelles. In this review we discuss current themes in relation to the origin and evolution of organellar proteomes. Throughout the text, a special focus is set on the evolution of mitochondrial and peroxisomal proteomes, which are two organelles for which extensive proteomic and evolutionary studies have been performed.
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Affiliation(s)
- Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Alexandros A Pittis
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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31
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Abstract
Eukaryotic cells contain a multitude of membrane structures that are connected through a highly dynamic and complex exchange of their constituents. The vibrant instability of these structures challenges the classical view of defined, static compartments that are connected by different types of vesicles. Despite this astonishing complexity, proteins and lipids are accurately transported into the different intracellular membrane systems. Over the past few decades many factors have been identified that either mediate or regulate intracellular membrane trafficking. Like in a modern parcel sorting system of a logistics center, the cargo typically passes through several sequential sorting stations until it finally reaches the location that is specified by its individual address label. While each membrane system employs specific sets of factors, the transport processes typically operate on common principles. With the advent of genome- and proteome-wide screens, the availability of mutant collections, exciting new developments in microscope technology and sophisticated methods to study their dynamics, the future promises a broad and comprehensive picture of the processes by which eukaryotic cells sort their proteins.
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Engelke R, Riede J, Hegermann J, Wuerch A, Eimer S, Dengjel J, Mittler G. The Quantitative Nuclear Matrix Proteome as a Biochemical Snapshot of Nuclear Organization. J Proteome Res 2014; 13:3940-56. [DOI: 10.1021/pr500218f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rudolf Engelke
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Julia Riede
- Freiburg
Institute for Advanced Studies, School of Life Sciences − LifeNet, University of Freiburg, Albertstrasse 19, 79104 Freiburg, Germany
- Center
for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse
49, 79104 Freiburg, Germany
| | - Jan Hegermann
- European Neuroscience Institute and Center for Molecular Physiology of the Brain (CMPB), 37077 Göttingen, Germany
| | - Andreas Wuerch
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Stefan Eimer
- European Neuroscience Institute and Center for Molecular Physiology of the Brain (CMPB), 37077 Göttingen, Germany
| | - Joern Dengjel
- Freiburg
Institute for Advanced Studies, School of Life Sciences − LifeNet, University of Freiburg, Albertstrasse 19, 79104 Freiburg, Germany
- Center
for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse
49, 79104 Freiburg, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
- BIOSS,
Center for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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Yen TY, Dutta SM, Litsakos-Cheung C, Corona AA, Timpe LC, Macher BA. Overcoming challenges and opening new opportunities in glycoproteomics. Biomolecules 2014; 3:270-86. [PMID: 24790834 PMCID: PMC4002168 DOI: 10.3390/biom3020270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Glycoproteomics has emerged as a prime area of interest within the field of proteomics because glycoproteins have been shown to function as biomarkers for disease and as promising therapeutic targets. A significant challenge in the study of glycoproteins is the fact that they are expressed in relatively low abundance in cells. In response, various enrichment methods have been developed to improve the detection of glycoproteins. One such method involves their capture via oxidation of their glycan chains and covalent attachment with hydrazide resins which, when catalyzed by PNGase F, release N-linked glycans and convert the glycosite Asn to Asp; this conversion is identifiable with LC/ESI-MS/MS as a corresponding increase of 0.984 Da in molecular weight. The present study builds on this body of work, providing evidence of three additional strategies that improve glycoprotein identification: (1) use of a high resolution mass spectrometer—the Q Exactive MS—which delivers 2–3 times more glycoprotein identifications than a low resolution MS; (2) optimization of instrument settings and database search parameters to reduce misidentification of N-linked glycopeptides to ~1 percent; and (3) labeling glycopeptides with 18O during PNGase F treatment to locate N-linked glycosites within peptides containing multiple N-linked sequons.
