3201
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Wierer M, Mann M. Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes. Hum Mol Genet 2016; 25:R106-R114. [PMID: 27402878 PMCID: PMC5036873 DOI: 10.1093/hmg/ddw208] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/24/2016] [Indexed: 01/30/2023] Open
Abstract
High-resolution mass spectrometry (MS)-based proteomics is a powerful method for the identification of soluble protein complexes and large-scale affinity purification screens can decode entire protein interaction networks. In contrast, protein complexes residing on chromatin have been much more challenging, because they are difficult to purify and often of very low abundance. However, this is changing due to recent methodological and technological advances in proteomics. Proteins interacting with chromatin marks can directly be identified by pulldowns with synthesized histone tails containing posttranslational modifications (PTMs). Similarly, pulldowns with DNA baits harbouring single nucleotide polymorphisms or DNA modifications reveal the impact of those DNA alterations on the recruitment of transcription factors. Accurate quantitation – either isotope-based or label free – unambiguously pinpoints proteins that are significantly enriched over control pulldowns. In addition, protocols that combine classical chromatin immunoprecipitation (ChIP) methods with mass spectrometry (ChIP-MS) target gene regulatory complexes in their in-vivo context. Similar to classical ChIP, cells are crosslinked with formaldehyde and chromatin sheared by sonication or nuclease digested. ChIP-MS baits can be proteins in tagged or endogenous form, histone PTMs, or lncRNAs. Locus-specific ChIP-MS methods would allow direct purification of a single genomic locus and the proteins associated with it. There, loci can be targeted either by artificial DNA-binding sites and corresponding binding proteins or via proteins with sequence specificity such as TAL or nuclease deficient Cas9 in combination with a specific guide RNA. We predict that advances in MS technology will soon make such approaches generally applicable tools in epigenetics.
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Affiliation(s)
- Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
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3202
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Pertl-Obermeyer H, Wu XN, Schrodt J, Müdsam C, Obermeyer G, Schulze WX. Identification of Cargo for Adaptor Protein (AP) Complexes 3 and 4 by Sucrose Gradient Profiling. Mol Cell Proteomics 2016; 15:2877-89. [PMID: 27371946 DOI: 10.1074/mcp.m116.060129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 11/06/2022] Open
Abstract
Intracellular vesicle trafficking is a fundamental process in eukaryotic cells. It enables cellular polarity and exchange of proteins between subcellular compartments such as the plasma membrane or the vacuole. Adaptor protein complexes participate in the vesicle formation by specific selection of the transported cargo. We investigated the role of the adaptor protein complex 3 (AP-3) and adaptor protein complex 4 (AP-4) in this selection process by screening for AP-3 and AP-4 dependent cargo proteins. Specific cargo proteins are expected to be mis-targeted in knock-out mutants of adaptor protein complex components. Thus, we screened for altered distribution profiles across a density gradient of membrane proteins in wild type versus ap-3β and ap-4β knock-out mutants. In ap-3β mutants, especially proteins with transport functions, such as aquaporins and plasma membrane ATPase, as well as vesicle trafficking proteins showed differential protein distribution profiles across the density gradient. In the ap-4β mutant aquaporins but also proteins from lipid metabolism were differentially distributed. These proteins also showed differential phosphorylation patterns in ap-3β and ap-4β compared with wild type. Other proteins, such as receptor kinases were depleted from the AP-3 mutant membrane system, possibly because of degradation after mis-targeting. In AP-4 mutants, membrane fractions were depleted for cytochrome P450 proteins, cell wall proteins and receptor kinases. Analysis of water transport capacity in wild type and mutant mesophyll cells confirmed aquaporins as cargo proteins of AP-3 and AP-4. The combination of organelle density gradients with proteome analysis turned out as a suitable experimental strategy for large-scale analyses of protein trafficking.
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Affiliation(s)
- Heidi Pertl-Obermeyer
- From the ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Xu Na Wu
- From the ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Jens Schrodt
- From the ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Christina Müdsam
- ¶Molecular Plant Physiology, University of Erlangen, Staudtstraβe 5, 91058 Erlangen, Germany
| | - Gerhard Obermeyer
- §Molecular Plant Biophysics and Biochemistry, Department of Molecular Biology, University of Salzburg, Billrothstraβe 11, 5020 Salzburg, Austria
| | - Waltraud X Schulze
- From the ‡Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany;
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3203
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Larance M, Kirkwood KJ, Tinti M, Brenes Murillo A, Ferguson MAJ, Lamond AI. Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling. Mol Cell Proteomics 2016; 15:2476-90. [PMID: 27114452 PMCID: PMC4937518 DOI: 10.1074/mcp.o115.055467] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/11/2016] [Indexed: 12/30/2022] Open
Abstract
We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754).
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Affiliation(s)
- Mark Larance
- From the ‡Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kathryn J Kirkwood
- From the ‡Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michele Tinti
- §Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Alejandro Brenes Murillo
- From the ‡Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael A J Ferguson
- §Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Angus I Lamond
- From the ‡Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
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3204
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Delconte RB, Kolesnik TB, Dagley LF, Rautela J, Shi W, Putz EM, Stannard K, Zhang JG, Teh C, Firth M, Ushiki T, Andoniou CE, Degli-Esposti MA, Sharp PP, Sanvitale CE, Infusini G, Liau NPD, Linossi EM, Burns CJ, Carotta S, Gray DHD, Seillet C, Hutchinson DS, Belz GT, Webb AI, Alexander WS, Li SS, Bullock AN, Babon JJ, Smyth MJ, Nicholson SE, Huntington ND. CIS is a potent checkpoint in NK cell-mediated tumor immunity. Nat Immunol 2016; 17:816-24. [PMID: 27213690 DOI: 10.1038/ni.3470] [Citation(s) in RCA: 259] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 04/27/2016] [Indexed: 12/14/2022]
Abstract
The detection of aberrant cells by natural killer (NK) cells is controlled by the integration of signals from activating and inhibitory ligands and from cytokines such as IL-15. We identified cytokine-inducible SH2-containing protein (CIS, encoded by Cish) as a critical negative regulator of IL-15 signaling in NK cells. Cish was rapidly induced in response to IL-15, and deletion of Cish rendered NK cells hypersensitive to IL-15, as evidenced by enhanced proliferation, survival, IFN-γ production and cytotoxicity toward tumors. This was associated with increased JAK-STAT signaling in NK cells in which Cish was deleted. Correspondingly, CIS interacted with the tyrosine kinase JAK1, inhibiting its enzymatic activity and targeting JAK for proteasomal degradation. Cish(-/-) mice were resistant to melanoma, prostate and breast cancer metastasis in vivo, and this was intrinsic to NK cell activity. Our data uncover a potent intracellular checkpoint in NK cell-mediated tumor immunity and suggest possibilities for new cancer immunotherapies directed at blocking CIS function.
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Affiliation(s)
- Rebecca B Delconte
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Tatiana B Kolesnik
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Jai Rautela
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Wei Shi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Eva M Putz
- Immunology in Cancer and Infection Laboratory QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Kimberley Stannard
- Immunology in Cancer and Infection Laboratory QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jian-Guo Zhang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Charis Teh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Matt Firth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Takashi Ushiki
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Christopher E Andoniou
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia and Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia and Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Phillip P Sharp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | | | - Giuseppe Infusini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Nicholas P D Liau
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Edmond M Linossi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Christopher J Burns
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Sebastian Carotta
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Daniel H D Gray
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Cyril Seillet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Dana S Hutchinson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Gabrielle T Belz
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Shawn S Li
- Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Alex N Bullock
- Structural Genomics Consortium (SGC), University of Oxford, Oxford, UK
| | - Jeffery J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Sandra E Nicholson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Nicholas D Huntington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
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3205
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Pettersen VK, Mosevoll KA, Lindemann PC, Wiker HG. Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis. Mol Cell Proteomics 2016; 15:2890-907. [PMID: 27364158 PMCID: PMC5013306 DOI: 10.1074/mcp.m116.060582] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 02/06/2023] Open
Abstract
One of the trademarks of extraintestinal pathogenic Escherichia coli is adaptation of metabolism and basic physiology to diverse host sites. However, little is known how this common human pathogen adapts to permit survival and growth in blood. We used label-free quantitative proteomics to characterize five E. coli strains purified from clinical blood cultures associated with sepsis and urinary tract infections. Further comparison of proteome profiles of the clinical strains and a reference uropathogenic E. coli strain 536 cultivated in blood culture and on two different solid media distinguished cellular features altered in response to the pathogenically relevant condition. The analysis covered nearly 60% of the strains predicted proteomes, and included quantitative description based on label-free intensity scores for 90% of the detected proteins. Statistical comparison of anaerobic and aerobic blood cultures revealed 32 differentially expressed proteins (1.5% of the shared proteins), mostly associated with acquisition and utilization of metal ions critical for anaerobic or aerobic respiration. Analysis of variance identified significantly altered amounts of 47 proteins shared by the strains (2.7%), including proteins involved in vitamin B6 metabolism and virulence. Although the proteomes derived from blood cultures were fairly similar for the investigated strains, quantitative proteomic comparison to the growth on solid media identified 200 proteins with substantially changed levels (11% of the shared proteins). Blood culture was characterized by up-regulation of anaerobic fermentative metabolism and multiple virulence traits, including cell motility and iron acquisition. In a response to the growth on solid media there were increased levels of proteins functional in aerobic respiration, catabolism of medium-specific carbon sources and protection against oxidative and osmotic stresses. These results demonstrate on the expressed proteome level that expression of extraintestinal virulence factors and overall cellular metabolism closely reflects specific growth conditions. Data are available via ProteomeXchange with identifier PXD002912.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway;
| | | | - Paul Christoffer Lindemann
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; ¶Department of Microbiology; Haukeland University Hospital, N-5021 Bergen, Norway
| | - Harald G Wiker
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; ¶Department of Microbiology; Haukeland University Hospital, N-5021 Bergen, Norway
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3206
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Rinschen MM, Schroeter CB, Koehler S, Ising C, Schermer B, Kann M, Benzing T, Brinkkoetter PT. Quantitative deep mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation. Am J Physiol Cell Physiol 2016; 311:C404-17. [PMID: 27357545 DOI: 10.1152/ajpcell.00121.2016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/27/2016] [Indexed: 11/22/2022]
Abstract
The renal filtration barrier is maintained by the renal podocyte, an epithelial postmitotic cell. Immortalized mouse podocyte cell lines-both in the differentiated and undifferentiated state-are widely utilized tools to estimate podocyte injury and cytoskeletal rearrangement processes in vitro. Here, we mapped the cultured podocyte proteome at a depth of more than 8,800 proteins and quantified 7,240 proteins. Copy numbers of proteins mutated in forms of hereditary nephrotic syndrome or focal segmental glomerulosclerosis (FSGS) were assessed. We found that cultured podocytes express abundant copy numbers of endogenous receptors, such as tyrosine kinase membrane receptors, the G protein-coupled receptor (GPCR), NPR3 (ANP receptor), and several poorly characterized GPCRs. The data set was correlated with deep mapping mRNA sequencing ("mRNAseq") data from the native mouse podocyte, the native mouse podocyte proteome and staining intensities from the human protein atlas. The generated data set was similar to these previously published resources, but several native and high-abundant podocyte-specific proteins were not identified in the data set. Notably, this data set detected general perturbations in proteostatic mechanisms as a dominant alteration during podocyte differentiation, with high proteasome activity in the undifferentiated state and markedly increased expression of lysosomal proteins in the differentiated state. Phosphoproteomics analysis of mouse podocytes at a resolution of more than 3,000 sites suggested a preference of phosphorylation of actin filament-associated proteins in the differentiated state. The data set obtained here provides a resource and provides the means for deep mapping of the native podocyte proteome and phosphoproteome in a similar manner.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; and Systems Biology of Ageing Cologne, SybaCol, Cologne, Germany
| | - Christina B Schroeter
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Sybille Koehler
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Christina Ising
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; and Systems Biology of Ageing Cologne, SybaCol, Cologne, Germany
| | - Martin Kann
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; and Systems Biology of Ageing Cologne, SybaCol, Cologne, Germany
| | - Paul T Brinkkoetter
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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3207
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von Stechow L, Francavilla C, Olsen JV. Recent findings and technological advances in phosphoproteomics for cells and tissues. Expert Rev Proteomics 2016; 12:469-87. [PMID: 26400465 PMCID: PMC4819829 DOI: 10.1586/14789450.2015.1078730] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Site-specific phosphorylation is a fast and reversible covalent post-translational modification that is tightly regulated in cells. The cellular machinery of enzymes that write, erase and read these modifications (kinases, phosphatases and phospho-binding proteins) is frequently deregulated in different diseases, including cancer. Large-scale studies of phosphoproteins – termed phosphoproteomics – strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed and reproducibility in tissues and cells. Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed.
