101
|
Young AI, Timpson P, Gallego-Ortega D, Ormandy CJ, Oakes SR. Myeloid cell leukemia 1 (MCL-1), an unexpected modulator of protein kinase signaling during invasion. Cell Adh Migr 2017; 12:513-523. [PMID: 29166822 PMCID: PMC6363037 DOI: 10.1080/19336918.2017.1393591] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Myeloid cell leukemia-1 (MCL-1), closely related to B-cell lymphoma 2 (BCL-2), has a well-established role in cell survival and has emerged as an important target for cancer therapeutics. We have demonstrated that inhibiting MCL-1 is efficacious in suppressing tumour progression in pre-clinical models of breast cancer and revealed that in addition to its role in cell survival, MCL-1 modulated cellular invasion. Utilizing a MCL-1-specific genetic antagonist, we found two possible mechanisms; firstly MCL-1 directly binds to and alters the phosphorylation of the cytoskeletal remodeling protein, Cofilin, a protein important for cytoskeletal remodeling during invasion, and secondly MCL-1 modulates the levels SRC family kinases (SFKs) and their targets. These data provide evidence that MCL-1 activities are not limited to endpoints of extracellular and intracellular signaling culminating in cell survival as previously thought, but can directly modulate the output of SRC family kinases signaling during cellular invasion. Here we review the pleotropic roles of MCL-1 and discuss the implications of this newly discovered effect on protein kinase signaling for the development of cancer therapeutics.
Collapse
Affiliation(s)
- Adelaide Ij Young
- a Cancer Research Division , Garvan Institute of Medical Research and the Kinghorn Cancer Centre , 384 Victoria Street, Darlinghurst , NSW , Australia
| | - Paul Timpson
- a Cancer Research Division , Garvan Institute of Medical Research and the Kinghorn Cancer Centre , 384 Victoria Street, Darlinghurst , NSW , Australia.,b St. Vincent's Clinical School, UNSW Medicine , Victoria Street, Darlinghurst , NSW , Australia
| | - David Gallego-Ortega
- a Cancer Research Division , Garvan Institute of Medical Research and the Kinghorn Cancer Centre , 384 Victoria Street, Darlinghurst , NSW , Australia.,b St. Vincent's Clinical School, UNSW Medicine , Victoria Street, Darlinghurst , NSW , Australia
| | - Christopher J Ormandy
- a Cancer Research Division , Garvan Institute of Medical Research and the Kinghorn Cancer Centre , 384 Victoria Street, Darlinghurst , NSW , Australia.,b St. Vincent's Clinical School, UNSW Medicine , Victoria Street, Darlinghurst , NSW , Australia
| | - Samantha R Oakes
- a Cancer Research Division , Garvan Institute of Medical Research and the Kinghorn Cancer Centre , 384 Victoria Street, Darlinghurst , NSW , Australia.,b St. Vincent's Clinical School, UNSW Medicine , Victoria Street, Darlinghurst , NSW , Australia
| |
Collapse
|
102
|
Dutta SM, Hadley MM, Peterman S, Jewell JS, Duncan VD, Britten RA. Quantitative Proteomic Analysis of the Hippocampus of Rats with GCR-Induced Spatial Memory Impairment. Radiat Res 2017; 189:136-145. [PMID: 29206597 DOI: 10.1667/rr14822.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
NASA is planning future missions to Mars, which will result in astronauts being exposed to ∼13 cGy/year of galactic cosmic radiation (GCR). Previous ground-based experiments have demonstrated that low (15 cGy) doses of 1 GeV/n 56Fe ions impair hippocampus-dependent spatial memory in rats. However, some irradiated rats maintain a spatial memory performance comparable to that seen in the sham-irradiated rats, suggesting that some of these animals are able to ameliorate the deleterious effects of the GCR, while others are not. This rat model provides a unique opportunity to increase our understanding of how GCR affects neurophysiology, what adaptive responses can be invoked to prevent the emergence of GCR-induced spatial memory impairment, as well as the pathways that are altered when spatial memory impairment occurs. A label-free, unbiased proteomic profiling approach involving quantitative protein/peptide profiling followed by Cytoscape analysis has established the composition of the hippocampal proteome in male Wistar rats after exposure to 15 cGy of 1 GeV/n 56Fe, and identified proteins whose expression is altered with respect to: 1. radiation exposure and 2. impaired spatial memory performance. We identified 30 proteins that were classified as "GCR exposure marker" (GEM) proteins (expressed solely or at higher levels in the irradiated rats but not related to spatial memory performance), most notably CD98, Cadps and GMFB. Conversely, there were 252 proteins that were detected only in the sham-irradiated samples, i.e., they were not detected in either of the irradiated cohorts; of these 10% have well-documented roles in neurotransmission. The second aspect of our data mining was to identify proteins whose expression was associated with either impaired or functional spatial memory. While there are multiple changes in the hippocampal proteome in the irradiated rats that have impaired spatial memory performance, with 203 proteins being detected (or upregulated) only in these rats, it would appear that spatial memory impairment may also arise from an inability of these rats to express "good spatial memory" (GSM) proteins, many of which play an important role in neuronal homeostasis and function, axonogenesis, presynaptic membrane organization and G-protein coupled receptor (GCPR) signaling. It may be possible to use this knowledge to develop two alternative countermeasure strategies, one that preserves critical pathways prophylactically and one that invokes restorative pathways after GCR exposure.
Collapse
Affiliation(s)
- Sucharita M Dutta
- a Leroy T. Canoles Jr. Cancer Research Center and.,b Departments of Microbiology and Molecular Cell Biology and
| | - Melissa M Hadley
- c Radiation Oncology, Eastern Virginia Medical School, Norfolk, Virginia 23507; and
| | - Scott Peterman
- d BRIMS, Thermo Fisher Scientific, Cambridge, Massachusetts 02139
| | - Jessica S Jewell
- c Radiation Oncology, Eastern Virginia Medical School, Norfolk, Virginia 23507; and
| | - Vania D Duncan
- c Radiation Oncology, Eastern Virginia Medical School, Norfolk, Virginia 23507; and
| | - Richard A Britten
- a Leroy T. Canoles Jr. Cancer Research Center and.,b Departments of Microbiology and Molecular Cell Biology and.,c Radiation Oncology, Eastern Virginia Medical School, Norfolk, Virginia 23507; and
| |
Collapse
|
103
|
Hosp F, Mann M. A Primer on Concepts and Applications of Proteomics in Neuroscience. Neuron 2017; 96:558-571. [DOI: 10.1016/j.neuron.2017.09.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/29/2017] [Accepted: 09/14/2017] [Indexed: 02/06/2023]
|
104
|
Tanimura S, Takeda K. ERK signalling as a regulator of cell motility. J Biochem 2017; 162:145-154. [PMID: 28903547 DOI: 10.1093/jb/mvx048] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/17/2017] [Indexed: 01/21/2023] Open
Abstract
Cell motility is regulated by multiple processes, including cell protrusion, cell retraction, cell-matrix adhesion, polarized exocytosis and polarized vesicle trafficking, each of which is spatiotemporally controlled by various intracellular signalling pathways. Dysregulation of cell motility leads to pathological conditions, such as tumour invasion and metastasis. Accumulating evidence has revealed that extracellular signal-regulated kinase (ERK) signalling is one of the critical regulators of cell motility, although it is classically known as an important regulator of cell proliferation, differentiation and survival through regulation of gene expression. ERK and its downstream kinase, p90 ribosomal S6 kinase (RSK), dynamically regulate cell motility mainly through direct phosphorylation of various molecules that are not necessarily involved in the regulation of gene transcription and translation. In this review, we summarize how ERK signalling regulates cell motility by focusing on the components of the cell motility machinery that are directly regulated by ERK or RSK.
Collapse
Affiliation(s)
- Susumu Tanimura
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kohsuke Takeda
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| |
Collapse
|
105
|
Ishii K, Zhou M, Uchiyama S. Native mass spectrometry for understanding dynamic protein complex. Biochim Biophys Acta Gen Subj 2017; 1862:275-286. [PMID: 28965879 DOI: 10.1016/j.bbagen.2017.09.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/17/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022]
Abstract
Biomolecules have evolved to perform specific and sophisticated activities in a highly coordinated manner organizing into multi-component complexes consisting of proteins, nucleic acids, cofactors or ligands. Understanding such complexes represents a task in earnest for modern bioscience. Traditional structural techniques when extrapolating to macromolecules of ever increasing sizes are confronted with limitations posed by the difficulty in enrichment, solubility, stability as well as lack of homogeneity of these complexes. Alternative approaches are therefore prompted to bridge the gap, one of which is native mass spectrometry. Here we demonstrate the strength of native mass spectrometry, used alone or in combination with other biophysical methods such as analytical ultracentrifugation, small-angle neutron scattering, and small-angle X-ray scattering etc., in addressing dynamic aspects of protein complexes including structural reorganization, subunit exchange, as well as the assembly/disassembly processes in solution that are dictated by transient non-covalent interactions. We review recent studies from our laboratories and others applying native mass spectrometry to both soluble and membrane-embedded assemblies. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
Collapse
Affiliation(s)
- Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China.