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Affiliation(s)
- Ten-Yang Yen
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA; E-Mails: (T.-Y.Y.); (C.L.C.); (A.A.C.); (L.C.T.)
| | | | - Christina Litsakos-Cheung
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA; E-Mails: (T.-Y.Y.); (C.L.C.); (A.A.C.); (L.C.T.)
| | - Alejandro A. Corona
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA; E-Mails: (T.-Y.Y.); (C.L.C.); (A.A.C.); (L.C.T.)
| | - Leslie C. Timpe
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA; E-Mails: (T.-Y.Y.); (C.L.C.); (A.A.C.); (L.C.T.)
| | - Bruce A. Macher
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA; E-Mails: (T.-Y.Y.); (C.L.C.); (A.A.C.); (L.C.T.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-415-338-6078; Fax: +1-415-338-6253
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Billing AM, Kessler JR, Revets D, Sausy A, Schmitz S, Barra C, Muller CP. Proteome profiling of virus-host interactions of wild type and attenuated measles virus strains. J Proteomics 2014; 108:325-36. [PMID: 24914991 DOI: 10.1016/j.jprot.2014.05.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 11/18/2022]
Abstract
UNLABELLED Quantitative gel-based proteomics (2D DIGE coupled to MALDI-TOF/TOF MS) has been used to investigate the effects of different measles virus (MV) strains on the host cell proteome. A549/hSLAM cells were infected either with wild type MV strains, an attenuated vaccine or a multiple passaged Vero cell adapted strain. By including interferon beta treatment as a control it was possible to distinguish between the classical antiviral response and changes induced specifically by the different strains. Of 38 differentially expressed proteins in total (p-value ≤0.05, fold change ≥2), 18 proteins were uniquely modulated following MV infection with up to 9 proteins specific per individual strain. Interestingly, wt strains displayed distinct protein patterns particularly during the late phase of infection. Proteins were grouped into cytoskeleton, metabolism, transcription/translation, immune response and mitochondrial proteins. Bioinformatics analysis revealed mostly changes in proteins regulating cell death and apoptosis. Surprisingly, wt strains affected the cytokeratin system much stronger than the vaccine strain. To our knowledge, this is the first study on the MV-host proteome addressing interstrain differences. BIOLOGICAL SIGNIFICANCE In the present study we investigated the host cell proteome upon measles virus (MV) infection. The novelty about this study is the side-by side comparison of different strains from the same virus, which has not been done at the proteome level for any other virus including MV. We used different virus strains including a vaccine strain, wild type isolates derived from MV-infected patients as well as a Vero cell adapted strain, which serves as an intermediate between vaccine and wild type strain. We observed differences between vaccine and wild type strains as well as common features between different wild type strains. Perhaps one of the most surprising findings was that differences did not only occur between wild type and vaccine or Vero cell adapted strains but also between different wild type strains. In fact our study suggests that besides the cytokeratin and the IFN system wild type viruses seem to differ as much among each other than from vaccine strains. Thus our results are suggestive of complex and diverse virus-host interactions which differ considerably between different wild type strains. Our data indicate that interstrain differences are prominent and have so far been neglected by proteomics studies.
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Affiliation(s)
- Anja M Billing
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Julia R Kessler
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Dominique Revets
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Aurélie Sausy
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Stephanie Schmitz
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Claire Barra
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
| | - Claude P Muller
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg.
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Drissi R, Dubois ML, Boisvert FM. Proteomics methods for subcellular proteome analysis. FEBS J 2013; 280:5626-34. [PMID: 24034475 DOI: 10.1111/febs.12502] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 08/14/2013] [Accepted: 08/22/2013] [Indexed: 01/29/2023]
Abstract
The elucidation of the subcellular distribution of proteins under different conditions is a major challenge in cell biology. This challenge is further complicated by the multicompartmental and dynamic nature of protein localization. To address this issue, quantitative proteomics workflows have been developed to reliably identify the protein complement of whole organelles, as well as for protein assignment to subcellular location and relative protein quantification based on different cell culture conditions. Here, we review quantitative MS-based approaches that combine cellular fractionation with proteomic analysis. The application of these methods to the characterization of organellar composition and to the determination of the dynamic nature of protein complexes is improving our understanding of protein functions and dynamics.