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Affiliation(s)
- Louise von Stechow
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Chiara Francavilla
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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3208
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Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, Mann M, Cox J. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods 2016; 13:731-40. [DOI: 10.1038/nmeth.3901] [Citation(s) in RCA: 4028] [Impact Index Per Article: 503.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/10/2016] [Indexed: 02/06/2023]
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3209
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Zhang X, Ning Z, Mayne J, Moore JI, Li J, Butcher J, Deeke SA, Chen R, Chiang CK, Wen M, Mack D, Stintzi A, Figeys D. MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota. MICROBIOME 2016; 4:31. [PMID: 27343061 PMCID: PMC4919841 DOI: 10.1186/s40168-016-0176-z] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/02/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND The gut microbiota has been shown to be closely associated with human health and disease. While next-generation sequencing can be readily used to profile the microbiota taxonomy and metabolic potential, metaproteomics is better suited for deciphering microbial biological activities. However, the application of gut metaproteomics has largely been limited due to the low efficiency of protein identification. Thus, a high-performance and easy-to-implement gut metaproteomic approach is required. RESULTS In this study, we developed a high-performance and universal workflow for gut metaproteome identification and quantification (named MetaPro-IQ) by using the close-to-complete human or mouse gut microbial gene catalog as database and an iterative database search strategy. An average of 38 and 33 % of the acquired tandem mass spectrometry (MS) spectra was confidently identified for the studied mouse stool and human mucosal-luminal interface samples, respectively. In total, we accurately quantified 30,749 protein groups for the mouse metaproteome and 19,011 protein groups for the human metaproteome. Moreover, the MetaPro-IQ approach enabled comparable identifications with the matched metagenome database search strategy that is widely used but needs prior metagenomic sequencing. The response of gut microbiota to high-fat diet in mice was then assessed, which showed distinct metaproteome patterns for high-fat-fed mice and identified 849 proteins as significant responders to high-fat feeding in comparison to low-fat feeding. CONCLUSIONS We present MetaPro-IQ, a metaproteomic approach for highly efficient intestinal microbial protein identification and quantification, which functions as a universal workflow for metaproteomic studies, and will thus facilitate the application of metaproteomics for better understanding the functions of gut microbiota in health and disease.
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Affiliation(s)
- Xu Zhang
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Zhibin Ning
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Janice Mayne
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Jasmine I. Moore
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Jennifer Li
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - James Butcher
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Shelley Ann Deeke
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Rui Chen
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Cheng-Kang Chiang
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Ming Wen
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - David Mack
- />Department of Paediatrics, CHEO Inflammatory Bowel Disease Centre and Research Institute, University of Ottawa, Ottawa, ON Canada
| | - Alain Stintzi
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Daniel Figeys
- />Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
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3210
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Abstract
Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing.
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3211
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Nuez-Ortín WG, Carter CG, Nichols PD, Wilson R. Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon (Salmo salar). Proteomics 2016; 16:2043-7. [PMID: 27272914 DOI: 10.1002/pmic.201600051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 05/05/2016] [Accepted: 06/02/2016] [Indexed: 11/05/2022]
Abstract
Understanding diet- and environmentally induced physiological changes in fish larvae is a major goal for the aquaculture industry. Proteomic analysis of whole fish larvae comprising multiple tissues offers considerable potential but is challenging due to the very large dynamic range of protein abundance. To extend the coverage of the larval phase of the Atlantic salmon (Salmo salar) proteome, we applied a two-step sequential extraction (SE) method, based on differential protein solubility, using a nondenaturing buffer containing 150 mM NaCl followed by a denaturing buffer containing 7 M urea and 2 M thiourea. Extracts prepared using SE and one-step direct extraction were characterized via label-free shotgun proteomics using nanoLC-MS/MS (LTQ-Orbitrap). SE partitioned the proteins into two fractions of approximately equal amounts, but with very distinct protein composition, leading to identification of ∼40% more proteins than direct extraction. This fractionation strategy enabled the most detailed characterization of the salmon larval proteome to date and provides a platform for greater understanding of physiological changes in whole fish larvae. The MS data are available via the ProteomeXchange Consortium PRIDE partner repository, dataset PXD003366.
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Affiliation(s)
- Waldo G Nuez-Ortín
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia.,CSIRO Food and Nutrition, Oceans and Atmosphere, Hobart, TAS, Australia
| | - Chris G Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Peter D Nichols
- CSIRO Food and Nutrition, Oceans and Atmosphere, Hobart, TAS, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS, Australia
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3212
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Sun L, Dubiak KM, Peuchen EH, Zhang Z, Zhu G, Huber PW, Dovichi NJ. Single Cell Proteomics Using Frog (Xenopus laevis) Blastomeres Isolated from Early Stage Embryos, Which Form a Geometric Progression in Protein Content. Anal Chem 2016; 88:6653-7. [PMID: 27314579 DOI: 10.1021/acs.analchem.6b01921] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Single cell analysis is required to understand cellular heterogeneity in biological systems. We propose that single cells (blastomeres) isolated from early stage invertebrate, amphibian, or fish embryos are ideal model systems for the development of technologies for single cell analysis. For these embryos, although cell cleavage is not exactly symmetric, the content per blastomere decreases roughly by half with each cell division, creating a geometric progression in cellular content. This progression forms a ladder of single-cell targets for the development of successively higher sensitivity instruments. In this manuscript, we performed bottom-up proteomics on single blastomeres isolated by microdissection from 2-, 4-, 8-, 16-, 32-, and 50-cell Xenopus laevis (African clawed frog) embryos. Over 1 400 protein groups were identified in single-run reversed-phase liquid chromatography-electrospray ionization-tandem mass spectrometry from single balstomeres isolated from a 16-cell embryo. When the mass of yolk-free proteins in single blastomeres decreased from ∼0.8 μg (16-cell embryo) to ∼0.2 μg (50-cell embryo), the number of protein group identifications declined from 1 466 to 644. Around 800 protein groups were quantified across four blastomeres isolated from a 16-cell embryo. By comparing the protein expression among different blastomeres, we observed that the blastomere-to-blastomere heterogeneity in 8-, 16-, 32-, and 50-cell embryos increases with development stage, presumably due to cellular differentiation. These results suggest that comprehensive quantitative proteomics on single blastomeres isolated from these early stage embryos can provide valuable insights into cellular differentiation and organ development.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Kyle M Dubiak
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Elizabeth H Peuchen
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Paul W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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3213
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Ruhe J, Agler MT, Placzek A, Kramer K, Finkemeier I, Kemen EM. Obligate Biotroph Pathogens of the Genus Albugo Are Better Adapted to Active Host Defense Compared to Niche Competitors. FRONTIERS IN PLANT SCIENCE 2016; 7:820. [PMID: 27379119 PMCID: PMC4913113 DOI: 10.3389/fpls.2016.00820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/25/2016] [Indexed: 05/23/2023]
Abstract
Recent research suggested that plants behave differently under combined versus single abiotic and biotic stress conditions in controlled environments. While this work has provided a glimpse into how plants might behave under complex natural conditions, it also highlights the need for field experiments using established model systems. In nature, diverse microbes colonize the phyllosphere of Arabidopsis thaliana, including the obligate biotroph oomycete genus Albugo, causal agent of the common disease white rust. Biotrophic, as well as hemibiotrophic plant pathogens are characterized by efficient suppression of host defense responses. Lab experiments have even shown that Albugo sp. can suppress non-host resistance, thereby enabling otherwise avirulent pathogen growth. We asked how a pathogen that is vitally dependent on a living host can compete in nature for limited niche space while paradoxically enabling colonization of its host plant for competitors? To address this question, we used a proteomics approach to identify differences and similarities between lab and field samples of Albugo sp.-infected and -uninfected A. thaliana plants. We could identify highly similar apoplastic proteomic profiles in both infected and uninfected plants. In wild plants, however, a broad range of defense-related proteins were detected in the apoplast regardless of infection status, while no or low levels of defense-related proteins were detected in lab samples. These results indicate that Albugo sp. do not strongly affect immune responses and leave distinct branches of the immune signaling network intact. To validate our findings and to get mechanistic insights, we tested a panel of A. thaliana mutant plants with induced or compromised immunity for susceptibility to different biotrophic pathogens. Our findings suggest that the biotroph pathogen Albugo selectively interferes with host defense under different environmental and competitive pressures to maintain its ecological niche dominance. Adaptation to host immune responses while maintaining a partially active host immunity seems advantageous against competitors. We suggest a model for future research that considers not only host-microbe but in addition microbe-microbe and microbe-host environment factors.
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Affiliation(s)
- Jonas Ruhe
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Matthew T. Agler
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Katharina Kramer
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Iris Finkemeier
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Institute of Plant Biology and Biotechnology, University of MuensterMünster, Germany
| | - Eric M. Kemen
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
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3214
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Alves MJM, Kawahara R, Viner R, Colli W, Mattos EC, Thaysen-Andersen M, Larsen MR, Palmisano G. Comprehensive glycoprofiling of the epimastigote and trypomastigote stages of Trypanosoma cruzi. J Proteomics 2016; 151:182-192. [PMID: 27318177 DOI: 10.1016/j.jprot.2016.05.034] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/23/2016] [Accepted: 05/30/2016] [Indexed: 12/17/2022]
Abstract
Trypanosoma cruzi, the protozoan that causes Chagas disease, has a complex life cycle involving insect and mammalian hosts and distinct developmental stages. During T. cruzi developmental stages, glycoproteins play important role in the host-parasite interaction, such as cellular recognition, host cell invasion and adhesion, and immune evasion. In this study, comprehensive glycoprofiling analysis was performed in the epimastigote and trypomastigote stages of T. cruzi using two glycopeptide enrichment strategies, lectin-based and hydrophilic interaction liquid chromatography, followed by high resolution LC-MS/MS. Following deglycosylation, a total of 1306 N-glycosylation sites in NxS/T/C motifs were identified from 690 T. cruzi glycoproteins. Among them, 170 and 334 glycoproteins were exclusively identified in epimastigotes and trypomastigotes, respectively. Besides, global site-specific characterization of the N- and O-linked glycan heterogeneity in the two life stages of T. cruzi was achieved by intact glycopeptide analysis, revealing 144/466 unique N-linked and 10/97 unique O-linked intact glycopeptides in epimastigotes/trypomastigotes, respectively. Conclusively, this study documents the significant T. cruzi stage-specific expression of glycoproteins that can help to better understand the T. cruzi phenotype and response caused by the interaction with different hosts during its complex life cycle. BIOLOGICAL SIGNIFICANCE Chagas disease caused by the protozoan Trypanosoma cruzi is a neglected disease which affects millions of people especially in Latin America. The absence of efficient drugs and vaccines against Chagas disease stimulates the search for novel targets. Glycoproteins are very attractive therapeutic candidate targets since they mediate key processes in the host-parasite interaction, such as cellular recognition, host cell invasion and adhesion, and immune evasion. This study aimed to provide an in depth characterization of the N-linked and O-linked glycoproteome of two T. cruzi life stages: epimastigotes and trypomastigotes. Mass spectrometry-based proteomics showed interesting stage-specific glycoproteome signatures that are valuable to better understand the importance of protein glycosylation in epimastigotes and trypomastigotes and to expand the repertoire of potential therapeutic targets against Chagas disease.