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
106
|
Abstract
Cellular signaling, predominantly mediated by phosphorylation through protein kinases, is found to be deregulated in most cancers. Accordingly, protein kinases have been subject to intense investigations in cancer research, to understand their role in oncogenesis and to discover new therapeutic targets. Despite great advances, an understanding of kinase dysfunction in cancer is far from complete.A powerful tool to investigate phosphorylation is mass-spectrometry (MS)-based phosphoproteomics, which enables the identification of thousands of phosphorylated peptides in a single experiment. Since every phosphorylation event results from the activity of a protein kinase, high-coverage phosphoproteomics data should indirectly contain comprehensive information about the activity of protein kinases.In this chapter, we discuss the use of computational methods to predict kinase activity scores from MS-based phosphoproteomics data. We start with a short explanation of the fundamental features of the phosphoproteomics data acquisition process from the perspective of the computational analysis. Next, we briefly review the existing databases with experimentally verified kinase-substrate relationships and present a set of bioinformatic tools to discover novel kinase targets. We then introduce different methods to infer kinase activities from phosphoproteomics data and these kinase-substrate relationships. We illustrate their application with a detailed protocol of one of the methods, KSEA (Kinase Substrate Enrichment Analysis). This method is implemented in Python within the framework of the open-source Kinase Activity Toolbox (kinact), which is freely available at http://github.com/saezlab/kinact/ .
Collapse
Affiliation(s)
- Jakob Wirbel
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, MTZ Pauwelsstrasse 19, D-52074, Aachen, Germany
- Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, 69120, Heidelberg, Germany
| | - Pedro Cutillas
- Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Julio Saez-Rodriguez
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, MTZ Pauwelsstrasse 19, D-52074, Aachen, Germany.
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
| |
Collapse
|
107
|
Sun B, Kovatch JR, Badiong A, Merbouh N. Optimization and Modeling of Quadrupole Orbitrap Parameters for Sensitive Analysis toward Single-Cell Proteomics. J Proteome Res 2017; 16:3711-3721. [PMID: 28825293 DOI: 10.1021/acs.jproteome.7b00416] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Single-cell proteomics represents a field of extremely sensitive proteomic analysis, owing to the minute amount of yet complex proteins in a single cell. Without amplification potential as of nucleic acids, single-cell mass spectrometry (MS) analysis demands special instrumentation running with optimized parameters to maximize the sensitivity and throughput for comprehensive proteomic discovery. To facilitate such analysis, we here investigated two factors critical to peptide sequencing and protein detection in shotgun proteomics, i.e. precursor ion isolation window (IW) and maximum precursor ion injection time (ITmax), on an ultrahigh-field quadrupole Orbitrap (Q-Exactive HF). Counterintuitive to the frequently used proteomic parameters for bulk samples (>100 ng), our experimental data and subsequent modeling suggested a universally optimal IW of 4.0 Th for sample quantity ranging from 100 ng to 1 ng, and a sample-quantity dependent ITmax of more than 250 ms for 1-ng samples. Compared with the benchmark condition of IW = 2.0 Th and ITmax = 50 ms, our optimization generated up to 300% increase to the detected protein groups for 1-ng samples. The additionally identified proteins allowed deeper penetration of proteome for better revealing crucial cellular functions such as signaling and cell adhesion. We hope this effort can prompt single-cell and trace proteomic analysis and enable a rational selection of MS parameters.
Collapse
Affiliation(s)
- Bingyun Sun
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Faculty of Health Science, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada
| | - Jessica Rae Kovatch
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Faculty of Health Science, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada
| | - Albert Badiong
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Faculty of Health Science, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada
| | - Nabyl Merbouh
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Faculty of Health Science, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
108
|
Liu J, Wang Q, Jiang X, Yang H, Zhao D, Han J, Luo Y, Xiang H. Systematic Analysis of Lysine Acetylation in the Halophilic Archaeon Haloferax mediterranei. J Proteome Res 2017; 16:3229-3241. [DOI: 10.1021/acs.jproteome.7b00222] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jingfang Liu
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Wang
- Core Facility of Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiongjian Jiang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College
of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haibo Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College
of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dahe Zhao
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College
of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Han
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanming Luo
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Xiang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College
of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
109
|
Rezeli M, Sjödin K, Lindberg H, Gidlöf O, Lindahl B, Jernberg T, Spaak J, Erlinge D, Marko-Varga G. Quantitation of 87 Proteins by nLC-MRM/MS in Human Plasma: Workflow for Large-Scale Analysis of Biobank Samples. J Proteome Res 2017; 16:3242-3254. [PMID: 28738677 DOI: 10.1021/acs.jproteome.7b00235] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A multiple reaction monitoring (MRM) assay was developed for precise quantitation of 87 plasma proteins including the three isoforms of apolipoprotein E (APOE) associated with cardiovascular diseases using nanoscale liquid chromatography separation and stable isotope dilution strategy. The analytical performance of the assay was evaluated and we found an average technical variation of 4.7% in 4-5 orders of magnitude dynamic range (≈0.2 mg/L to 4.5 g/L) from whole plasma digest. Here, we report a complete workflow, including sample processing adapted to 96-well plate format and normalization strategy for large-scale studies. To further investigate the MS-based quantitation the amount of six selected proteins was measured by routinely used clinical chemistry assays as well and the two methods showed excellent correlation with high significance (p-value < 10e-5) for the six proteins, in addition for the cardiovascular predictor factor, APOB: APOA1 ratio (r = 0.969, p-value < 10e-5). Moreover, we utilized the developed assay for screening of biobank samples from patients with myocardial infarction and performed the comparative analysis of patient groups with STEMI (ST- segment elevation myocardial infarction), NSTEMI (non ST- segment elevation myocardial infarction) and type-2 AMI (type-2 myocardial infarction) patients.
Collapse
Affiliation(s)
- Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University , BMC D13, Lund SE-221 84, Sweden
| | - Karin Sjödin
- Department of Drug Metabolism, H Lundbeck & Co AS , Copenhagen, DK-2500, Denmark
| | - Henrik Lindberg
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University , BMC D13, Lund SE-221 84, Sweden
| | - Olof Gidlöf
- Department of Cardiology, Clinical Sciences, Lund University, Skåne University Hospital , Lund, SE-221 85, Sweden
| | - Bertil Lindahl
- Department of Medical Sciences, Cardiology & Uppsala Clinical Research Center, Uppsala University , Uppsala, SE-751 83, Sweden
| | - Tomas Jernberg
- Department of Clinical Sciences, Danderyd University Hospital, Karolinska Institutet , Stockholm, SE-182 88, Sweden
| | - Jonas Spaak
- Department of Clinical Sciences, Danderyd University Hospital, Karolinska Institutet , Stockholm, SE-182 88, Sweden
| | - David Erlinge
- Department of Cardiology, Clinical Sciences, Lund University, Skåne University Hospital , Lund, SE-221 85, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University , BMC D13, Lund SE-221 84, Sweden
| |
Collapse
|
110
|
Cox RS, McLaughlin JA, Grünberg R, Beal J, Wipat A, Sauro HM. A Visual Language for Protein Design. ACS Synth Biol 2017; 6:1120-1123. [PMID: 28173698 DOI: 10.1021/acssynbio.6b00286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As protein engineering becomes more sophisticated, practitioners increasingly need to share diagrams for communicating protein designs. To this end, we present a draft visual language, Protein Language, that describes the high-level architecture of an engineered protein with easy-to-draw glyphs, intended to be compatible with other biological diagram languages such as SBOL Visual and SBGN. Protein Language consists of glyphs for representing important features (e.g., globular domains, recognition and localization sequences, sites of covalent modification, cleavage and catalysis), rules for composing these glyphs to represent complex architectures, and rules constraining the scaling and styling of diagrams. To support Protein Language we have implemented an extensible web-based software diagram tool, Protein Designer, that uses Protein Language in a "drag and drop" interface for visualization and computer-aided-design of engineered proteins, as well as conversion of annotated protein sequences to Protein Language diagrams and figure export. Protein Designer can be accessed at http://biocad.ncl.ac.uk/protein-designer/ .
Collapse
Affiliation(s)
- Robert Sidney Cox
- Material
Science Institute, University of Oregon, Eugene, Oregon 97403, United States
| | | | - Raik Grünberg
- Computational
Bioscience Research Center, King Abdullah University for Science and Technology, Thuwal 23955, Saudi Arabia
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Anil Wipat
- School
of Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Herbert M. Sauro
- Department
of Bioengineering, University of Washington, Seattle, Washington 98105, United States
| |
Collapse
|
111
|
Mullari M, Lyon D, Jensen LJ, Nielsen ML. Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification. J Proteome Res 2017. [PMID: 28648085 DOI: 10.1021/acs.jproteome.7b00042] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-transcriptional regulation of gene expression, and aberrations in RBP functions have been linked to many diseases, including neurological disorders and cancer. Human cells encode thousands of RNA-binding proteins with unique RNA-binding properties. These properties are regulated through modularity of a large variety of RNA-binding domains, rendering RNA-protein interactions difficult to study. Recently, the introduction of proteomics methods has provided novel insights into RNA-binding proteins at a systems level. However, determining the exact protein sequence regions that interact with RNA remains challenging and laborious, especially considering that many RBPs lack canonical RNA-binding domains. Here we describe a streamlined proteomic workflow called peptide cross-linking and affinity purification (pCLAP) that allows rapid characterization of RNA-binding regions in proteins. pCLAP is based upon the combined use of UV cross-linking and enzymatic digestion of RNA-bound proteins followed by single-shot mass spectrometric analysis. To benchmark our method, we identified the binding regions for polyadenylated RNA-binding proteins in HEK293 cells, allowing us to map the mRNA interaction regions of more than 1000 RBPs with very high reproducibility from replicate single-shot analyses. Our results show specific enrichment of many known RNA-binding regions on many known RNA-binding proteins, confirming the specificity of our approach.