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Affiliation(s)
- Romain Drissi
- Department of Anatomy and Cell Biology, Université de Sherbrooke, Québec, Canada
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37
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Lin Y, Wang K, Yan Y, Lin H, Peng B, Liu Z. Evaluation of the combinative application of SDS and sodium deoxycholate to the LC-MS-based shotgun analysis of membrane proteomes. J Sep Sci 2013; 36:3026-34. [DOI: 10.1002/jssc.201300413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 06/06/2013] [Accepted: 06/21/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Yong Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Kunbo Wang
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Yujun Yan
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
| | - Haiyan Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Bin Peng
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Zhonghua Liu
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
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Hernandez-Fernaud JR, Reid SE, Neilson LJ, Zanivan S. Quantitative mass spectrometry-based proteomics in angiogenesis. Proteomics Clin Appl 2013; 7:464-76. [PMID: 23161605 DOI: 10.1002/prca.201200055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 10/13/2012] [Accepted: 10/25/2012] [Indexed: 12/29/2022]
Abstract
The process of new blood vessel formation from pre-existing ones is called angiogenesis. Beyond playing a critical role in the physiological development of the vascular system, angiogenesis is a well-recognised hallmark of cancer. Unbiased system-wide approaches are required to complement the current knowledge, and intimately understand the molecular mechanisms regulating this process in physiological and pathological conditions. In this review we describe the cellular and molecular dynamics regulating the physiological growth of vessels and their deregulation in cancer, survey in vitro and in vivo models currently exploited to investigate various aspects of angiogenesis and describe state-of-the-art and most widespread methods and technologies in MS shotgun proteomics. Finally, we focus on current applications of MS to better understand endothelial cell behaviour and propose how modern proteomics can impact on angiogenesis research.
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Schwake M, Schröder B, Saftig P. Lysosomal membrane proteins and their central role in physiology. Traffic 2013; 14:739-48. [PMID: 23387372 DOI: 10.1111/tra.12056] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/01/2013] [Accepted: 02/06/2013] [Indexed: 12/19/2022]
Abstract
The lysosomal membrane was thought for a long time to primarily act as a physical barrier separating the luminal acidic milieu from the cytoplasmic environment. Meanwhile, it has been realized that unique lysosomal membranes play essential roles in a number of cellular events ranging from phagocytosis, autophagy, cell death, virus infection to membrane repair. This review provides an overview about the most interesting emerging functions of lysosomal membrane proteins and how they contribute to health and disease. Their importance is exemplified by their role in acidification, transport of metabolites and ions across the membrane, intracellular transport of hydrolases and the regulation of membrane fusion events. Studies in patient cells, non-mammalian model organisms and knockout mice contributed to our understanding of how the different lysosomal membrane proteins affect cellular homeostasis, developmental processes as well as tissue functions. Because these proteins are central for the biogenesis of this compartment they are also considered as attractive targets to modulate the lysosomal machinery in cases where impaired lysosomal degradation leads to cellular pathologies. We are only beginning to understand the complex composition and function of these proteins which are tightly linked to processes occurring throughout the endocytic and biosynthetic pathways.
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Affiliation(s)
- Michael Schwake
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, D-24098, Kiel, Germany
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Liberski AR, Al-Noubi MN, Rahman ZH, Halabi NM, Dib SS, Al-Mismar R, Billing AM, Krishnankutty R, Ahmad FS, Raynaud CM, Rafii A, Engholm-Keller K, Graumann J. Adaptation of a commonly used, chemically defined medium for human embryonic stem cells to stable isotope labeling with amino acids in cell culture. J Proteome Res 2013; 12:3233-45. [PMID: 23734825 DOI: 10.1021/pr400099j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metabolic labeling with stable isotopes is a prominent technique for comparative quantitative proteomics, and stable isotope labeling with amino acids in cell culture (SILAC) is the most commonly used approach. SILAC is, however, traditionally limited to simple tissue culture regimens and only rarely employed in the context of complex culturing conditions as those required for human embryonic stem cells (hESCs). Classic hESC culture is based on the use of mouse embryonic fibroblasts (MEFs) as a feeder layer, and as a result, possible xenogeneic contamination, contribution of unlabeled amino acids by the feeders, interlaboratory variability of MEF preparation, and the overall complexity of the culture system are all of concern in conjunction with SILAC. We demonstrate a feeder-free SILAC culture system based on a customized version of a commonly used, chemically defined hESC medium developed by Ludwig et al. and commercially available as mTeSR1 [mTeSR1 is a trade mark of WiCell (Madison, WI) licensed to STEMCELL Technologies (Vancouver, Canada)]. This medium, together with adjustments to the culturing protocol, facilitates reproducible labeling that is easily scalable to the protein amounts required by proteomic work flows. It greatly enhances the usability of quantitative proteomics as a tool for the study of mechanisms underlying hESCs differentiation and self-renewal. Associated data have been deposited to the ProteomeXchange with the identifier PXD000151.