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Affiliation(s)
- Maria Julia Manso Alves
- Instituto de Química, Departamento de Bioquímica, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Rebeca Kawahara
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, USA
| | - Walter Colli
- Instituto de Química, Departamento de Bioquímica, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Eliciane Cevolani Mattos
- Instituto de Química, Departamento de Bioquímica, Universidade de São Paulo, USP, São Paulo, Brazil
| | | | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology, University of Southern, Odense, DK, Denmark
| | - Giuseppe Palmisano
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, USP, São Paulo, Brazil.
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3215
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Madeira JP, Omer H, Alpha-Bazin B, Armengaud J, Duport C. Deciphering the interactions between the Bacillus cereus linear plasmid, pBClin15, and its host by high-throughput comparative proteomics. J Proteomics 2016; 146:25-33. [PMID: 27321915 DOI: 10.1016/j.jprot.2016.06.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 04/22/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
UNLABELLED The pathogen, Bacillus cereus, is able to adapt its metabolism to various environmental conditions. The reference strain, Bacillus cereus ATCC 14579, harbors a linear plasmid, pBClin15, which displays a cryptic prophage behavior. Here, we studied the impact of pBClin15 on the aerobic respiratory metabolism of B. cereus by curing its host strain. We compared, by means of a high-throughput shotgun proteomic approach, both the cellular proteome and the exoproteome of B. cereus ATCC 14579 in the presence and absence of pBClin15 at the early, late and stationary growth phases. The results were visualized through a hierarchical cluster analysis of proteomic data. We found that pBClin15 contributes significantly to the metabolic efficiency of B. cereus by restricting the production of chromosome-encoded phage proteins in the extracellular milieu. The data also revealed intricate regulatory mechanisms between pBClin15 and its host. Finally, we show that pBClin15 provides benefit to its host to adapt to different ecologic niches. BIOLOGICAL SIGNIFICANCE Bacteria belonging to the Bacillus cereus group include B. cereus, a notorious food borne pathogen which causes gastroenteritis. The B. cereus type, strain ATCC 14579, harbors a linear plasmid, pBClin15, which displays cryptic prophage behavior. Here, we present data supporting the idea that pBClin15 may have a much greater role in B. cereus metabolism that has hitherto been suspected. Specifically, our comparative proteomic analyses reveal that pBClin15 manages B. cereus central metabolism to optimize energy and carbon utilization through the repression of several chromosome-encoded phage proteins. These results suggest that pBClin15 provides benefit to the host for surviving adverse environmental conditions.
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Affiliation(s)
- Jean-Paul Madeira
- SQPOV, UMR0408, Avignon Université, INRA, F-84914 Avignon, France; CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory "Innovative technologies for Detection and Diagnostics", Bagnols-sur-Cèze F-30200, France
| | - Hélène Omer
- SQPOV, UMR0408, Avignon Université, INRA, F-84914 Avignon, France; CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory "Innovative technologies for Detection and Diagnostics", Bagnols-sur-Cèze F-30200, France
| | - Béatrice Alpha-Bazin
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory "Innovative technologies for Detection and Diagnostics", Bagnols-sur-Cèze F-30200, France
| | - Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory "Innovative technologies for Detection and Diagnostics", Bagnols-sur-Cèze F-30200, France
| | - Catherine Duport
- SQPOV, UMR0408, Avignon Université, INRA, F-84914 Avignon, France.
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3216
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Chen ZA, Fischer L, Cox J, Rappsilber J. Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant. Mol Cell Proteomics 2016; 15:2769-78. [PMID: 27302889 PMCID: PMC4974350 DOI: 10.1074/mcp.m115.056481] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 12/20/2022] Open
Abstract
The conceptually simple step from cross-linking/mass spectrometry (CLMS) to quantitative cross-linking/mass spectrometry (QCLMS) is compounded by technical challenges. Currently, quantitative proteomics software is tightly integrated with the protein identification workflow. This prevents automatically quantifying other m/z features in a targeted manner including those associated with cross-linked peptides. Here we present a new release of MaxQuant that permits starting the quantification process from an m/z feature list. Comparing the automated quantification to a carefully manually curated test set of cross-linked peptides obtained by cross-linking C3 and C3b with BS3 and isotope-labeled BS3-d4 revealed a number of observations: (1) Fully automated process using MaxQuant can quantify cross-links in our reference data set with 68% recall rate and 88% accuracy. (2) Hidden quantification errors can be converted into exposed failures by label-swap replica, which makes label-swap replica an essential part of QCLMS. (3) Cross-links that failed during automated quantification can be recovered by semi-automated re-quantification. The integrated workflow of MaxQuant and semi-automated assessment provides the maximum of quantified cross-links. In contrast, work on larger data sets or by less experienced users will benefit from full automation in MaxQuant.
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Affiliation(s)
- Zhuo A Chen
- From the ‡Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Lutz Fischer
- From the ‡Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jürgen Cox
- §Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Juri Rappsilber
- From the ‡Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; ¶Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
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3217
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Lasonder E, Rijpma SR, van Schaijk BCL, Hoeijmakers WAM, Kensche PR, Gresnigt MS, Italiaander A, Vos MW, Woestenenk R, Bousema T, Mair GR, Khan SM, Janse CJ, Bártfai R, Sauerwein RW. Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes: molecular insight into sex-specific processes and translational repression. Nucleic Acids Res 2016; 44:6087-101. [PMID: 27298255 PMCID: PMC5291273 DOI: 10.1093/nar/gkw536] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/06/2016] [Indexed: 12/15/2022] Open
Abstract
Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these ‘repressed transcripts’ have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies.
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Affiliation(s)
- Edwin Lasonder
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth PL4 8AA, UK
| | - Sanna R Rijpma
- Parasitology, Department of Medical Microbiology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Ben C L van Schaijk
- Parasitology, Department of Medical Microbiology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands Malaria Epigenomics Group, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Wieteke A M Hoeijmakers
- Malaria Epigenomics Group, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Philip R Kensche
- Malaria Epigenomics Group, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Mark S Gresnigt
- Parasitology, Department of Medical Microbiology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Annet Italiaander
- Parasitology, Department of Medical Microbiology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Martijn W Vos
- Parasitology, Department of Medical Microbiology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Rob Woestenenk
- Flow Cytometry Facility, Department of Laboratory Medicine, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Teun Bousema
- Parasitology, Department of Medical Microbiology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Gunnar R Mair
- Parasitology, Department of Infectious Diseases, University of Heidelberg Medical School, D-69120 Heidelberg, Germany
| | - Shahid M Khan
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Chris J Janse
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Richárd Bártfai
- Malaria Epigenomics Group, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Robert W Sauerwein
- Parasitology, Department of Medical Microbiology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
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3218
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Gillet LC, Leitner A, Aebersold R. Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:449-72. [PMID: 27049628 DOI: 10.1146/annurev-anchem-071015-041535] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Proteins constitute a key class of molecular components that perform essential biochemical reactions in living cells. Whether the aim is to extensively characterize a given protein or to perform high-throughput qualitative and quantitative analysis of the proteome content of a sample, liquid chromatography coupled to tandem mass spectrometry has become the technology of choice. In this review, we summarize the current state of mass spectrometry applied to bottom-up proteomics, the approach that focuses on analyzing peptides obtained from proteolytic digestion of proteins. With the recent advances in instrumentation and methodology, we show that the field is moving away from providing qualitative identification of long lists of proteins to delivering highly consistent and accurate quantification values for large numbers of proteins across large numbers of samples. We believe that this shift will have a profound impact for the field of proteomics and life science research in general.
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Affiliation(s)
- Ludovic C Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland;
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland;
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland;
- Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
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3219
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Wright MH, Paape D, Price HP, Smith DF, Tate EW. Global Profiling and Inhibition of Protein Lipidation in Vector and Host Stages of the Sleeping Sickness Parasite Trypanosoma brucei. ACS Infect Dis 2016; 2:427-441. [PMID: 27331140 PMCID: PMC4906374 DOI: 10.1021/acsinfecdis.6b00034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Indexed: 01/05/2023]
Abstract
The enzyme N-myristoyltransferase (NMT) catalyzes the essential fatty acylation of substrate proteins with myristic acid in eukaryotes and is a validated drug target in the parasite Trypanosoma brucei, the causative agent of African trypanosomiasis (sleeping sickness). N-Myristoylation typically mediates membrane localization of proteins and is essential to the function of many. However, only a handful of proteins are experimentally validated as N-myristoylated in T. brucei. Here, we perform metabolic labeling with an alkyne-tagged myristic acid analogue, enabling the capture of lipidated proteins in insect and host life stages of T. brucei. We further compare this with a longer chain palmitate analogue to explore the chain length-specific incorporation of fatty acids into proteins. Finally, we combine the alkynyl-myristate analogue with NMT inhibitors and quantitative chemical proteomics to globally define N-myristoylated proteins in the clinically relevant bloodstream form parasites. This analysis reveals five ARF family small GTPases, calpain-like proteins, phosphatases, and many uncharacterized proteins as substrates of NMT in the parasite, providing a global view of the scope of this important protein modification and further evidence for the crucial and pleiotropic role of NMT in the cell.