Collapse
Affiliation(s)
- Meeli Mullari
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| | - David Lyon
- Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| | - Michael L Nielsen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark
| |
Collapse
|
112
|
Ahsan N, Belmont J, Chen Z, Clifton JG, Salomon AR. Highly reproducible improved label-free quantitative analysis of cellular phosphoproteome by optimization of LC-MS/MS gradient and analytical column construction. J Proteomics 2017. [PMID: 28634120 DOI: 10.1016/j.jprot.2017.06.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Expanding the sequencing depth of the peptides with a statistically significant quantitative change derived from a biological stimulation is critical. Here we demonstrate that optimization of LC gradient and analytical column construction can reveal over 30,000 unique peptides and 23,000 phosphopeptides at high confidence. The quantitative reproducibility of different analytical workflows was evaluated by comparing the phosphoproteome of CD3/4 stimulated and unstimulated T-cells as a model system. A fritless, 50cm-long column packed with 1.9μm particles operated with a standard pressure HPLC significantly improved the sequencing depth 51% and decreased the selected ion chromatogram peak spreading. Most importantly, under the optimal workflow we observed an improvement of over 300% in detection of significantly changed phosphopeptides in the stimulated cells compared with the other workflows. The discovery power of the optimized column configuration was illustrated by identification of significantly altered phosphopeptides harboring novel sites from proteins previously established as important in T cell signaling including A-Raf, B-Raf, c-Myc, CARMA1, Fyn, ITK, LAT, NFAT1/2/3, PKCα, PLCγ1/2, RAF1, and SOS1. Taken together, our results reveal the analytical power of optimized chromatography using sub 2μm particles for the analysis of the T cell phosphoproteome to reveal a vast landscape of significantly altered phosphorylation changes in response to T cell receptor stimulation.
Collapse
Affiliation(s)
- Nagib Ahsan
- Division of Biology and Medicine, Brown University, Providence, RI 02903, USA; Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI 02903, USA
| | - Judson Belmont
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Zhuo Chen
- Department of Chemistry, Brown University, Providence, RI 02912, USA
| | - James G Clifton
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown, University, Providence, RI 02912, USA
| | - Arthur R Salomon
- Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI 02903, USA; Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA; Department of Chemistry, Brown University, Providence, RI 02912, USA.
| |
Collapse
|
113
|
Henry M, Power M, Kaushik P, Coleman O, Clynes M, Meleady P. Differential Phosphoproteomic Analysis of Recombinant Chinese Hamster Ovary Cells Following Temperature Shift. J Proteome Res 2017; 16:2339-2358. [DOI: 10.1021/acs.jproteome.6b00868] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael Henry
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Power
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Prashant Kaushik
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Orla Coleman
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| |
Collapse
|
114
|
Battaglia RA, Kabiraj P, Willcockson HH, Lian M, Snider NT. Isolation of Intermediate Filament Proteins from Multiple Mouse Tissues to Study Aging-associated Post-translational Modifications. J Vis Exp 2017. [PMID: 28570536 DOI: 10.3791/55655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Intermediate filaments (IFs), together with actin filaments and microtubules, form the cytoskeleton - a critical structural element of every cell. Normal functioning IFs provide cells with mechanical and stress resilience, while a dysfunctional IF cytoskeleton compromises cellular health and has been associated with many human diseases. Post-translational modifications (PTMs) critically regulate IF dynamics in response to physiological changes and under stress conditions. Therefore, the ability to monitor changes in the PTM signature of IFs can contribute to a better functional understanding, and ultimately conditioning, of the IF system as a stress responder during cellular injury. However, the large number of IF proteins, which are encoded by over 70 individual genes and expressed in a tissue-dependent manner, is a major challenge in sorting out the relative importance of different PTMs. To that end, methods that enable monitoring of PTMs on IF proteins on an organism-wide level, rather than for isolated members of the family, can accelerate research progress in this area. Here, we present biochemical methods for the isolation of the total, detergent-soluble, and detergent-resistant fraction of IF proteins from 9 different mouse tissues (brain, heart, lung, liver, small intestine, large intestine, pancreas, kidney, and spleen). We further demonstrate an optimized protocol for rapid isolation of IF proteins by using lysing matrix and automated homogenization of different mouse tissues. The automated protocol is useful for profiling IFs in experiments with high sample volume (such as in disease models involving multiple animals and experimental groups). The resulting samples can be utilized for various downstream analyses, including mass spectrometry-based PTM profiling. Utilizing these methods, we provide new data to show that IF proteins in different mouse tissues (brain and liver) undergo parallel changes with respect to their expression levels and PTMs during aging.
Collapse
Affiliation(s)
- Rachel A Battaglia
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina at Chapel Hill
| | - Parijat Kabiraj
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina at Chapel Hill
| | - Helen H Willcockson
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina at Chapel Hill
| | - Melinda Lian
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina at Chapel Hill
| | - Natasha T Snider
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina at Chapel Hill;
| |
Collapse
|
115
|
Wootton CA, Lam YPY, Willetts M, van Agthoven MA, Barrow MP, Sadler PJ, O Connor PB. Automatic assignment of metal-containing peptides in proteomic LC-MS and MS/MS data sets. Analyst 2017; 142:2029-2037. [PMID: 28513638 DOI: 10.1039/c7an00075h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Transition metal-containing proteins and enzymes are critical for the maintenance of cellular function and metal-based (metallo)drugs are commonly used for the treatment of many diseases, such as cancer. Detection and characterisation of metallodrug targets is crucial for improving drug-design and therapeutic efficacy. Due to the unique isotopic ratios of many metal species, and the complexity of proteomic samples, standard MS data analysis of these species is unsuitable for accurate assignment. Herein a new method for differentiating metal-containing species within complex LCMS data is presented based upon the Smart Numerical Annotation Procedure (SNAP). SNAP-LC accounts for the change in isotopic envelopes for analytes containing non-standard species, such as metals, and will accurately identify, record, and display the particular spectra within extended LCMS runs that contain target species, and produce accurate lists of matched peaks, greatly assisting the identification and assignment of modified species and tailored to the metals of interest. Analysis of metallated species obtained from tryptic digests of common blood proteins after reactions with three candidate metallodrugs is presented as proof-of-concept examples and demonstrates the effectiveness of SNAP-LC for the fast and accurate elucidation of metallodrug targets.
Collapse
Affiliation(s)
| | - Yuko P Y Lam
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | | | | | - Mark P Barrow
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - Peter B O Connor
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| |
Collapse
|
116
|
Abstract
High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which gave rise to the field of “integrative genetics”. Other omics technologies, such as proteomics and metabolomics, are now often incorporated into the everyday methodology of biological researchers. In this review, we provide an overview of such omics technologies and focus on methods for their integration across multiple omics layers. As compared to studies of a single omics type, multi-omics offers the opportunity to understand the flow of information that underlies disease.
Collapse
Affiliation(s)
- Yehudit Hasin
- Department of Medicine, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA.,Department of Human Genetics, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA
| | - Marcus Seldin
- Department of Medicine, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA
| | - Aldons Lusis
- Department of Medicine, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA. .,Department of Microbiology, Immunology and Molecular Genetics, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA. .,Department of Human Genetics, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA.
| |
Collapse
|
117
|
Ishida YI, Aki M, Fujiwara S, Nagahama M, Ogasawara Y. Peroxidatic cysteine residue of peroxiredoxin 2 separated from human red blood cells treated by tert-butyl hydroperoxide is hyperoxidized into sulfinic and sulfonic acids. Hum Cell 2017; 30:279-289. [DOI: 10.1007/s13577-017-0171-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/08/2017] [Indexed: 01/21/2023]
|
118
|
Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO. Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. BMC Genomics 2017; 18:301. [PMID: 28412930 PMCID: PMC5392934 DOI: 10.1186/s12864-017-3676-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 03/31/2017] [Indexed: 01/24/2023] Open
Abstract
Background Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects. Results We utilized a deeply-sampled dataset of MS/MS proteomic analysis covering 9 timepoints spanning the Escherichia coli growth cycle and an unbiased PTM search strategy to construct a temporal map of abundance for all PTMs within a 400 Da window of mass shifts. Using this map, we are able to identify novel targets and temporal patterns for N-terminal N α acetylation, C-terminal glutamylation, and asparagine deamidation. Furthermore, we identify a possible relationship between N-terminal N α acetylation and regulation of protein degradation in stationary phase, pointing to a previously unrecognized biological function for this poorly-understood PTM. Conclusions Unbiased detection of PTM in MS/MS proteomics data facilitates the discovery of novel modification types and previously unobserved dynamic changes in modification across growth timepoints. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3676-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Colin W Brown
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Viswanadham Sridhara
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, USA
| | - Daniel R Boutz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Maria D Person
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Edward M Marcotte
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Jeffrey E Barrick
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Claus O Wilke
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA. .,Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, USA. .,Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA.
| |
Collapse
|
119
|
Brooks J, Watson A, Korcsmaros T. Omics Approaches to Identify Potential Biomarkers of Inflammatory Diseases in the Focal Adhesion Complex. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:101-109. [PMID: 28373027 PMCID: PMC5414711 DOI: 10.1016/j.gpb.2016.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 12/12/2022]
Abstract
Inflammatory diseases such as inflammatory bowel disease (IBD) require recurrent invasive tests, including blood tests, radiology, and endoscopic evaluation both to diagnose and assess disease activity, and to determine optimal therapeutic strategies. Simple ‘bedside’ biomarkers could be used in all phases of patient management to avoid unnecessary investigation and guide further management. The focal adhesion complex (FAC) has been implicated in the pathogenesis of multiple inflammatory diseases, including IBD, rheumatoid arthritis, and multiple sclerosis. Utilizing omics technologies has proven to be an efficient approach to identify biomarkers from within the FAC in the field of cancer medicine. Predictive biomarkers are paving the way for the success of precision medicine for cancer patients, but inflammatory diseases have lagged behind in this respect. This review explores the current status of biomarker prediction for inflammatory diseases from within the FAC using omics technologies and highlights the benefits of future potential biomarker identification approaches.