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Lim CW, Le HT, Han JH, Kim DH, Jang JG, Kim TW. New Water-soluble Alkynylating Agent for Cell Surface Protein: Sulfosuccinimidyl 4-Pentynoate. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.6.1895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Gronemeyer T, Wiese S, Ofman R, Bunse C, Pawlas M, Hayen H, Eisenacher M, Stephan C, Meyer HE, Waterham HR, Erdmann R, Wanders RJ, Warscheid B. The proteome of human liver peroxisomes: identification of five new peroxisomal constituents by a label-free quantitative proteomics survey. PLoS One 2013; 8:e57395. [PMID: 23460848 PMCID: PMC3583843 DOI: 10.1371/journal.pone.0057395] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 01/24/2013] [Indexed: 01/11/2023] Open
Abstract
The peroxisome is a key organelle of low abundance that fulfils various functions essential for human cell metabolism. Severe genetic diseases in humans are caused by defects in peroxisome biogenesis or deficiencies in the function of single peroxisomal proteins. To improve our knowledge of this important cellular structure, we studied for the first time human liver peroxisomes by quantitative proteomics. Peroxisomes were isolated by differential and Nycodenz density gradient centrifugation. A label-free quantitative study of 314 proteins across the density gradient was accomplished using high resolution mass spectrometry. By pairing statistical data evaluation, cDNA cloning and in vivo colocalization studies, we report the association of five new proteins with human liver peroxisomes. Among these, isochorismatase domain containing 1 protein points to the existence of a new metabolic pathway and hydroxysteroid dehydrogenase like 2 protein is likely involved in the transport or β-oxidation of fatty acids in human peroxisomes. The detection of alcohol dehydrogenase 1A suggests the presence of an alternative alcohol-oxidizing system in hepatic peroxisomes. In addition, lactate dehydrogenase A and malate dehydrogenase 1 partially associate with human liver peroxisomes and enzyme activity profiles support the idea that NAD+ becomes regenerated during fatty acid β-oxidation by alternative shuttling processes in human peroxisomes involving lactate dehydrogenase and/or malate dehydrogenase. Taken together, our data represent a valuable resource for future studies of peroxisome biochemistry that will advance research of human peroxisomes in health and disease.
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Affiliation(s)
- Thomas Gronemeyer
- Department of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany
| | - Sebastian Wiese
- Institut für Biologie II, Funktionelle Proteomik, Fakultät für Biologie and BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - Rob Ofman
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Christian Bunse
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Magdalena Pawlas
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Heiko Hayen
- Leibniz-Institut für Analytische Wissenschaften - ISAS e.V., Dortmund, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Christian Stephan
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Helmut E. Meyer
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Hans R. Waterham
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, Bochum, Germany
| | - Ronald J. Wanders
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bettina Warscheid
- Institut für Biologie II, Funktionelle Proteomik, Fakultät für Biologie and BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
- * E-mail:
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Krahmer N, Hilger M, Kory N, Wilfling F, Stoehr G, Mann M, Farese RV, Walther TC. Protein correlation profiles identify lipid droplet proteins with high confidence. Mol Cell Proteomics 2013; 12:1115-26. [PMID: 23319140 DOI: 10.1074/mcp.m112.020230] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues.
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Affiliation(s)
- Natalie Krahmer
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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Lubchenko GA, Kyiv National Taras Shevchenko University. FLUORESCENT PROTEINS USING FOR LYMPHOCYTE ACTIVATION ASSAYING. BIOTECHNOLOGIA ACTA 2013. [DOI: 10.15407/biotech6.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Lin Y, Liu H, Liu Z, Liu Y, He Q, Chen P, Wang X, Liang S. Development and evaluation of an entirely solution-based combinative sample preparation method for membrane proteomics. Anal Biochem 2013; 432:41-8. [DOI: 10.1016/j.ab.2012.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 08/31/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
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47
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Fagerberg L, Oksvold P, Skogs M, Algenäs C, Lundberg E, Pontén F, Sivertsson A, Odeberg J, Klevebring D, Kampf C, Asplund A, Sjöstedt E, Al-Khalili Szigyarto C, Edqvist PH, Olsson I, Rydberg U, Hudson P, Ottosson Takanen J, Berling H, Björling L, Tegel H, Rockberg J, Nilsson P, Navani S, Jirström K, Mulder J, Schwenk JM, Zwahlen M, Hober S, Forsberg M, von Feilitzen K, Uhlén M. Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP). J Proteome Res 2012; 12:2439-48. [PMID: 23276153 DOI: 10.1021/pr300924j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few tissue-specific proteins and approximately half of the genes expressed in all the analyzed cells. The status for each gene with regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas ( www.proteinatlas.org ).