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Affiliation(s)
- Megan H. Wright
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Daniel Paape
- Centre for Immunology and Infection, Department
of Biology, University of York, York YO10 5DD, United Kingdom
| | - Helen P. Price
- Centre for Immunology and Infection, Department
of Biology, University of York, York YO10 5DD, United Kingdom
| | - Deborah F. Smith
- Centre for Immunology and Infection, Department
of Biology, University of York, York YO10 5DD, United Kingdom
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
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3220
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Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE. Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells. J Proteome Res 2016; 15:2178-86. [DOI: 10.1021/acs.jproteome.6b00134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Marco Lodrini
- Department
of Pediatric Hematology/Oncology/Stem Cell Transplantation Charité − Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger
Platz 1, 13353 Berlin, Germany
| | - Gereon Poschmann
- Molecular
Proteomics Laboratory, Biological Medical Research Centre, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Victoria Schmidt
- Clinical
Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), INF 280, 69120 Heidelberg, Germany
| | - Jasmin Wünschel
- Department
of Pediatric Hematology/Oncology/Stem Cell Transplantation Charité − Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger
Platz 1, 13353 Berlin, Germany
| | - Daniel Dreidax
- Division
Neuroblastoma Genetics, DKFZ, INF 280, 69120 Heidelberg, Germany
| | - Olaf Witt
- Clinical
Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), INF 280, 69120 Heidelberg, Germany
- Center
for Individualized Pediatric Oncology (ZIPO) and Brain Tumors, Department
of Pediatric Hematology/Oncology, University of Heidelberg and National Center for Tumor Diseases (NCT), INF 430, 69120 Heidelberg, Germany
| | - Thomas Höfer
- Division
of Theoretical Systems Biology, DKFZ, INF 280, 69120 Heidelberg, Germany
| | - Helmut E. Meyer
- Leibniz-Institut
für Analytische Wissenschaften − ISAS − e.V., Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany
| | - Kai Stühler
- Molecular
Proteomics Laboratory, Biological Medical Research Centre, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Institute
for Molecular Medicine, University Hospital Düsseldorf, Universitätsstraße
1, 40225 Düsseldorf, Germany
| | - Angelika Eggert
- Department
of Pediatric Hematology/Oncology/Stem Cell Transplantation Charité − Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger
Platz 1, 13353 Berlin, Germany
| | - Hedwig E. Deubzer
- Department
of Pediatric Hematology/Oncology/Stem Cell Transplantation Charité − Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger
Platz 1, 13353 Berlin, Germany
- Clinical
Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), INF 280, 69120 Heidelberg, Germany
- Center
for Individualized Pediatric Oncology (ZIPO) and Brain Tumors, Department
of Pediatric Hematology/Oncology, University of Heidelberg and National Center for Tumor Diseases (NCT), INF 430, 69120 Heidelberg, Germany
- Junior
Neuroblastoma Research Group, Experimental and Clinical Research Center
of the Max-Delbrück Center for Molecular Medicine and the Charité − Universitätsmedizin Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
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3221
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Itzhak DN, Tyanova S, Cox J, Borner GH. Global, quantitative and dynamic mapping of protein subcellular localization. eLife 2016; 5. [PMID: 27278775 PMCID: PMC4959882 DOI: 10.7554/elife.16950] [Citation(s) in RCA: 382] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/08/2016] [Indexed: 01/01/2023] Open
Abstract
Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology. DOI:http://dx.doi.org/10.7554/eLife.16950.001 The interior of every cell is highly organised, and contains many compartments, called organelles, that are dedicated to specific roles. Proteins are the tools and machines of the cell, and each organelle has its own set of proteins that it requires to work correctly. Each cell contains ten or more organelles, and several thousand different types of proteins. The exact location of proteins in the cell is important; once we know what compartment a protein is in, it is easier to narrow down what it might be doing. The location of many proteins in a cell is unclear or simply not known. Moreover, since changing the location of a protein can change its activity, it is also important to be able to detect changes in the location of proteins under different circumstances, such as before and after drug treatment. Itzhak et al. set out to develop a method that reveals the locations of all the proteins in a cell at any given time. The resulting technique maps the location of most of the proteins in a human cancer cell line and, in addition, determines how many copies of each protein there are. Combining these two types of information produces a model of the cell’s architecture. Importantly, Itzhak et al. were able to compare such a model of the cell under normal circumstances to a model made after the cell had been stimulated with a growth factor. This revealed which proteins had changed location, identifying these proteins as important for the cell’s response to the growth factor. The new mapping method could be used in the future to analyse the anatomy of different cell types, such as nerve cells and cells of the immune system. Itzhak et al. also want to investigate the differences between healthy cells and cells from people with neurological disorders to understand how such diseases arise. DOI:http://dx.doi.org/10.7554/eLife.16950.002
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Affiliation(s)
- Daniel N Itzhak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefka Tyanova
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Georg Hh Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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3222
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Raj R, Lercher L, Mohammed S, Davis BG. Synthetic Nucleosomes Reveal that GlcNAcylation Modulates Direct Interaction with the FACT Complex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ritu Raj
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Lukas Lercher
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Shabaz Mohammed
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Benjamin G. Davis
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
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3223
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Much C, Auchynnikava T, Pavlinic D, Buness A, Rappsilber J, Benes V, Allshire R, O’Carroll D. Endogenous Mouse Dicer Is an Exclusively Cytoplasmic Protein. PLoS Genet 2016; 12:e1006095. [PMID: 27254021 PMCID: PMC4890738 DOI: 10.1371/journal.pgen.1006095] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/10/2016] [Indexed: 12/25/2022] Open
Abstract
Dicer is a large multi-domain protein responsible for the ultimate step of microRNA and short-interfering RNA biogenesis. In human and mouse cell lines, Dicer has been shown to be important in the nuclear clearance of dsRNA as well as the establishment of chromatin modifications. Here we set out to unambiguously define the cellular localization of Dicer in mice to understand if this is a conserved feature of mammalian Dicer in vivo. To this end, we utilized an endogenously epitope tagged Dicer knock-in mouse allele. From primary mouse cell lines and adult tissues, we determined with certainty by biochemical fractionation and confocal immunofluorescence microscopy that endogenous Dicer is exclusively cytoplasmic. We ruled out the possibility that a fraction of Dicer shuttles to and from the nucleus as well as that FGF or DNA damage signaling induce Dicer nuclear translocation. We also explored Dicer localization during the dynamic and developmental context of embryogenesis, where Dicer is ubiquitously expressed and strictly cytoplasmic in all three germ layers as well as extraembryonic tissues. Our data exclude a direct role for Dicer in the nuclear RNA processing in the mouse.
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Affiliation(s)
- Christian Much
- Mouse Biology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, Italy
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Tania Auchynnikava
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Dinko Pavlinic
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Buness
- Mouse Biology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, Italy
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Robin Allshire
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Dónal O’Carroll
- Mouse Biology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, Italy
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- * E-mail:
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3224
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Synergic stress in striped catfish (Pangasianodon hypophthalmus, S.) exposed to chronic salinity and bacterial infection: Effects on kidney protein expression profile. J Proteomics 2016; 142:91-101. [DOI: 10.1016/j.jprot.2016.04.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 12/14/2022]
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3225
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Devaux S, Cizkova D, Quanico J, Franck J, Nataf S, Pays L, Hauberg-Lotte L, Maass P, Kobarg JH, Kobeissy F, Mériaux C, Wisztorski M, Slovinska L, Blasko J, Cigankova V, Fournier I, Salzet M. Proteomic Analysis of the Spatio-temporal Based Molecular Kinetics of Acute Spinal Cord Injury Identifies a Time- and Segment-specific Window for Effective Tissue Repair. Mol Cell Proteomics 2016; 15:2641-70. [PMID: 27250205 DOI: 10.1074/mcp.m115.057794] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Indexed: 12/11/2022] Open
Abstract
Spinal cord injury (SCI) represents a major debilitating health issue with a direct socioeconomic burden on the public and private sectors worldwide. Although several studies have been conducted to identify the molecular progression of injury sequel due from the lesion site, still the exact underlying mechanisms and pathways of injury development have not been fully elucidated. In this work, based on OMICs, 3D matrix-assisted laser desorption ionization (MALDI) imaging, cytokines arrays, confocal imaging we established for the first time that molecular and cellular processes occurring after SCI are altered between the lesion proximity, i.e. rostral and caudal segments nearby the lesion (R1-C1) whereas segments distant from R1-C1, i.e. R2-C2 and R3-C3 levels coexpressed factors implicated in neurogenesis. Delay in T regulators recruitment between R1 and C1 favor discrepancies between the two segments. This is also reinforced by presence of neurites outgrowth inhibitors in C1, absent in R1. Moreover, the presence of immunoglobulins (IgGs) in neurons at the lesion site at 3 days, validated by mass spectrometry, may present additional factor that contributes to limited regeneration. Treatment in vivo with anti-CD20 one hour after SCI did not improve locomotor function and decrease IgG expression. These results open the door of a novel view of the SCI treatment by considering the C1 as the therapeutic target.
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Affiliation(s)
- Stephanie Devaux
- From the ‡Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France; §Institute of Neurobiology, Slovak Academy of Sciences, Center of Excellence for Brain Research, Soltesovej 4-6 Kosice, Slovakia; §§Department of Anatomy, Histology and Physiology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Dasa Cizkova
- From the ‡Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France; §Institute of Neurobiology, Slovak Academy of Sciences, Center of Excellence for Brain Research, Soltesovej 4-6 Kosice, Slovakia; §§Department of Anatomy, Histology and Physiology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Jusal Quanico
- From the ‡Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Julien Franck
- From the ‡Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Serge Nataf
- ¶Inserm U-1060, CarMeN Laboratory, Banque de Tissus et de Cellules des Hospices Civils de Lyon, Université Lyon-1, France
| | - Laurent Pays
- ¶Inserm U-1060, CarMeN Laboratory, Banque de Tissus et de Cellules des Hospices Civils de Lyon, Université Lyon-1, France
| | - Lena Hauberg-Lotte
- ‖Center for industrial mathematics, University of Bremen, Bibliothek straβe 1, MZH, Room 2060, 28359 Bremen, Germany
| | - Peter Maass
- ‖Center for industrial mathematics, University of Bremen, Bibliothek straβe 1, MZH, Room 2060, 28359 Bremen, Germany
| | - Jan H Kobarg
- **Steinbeis Innovation Center SCiLS Research, Fahrenheitstr. 1, 28359 Bremen, Germany
| | - Firas Kobeissy
- ‡‡Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut
| | - Céline Mériaux
- From the ‡Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Maxence Wisztorski
- From the ‡Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Lucia Slovinska
- §Institute of Neurobiology, Slovak Academy of Sciences, Center of Excellence for Brain Research, Soltesovej 4-6 Kosice, Slovakia
| | - Juraj Blasko
- §Institute of Neurobiology, Slovak Academy of Sciences, Center of Excellence for Brain Research, Soltesovej 4-6 Kosice, Slovakia
| | - Viera Cigankova
- §§Department of Anatomy, Histology and Physiology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Isabelle Fournier
- From the ‡Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Michel Salzet
- From the ‡Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France; **Steinbeis Innovation Center SCiLS Research, Fahrenheitstr. 1, 28359 Bremen, Germany
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3226
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Temporal Regulation of the Bacillus subtilis Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth. mSystems 2016; 1. [PMID: 27376153 PMCID: PMC4927096 DOI: 10.1128/msystems.00005-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The past decade highlighted Nε-lysine acetylation as a prevalent posttranslational modification in bacteria. However, knowledge regarding the physiological importance and temporal regulation of acetylation has remained limited. To uncover potential regulatory roles for acetylation, we analyzed how acetylation patterns and abundances change between growth phases in B. subtilis. To demonstrate that the identification of cell growth-dependent modifications can point to critical regulatory acetylation events, we further characterized MreB, the cell shape-determining protein. Our findings led us to propose a role for MreB acetylation in controlling cell width by restricting cell wall growth. Nε-Lysine acetylation has been recognized as a ubiquitous regulatory posttranslational modification that influences a variety of important biological processes in eukaryotic cells. Recently, it has been realized that acetylation is also prevalent in bacteria. Bacteria contain hundreds of acetylated proteins, with functions affecting diverse cellular pathways. Still, little is known about the regulation or biological relevance of nearly all of these modifications. Here we characterize the cellular growth-associated regulation of the Bacillus subtilis acetylome. Using acetylation enrichment and quantitative mass spectrometry, we investigate the logarithmic and stationary growth phases, identifying over 2,300 unique acetylation sites on proteins that function in essential cellular pathways. We determine an acetylation motif, EK(ac)(D/Y/E), which resembles the eukaryotic mitochondrial acetylation signature, and a distinct stationary-phase-enriched motif. By comparing the changes in acetylation with protein abundances, we discover a subset of critical acetylation events that are temporally regulated during cell growth. We functionally characterize the stationary-phase-enriched acetylation on the essential shape-determining protein MreB. Using bioinformatics, mutational analysis, and fluorescence microscopy, we define a potential role for the temporal acetylation of MreB in restricting cell wall growth and cell diameter. IMPORTANCE The past decade highlighted Nε-lysine acetylation as a prevalent posttranslational modification in bacteria. However, knowledge regarding the physiological importance and temporal regulation of acetylation has remained limited. To uncover potential regulatory roles for acetylation, we analyzed how acetylation patterns and abundances change between growth phases in B. subtilis. To demonstrate that the identification of cell growth-dependent modifications can point to critical regulatory acetylation events, we further characterized MreB, the cell shape-determining protein. Our findings led us to propose a role for MreB acetylation in controlling cell width by restricting cell wall growth.