Collapse
Affiliation(s)
- Johanne Brooks
- Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom; Gastroenterology Department, Norfolk and Norwich University Hospital, Norwich NR4 7UY, United Kingdom
| | - Alastair Watson
- Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom; Gastroenterology Department, Norfolk and Norwich University Hospital, Norwich NR4 7UY, United Kingdom
| | - Tamas Korcsmaros
- Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom.
| |
Collapse
|
120
|
Yi S, Lin S, Li Y, Zhao W, Mills GB, Sahni N. Functional variomics and network perturbation: connecting genotype to phenotype in cancer. Nat Rev Genet 2017; 18:395-410. [PMID: 28344341 DOI: 10.1038/nrg.2017.8] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteins interact with other macromolecules in complex cellular networks for signal transduction and biological function. In cancer, genetic aberrations have been traditionally thought to disrupt the entire gene function. It has been increasingly appreciated that each mutation of a gene could have a subtle but unique effect on protein function or network rewiring, contributing to diverse phenotypic consequences across cancer patient populations. In this Review, we discuss the current understanding of cancer genetic variants, including the broad spectrum of mutation classes and the wide range of mechanistic effects on gene function in the context of signalling networks. We highlight recent advances in computational and experimental strategies to study the diverse functional and phenotypic consequences of mutations at the base-pair resolution. Such information is crucial to understanding the complex pleiotropic effect of cancer genes and provides a possible link between genotype and phenotype in cancer.
Collapse
Affiliation(s)
- Song Yi
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shengda Lin
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Yongsheng Li
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Wei Zhao
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Nidhi Sahni
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
121
|
Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells. PLoS Comput Biol 2017; 13:e1005432. [PMID: 28306714 PMCID: PMC5376343 DOI: 10.1371/journal.pcbi.1005432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/31/2017] [Accepted: 02/20/2017] [Indexed: 11/19/2022] Open
Abstract
The ability to build in-depth cell signaling networks from vast experimental data is a key objective of computational biology. The spleen tyrosine kinase (Syk) protein, a well-characterized key player in immune cell signaling, was surprisingly first shown by our group to exhibit an onco-suppressive function in mammary epithelial cells and corroborated by many other studies, but the molecular mechanisms of this function remain largely unsolved. Based on existing proteomic data, we report here the generation of an interaction-based network of signaling pathways controlled by Syk in breast cancer cells. Pathway enrichment of the Syk targets previously identified by quantitative phospho-proteomics indicated that Syk is engaged in cell adhesion, motility, growth and death. Using the components and interactions of these pathways, we bootstrapped the reconstruction of a comprehensive network covering Syk signaling in breast cancer cells. To generate in silico hypotheses on Syk signaling propagation, we developed a method allowing to rank paths between Syk and its targets. We first annotated the network according to experimental datasets. We then combined shortest path computation with random walk processes to estimate the importance of individual interactions and selected biologically relevant pathways in the network. Molecular and cell biology experiments allowed to distinguish candidate mechanisms that underlie the impact of Syk on the regulation of cortactin and ezrin, both involved in actin-mediated cell adhesion and motility. The Syk network was further completed with the results of our biological validation experiments. The resulting Syk signaling sub-networks can be explored via an online visualization platform.
Collapse
|
122
|
Wang ZK, Cai Q, Liu J, Ying SH, Feng MG. Global Insight into Lysine Acetylation Events and Their Links to Biological Aspects in Beauveria bassiana, a Fungal Insect Pathogen. Sci Rep 2017; 7:44360. [PMID: 28295016 PMCID: PMC5353618 DOI: 10.1038/srep44360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 02/08/2017] [Indexed: 01/02/2023] Open
Abstract
Lysine acetylation (Kac) events in filamentous fungi are poorly explored. Here we show a lysine acetylome generated by LC-MS/MS analysis of immunoaffinity-based Kac peptides from normal hyphal cells of Beauveria bassiana, a fungal entomopathogen. The acetylome comprised 283 Kac proteins and 464 Kac sites. These proteins were enriched to eight molecular functions, 20 cellular components, 27 biological processes, 20 KEGG pathways and 12 subcellular localizations. All Kac sites were characterized as six Kac motifs, including a novel motif (KacW) for 26 Kac sites of 17 unknown proteins. Many Kac sites were predicted to be multifunctional, largely expanding the fungal Kac events. Biological importance of identified Kac sites was confirmed through functional analysis of Kac sites on Pmt1 and Pmt4, two O-mannosyltransferases. Singular site mutations (K88R and K482R) of Pmt1 resulted in impaired conidiation, attenuated virulence and decreased tolerance to oxidation and cell wall perturbation. These defects were close to or more severe than those caused by the deletion of pmt1. The Pmt4 K360R mutation facilitated colony growth under normal and stressful conditions and enhanced the fungal virulence. Our findings provide the first insight into the Kac events of B. bassiana and their links to the fungal potential against insect pests.
Collapse
Affiliation(s)
- Zhi-Kang Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Qilu University of Technology, Jinan, Shandong, 250353, China
| | - Qing Cai
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jin Liu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
123
|
Imamura H, Wagih O, Niinae T, Sugiyama N, Beltrao P, Ishihama Y. Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring. J Proteome Res 2017; 16:1825-1830. [DOI: 10.1021/acs.jproteome.7b00087] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Haruna Imamura
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- European Bioinformatics Institute, European Molecular
Biology Laboratory, Wellcome
Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Omar Wagih
- European Bioinformatics Institute, European Molecular
Biology Laboratory, Wellcome
Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Tomoya Niinae
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Pedro Beltrao
- European Bioinformatics Institute, European Molecular
Biology Laboratory, Wellcome
Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Yasushi Ishihama
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
124
|
Britten RA, Jewell JS, Davis LK, Miller VD, Hadley MM, Semmes OJ, Lonart G, Dutta SM. Changes in the Hippocampal Proteome Associated with Spatial Memory Impairment after Exposure to Low (20 cGy) Doses of 1 GeV/n 56Fe Radiation. Radiat Res 2017; 187:287-297. [PMID: 28156212 DOI: 10.1667/rr14067.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Exposure to low (∼20 cGy) doses of high-energy charged (HZE) particles, such as 1 GeV/n 56Fe, results in impaired hippocampal-dependent learning and memory (e.g., novel object recognition and spatial memory) in rodents. While these findings raise the possibility that astronauts on deep-space missions may develop cognitive deficits, not all rats develop HZE-induced cognitive impairments, even after exposure to high (200 cGy) HZE doses. The reasons for this differential sensitivity in some animals that develop HZE-induced cognitive failure remain speculative. We employed a robust quantitative mass spectrometry-based workflow, which links early-stage discovery to next-stage quantitative verification, to identify differentially active proteins/pathways in rats that developed spatial memory impairment at three months after exposure to 20 cGy of 1 GeV/n 56Fe (20/impaired), and in those rats that managed to maintain normal cognitive performance (20/functional). Quantitative data were obtained on 665-828 hippocampal proteins in the various cohorts of rats studied, of which 580 were expressed in all groups. A total of 107 proteins were upregulated in the irradiated rats irrespective of their spatial memory performance status, which included proteins involved in oxidative damage response, calcium transport and signaling. Thirty percent (37/107) of these "radiation biomarkers" formed a functional interactome of the proteasome and the COP9 signalosome. These data suggest that there is persistent oxidative stress, ongoing autophagy and altered synaptic plasticity in the irradiated hippocampus, irrespective of the spatial memory performance status, suggesting that the ultimate phenotype may be determined by how well the hippocampal neurons compensate to the ongoing oxidative stress and associated side effects. There were 67 proteins with expression that correlated with impaired spatial memory performance. Several of the "impaired biomarkers" have been implicated in poor spatial memory performance, neurodegeneration, neuronal loss or neuronal susceptibility to apoptosis, or neuronal synaptic or structural plasticity. Therefore, in addition to the baseline oxidative stress and altered adenosine metabolism observed in all irradiated rats, the 20/impaired rats expressed proteins that led to poor spatial memory performance, enhanced neuronal loss and apoptosis, changes in synaptic plasticity and dendritic remodeling. A total of 46 proteins, which were differentially upregulated in the sham-irradiated and 20/functional rat cohorts, can thus be considered as markers of good spatial memory, while another 95 proteins are associated with the maintenance of good spatial memory in the 20/functional rats. The loss or downregulation of these "good spatial memory" proteins would most likely exacerbate the situation in the 20/impaired rats, having a major impact on their neurocognitive status, given that many of those proteins play an important role in neuronal homeostasis and function. Our large-scale comprehensive proteomic analysis has provided some insight into the processes that are altered after exposure, and the collective data suggests that there are multiple problems with the functionality of the neurons and astrocytes in the irradiated hippocampi, which appear to be further exacerbated in the rats that have impaired spatial memory performance or partially compensated for in the rats with good spatial memory.