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Affiliation(s)
- Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
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48
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Lin Y, Jiang H, Yan Y, Peng B, Chen J, Lin H, Liu Z. Shotgun analysis of membrane proteomes by an improved SDS-assisted sample preparation method coupled with liquid chromatography–tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 911:6-14. [DOI: 10.1016/j.jchromb.2012.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
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49
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Bousette N, Gramolini AO, Kislinger T. Proteomics-based investigations of animal models of disease. Proteomics Clin Appl 2012; 2:638-53. [PMID: 21136864 DOI: 10.1002/prca.200780043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cells contain a large yet, constant genome, which contains all the coding information necessary to sustain cellular physiology. However, proteins are the end products of genes, and hence dictate the phenotype of cells and tissues. Therefore, proteomics can provide key information for the elucidation of physiological and pathophysiological mechanisms by identifying the protein profile from cells and tissues. The relatively novel techniques used for the study of proteomics thus have the potential to improve diagnostic, prognostic, as well as therapeutic avenues. In this review, we first discuss the benefits of animal models over the use of human samples for the proteomic analysis of human disease. Next, we aim to demonstrate the potential of proteomics in the elucidation of disease mechanisms that may not be possible by other conventional technologies. Following this, we describe the use of proteomics for the analysis of PTM and protein interactions in animal models and their relevance to the study of human disease. Finally, we discuss the development of clinical biomarkers for the early diagnosis of disease via proteomic analysis of animal models. We also discuss the development of standard proteomes and relate how this data will benefit future proteomic research. A comprehensive review of all animal models used in conjunction with proteomics is beyond the scope of this manuscript. Therefore, we aimed to cover a large breadth of topics, which together, demonstrate the potential of proteomics as a powerful tool in biomedical research.
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Affiliation(s)
- Nicolas Bousette
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada; Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Toronto, Ontario, Canada
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50
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Tardif M, Atteia A, Specht M, Cogne G, Rolland N, Brugière S, Hippler M, Ferro M, Bruley C, Peltier G, Vallon O, Cournac L. PredAlgo: a new subcellular localization prediction tool dedicated to green algae. Mol Biol Evol 2012; 29:3625-39. [PMID: 22826458 DOI: 10.1093/molbev/mss178] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a prime model for deciphering processes occurring in the intracellular compartments of the photosynthetic cell. Organelle-specific proteomic studies have started to delineate its various subproteomes, but sequence-based prediction software is necessary to assign proteins subcellular localizations at whole genome scale. Unfortunately, existing tools are oriented toward land plants and tend to mispredict the localization of nuclear-encoded algal proteins, predicting many chloroplast proteins as mitochondrion targeted. We thus developed a new tool called PredAlgo that predicts intracellular localization of those proteins to one of three intracellular compartments in green algae: the mitochondrion, the chloroplast, and the secretory pathway. At its core, a neural network, trained using carefully curated sets of C. reinhardtii proteins, divides the N-terminal sequence into overlapping 19-residue windows and scores the probability that they belong to a cleavable targeting sequence for one of the aforementioned organelles. A targeting prediction is then deduced for the protein, and a likely cleavage site is predicted based on the shape of the scoring function along the N-terminal sequence. When assessed on an independent benchmarking set of C. reinhardtii sequences, PredAlgo showed a highly improved discrimination capacity between chloroplast- and mitochondrion-localized proteins. Its predictions matched well the results of chloroplast proteomics studies. When tested on other green algae, it gave good results with Chlorophyceae and Trebouxiophyceae but tended to underpredict mitochondrial proteins in Prasinophyceae. Approximately 18% of the nuclear-encoded C. reinhardtii proteome was predicted to be targeted to the chloroplast and 15% to the mitochondrion.
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