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3227
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Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG. Proteomic investigation of the secretome ofCellvibrio japonicusduring growth on chitin. Proteomics 2016; 16:1904-14. [DOI: 10.1002/pmic.201500419] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 04/05/2016] [Accepted: 05/09/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tina Rise Tuveng
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Magnus Øverlie Arntzen
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Oskar Bengtsson
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Jeffrey G. Gardner
- Department of Biological Sciences; University of Maryland - Baltimore County; Baltimore MD USA
| | - Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Vincent G.H. Eijsink
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
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3228
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Proteomic dataset for altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells. Data Brief 2016; 8:342-9. [PMID: 27331112 PMCID: PMC4908283 DOI: 10.1016/j.dib.2016.05.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/12/2016] [Accepted: 05/24/2016] [Indexed: 01/20/2023] Open
Abstract
This article contains raw and processed data related to research published in "Role of the polypeptide N-acetylgalactosaminyltransferase 3 in ovarian cancer progression: possible implications in abnormal mucin O-glycosylation" [1]. The data presented here was obtained with the application of a bioorthogonal chemical reporter strategy analyzing differential glycoprotein expression following the knock-down (KD) of the GALNT3 gene in the epithelial ovarian cancer (EOC) cell line A2780s. LC-MS/MS mass spectrometry analysis was then performed and the processed data related to the identified glycoproteins show that several hundred proteins are differentially expressed between control and GALNT3 KD A2780s cells. The obtained data also uncover numerous novel glycoproteins; some of which could represent new potential EOC biomarkers and/or therapeutic targets.
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3229
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Virant-Klun I, Leicht S, Hughes C, Krijgsveld J. Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes. Mol Cell Proteomics 2016; 15:2616-27. [PMID: 27215607 DOI: 10.1074/mcp.m115.056887] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Indexed: 12/25/2022] Open
Abstract
Oocytes undergo a range of complex processes via oogenesis, maturation, fertilization, and early embryonic development, eventually giving rise to a fully functioning organism. To understand proteome composition and diversity during maturation of human oocytes, here we have addressed crucial aspects of oocyte collection and proteome analysis, resulting in the first proteome and secretome maps of human oocytes. Starting from 100 oocytes collected via a novel serum-free hanging drop culture system, we identified 2,154 proteins, whose function indicate that oocytes are largely resting cells with a proteome that is tailored for homeostasis, cellular attachment, and interaction with its environment via secretory factors. In addition, we have identified 158 oocyte-enriched proteins (such as ECAT1, PIWIL3, NLRP7)(1) not observed in high-coverage proteomics studies of other human cell lines or tissues. Exploiting SP3, a novel technology for proteomic sample preparation using magnetic beads, we scaled down proteome analysis to single cells. Despite the low protein content of only ∼100 ng per cell, we consistently identified ∼450 proteins from individual oocytes. When comparing individual oocytes at the germinal vesicle (GV) and metaphase II (MII) stage, we found that the Tudor and KH domain-containing protein (TDRKH) is preferentially expressed in immature oocytes, while Wee2, PCNA, and DNMT1 were enriched in mature cells, collectively indicating that maintenance of genome integrity is crucial during oocyte maturation. This study demonstrates that an innovative proteomics workflow facilitates analysis of single human oocytes to investigate human oocyte biology and preimplantation development. The approach presented here paves the way for quantitative proteomics in other quantity-limited tissues and cell types. Data associated with this study are available via ProteomeXchange with identifier PXD004142.
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Affiliation(s)
- Irma Virant-Klun
- From the ‡Reproductive Unit, Department of Obstetrics and Gynecology, University Medical Centre Ljubljana, Slajmerjeva 3, 1000 Ljubljana, Slovenia
| | - Stefan Leicht
- §European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christopher Hughes
- ¶British Columbia Cancer Research Agency, 675 West 10th Avenue, Vancouver, Canada
| | - Jeroen Krijgsveld
- §European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany; ‖German Cancer Research Center and Heidelberg University, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
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3230
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Klaeger S, Gohlke B, Perrin J, Gupta V, Heinzlmeir S, Helm D, Qiao H, Bergamini G, Handa H, Savitski MM, Bantscheff M, Médard G, Preissner R, Kuster B. Chemical Proteomics Reveals Ferrochelatase as a Common Off-target of Kinase Inhibitors. ACS Chem Biol 2016; 11:1245-54. [PMID: 26863403 DOI: 10.1021/acschembio.5b01063] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many protein kinases are valid drug targets in oncology because they are key components of signal transduction pathways. The number of clinical kinase inhibitors is on the rise, but these molecules often exhibit polypharmacology, potentially eliciting desired and toxic effects. Therefore, a comprehensive assessment of a compound's target space is desirable for a better understanding of its biological effects. The enzyme ferrochelatase (FECH) catalyzes the conversion of protoporphyrin IX into heme and was recently found to be an off-target of the BRAF inhibitor Vemurafenib, likely explaining the phototoxicity associated with this drug in melanoma patients. This raises the question of whether FECH binding is a more general feature of kinase inhibitors. To address this, we applied a chemical proteomics approach using kinobeads to evaluate 226 clinical kinase inhibitors for their ability to bind FECH. Surprisingly, low or submicromolar FECH binding was detected for 29 of all compounds tested and isothermal dose response measurements confirmed target engagement in cells. We also show that Vemurafenib, Linsitinib, Neratinib, and MK-2461 reduce heme levels in K562 cells, verifying that drug binding leads to a loss of FECH activity. Further biochemical and docking experiments identified the protoporphyrin pocket in FECH as one major drug binding site. Since the genetic loss of FECH activity leads to photosensitivity in humans, our data strongly suggest that FECH inhibition by kinase inhibitors is the molecular mechanism triggering photosensitivity in patients. We therefore suggest that a FECH assay should generally be part of the preclinical molecular toxicology package for the development of kinase inhibitors.
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Affiliation(s)
- Susan Klaeger
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bjoern Gohlke
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Structural
Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
| | | | - Vipul Gupta
- Department
of Nanoparticle Translational Research, Tokyo Medical University, Tokyo, Japan
| | - Stephanie Heinzlmeir
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Helm
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Huichao Qiao
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Hiroshi Handa
- Department
of Nanoparticle Translational Research, Tokyo Medical University, Tokyo, Japan
| | | | | | - Guillaume Médard
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Robert Preissner
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Structural
Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
| | - Bernhard Kuster
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bavarian
Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany
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3231
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Tsolis KC, Bagli E, Kanaki K, Zografou S, Carpentier S, Bei ES, Christoforidis S, Zervakis M, Murphy C, Fotsis T, Economou A. Proteome Changes during Transition from Human Embryonic to Vascular Progenitor Cells. J Proteome Res 2016; 15:1995-2007. [DOI: 10.1021/acs.jproteome.6b00180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Konstantinos C. Tsolis
- Department
of Protein structure and Proteomics Facility, Institute of Molecular Biology and Biotechnology - FORTH, 70013 Iraklio, Crete, Greece
- Department
of Biology, University of Crete, 70013 Iraklio, Crete, Greece
| | - Eleni Bagli
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
| | - Katerina Kanaki
- Department
of Protein structure and Proteomics Facility, Institute of Molecular Biology and Biotechnology - FORTH, 70013 Iraklio, Crete, Greece
| | - Sofia Zografou
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
| | - Sebastien Carpentier
- SYBIOMA, KU Leuven facility for Systems Biology Based Mass Spectrometry, B-3000 Leuven Belgium
| | - Ekaterini S. Bei
- School
of Electronic and Computer Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Savvas Christoforidis
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
- Laboratory
of Biological Chemistry, Medical School, University of Ioannina, 45110 Ioannina, Greece
| | - Michalis Zervakis
- School
of Electronic and Computer Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Carol Murphy
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
- School
of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Theodore Fotsis
- Division
of Biomedical Research, Institute of Molecular Biology and Biotechnology - FORTH, 45110 Ioaninna, Greece
- Laboratory
of Biological Chemistry, Medical School, University of Ioannina, 45110 Ioannina, Greece
- School
of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Anastassios Economou
- Department
of Protein structure and Proteomics Facility, Institute of Molecular Biology and Biotechnology - FORTH, 70013 Iraklio, Crete, Greece
- Department
of Biology, University of Crete, 70013 Iraklio, Crete, Greece
- SYBIOMA, KU Leuven facility for Systems Biology Based Mass Spectrometry, B-3000 Leuven Belgium
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3232
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de Jesus TCL, Nunes VS, Lopes MDC, Martil DE, Iwai LK, Moretti NS, Machado FC, de Lima-Stein ML, Thiemann OH, Elias MC, Janzen C, Schenkman S, da Cunha JPC. Chromatin Proteomics Reveals Variable Histone Modifications during the Life Cycle of Trypanosoma cruzi. J Proteome Res 2016; 15:2039-51. [DOI: 10.1021/acs.jproteome.6b00208] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Teresa Cristina Leandro de Jesus
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
- Departamento
de Física e Informática, Instituto de Física
de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo 13563-120, Brazil
| | - Vinícius Santana Nunes
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Mariana de Camargo Lopes
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Daiana Evelin Martil
- Departamento
de Física e Informática, Instituto de Física
de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo 13563-120, Brazil
| | - Leo Kei Iwai
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Nilmar Silvio Moretti
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Fabrício Castro Machado
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Mariana L. de Lima-Stein
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Otavio Henrique Thiemann
- Departamento
de Física e Informática, Instituto de Física
de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo 13563-120, Brazil
| | - Maria Carolina Elias
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Christian Janzen
- Department
of Cell and Developmental Biology, Theodor-Boveri-Institute at the
Biocenter, University of Würzburg, 97070 Germany
| | - Sergio Schenkman
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
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3233
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Yi Z, Manil-Ségalen M, Sago L, Glatigny A, Redeker V, Legouis R, Mucchielli-Giorgi MH. SAFER, an Analysis Method of Quantitative Proteomic Data, Reveals New Interactors of the C. elegans Autophagic Protein LGG-1. J Proteome Res 2016; 15:1515-23. [PMID: 26999449 DOI: 10.1021/acs.jproteome.5b01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Affinity purifications followed by mass spectrometric analysis are used to identify protein-protein interactions. Because quantitative proteomic data are noisy, it is necessary to develop statistical methods to eliminate false-positives and identify true partners. We present here a novel approach for filtering false interactors, named "SAFER" for mass Spectrometry data Analysis by Filtering of Experimental Replicates, which is based on the reproducibility of the replicates and the fold-change of the protein intensities between bait and control. To identify regulators or targets of autophagy, we characterized the interactors of LGG1, a ubiquitin-like protein involved in autophagosome formation in C. elegans. LGG-1 partners were purified by affinity, analyzed by nanoLC-MS/MS mass spectrometry, and quantified by a label-free proteomic approach based on the mass spectrometric signal intensity of peptide precursor ions. Because the selection of confident interactions depends on the method used for statistical analysis, we compared SAFER with several statistical tests and different scoring algorithms on this set of data. We show that SAFER recovers high-confidence interactors that have been ignored by the other methods and identified new candidates involved in the autophagy process. We further validated our method on a public data set and conclude that SAFER notably improves the identification of protein interactors.
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Affiliation(s)
- Zhou Yi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Marion Manil-Ségalen
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Laila Sago
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.,Service d'Identification et de Caractérisation des Protéines par Spectrométrie de masse (SICaPS), CNRS, 91198 Gif-sur-Yvette, France
| | - Annie Glatigny
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Virginie Redeker
- Service d'Identification et de Caractérisation des Protéines par Spectrométrie de masse (SICaPS), CNRS, 91198 Gif-sur-Yvette, France.,Paris-Saclay Institute of Neuroscience (Neuro-PSI), CNRS, 91198 Gif-sur-Yvette cedex, France
| | - Renaud Legouis
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Marie-Hélène Mucchielli-Giorgi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.,Sorbonne Universités , UPMC Univ Paris 06, UFR927, F-75005, Paris, France
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3234
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Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A. Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches. J Proteome Res 2016; 15:1659-69. [PMID: 27049334 DOI: 10.1021/acs.jproteome.6b00126] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Nucleolin (NCL) is a major component of the cell nucleolus, which has the ability to rapidly shuttle to several other cells' compartments. NCL plays important roles in a variety of essential functions, among which are ribosome biogenesis, gene expression, and cell growth. However, the precise mechanisms underlying NCL functions are still unclear. Our study aimed to provide new information on NCL functions via the identification of its nuclear interacting partners. Using an interactomics approach, we identified 140 proteins co-purified with NCL, among which 100 of them were specifically found to be associated with NCL after RNase digestion. The functional classification of these proteins confirmed the prominent role of NCL in ribosome biogenesis and additionally revealed the possible involvement of nuclear NCL in several pre-mRNA processing pathways through its interaction with RNA helicases and proteins participating in pre-mRNA splicing, transport, or stability. NCL knockdown experiments revealed that NCL regulates the localization of EXOSC10 and the amount of ZC3HAV1, two components of the RNA exosome, further suggesting its involvement in the control of mRNA stability. Altogether, this study describes the first nuclear interactome of human NCL and provides the basis for further understanding the mechanisms underlying the essential functions of this nucleolar protein.