Collapse
Affiliation(s)
- Richard A Britten
- Department of a Radiation Oncology, Eastern Virginia Medical School, Norfolk, Virginia 23507.,b Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507.,c Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Jessica S Jewell
- Department of a Radiation Oncology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Leslie K Davis
- Department of a Radiation Oncology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Vania D Miller
- Department of a Radiation Oncology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Melissa M Hadley
- Department of a Radiation Oncology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - O John Semmes
- b Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507.,c Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507.,d Department of Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - György Lonart
- d Department of Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Sucharita M Dutta
- c Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507
| |
Collapse
|
125
|
Ma Z, Fung V, D'Orso I. Tandem Affinity Purification of Protein Complexes from Eukaryotic Cells. J Vis Exp 2017. [PMID: 28190026 DOI: 10.3791/55236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The purification of active protein-protein and protein-nucleic acid complexes is crucial for the characterization of enzymatic activities and de novo identification of novel subunits and post-translational modifications. Bacterial systems allow for the expression and purification of a wide variety of single polypeptides and protein complexes. However, this system does not enable the purification of protein subunits that contain post-translational modifications (e.g., phosphorylation and acetylation), and the identification of novel regulatory subunits that are only present/expressed in the eukaryotic system. Here, we provide a detailed description of a novel, robust, and efficient tandem affinity purification (TAP) method using STREP- and FLAG-tagged proteins that facilitates the purification of protein complexes with transiently or stably expressed epitope-tagged proteins from eukaryotic cells. This protocol can be applied to characterize protein complex functionality, to discover post-translational modifications on complex subunits, and to identify novel regulatory complex components by mass spectrometry. Notably, this TAP method can be applied to study protein complexes formed by eukaryotic or pathogenic (viral and bacterial) components, thus yielding a wide array of downstream experimental opportunities. We propose that researchers working with protein complexes could utilize this approach in many different ways.
Collapse
Affiliation(s)
- Zheng Ma
- Department of Microbiology, The University of Texas Southwestern Medical Center
| | - Victor Fung
- Department of Microbiology, The University of Texas Southwestern Medical Center
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center;
| |
Collapse
|
126
|
Waardenberg AJ. Statistical Analysis of ATM-Dependent Signaling in Quantitative Mass Spectrometry Phosphoproteomics. Methods Mol Biol 2017; 1599:229-244. [PMID: 28477123 DOI: 10.1007/978-1-4939-6955-5_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ataxia-telangiectasia mutated (ATM) is a serine/threonine protein kinase, which when perturbed is associated with modified protein signaling that ultimately leads to a range of neurological and DNA repair defects. Recent advances in phospho-proteomics coupled with high-resolution mass-spectrometry provide new opportunities to dissect signaling pathways that ATM utilize under a number of conditions. This chapter begins by providing a brief overview of ATM function, its various regulatory roles and then leads into a workflow focused on the use of the statistical programming language R, together with code, for the identification of ATM-dependent substrates in the cytoplasm. This chapter cannot cover statistical properties in depth nor the range of possible methods in great detail, but instead aims to equip researchers with a set of tools to perform analysis between two conditions through examples with R functions.
Collapse
Affiliation(s)
- Ashley J Waardenberg
- Children's Medical Research Institute, University of Sydney, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia.
| |
Collapse
|
127
|
Lassowskat I, Hartl M, Hosp F, Boersema PJ, Mann M, Finkemeier I. Dimethyl-Labeling-Based Quantification of the Lysine Acetylome and Proteome of Plants. Methods Mol Biol 2017; 1653:65-81. [PMID: 28822126 DOI: 10.1007/978-1-4939-7225-8_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Photorespiratory enzymes in different cellular compartments have been reported to be posttranslational modified by phosphorylation, disulfide formation, S-nitrosylation, glutathionylation, and lysine acetylation. However, not much is known yet about the function of these modifications to regulate the activities, localizations, or interactions of the proteins in this metabolic pathway. Hence, it will be of great importance to study these modifications and their temporal and conditional occurrence in more detail. Here, we focus on the analysis of lysine acetylation as a relatively newly discovered modification on plant metabolic enzymes. The acetylation of lysine residues within proteins is a highly conserved and reversible posttranslational modification which occurs in all living organisms. First discovered on histones and implied in the regulation of gene expression, lysine acetylation also occurs on a diverse set of cellular proteins in different subcellular compartments and is particularly abundant on metabolic enzymes. Upon lysine acetylation, the function of proteins can be modulated due to the loss of the positive charge of the lysine residue. Lysine acetylation was also discovered on proteins involved in photosynthesis and novel tools are needed to study the regulation of this modification in dependence on the environmental conditions, tissues, or plant genotype. This chapter describes a method for the identification and relative quantification of lysine-acetylated proteins in plant tissues using a dimethyl labeling technique combined with an anti-acetyl lysine antibody enrichment strategy. Here, we describe the protein purification, labeling of trypsinated peptides, as well as immuno-enrichment of lysine-acetylated peptides followed by liquid chromatography tandem mass spectrometry (LC-MS/MS) data acquisition and analysis.
Collapse
Affiliation(s)
- Ines Lassowskat
- Plant Proteomics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Köln, Germany
| | - Markus Hartl
- Plant Proteomics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Köln, Germany
- Mass Spectrometry Facility, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Fabian Hosp
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Paul J Boersema
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Department of Biology, Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093, Zurich, Switzerland
| | - Matthias Mann
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Iris Finkemeier
- Plant Proteomics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Köln, Germany.
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, 48149, Münster, Germany.
| |
Collapse
|
128
|
Abstract
Understanding cell growth and cell division involves the study of regulatory events that occur in a cell cycle phase-dependent manner. Studies analyzing cell cycle regulatory mechanisms and cell cycle progression invariably require synchronization of cell populations at specific cell cycle stages. Several methods have been established to synchronize cells, including serum deprivation, contact inhibition, centrifugal elutriation, and drug-dependent synchronization. Despite potential adverse cellular consequences of synchronizing cells by pharmacological agents, drug-dependent methods can be advantageous when studying later cell cycle events to ensure specific enrichment at selected mitotic stages. This chapter describes protocols used in our laboratory for isolating mitotic mammalian cells in a large-scale manner. In particular, we discuss the technical aspects of adherent or suspension cell isolation, the methods necessary to enrich cells at different mitotic stages and the optimized culture conditions.
Collapse
Affiliation(s)
- Kalyan Dulla
- Department of Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Molecular Diagnostics, Philips Corporate Technologies, AE Eindhoven, The Netherlands
| | - Anna Santamaria Margalef
- Cell Cycle and Cancer, Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) - UAB, Barcelona, 08035, Spain.
| |
Collapse
|
129
|
Henry M, Coleman O, Clynes M, Meleady P. Phosphopeptide Enrichment and LC-MS/MS Analysis to Study the Phosphoproteome of Recombinant Chinese Hamster Ovary Cells. Methods Mol Biol 2017; 1603:195-208. [PMID: 28493132 DOI: 10.1007/978-1-4939-6972-2_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The reversible phosphorylation of proteins on serine, threonine, and tyrosine residues is one of the most important post-translational modifications that regulates many biological processes. The phosphoproteome has not been studied in any great detail in recombinant Chinese hamster ovary (CHO) cells to date despite phosphorylation playing a crucial role in regulating many molecular and cellular processes relevant to bioprocess phenotypes including, for example, transcription, translation, growth, apoptosis, and signal transduction. In this chapter, we provide a protocol for the phosphoproteomic analysis of Chinese hamster ovary cells using phosphopeptide enrichment with metal oxide affinity chromatography (MOAC) and immobilized metal affinity chromatography (IMAC) techniques, followed by site-specific identification of phosphorylated residues using LC-MS (MS2 and MS3) strategies.
Collapse
Affiliation(s)
- Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Orla Coleman
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| |
Collapse
|
130
|
Kang UB, Marto JA. Leucine-rich repeat kinase 2 and Parkinson's disease. Proteomics 2016; 17. [PMID: 27723254 DOI: 10.1002/pmic.201600092] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/13/2016] [Accepted: 10/06/2016] [Indexed: 12/21/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large multidomain protein that is expressed in many tissues and participates in numerous biological pathways. Mutations in LRRK2 are recognized as genetic risk factors for familial Parkinson's disease (PD) and may also represent causal factors in the more common sporadic form of PD. The structure of LRRK2 comprises a combination of GTPase, kinase, and scaffolding domains. This functional diversity, combined with a potentially central role in genetic and idiopathic PD motivates significant effort to further credential LRRK2 as a therapeutic target. Here, we review the current understanding for LRRK2 function in normal physiology and PD, with emphasis on insight gained from proteomic approaches.
Collapse
Affiliation(s)
- Un-Beom Kang
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
131
|
Kim MS, Zhong J, Pandey A. Common errors in mass spectrometry-based analysis of post-translational modifications. Proteomics 2016; 16:700-14. [PMID: 26667783 DOI: 10.1002/pmic.201500355] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/05/2015] [Accepted: 12/08/2015] [Indexed: 12/29/2022]
Abstract
Mass spectrometry (MS) is a powerful tool to analyze complex mixtures of proteins in a high-throughput fashion. Proteome analysis has already become a routine task in biomedical research with the emergence of proteomics core facilities in most research institutions. Post-translational modifications (PTMs) represent a mechanism by which complex biological processes are orchestrated dynamically at the systems level. MS is rapidly becoming popular to discover new modifications and novel sites of known PTMs, revolutionizing the current understanding of diverse signaling pathways and biological processes. However, MS-based analysis of PTMs has its own caveats and pitfalls that can lead to erroneous conclusions. Here, we review the most common errors in MS-based PTM analyses with the goal of adopting strategies that maximize correct interpretation in the context of biological questions that are being addressed. Finally, we provide suggestions that should help mass spectrometrists, bioinformaticians and biologists to perform and interpret MS-based PTM analyses more accurately.