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Affiliation(s)
- Anna Salvetti
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308 , 69007 Lyon, France
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
- Labex Ecofect Université de Lyon , 69007 Lyon, France
| | - Yohann Couté
- Université Grenoble Alpes , 38000 Grenoble, France
- CEA, BIG-BGE , 38000 Grenoble, France
- INSERM, BGE , 38000 Grenoble, France
| | - Alberto Epstein
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308 , 69007 Lyon, France
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
- Labex Ecofect Université de Lyon , 69007 Lyon, France
| | - Loredana Arata
- Subdepartment of Molecular Genetics, Public Health Institute of Chile , Santiago, Chile
| | - Alexandra Kraut
- Université Grenoble Alpes , 38000 Grenoble, France
- CEA, BIG-BGE , 38000 Grenoble, France
- INSERM, BGE , 38000 Grenoble, France
| | - Vincent Navratil
- Pôle Rhône Alpes de Bioinformatique (PRABI), Université Lyon 1 , 69100 Villeurbanne, France
| | - Philippe Bouvet
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
- Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR5286 , 69003 Lyon, France
| | - Anna Greco
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308 , 69007 Lyon, France
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
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3235
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Huang H, Lai W, Cui M, Liang L, Lin Y, Fang Q, Liu Y, Xie L. An Evaluation of Blood Compatibility of Silver Nanoparticles. Sci Rep 2016; 6:25518. [PMID: 27145858 PMCID: PMC4857076 DOI: 10.1038/srep25518] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/15/2016] [Indexed: 12/12/2022] Open
Abstract
Silver nanoparticles (AgNPs) have tremendous potentials in medical devices due to their excellent antimicrobial properties. Blood compatibility should be investigated for AgNPs due to the potential blood contact. However, so far, most studies are not systematic and have not provided insights into the mechanisms for blood compatibility of AgNPs. In this study, we have investigated the blood biological effects, including hemolysis, lymphocyte proliferation, platelet aggregation, coagulation and complement activation, of 20 nm AgNPs with two different surface coatings (polyvinyl pyrrolidone and citrate). Our results have revealed AgNPs could elicit hemolysis and severely impact the proliferation and viability of lymphocytes at all investigated concentrations (10, 20, 40 μg/mL). Nevertheless, AgNPs didn't show any effect on platelet aggregation, coagulation process, or complement activation at up to ~40 μg/mL. Proteomic analysis on AgNPs plasma proteins corona has revealed that acidic and small molecular weight blood plasma proteins were preferentially adsorbed onto AgNPs, and these include some important proteins relevant to hemostasis, coagulation, platelet, complement activation and immune responses. The predicted biological effects of AgNPs by proteomic analysis are mostly consistent with our experimental data since there were few C3 components on AgNPs and more negative than positive factors involving platelet aggregation and thrombosis.
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Affiliation(s)
- He Huang
- Key Laboratory of Standardization and Measurement for Nanotechnology of Chinese Academy of Sciences, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Wenjia Lai
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety of Chinese Academy of Sciences, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Menghua Cui
- Key Laboratory of Standardization and Measurement for Nanotechnology of Chinese Academy of Sciences, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Ling Liang
- Key Laboratory of Standardization and Measurement for Nanotechnology of Chinese Academy of Sciences, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, P. R. China
| | - Yuchen Lin
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety of Chinese Academy of Sciences, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Qiaojun Fang
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety of Chinese Academy of Sciences, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Ying Liu
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety of Chinese Academy of Sciences, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Liming Xie
- Key Laboratory of Standardization and Measurement for Nanotechnology of Chinese Academy of Sciences, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
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3236
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Wu J, Qin H, Li T, Cheng K, Dong J, Tian M, Chai N, Guo H, Li J, You X, Dong M, Ye M, Nie Y, Zou H, Fan D. Characterization of site-specific glycosylation of secreted proteins associated with multi-drug resistance of gastric cancer. Oncotarget 2016; 7:25315-27. [PMID: 27015365 PMCID: PMC5041906 DOI: 10.18632/oncotarget.8287] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/06/2016] [Indexed: 01/14/2023] Open
Abstract
Multi-drug resistance (MDR) remains a great obstacle to effective chemotherapy for gastric cancer. A number of secreted glycoproteins have been reported to be involved in the development of MDR in gastric cancer. However, whether glycosylation of secreted glycoproteins changes during MDR of gastric cancer is unclear. Our present work manifested that N-glycosites and site-specific glycoforms of secreted proteins in drug-resistant cell lines were distinctly different from those in the parental cell line for the first time. Further characterization highlighted the significance of some aberrantly glycosylated secretory proteins in MDR, suggesting that manipulating the glycosylation of specific glycoproteins could be a potential target for overcoming multi-drug resistance in gastric cancer.
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Affiliation(s)
- Jian Wu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Hongqiang Qin
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ting Li
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Kai Cheng
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jiaqiang Dong
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Miaomiao Tian
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Na Chai
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Hao Guo
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Jinjing Li
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Xin You
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingming Dong
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingliang Ye
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Hanfa Zou
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
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3237
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Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M. In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics. Mol Cell Proteomics 2016; 15:1642-57. [PMID: 26912668 PMCID: PMC4858945 DOI: 10.1074/mcp.m115.053975] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 02/24/2016] [Indexed: 01/20/2023] Open
Abstract
Studying protein interactions in whole organisms is fundamental to understanding development. Here, we combine in vivo expressed GFP-tagged proteins with quantitative proteomics to identify protein-protein interactions of selected key proteins involved in early C. elegans embryogenesis. Co-affinity purification of interaction partners for eight bait proteins resulted in a pilot in vivo interaction map of proteins with a focus on early development. Our network reflects known biology and is highly enriched in functionally relevant interactions. To demonstrate the utility of the map, we looked for new regulators of P granule dynamics and found that GEI-12, a novel binding partner of the DYRK family kinase MBK-2, is a key regulator of P granule formation and germline maintenance. Our data corroborate a recently proposed model in which the phosphorylation state of GEI-12 controls P granule dynamics. In addition, we find that GEI-12 also induces granule formation in mammalian cells, suggesting a common regulatory mechanism in worms and humans. Our results show that in vivo interaction proteomics provides unique insights into animal development.
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Affiliation(s)
- Jia-Xuan Chen
- From the ‡Max Delbrück Center for Molecular Medicine, D-13092 Berlin, Germany; §Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Patricia G Cipriani
- §Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003; ¶New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Desirea Mecenas
- §Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Jolanta Polanowska
- §Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003; ‖INSERM, U1104, 13288 Marseille, France
| | - Fabio Piano
- §Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003; ¶New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin C Gunsalus
- §Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003; ¶New York University Abu Dhabi, Abu Dhabi, United Arab Emirates;
| | - Matthias Selbach
- From the ‡Max Delbrück Center for Molecular Medicine, D-13092 Berlin, Germany; **Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.
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3238
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Comprehensive Identification of Immunodominant Proteins of Brucella abortus and Brucella melitensis Using Antibodies in the Sera from Naturally Infected Hosts. Int J Mol Sci 2016; 17:ijms17050659. [PMID: 27144565 PMCID: PMC4881485 DOI: 10.3390/ijms17050659] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/15/2016] [Accepted: 04/22/2016] [Indexed: 12/20/2022] Open
Abstract
Brucellosis is a debilitating zoonotic disease that affects humans and animals. The diagnosis of brucellosis is challenging, as accurate species level identification is not possible with any of the currently available serology-based diagnostic methods. The present study aimed at identifying Brucella (B.) species-specific proteins from the closely related species B. abortus and B. melitensis using sera collected from naturally infected host species. Unlike earlier reported investigations with either laboratory-grown species or vaccine strains, in the present study, field strains were utilized for analysis. The label-free quantitative proteomic analysis of the naturally isolated strains of these two closely related species revealed 402 differentially expressed proteins, among which 63 and 103 proteins were found exclusively in the whole cell extracts of B. abortus and B. melitensis field strains, respectively. The sera from four different naturally infected host species, i.e., cattle, buffalo, sheep, and goat were applied to identify the immune-binding protein spots present in the whole protein extracts from the isolated B. abortus and B. melitensis field strains and resolved on two-dimensional gel electrophoresis. Comprehensive analysis revealed that 25 proteins of B. abortus and 20 proteins of B. melitensis were distinctly immunoreactive. Dihydrodipicolinate synthase, glyceraldehyde-3-phosphate dehydrogenase and lactate/malate dehydrogenase from B. abortus, amino acid ABC transporter substrate-binding protein from B. melitensis and fumarylacetoacetate hydrolase from both species were reactive with the sera of all the tested naturally infected host species. The identified proteins could be used for the design of serological assays capable of detecting pan-Brucella, B. abortus- and B. melitensis-specific antibodies.
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3239
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Peuchen EH, Sun L, Dovichi NJ. Optimization and comparison of bottom-up proteomic sample preparation for early-stage Xenopus laevis embryos. Anal Bioanal Chem 2016; 408:4743-9. [PMID: 27137514 DOI: 10.1007/s00216-016-9564-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/22/2016] [Accepted: 04/14/2016] [Indexed: 01/21/2023]
Abstract
Xenopus laevis is an important model organism in developmental biology. While there is a large literature on changes in the organism's transcriptome during development, the study of its proteome is at an embryonic state. Several papers have been published recently that characterize the proteome of X. laevis eggs and early-stage embryos; however, proteomic sample preparation optimizations have not been reported. Sample preparation is challenging because a large fraction (~90 % by weight) of the egg or early-stage embryo is yolk. We compared three common protein extraction buffer systems, mammalian Cell-PE LB(TM) lysing buffer (NP40), sodium dodecyl sulfate (SDS), and 8 M urea, in terms of protein extraction efficiency and protein identifications. SDS extracts contained the highest concentration of proteins, but this extract was dominated by a high concentration of yolk proteins. In contrast, NP40 extracts contained ~30 % of the protein concentration as SDS extracts, but excelled in discriminating against yolk proteins, which resulted in more protein and peptide identifications. We then compared digestion methods using both SDS and NP40 extraction methods with one-dimensional reverse-phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS). NP40 coupled to a filter-aided sample preparation (FASP) procedure produced nearly twice the number of protein and peptide identifications compared to alternatives. When NP40-FASP samples were subjected to two-dimensional RPLC-ESI-MS/MS, a total of 5171 proteins and 38,885 peptides were identified from a single stage of embryos (stage 2), increasing the number of protein identifications by 23 % in comparison to other traditional protein extraction methods.
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Affiliation(s)
| | - Liangliang Sun
- University of Notre Dame, Stepan Chemistry 425, Notre Dame, IN, 46556, USA
| | - Norman J Dovichi
- University of Notre Dame, Stepan Chemistry 425, Notre Dame, IN, 46556, USA.
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3240
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Manakov D, Ujcikova H, Pravenec M, Novotny J. Alterations in the cardiac proteome of the spontaneously hypertensive rat induced by transgenic expression of CD36. J Proteomics 2016; 145:177-186. [PMID: 27132684 DOI: 10.1016/j.jprot.2016.04.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 01/08/2023]
Abstract
Fatty acid translocase (FAT/CD36) plays an important role in fatty acid uptake by different cell types and may also participate in regulation of calcium homeostasis and eicosanoid production. CD36 deficiency or polymorphisms in the CD36 gene are linked to some physiological irregularities. It is known that the expression of FAT/CD36 is aberrant in the spontaneously hypertensive rat (SHR), one of the most widely studied rat strains in cardiovascular research. In this work, we compared the cardiac proteome of SHR and transgenic SHR-Cd36 rats, who carry a copy of the wild type CD36 gene. Protein expression profiling was based on two-dimensional gel electrophoresis (2DE) coupled to tandem mass spectrometry and label-free LC/MS. These two complementary proteomic approaches allowed us to investigate proteome differences in the left and right heart ventricles of SHR and SHR-Cd36 rats. In total, we identified 26 differently expressed myocardial proteins, out of which 18 were found in the right ventricles and 8 in the left ventricles. Besides that, we determined a great number of proteins uniquely expressed either in the left or right ventricles. These data indicate a large qualitative disparity between the left and right ventricles. Genetic manipulations may affect different proteins in both heart ventricles. Biological significance: This is the first report revealing a relatively broad impact of transgenic expression of CD36 on the heart at the proteome level. Comparison of the protein profiles in both the left and right ventricles revealed differences in several proteins involved especially in energy metabolism. The observed downregulation of the respiratory chain enzymes in transgenic SHR-Cd36 rats may suggest a shift in regulation of energy metabolism due to expression of fatty acid translocase FAT/CD36. This study highlights the important role of cardiac tissue proteomic profiling for mapping of proteins which might be altered by targeted genetic manipulations.
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Affiliation(s)
- Dmitry Manakov
- Department of Physiology, Faculty of Science, Charles University in Prague, Czech Republic
| | - Hana Ujcikova
- Department of Physiology, Faculty of Science, Charles University in Prague, Czech Republic; Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Novotny
- Department of Physiology, Faculty of Science, Charles University in Prague, Czech Republic.
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3241
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Pavelek Z, Vyšata O, Tambor V, Pimková K, Vu DL, Kuča K, Šťourač P, Vališ M. Proteomic analysis of cerebrospinal fluid for relapsing-remitting multiple sclerosis and clinically isolated syndrome. Biomed Rep 2016; 5:35-40. [PMID: 27347402 PMCID: PMC4906564 DOI: 10.3892/br.2016.668] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/25/2016] [Indexed: 01/21/2023] Open
Abstract
Early diagnosis and treatment of multiple sclerosis (MS) in the initial stages of the disease can significantly retard its progression. The aim of the present study was to identify changes in the cerebrospinal fluid proteome in patients with relapsing-remitting MS and clinically isolated MS syndrome who are at high risk of developing MS (case group) compared to healthy population (control) in order to identify potential new markers, which could ultimately aid in early diagnosis of MS. The protein concentrations of each of the 11 case and 15 control samples were determined using a bicinchoninic acid assay. Nanoscale liquid chromatography coupled with tandem mass spectrometry was used for protein identification. Proteomics data were processed using the Perseus software suite and R. The results were filtered using the Benjamini-Hochberg procedure for the false discovery rate (FDR) correction (FDR<0.05). The results showed that, 26 proteins were significantly dysregulated in case samples compared to the controls. Nine proteins were found to be significantly less abundant in case samples, while the abundance of 17 proteins was significantly increased in case samples compared to controls. Three of the proteins were previously linked to RR MS, including immunoglobulin (Ig) γ-1 chain C region, Ig heavy chain V–III region BRO and Ig κ chain C region. Three proteins that were uniquely expressed in patients with RR MS were identified and these proteins may serve as prognostic biomarkers for identifying patients with a high risk of developing RR MS.
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Affiliation(s)
- Zbyšek Pavelek
- Department of Neurology, Faculty of Medicine and University Hospital Hradec Králové, Charles University in Prague, CZ-500 05 Hradec Králové, Czech Republic
| | - Oldřich Vyšata
- Department of Neurology, Faculty of Medicine and University Hospital Hradec Králové, Charles University in Prague, CZ-500 05 Hradec Králové, Czech Republic
| | - Vojtěch Tambor
- Biomedical Research Center, University Hospital Hradec Králové, CZ-500 05 Hradec Králové, Czech Republic
| | - Kristýna Pimková
- Biomedical Research Center, University Hospital Hradec Králové, CZ-500 05 Hradec Králové, Czech Republic
| | - Dai Long Vu
- Biomedical Research Center, University Hospital Hradec Králové, CZ-500 05 Hradec Králové, Czech Republic
| | - Kamil Kuča
- Biomedical Research Center, University Hospital Hradec Králové, CZ-500 05 Hradec Králové, Czech Republic
| | - Pavel Šťourač
- Department of Neurology, Faculty of Medicine and University Hospital Brno, CZ-639 00 Brno, Czech Republic
| | - Martin Vališ
- Department of Neurology, Faculty of Medicine and University Hospital Hradec Králové, Charles University in Prague, CZ-500 05 Hradec Králové, Czech Republic
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3242
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De Marchi T, Braakman RBH, Stingl C, van Duijn MM, Smid M, Foekens JA, Luider TM, Martens JWM, Umar A. The advantage of laser-capture microdissection over whole tissue analysis in proteomic profiling studies. Proteomics 2016; 16:1474-85. [PMID: 27030549 DOI: 10.1002/pmic.201600004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/29/2016] [Accepted: 03/24/2016] [Indexed: 12/29/2022]
Abstract
Laser-capture microdissection (LCM) offers a reliable cell population enrichment tool and has been successfully coupled to MS analysis. Despite this, most proteomic studies employ whole tissue lysate (WTL) analysis in the discovery of disease biomarkers and in profiling analyses. Furthermore, the influence of tissue heterogeneity in WTL analysis, nor its impact in biomarker discovery studies have been completely elucidated. In order to address this, we compared previously obtained high resolution MS data from a cohort of 38 breast cancer tissues, of which both LCM enriched tumor epithelial cells and WTL samples were analyzed. Label-free quantification (LFQ) analysis through MaxQuant software showed a significantly higher number of identified and quantified proteins in LCM enriched samples (3404) compared to WTLs (2837). Furthermore, WTL samples displayed a higher amount of missing data compared to LCM both at peptide and protein levels (p-value < 0.001). 2D analysis on co-expressed proteins revealed discrepant expression of immune system and lipid metabolisms related proteins between LCM and WTL samples. We hereby show that LCM better dissected the biology of breast tumor epithelial cells, possibly due to lower interference from surrounding tissues and highly abundant proteins. All data have been deposited in the ProteomeXchange with the dataset identifier PXD002381 (http://proteomecentral.proteomexchange.org/dataset/PXD002381).
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Affiliation(s)
- Tommaso De Marchi
- Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rene B H Braakman
- Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,TNO-Rijswijk, CBRN Protection, Rijswijk, The Netherlands
| | - Christoph Stingl
- Department of Neurology, Erasmus University Medical Center Rotterdam, The Netherlands
| | - Martijn M van Duijn
- Department of Neurology, Erasmus University Medical Center Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A Foekens
- Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus University Medical Center Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Cancer Genomics, Netherlands
| | - Arzu Umar
- Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
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3243
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Aretz I, Meierhofer D. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology. Int J Mol Sci 2016; 17:ijms17050632. [PMID: 27128910 PMCID: PMC4881458 DOI: 10.3390/ijms17050632] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/22/2022] Open
Abstract
Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.
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Affiliation(s)
- Ina Aretz
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
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3244
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Yu C, Yang Y, Wang X, Guan S, Fang L, Liu F, Walters KJ, Kaiser P, Huang L. Characterization of Dynamic UbR-Proteasome Subcomplexes by In vivo Cross-linking (X) Assisted Bimolecular Tandem Affinity Purification (XBAP) and Label-free Quantitation. Mol Cell Proteomics 2016; 15:2279-92. [PMID: 27114451 DOI: 10.1074/mcp.m116.058271] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 12/14/2022] Open
Abstract
Proteasomes are protein degradation machines that exist in cells as heterogeneous and dynamic populations. A group of proteins function as ubiquitin receptors (UbRs) that can recognize and deliver ubiquitinated substrates to proteasome complexes for degradation. Defining composition of proteasome complexes engaged with UbRs is critical to understand proteasome function. However, because of the dynamic nature of UbR interactions with the proteasome, it remains technically challenging to capture and isolate UbR-proteasome subcomplexes using conventional purification strategies. As a result, distinguishing the molecular differences among these subcomplexes remains elusive. We have developed a novel affinity purification strategy, in vivo cross-linking (X) assisted bimolecular tandem affinity purification strategy (XBAP), to effectively isolate dynamic UbR-proteasome subcomplexes and define their subunit compositions using label-free quantitative mass spectrometry. In this work, we have analyzed seven distinctive UbR-proteasome complexes and found that all of them contain the same type of the 26S holocomplex. However, selected UbRs interact with a group of proteasome interacting proteins that may link each UbR to specific cellular pathways. The compositional similarities and differences among the seven UbR-proteasome subcomplexes have provided new insights on functional entities of proteasomal degradation machineries. The strategy described here represents a general and useful proteomic tool for isolating and studying dynamic and heterogeneous protein subcomplexes in cells that have not been fully characterized.
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Affiliation(s)
- Clinton Yu
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Yingying Yang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Xiaorong Wang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Shenheng Guan
- §Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Lei Fang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Fen Liu
- ¶Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
| | - Kylie J Walters
- ¶Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
| | - Peter Kaiser
- ‖Department of Biological Chemistry, University of California, Irvine, California 92697
| | - Lan Huang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697;
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3245
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Grassl N, Kulak NA, Pichler G, Geyer PE, Jung J, Schubert S, Sinitcyn P, Cox J, Mann M. Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome. Genome Med 2016; 8:44. [PMID: 27102203 PMCID: PMC4841045 DOI: 10.1186/s13073-016-0293-0] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/24/2016] [Indexed: 12/21/2022] Open
Abstract
Background The oral cavity is home to one of the most diverse microbial communities of the human body and a major entry portal for pathogens. Its homeostasis is maintained by saliva, which fulfills key functions including lubrication of food, pre-digestion, and bacterial defense. Consequently, disruptions in saliva secretion and changes in the oral microbiome contribute to conditions such as tooth decay and respiratory tract infections. Here we set out to quantitatively map the saliva proteome in great depth with a rapid and in-depth mass spectrometry-based proteomics workflow. Methods We used recent improvements in mass spectrometry (MS)-based proteomics to develop a rapid workflow for mapping the saliva proteome quantitatively and at great depth. Standard clinical cotton swabs were used to collect saliva form eight healthy individuals at two different time points, allowing us to study inter-individual differences and interday changes of the saliva proteome. To accurately identify microbial proteins, we developed a method called “split by taxonomy id” that prevents peptides shared by humans and bacteria or between different bacterial phyla to contribute to protein identification. Results Microgram protein amounts retrieved from cotton swabs resulted in more than 3700 quantified human proteins in 100-min gradients or 5500 proteins after simple fractionation. Remarkably, our measurements also quantified more than 2000 microbial proteins from 50 bacterial genera. Co-analysis of the proteomics results with next-generation sequencing data from the Human Microbiome Project as well as a comparison to MALDI-TOF mass spectrometry on microbial cultures revealed strong agreement. The oral microbiome differs between individuals and changes drastically upon eating and tooth brushing. Conclusion Rapid shotgun and robust technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid and is therefore a valuable complement to genomic studies. This opens new frontiers for the study of host–pathogen interactions and clinical saliva diagnostics. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0293-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Niklas Grassl
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany
| | - Nils Alexander Kulak
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.,PreOmics GmbH, Am Klopferspitz 19, D-82152, Martinsried, Germany
| | - Garwin Pichler
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.,PreOmics GmbH, Am Klopferspitz 19, D-82152, Martinsried, Germany
| | - Philipp Emanuel Geyer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark
| | - Jette Jung
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Marchioninistr. 17, D-81377, München, Germany
| | - Sören Schubert
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Marchioninistr. 17, D-81377, München, Germany
| | - Pavel Sinitcyn
- Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany
| | - Juergen Cox
- Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany. .,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark.