Collapse
Affiliation(s)
- Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Zhong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
132
|
Li YL, Zhang XY, Leng Y, Wu YL, Li J, Wu YX. Global protein expression analysis of molecular markers of DS-1-47, a component of implantation-promoting traditional chinese medicine. ACTA ACUST UNITED AC 2016; 36:910-915. [PMID: 27924510 DOI: 10.1007/s11596-016-1683-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/25/2016] [Indexed: 01/01/2023]
Abstract
This study investigated the molecular markers of DS-1-47, a component of an implantation- promoting traditional Chinese medicine consisting of Astragalus mongholicus, Atractylodes macrocephala, Scutellaria baicalensis and Dipsacales, in an attempt to clarify the molecular mechanism and action targets of DS-1-47. Controlled ovarian stimulation (COS) method was used to establish the implantation dysfunction models of mice. Animals were divided into normal pregnant group, COS model group and DS-1-47 group. Laser capture microdissection-double dimensional electrophoresis-mass spectrum (LCM-DE-MS) was used to analyze the uterine protein molecules that were possibly involved in the promotion of implantation. Twenty-three proteins in DS-1-47 group were significantly changed as compared to those in COS model group, with 7 proteins down-regulated and 16 proteins up-regulated. Except for some constituent proteins, the down-regulated proteins included collagen α-1 (VI) chain, keratin 7, keratin 14, myosin regulatory light chain 12B, myosin light polypeptide 9, heat shock protein β-7, and C-U-editing enzyme APOBEC-2; the up-regulated proteins included apolipoprotein A-I, calcium regulated protein-3, proliferating cell nuclear antigen, L-xylulose reductase, and calcium binding protein. These 23 proteins that were regulated by DS-1-47 represented a broad diversity of molecule functions. The down-regulated proteins were associated with stress and immune response, and those up-regulated proteins were related to proliferation. It was suggested that these proteins were important in regulating the uterine environment for the blastocyst implantation. By identification of DS-1-47 markers, proteomic analysis coupled with functional assays is demonstrated to be a promising approach to better understand the molecular mechanism of traditional Chinese medicine.
Collapse
Affiliation(s)
- Yan-Ling Li
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiao-Yan Zhang
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yu Leng
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yan-Li Wu
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Li
- Department of Emergency, Hubei General Hospital of Chinese People's Armed Police Forces, Wuhan, 430061, China.
| | - Yun-Xia Wu
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China.
| |
Collapse
|
133
|
Ren J, Xu N, Ma Z, Li Y, Li C, Wang Y, Tian Y, Liu X, Kang X. Characteristics of expression and regulation of sirtuins in chicken (Gallus gallus). Genome 2016; 60:431-440. [PMID: 28177837 DOI: 10.1139/gen-2016-0125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sirtuins (SIRT1-SIRT7) are a family of NAD+-dependent protein deacetylases that are linked to post-translational regulation of many metabolic processes. There are few reports available for chicken sirtuins (designated cSIRT1-cSIRT7), whose expression and regulation in the liver have yet to be explored. In the present study, we characterized the expression and regulation of sirtuin family members in chicken liver. The results showed that the sirtuin family members in chicken share the same conserved functional SIR2 domains. All the sirtuin family members were expressed extensively in all tissues examined, and the expression levels of cSIRT1, cSIRT2, cSIRT4, cSIRT6, and cSIRT7 in the liver increased significantly with sexual maturity. However, all sirtuin family members were downregulated (P < 0.05) in chicken livers and cultured primary hepatocytes treated with 17β-estradiol. We concluded that the expression levels of some chicken sirtuin family members in the liver were upregulated with sexual maturation, but might not be regulated directly by estrogen. Whereas estrogen could be used as an inhibitor of all sirtuins, both in vivo and in vitro.
Collapse
Affiliation(s)
- Junxiao Ren
- a College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Naiyi Xu
- a College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Zheng Ma
- a College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanmin Li
- a College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Cuicui Li
- a College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.,b Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China.,c International Joint Research Laboratory for Poultry Breeding of Henan, Henan, Zhengzhou 450002, China
| | - Yanbin Wang
- a College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.,b Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China.,c International Joint Research Laboratory for Poultry Breeding of Henan, Henan, Zhengzhou 450002, China
| | - Yadong Tian
- a College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.,b Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China.,c International Joint Research Laboratory for Poultry Breeding of Henan, Henan, Zhengzhou 450002, China
| | - Xiaojun Liu
- a College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.,b Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China.,c International Joint Research Laboratory for Poultry Breeding of Henan, Henan, Zhengzhou 450002, China
| | - Xiangtao Kang
- a College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.,b Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China.,c International Joint Research Laboratory for Poultry Breeding of Henan, Henan, Zhengzhou 450002, China
| |
Collapse
|
134
|
Raguz Nakic Z, Seisenbacher G, Posas F, Sauer U. Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2016; 10:104. [PMID: 27846849 PMCID: PMC5109706 DOI: 10.1186/s12918-016-0350-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 11/03/2016] [Indexed: 01/08/2023]
Abstract
Background Coordinated through a complex network of kinases and phosphatases, protein phosphorylation regulates essentially all cellular processes in eukaryotes. Recent advances in proteomics enable detection of thousands of phosphorylation sites (phosphosites) in single experiments. However, functionality of the vast majority of these sites remains unclear and we lack suitable approaches to evaluate functional relevance at a pace that matches their detection. Results Here, we assess functionality of 26 phosphosites by introducing phosphodeletion and phosphomimic mutations in 25 metabolic enzymes and regulators from the TOR and HOG signaling pathway in Saccharomyces cerevisiae by phenotypic analysis and untargeted metabolomics. We show that metabolomics largely outperforms growth analysis and recovers 10 out of the 13 previously characterized phosphosites and suggests functionality for several novel sites, including S79 on the TOR regulatory protein Tip41. We analyze metabolic profiles to identify consequences underlying regulatory phosphorylation events and detecting glycerol metabolism to have a so far unknown influence on arginine metabolism via phosphoregulation of the glycerol dehydrogenases. Further, we also find S508 in the MAPKK Pbs2 as a potential link for cross-talking between HOG signaling and the cell wall integrity pathway. Conclusions We demonstrate that metabolic profiles can be exploited for gaining insight into regulatory consequences and biological roles of phosphosites. Altogether, untargeted metabolomics is a fast, sensitive and informative approach appropriate for future large-scale functional analyses of phosphosites. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0350-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zrinka Raguz Nakic
- Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard-Hof 1, Zürich, Switzerland.,PhD Program on Systems Biology, Life Science Zürich, Zürich, Switzerland
| | - Gerhard Seisenbacher
- Cell signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Posas
- Cell signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard-Hof 1, Zürich, Switzerland.
| |
Collapse
|
135
|
Hsu JL, Chen SH. Stable isotope dimethyl labelling for quantitative proteomics and beyond. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0364. [PMID: 27644970 PMCID: PMC5031631 DOI: 10.1098/rsta.2015.0364] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 05/21/2023]
Abstract
Stable-isotope reductive dimethylation, a cost-effective, simple, robust, reliable and easy-to- multiplex labelling method, is widely applied to quantitative proteomics using liquid chromatography-mass spectrometry. This review focuses on biological applications of stable-isotope dimethyl labelling for a large-scale comparative analysis of protein expression and post-translational modifications based on its unique properties of the labelling chemistry. Some other applications of the labelling method for sample preparation and mass spectrometry-based protein identification and characterization are also summarized.This article is part of the themed issue 'Quantitative mass spectrometry'.
Collapse
Affiliation(s)
- Jue-Liang Hsu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan, Republic of China
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan City, Taiwan, Republic of China
| |
Collapse
|
136
|
Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P. ATR inhibition rewires cellular signaling networks induced by replication stress. Proteomics 2016; 16:402-16. [PMID: 26572502 DOI: 10.1002/pmic.201500172] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 10/15/2015] [Accepted: 11/09/2015] [Indexed: 12/27/2022]
Abstract
The slowing down or stalling of replication forks is commonly known as replication stress and arises from multiple causes such as DNA lesions, nucleotide depletion, RNA-DNA hybrids, and oncogene activation. The ataxia telangiectasia and Rad3-related kinase (ATR) plays an essential role in the cellular response to replication stress and inhibition of ATR has emerged as therapeutic strategy for the treatment of cancers that exhibit high levels of replication stress. However, the cellular signaling induced by replication stress and the substrate spectrum of ATR has not been systematically investigated. In this study, we employed quantitative MS-based proteomics to define the cellular signaling after nucleotide depletion-induced replication stress and replication fork collapse following ATR inhibition. We demonstrate that replication stress results in increased phosphorylation of a subset of proteins, many of which are involved in RNA splicing and transcription and have previously not been associated with the cellular replication stress response. Furthermore, our data reveal the ATR-dependent phosphorylation following replication stress and discover novel putative ATR target sites on MCM6, TOPBP1, RAD51AP1, and PSMD4. We establish that ATR inhibition rewires cellular signaling networks induced by replication stress and leads to the activation of the ATM-driven double-strand break repair signaling.
Collapse
Affiliation(s)
- Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hannah Oehler
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Denis Dalic
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Anja Freiwald
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Hubert Serve
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| |
Collapse
|
137
|
Zakhartsev M, Pertl-Obermeyer H, Schulze WX. From Phosphoproteome to Modeling of Plant Signaling Pathways. Methods Mol Biol 2016; 1394:245-259. [PMID: 26700054 DOI: 10.1007/978-1-4939-3341-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Quantitative proteomic experiments in recent years became almost routine in many aspects of biology. Particularly the quantification of peptides and corresponding phosphorylated counterparts from a single experiment is highly important for understanding of dynamics of signaling pathways. We developed an analytical method to quantify phosphopeptides (pP) in relation to the quantity of the corresponding non-phosphorylated parent peptides (P). We used mixed-mode solid-phase extraction to purify total peptides from tryptic digest and separated them from most of the phosphorous-containing compounds (e.g., phospholipids, nucleotides) which enhances pP enrichment on TiO2 beads. Phosphoproteomic data derived with this designed method allows quantifying pP/P stoichiometry, and qualifying experimental data for mathematical modeling.
Collapse
Affiliation(s)
- Maksim Zakhartsev
- Plant Systems Biology, Plant Physiology, University of Hohenheim, Fruwirthstrasse 12, 70599, Stuttgart, Germany.
| | - Heidi Pertl-Obermeyer
- Plant Systems Biology, Plant Physiology, University of Hohenheim, Fruwirthstrasse 12, 70599, Stuttgart, Germany
| | - Waltraud X Schulze
- Plant Systems Biology, Plant Physiology, University of Hohenheim, Fruwirthstrasse 12, 70599, Stuttgart, Germany
| |
Collapse
|
138
|
Ye J, Zhang H, He W, Zhu B, Zhou D, Chen Z, Ashraf U, Wei Y, Liu Z, Fu ZF, Chen H, Cao S. Quantitative phosphoproteomic analysis identifies the critical role of JNK1 in neuroinflammation induced by Japanese encephalitis virus. Sci Signal 2016; 9:ra98. [DOI: 10.1126/scisignal.aaf5132] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
139
|
Calciolari E, Mardas N, Dereka X, Anagnostopoulos AK, Tsangaris GT, Donos N. The effect of experimental osteoporosis on bone regeneration: part 2, proteomics results. Clin Oral Implants Res 2016; 28:e135-e145. [PMID: 27580862 DOI: 10.1111/clr.12950] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 01/17/2023]
Abstract
OBJECTIVES To identify and describe protein expression in a Wistar rat calvarial critical size defect (CSD) model following treatment with guided bone regeneration in healthy and osteoporotic conditions. MATERIAL AND METHODS Thirty-six 10-month-old female Wistar rats were used. Half of them were ovariectomized (OVX) and fed with a low-calcium diet to induce an osteoporotic-like status. In each animal of both groups, two 5-mm calvarial CSDs were treated with deproteinized bovine bone mineral graft particles and a bilayer collagen membrane. Six OVX and six control rats were randomly euthanized at 7, 14, and 30 days. One defect/animal was randomly chosen for proteomic analysis. Differently expressed proteins between the two groups were identified with matrix-assisted laser desorption time-of-flight mass spectrometry and liquid chromatography-mass spectrometry/mass spectrometry. RESULTS At 7 days, 29 and 27 proteins were, respectively, identified in the healthy and OVX animals. At 14 days, 103 proteins were detected in the healthy controls and 20 proteins in the OVX rats, while at 30 days, 31 and 75 proteins were identified, respectively. Only limited proteins known to play a role in the later stages of bone formation and maturation were identified within the animals 'proteomes. DISCUSSION The osseous formation process was quite immature even at 30 days of healing. An overexpression of inflammatory and stress response pathways was detected in the OVX animals, as well as a tendency toward a delayed maturation of the osseous wound and a reduced/delayed differentiation of osteoblast cell precursors.
Collapse
Affiliation(s)
- E Calciolari
- Centre for Clinical Oral Research, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London (QMUL), London, UK.,Periodontology Department, UCL Eastman Dental Institute, London, UK
| | - N Mardas
- Centre for Adult Oral Health, Bart's & The London School of Dentistry & Medicine, Queen Mary University of London (QMUL), London, UK
| | - X Dereka
- Department of Periodontology, National and Kapodistrian University of Athens, Athens, Greece
| | - A K Anagnostopoulos
- Proteomics Research Unit, Centre of Basic Research II, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - G T Tsangaris
- Proteomics Research Unit, Centre of Basic Research II, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - N Donos
- Centre for Clinical Oral Research, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London (QMUL), London, UK
| |
Collapse
|
140
|
Incorporation of non-canonical amino acids into the developing murine proteome. Sci Rep 2016; 6:32377. [PMID: 27572480 PMCID: PMC5004113 DOI: 10.1038/srep32377] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/09/2016] [Indexed: 12/25/2022] Open
Abstract
Analysis of the developing proteome has been complicated by a lack of tools that can be easily employed to label and identify newly synthesized proteins within complex biological mixtures. Here, we demonstrate that the methionine analogs azidohomoalanine and homopropargylglycine can be globally incorporated into the proteome of mice through facile intraperitoneal injections. These analogs contain bio-orthogonal chemical handles to which fluorescent tags can be conjugated to identify newly synthesized proteins. We show these non-canonical amino acids are incorporated into various tissues in juvenile mice and in a concentration dependent manner. Furthermore, administration of these methionine analogs to pregnant dams during a critical stage of murine development, E10.5-12.5 when many tissues are assembling, does not overtly disrupt development as assessed by proteomic analysis and normal parturition and growth of pups. This successful demonstration that non-canonical amino acids can be directly administered in vivo will enable future studies that seek to characterize the murine proteome during growth, disease and repair.
Collapse
|
141
|
Coordinated Regulation of Cap-Dependent Translation and MicroRNA Function by Convergent Signaling Pathways. Mol Cell Biol 2016; 36:2360-73. [PMID: 27354062 DOI: 10.1128/mcb.01011-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/14/2016] [Indexed: 01/08/2023] Open
Abstract
Cell growth and proliferation require the coordinated activation of many cellular processes, including cap-dependent mRNA translation. MicroRNAs oppose cap-dependent translation and set thresholds for expression of target proteins. Emerging data suggest that microRNA function is enhanced by cellular activation due in part to induction of the RNA-induced silencing complex (RISC) scaffold protein GW182. In the current study, we demonstrate that increased expression of GW182 in activated or transformed immune cells results from effects of phosphoinositol 3-kinase-Akt-mechanistic target of rapamycin (PI3K-Akt-mTOR) and Jak-Stat-Pim signaling on the translation of GW182 mRNA. Both signaling pathways enhanced polysome occupancy and eukaryotic initiation factor 4E (eIF4E) binding to the 5' 7mG cap of GW182 mRNA. The effect of Jak-Stat-Pim signaling on polysome occupancy and expression of GW182 protein was greater than that of PI3K-Akt-mTOR signaling, likely resulting from enhanced eIF4A-dependent unwinding of G-quadruplexes in the 5' untranslated region of GW182 mRNA. Consistent with this, GW182 expression and microRNA function were reduced by inhibition of mTOR or Pim kinases, translation initiation complex assembly, or eIF4A function. Taken together, these data provide a mechanistic link between microRNA function and cap-dependent translation that allows activated immune cells to maintain microRNA-mediated repression of targets despite enhanced rates of protein synthesis.
Collapse
|
142
|
Singec I, Crain AM, Hou J, Tobe BTD, Talantova M, Winquist AA, Doctor KS, Choy J, Huang X, La Monaca E, Horn DM, Wolf DA, Lipton SA, Gutierrez GJ, Brill LM, Snyder EY. Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling. Stem Cell Reports 2016; 7:527-542. [PMID: 27569059 PMCID: PMC5032292 DOI: 10.1016/j.stemcr.2016.07.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 10/27/2022] Open
Abstract
Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt.
Collapse
Affiliation(s)
- Ilyas Singec
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Andrew M Crain
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Junjie Hou
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Brian T D Tobe
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Maria Talantova
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alicia A Winquist
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Kutbuddin S Doctor
- Informatics and Data Management, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jennifer Choy
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Xiayu Huang
- Informatics and Data Management, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Esther La Monaca
- Department of Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - David M Horn
- Thermo Fisher Scientific Inc., San Jose, CA 95134, USA
| | - Dieter A Wolf
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Stuart A Lipton
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Gustavo J Gutierrez
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Laurence M Brill
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Evan Y Snyder
- Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
143
|
Phosphorylation Sites Identified in the NEIL1 DNA Glycosylase Are Potential Targets for the JNK1 Kinase. PLoS One 2016; 11:e0157860. [PMID: 27518429 PMCID: PMC4982613 DOI: 10.1371/journal.pone.0157860] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/23/2016] [Indexed: 12/20/2022] Open
Abstract
The NEIL1 DNA glycosylase is one of eleven mammalian DNA glycosylases that partake in the first step of the base excision repair (BER) pathway. NEIL1 recognizes and cleaves mainly oxidized pyrimidines from DNA. The past decade has witnessed the identification of an increasing number of post-translational modifications (PTMs) in BER enzymes including phosphorylation, acetylation, and sumoylation, which modulate enzyme function. In this work, we performed the first comprehensive analysis of phosphorylation sites in human NEIL1 expressed in human cells. Mass spectrometry (MS) analysis revealed phosphorylation at three serine residues: S207, S306, and a third novel site, S61. We expressed, purified, and characterized phosphomimetic (glutamate) and phosphoablating (alanine) mutants of the three phosphorylation sites in NEIL1 revealed by the MS analysis. All mutant enzymes were active and bound tightly to DNA, indicating that phosphorylation does not affect DNA binding and enzyme activity at these three serine sites. We also characterized phosphomimetic mutants of two other sites of phosphorylation, Y263 and S269, reported previously, and observed that mutation of Y263 to E yielded a completely inactive enzyme. Furthermore, based on sequence motifs and kinase prediction algorithms, we identified the c-Jun N-terminal kinase 1 (JNK1) as the kinase involved in the phosphorylation of NEIL1. JNK1, a member of the mitogen activated protein kinase (MAPK) family, was detected in NEIL1 immunoprecipitates, interacted with NEIL1 in vitro, and was able to phosphorylate the enzyme at residues S207, S306, and S61.