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3246
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Chen W, Wang S, Adhikari S, Deng Z, Wang L, Chen L, Ke M, Yang P, Tian R. Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling. Anal Chem 2016; 88:4864-71. [PMID: 27062885 DOI: 10.1021/acs.analchem.6b00631] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Great efforts have been taken for developing high-sensitive mass spectrometry (MS)-based proteomic technologies, among which sample preparation is one of the major focus. Here, a simple and integrated spintip-based proteomics technology (SISPROT) consisting of strong cation exchange beads and C18 disk in one pipet tip was developed. Both proteomics sample preparation steps, including protein preconcentration, reduction, alkylation, and digestion, and reversed phase (RP)-based desalting and high-pH RP-based peptide fractionation can be achieved in a fully integrated manner for the first time. This easy-to-use technology achieved high sensitivity with negligible sample loss. Proteomic analysis of 2000 HEK 293 cells readily identified 1270 proteins within 1.4 h of MS time, while 7826 proteins were identified when 100000 cells were processed and analyzed within only 22 h of MS time. More importantly, the SISPROT can be easily multiplexed on a standard centrifuge with good reproducibility (Pearson correlation coefficient > 0.98) for both single-shot analysis and deep proteome profiling with five-step high-pH RP fractionation. The SISPROT was exemplified by the triplicate analysis of 100000 stem cells from human exfoliated deciduous teeth (SHED). This led to the identification of 9078 proteins containing 3771 annotated membrane proteins, which was the largest proteome data set for dental stem cells reported to date. We expect that the SISPROT will be well suited for deep proteome profiling for fewer than 100000 cells and applied for translational studies where multiplexed technology with good label-free quantification precision is required.
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Affiliation(s)
- Wendong Chen
- Department of Chemistry, Fudan University , Shanghai 200433, China
| | - Shuai Wang
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | - Zuhui Deng
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | | | | | - Pengyuan Yang
- Department of Chemistry, Fudan University , Shanghai 200433, China
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3247
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Riis S, Stensballe A, Emmersen J, Pennisi CP, Birkelund S, Zachar V, Fink T. Mass spectrometry analysis of adipose-derived stem cells reveals a significant effect of hypoxia on pathways regulating extracellular matrix. Stem Cell Res Ther 2016; 7:52. [PMID: 27075204 PMCID: PMC4831147 DOI: 10.1186/s13287-016-0310-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/09/2016] [Accepted: 03/31/2016] [Indexed: 12/21/2022] Open
Abstract
Background Adipose-derived stem cells (ASCs) are being increasingly recognized for their potential to promote tissue regeneration and wound healing. These effects appear to be partly mediated by paracrine signaling pathways, and are enhanced during hypoxia. Mass spectrometry (MS) is a valuable tool for proteomic profiling of cultured ASCs, which may help to reveal the identity of the factors secreted by the cells under different conditions. However, serum starvation which is essentially required to obtain samples compatible with secretome analysis by MS can have a significant influence on ASCs. Here, we present a novel and optimized culturing approach based on the use of a clinically relevant serum-free formulation, which was used to assess the effects of hypoxia on the ASC proteomic profile. Methods Human ASCs from three human donors were expanded in StemPro® MSC SFM XenoFree medium. Cells were cultured for 24 h in serum- and albumin-free supplements in either normoxic (20 %) or hypoxic (1 %) atmospheres, after which the cells and conditioned medium were collected, subfractionated, and analyzed using MS. Prior to analysis, the secreted proteins were further subdivided into a secretome (>30 kDa) and a peptidome (3–30 kDa) fraction. Results MS analysis revealed the presence of 342, 98, and 3228 proteins in the normoxic ASC secretome, peptidome, and proteome, respectively. A relatively small fraction of the proteome (9.6 %) was significantly affected by hypoxia, and the most regulated proteins were those involved in extracellular matrix (ECM) synthesis and cell metabolism. No proteins were found to be significantly modulated by hypoxic treatment across all cultures for the secretome and peptidome samples. Conclusions This study highlights ECM remodeling as a significant mechanism contributing to the ASC regenerative effect after hypoxic preconditioning, and further underscores considerable inter-individual differences in ASC response to hypoxia. The novel culture paradigm provides a basis for future proteomic studies under conditions that do not induce a stress response, so that the best responders can be accurately identified for prospective therapeutic use. Data are available via ProteomeXchange with identifier PXD003550. Electronic supplementary material The online version of this article (doi:10.1186/s13287-016-0310-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simone Riis
- Department of Health Science and Technology, Laboratory for Stem Cell Research, Aalborg University, Fredrik Bajers Vej 3B, Aalborg, 9220, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Laboratory for Medical Mass Spectrometry, Aalborg University, Aalborg, Denmark
| | - Jeppe Emmersen
- Department of Health Science and Technology, Laboratory for Stem Cell Research, Aalborg University, Fredrik Bajers Vej 3B, Aalborg, 9220, Denmark
| | - Cristian Pablo Pennisi
- Department of Health Science and Technology, Laboratory for Stem Cell Research, Aalborg University, Fredrik Bajers Vej 3B, Aalborg, 9220, Denmark
| | - Svend Birkelund
- Department of Health Science and Technology, Laboratory for Medical Mass Spectrometry, Aalborg University, Aalborg, Denmark
| | - Vladimir Zachar
- Department of Health Science and Technology, Laboratory for Stem Cell Research, Aalborg University, Fredrik Bajers Vej 3B, Aalborg, 9220, Denmark
| | - Trine Fink
- Department of Health Science and Technology, Laboratory for Stem Cell Research, Aalborg University, Fredrik Bajers Vej 3B, Aalborg, 9220, Denmark.
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3248
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Kovalchuk SI, Ziganshin RH, Starkov VG, Tsetlin VI, Utkin YN. Quantitative Proteomic Analysis of Venoms from Russian Vipers of Pelias Group: Phospholipases A₂ are the Main Venom Components. Toxins (Basel) 2016; 8:105. [PMID: 27077884 PMCID: PMC4848631 DOI: 10.3390/toxins8040105] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/28/2016] [Accepted: 04/05/2016] [Indexed: 02/06/2023] Open
Abstract
Venoms of most Russian viper species are poorly characterized. Here, by quantitative chromato-mass-spectrometry, we analyzed protein and peptide compositions of venoms from four Vipera species (V. kaznakovi, V. renardi, V. orlovi and V. nikolskii) inhabiting different regions of Russia. In all these species, the main components were phospholipases A2, their content ranging from 24% in V. orlovi to 65% in V. nikolskii. Altogether, enzyme content in venom of V. nikolskii reached ~85%. Among the non-enzymatic proteins, the most abundant were disintegrins (14%) in the V. renardi venom, C-type lectin like (12.5%) in V. kaznakovi, cysteine-rich venom proteins (12%) in V. orlovi and venom endothelial growth factors (8%) in V. nikolskii. In total, 210 proteins and 512 endogenous peptides were identified in the four viper venoms. They represented 14 snake venom protein families, most of which were found in the venoms of Vipera snakes previously. However, phospholipase B and nucleotide degrading enzymes were reported here for the first time. Compositions of V. kaznakovi and V. orlovi venoms were described for the first time and showed the greatest similarity among the four venoms studied, which probably reflected close relationship between these species within the “kaznakovi” complex.
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Affiliation(s)
- Sergey I Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
| | - Vladislav G Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
| | - Yuri N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
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3249
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Sindlinger J, Bierlmeier J, Geiger LC, Kramer K, Finkemeier I, Schwarzer D. Probing the structure-activity relationship of endogenous histone deacetylase complexes with immobilized peptide-inhibitors. J Pept Sci 2016; 22:352-9. [PMID: 27071932 DOI: 10.1002/psc.2875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/12/2016] [Accepted: 02/19/2016] [Indexed: 12/31/2022]
Abstract
Histone deacetylases (HDACs) are key regulators of numerous cellular proteins by removing acetylation marks from modified lysine residues. Peptide-based HDAC probes containing α-aminosuberic acid ω-hydroxamate have been established as useful tools for investigating substrate selectivity and composition of endogenous HDAC complexes in cellular lysates. Here we report a structure-activity study of potential HDAC-probes containing derivatives of the hydroxamate moieties. While most of these probes did not recruit significant amounts of endogenous HDACs from cellular lysates, peptides containing Nε-acetyl-Nε-hydroxy-L-lysine served as HDAC probe. The recruitment efficiency varied between HDACs and was generally lower than that of α-aminosuberic acid ω-hydroxamate probes, but showed a similar global interaction profile. These findings indicate that Nε-acetyl-Nε-hydroxy-L-lysine might be a useful tool for investigations on HDAC complexes and the development of HDAC inhibitors. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Julia Sindlinger
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, D-72076, Tübingen, Germany
| | - Jan Bierlmeier
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, D-72076, Tübingen, Germany
| | - Lydia-Christina Geiger
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, D-72076, Tübingen, Germany
| | - Katharina Kramer
- Plant Proteomics, Max Planck-Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany
| | - Iris Finkemeier
- Plant Proteomics, Max Planck-Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany.,Institute for Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, 48149, Muenster, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, D-72076, Tübingen, Germany
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3250
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Hoernstein SNW, Mueller SJ, Fiedler K, Schuelke M, Vanselow JT, Schuessele C, Lang D, Nitschke R, Igloi GL, Schlosser A, Reski R. Identification of Targets and Interaction Partners of Arginyl-tRNA Protein Transferase in the Moss Physcomitrella patens. Mol Cell Proteomics 2016; 15:1808-22. [PMID: 27067052 DOI: 10.1074/mcp.m115.057190] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Indexed: 12/15/2022] Open
Abstract
Protein arginylation is a posttranslational modification of both N-terminal amino acids of proteins and sidechain carboxylates and can be crucial for viability and physiology in higher eukaryotes. The lack of arginylation causes severe developmental defects in moss, affects the low oxygen response in Arabidopsis thaliana and is embryo lethal in Drosophila and in mice. Although several studies investigated impact and function of the responsible enzyme, the arginyl-tRNA protein transferase (ATE) in plants, identification of arginylated proteins by mass spectrometry was not hitherto achieved. In the present study, we report the identification of targets and interaction partners of ATE in the model plant Physcomitrella patens by mass spectrometry, employing two different immuno-affinity strategies and a recently established transgenic ATE:GUS reporter line (Schuessele et al., 2016 New Phytol. , DOI: 10.1111/nph.13656). Here we use a commercially available antibody against the fused reporter protein (β-glucuronidase) to pull down ATE and its interacting proteins and validate its in vivo interaction with a class I small heatshock protein via Förster resonance energy transfer (FRET). Additionally, we apply and modify a method that already successfully identified arginylated proteins from mouse proteomes by using custom-made antibodies specific for N-terminal arginine. As a result, we identify four arginylated proteins from Physcomitrella patens with high confidence.Data are available via ProteomeXchange with identifier PXD003228 and PXD003232.
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Affiliation(s)
- Sebastian N W Hoernstein
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Stefanie J Mueller
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Kathrin Fiedler
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Marc Schuelke
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Jens T Vanselow
- §Rudolf Virchow Center for Experimental Biomedicine, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Christian Schuessele
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Daniel Lang
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Roland Nitschke
- ¶ZBSA - Centre for Biological Systems Analysis, Life Imaging Center, University Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany; ‡‡BIOSS - Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - Gabor L Igloi
- ‖Institute of Biology 3, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Andreas Schlosser
- §Rudolf Virchow Center for Experimental Biomedicine, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Ralf Reski
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany; ¶ZBSA - Centre for Biological Systems Analysis, Life Imaging Center, University Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany; **FRIAS - Freiburg Institute for Advanced Studies, 79104 Freiburg, Germany; ‡‡BIOSS - Centre for Biological Signalling Studies, 79104 Freiburg, Germany
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