Collapse
|
144
|
Espinosa Angarica V, del Sol A. Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation. Bioessays 2016; 38:758-68. [PMID: 27321053 PMCID: PMC5094535 DOI: 10.1002/bies.201600103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Pluripotency can be considered a functional characteristic of pluripotent stem cells (PSCs) populations and their niches, rather than a property of individual cells. In this view, individual cells within the population independently adopt a variety of different expression states, maintained by different signaling, transcriptional, and epigenetics regulatory networks. In this review, we propose that generation of integrative network models from single cell data will be essential for getting a better understanding of the regulation of self-renewal and differentiation. In particular, we suggest that the identification of network stability determinants in these integrative models will provide important insights into the mechanisms mediating the transduction of signals from the niche, and how these signals can trigger differentiation. In this regard, the differential use of these stability determinants in subpopulation-specific regulatory networks would mediate differentiation into different cell fates. We suggest that this approach could offer a promising avenue for the development of novel strategies for increasing the efficiency and fidelity of differentiation, which could have a strong impact on regenerative medicine.
Collapse
Affiliation(s)
- Vladimir Espinosa Angarica
- Luxembourg Center for Systems Biomedicine (LCSB)University of Luxembourg, Campus BelvalBelvauxLuxembourg
| | - Antonio del Sol
- Luxembourg Center for Systems Biomedicine (LCSB)University of Luxembourg, Campus BelvalBelvauxLuxembourg
| |
Collapse
|
145
|
Abstract
Small ubiquitin-like modifiers (SUMOs) are essential for the regulation of several cellular processes and are potential therapeutic targets owing to their involvement in diseases such as cancer and Alzheimer disease. In the past decade, we have witnessed a rapid expansion of proteomic approaches for identifying sumoylated proteins, with recent advances in detecting site-specific sumoylation. In this Analysis, we combined all human SUMO proteomics data currently available into one cohesive database. We provide proteomic evidence for sumoylation of 3,617 proteins at 7,327 sumoylation sites, and insight into SUMO group modification by clustering the sumoylated proteins into functional networks. The data support sumoylation being a frequent protein modification (on par with other major protein modifications) with multiple nuclear functions, including in transcription, mRNA processing, DNA replication and the DNA-damage response.
Collapse
|
146
|
Croucher DR, Iconomou M, Hastings JF, Kennedy SP, Han JZR, Shearer RF, McKenna J, Wan A, Lau J, Aparicio S, Saunders DN. Bimolecular complementation affinity purification (BiCAP) reveals dimer-specific protein interactions for ERBB2 dimers. Sci Signal 2016; 9:ra69. [PMID: 27405979 DOI: 10.1126/scisignal.aaf0793] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The dynamic assembly of multiprotein complexes is a central mechanism of many cell signaling pathways. This process is key to maintaining the spatiotemporal specificity required for an accurate, yet adaptive, response to rapidly changing cellular conditions. We describe a technique for the specific isolation and downstream proteomic characterization of any two interacting proteins, to the exclusion of their individual moieties and competing binding partners. We termed the approach bimolecular complementation affinity purification (BiCAP) because it combines the use of conformation-specific nanobodies with a protein-fragment complementation assay with affinity purification. Using BiCAP, we characterized the specific interactome of the epidermal growth factor receptor (EGFR) family member ERBB2 when in the form of a homodimer or when in the form of a heterodimer with either EGFR or ERBB3. We identified dimer-specific interaction patterns for key adaptor proteins and identified a number of previously unknown interacting partners. Functional analysis for one of these newly identified partners revealed a noncanonical mechanism of extracellular signal-regulated kinase (ERK) activation that is specific to the ERBB2:ERBB3 heterodimer and acts through the adaptor protein FAM59A in breast cancer cells.
Collapse
Affiliation(s)
- David R Croucher
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. St. Vincent's Hospital Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia. School of Medicine, University College Dublin, Belfield, Dublin D4, Ireland.
| | - Mary Iconomou
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Jordan F Hastings
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Sean P Kennedy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. Systems Biology Ireland, University College Dublin, Belfield, Dublin D4, Ireland
| | - Jeremy Z R Han
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Robert F Shearer
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Jessie McKenna
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Adrian Wan
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Joseph Lau
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Darren N Saunders
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
| |
Collapse
|
147
|
Proteome-wide analysis of lysine acetylation in the plant pathogen Botrytis cinerea. Sci Rep 2016; 6:29313. [PMID: 27381557 PMCID: PMC4933888 DOI: 10.1038/srep29313] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 06/16/2016] [Indexed: 12/18/2022] Open
Abstract
Lysine acetylation is a dynamic and reversible post-translational modification that plays an important role in diverse cellular processes. Botrytis cinerea is the most thoroughly studied necrotrophic species due to its broad host range and huge economic impact. However, to date, little is known about the functions of lysine acetylation in this plant pathogen. In this study, we determined the lysine acetylome of B. cinerea through the combination of affinity enrichment and high-resolution LC-MS/MS analysis. Overall, 1582 lysine acetylation sites in 954 proteins were identified. Bioinformatics analysis shows that the acetylated proteins are involved in diverse biological functions and show multiple cellular localizations. Several particular amino acids preferred near acetylation sites, including KacY, KacH, Kac***R, KacF, FKac and Kac***K, were identified in this organism. Protein interaction network analysis demonstrates that a variety of interactions are modulated by protein acetylation. Interestingly, 6 proteins involved in virulence of B. cinerea, including 3 key components of the high-osmolarity glycerol pathway, were found to be acetylated, suggesting that lysine acetylation plays regulatory roles in pathogenesis. These data provides the first comprehensive view of the acetylome of B. cinerea and serves as a rich resource for functional analysis of lysine acetylation in this plant pathogen.
Collapse
|
148
|
van der Mijn JC, Broxterman HJ, Knol JC, Piersma SR, De Haas RR, Dekker H, Pham TV, Van Beusechem VW, Halmos B, Mier JW, Jiménez CR, Verheul HMW. Sunitinib activates Axl signaling in renal cell cancer. Int J Cancer 2016; 138:3002-10. [PMID: 26815723 DOI: 10.1002/ijc.30022] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 12/01/2015] [Accepted: 01/14/2016] [Indexed: 12/14/2022]
Abstract
Mass spectrometry-based phosphoproteomics provides a unique unbiased approach to evaluate signaling network in cancer cells. The tyrosine kinase inhibitor sunitinib is registered as treatment for patients with renal cell cancer (RCC). We investigated the effect of sunitinib on tyrosine phosphorylation in RCC tumor cells to get more insight in its mechanism of action and thereby to find potential leads for combination treatment strategies. Sunitinib inhibitory concentrations of proliferation (IC50) of 786-O, 769-p and A498 RCC cells were determined by MTT-assays. Global tyrosine phosphorylation was measured by LC-MS/MS after immunoprecipitation with the antiphosphotyrosine antibody p-TYR-100. Phosphoproteomic profiling of 786-O cells yielded 1519 phosphopeptides, corresponding to 675 unique proteins including 57 different phosphorylated protein kinases. Compared to control, incubation with sunitinib at its IC50 of 2 µM resulted in downregulation of 86 phosphopeptides including CDK5, DYRK3, DYRK4, G6PD, PKM and LDH-A, while 94 phosphopeptides including Axl, FAK, EPHA2 and p38α were upregulated. Axl- (y702), FAK- (y576) and p38α (y182) upregulation was confirmed by Western Blot in 786-O and A498 cells. Subsequent proliferation assays revealed that inhibition of Axl with a small molecule inhibitor (R428) sensitized 786-O RCC cells and immortalized endothelial cells to sunitinib up to 3 fold. In conclusion, incubation with sunitinib of RCC cells causes significant upregulation of multiple phosphopeptides including Axl. Simultaneous inhibition of Axl improves the antitumor activity of sunitinib. We envision that evaluation of phosphoproteomic changes by TKI treatment enables identification of new targets for combination treatment strategies.
Collapse
Affiliation(s)
- Johannes C van der Mijn
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Hematology/Oncology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Henk J Broxterman
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Richard R De Haas
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Victor W Van Beusechem
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Balazs Halmos
- Department of Hematology/Oncology, Columbia University Medical Center, New York, NY
| | - James W Mier
- Department of Hematology/Oncology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Connie R Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| |
Collapse
|
149
|
Wagner SA, Satpathy S, Beli P, Choudhary C. SPATA2 links CYLD to the TNF-α receptor signaling complex and modulates the receptor signaling outcomes. EMBO J 2016; 35:1868-84. [PMID: 27307491 DOI: 10.15252/embj.201694300] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/31/2016] [Indexed: 11/09/2022] Open
Abstract
TNF-α is a key regulator of innate immune and proinflammatory responses. However, the composition of the TNF-α receptor-associated signaling complexes (TNF-RSC) and the architecture of the downstream signaling networks are incompletely understood. We employed quantitative mass spectrometry to demonstrate that TNF-α stimulation induces widespread protein phosphorylation and that the scope of phosphorylation expands in a temporal manner. TNF-α stimulation also induces rapid ubiquitylation of components of the TNF-RSC Temporal analysis of the TNF-RSC composition identified SPATA2 as a novel component of the TNF-RSC The predicted PUB domain in the N-terminus of SPATA2 interacts with the USP domain of CYLD, whereas the C-terminus of SPATA2 interacts with HOIP SPATA2 is required for recruitment of CYLD to the TNF-RSC Downregulation of SPATA2 augments transcriptional activation of NF-κB and inhibits TNF-α-induced necroptosis, pointing to an important function of SPATA2 in modulating the outcomes of TNF-α signaling. Taken together, our study draws a detailed map of TNF-α signaling, identifies SPATA2 as a novel component of TNF-α signaling, and provides a rich resource for further functional investigations.
Collapse
Affiliation(s)
- Sebastian A Wagner
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark Department of Medicine, Hematology/Oncology, Goethe University School of Medicine, Frankfurt, Germany German Cancer Consortium (DKTK), Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Shankha Satpathy
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Petra Beli
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark Institute of Molecular Biology (IMB), Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
150
|
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.
Collapse
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
| |
Collapse
|