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Goto C, Hashizume S, Fukao Y, Hara-Nishimura I, Tamura K. Comprehensive nuclear proteome of Arabidopsis obtained by sequential extraction. Nucleus 2020; 10:81-92. [PMID: 30961429 PMCID: PMC6527390 DOI: 10.1080/19491034.2019.1603093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In eukaryotes, the nucleus plays key roles in fundamental cellular processes, including DNA replication, chromatin maintenance, transcription, and translation. To better understand the functional diversity of nuclei, we developed a method for the comprehensive extraction of the nuclear proteome from Arabidopsis. We used a buffer with a high sucrose concentration to purify nuclei and then conducted solubility-based fractionation to increase proteome coverage. We identified 1539 proteins and two novel nuclear envelope (NE) proteins in the nuclear fraction of Arabidopsis cultured cells. The localization of 25 proteins was determined by GFP fusion analyses; 23 of these proteins were localized either in the nucleus or the NE-associated endoplasmic reticulum. This result was indicative of the high quality of the proteome. These findings will be useful for clarifying novel nuclear functions in plants.
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Affiliation(s)
- Chieko Goto
- a Graduate School of Agricultural and Life Sciences , University of Tokyo , Tokyo , Japan
| | - Shoko Hashizume
- b Department of Botany , Graduate School of Science, Kyoto University , Kyoto , Japan
| | - Yoichiro Fukao
- c Department of Bioinformatics , College of Life Sciences, Ritsumeikan University , Shiga , Japan
| | | | - Kentaro Tamura
- e Department of Environmental and Life Sciences , University of Shizuoka , Shizuoka , Japan
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Aqueous peat extract exposes rhizobia to sub-lethal stress which may prime cells for improved desiccation tolerance. Appl Microbiol Biotechnol 2018; 102:7521-7539. [DOI: 10.1007/s00253-018-9086-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 01/25/2023]
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Intersectin goes nuclear: secret life of an endocytic protein. Biochem J 2018; 475:1455-1472. [PMID: 29599122 DOI: 10.1042/bcj20170897] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 01/22/2023]
Abstract
Intersectin 1-short (ITSN1-s) is a 1220 amino acid ubiquitously expressed scaffold protein presenting a multidomain structure that allows to spatiotemporally regulate the functional interaction of a plethora of proteins. Besides its well-established role in endocytosis, ITSN1-s is involved in the regulation of cell signaling and is implicated in tumorigenesis processes, although the signaling pathways involved are still poorly understood. Here, we identify ITSN1-s as a nucleocytoplasmic trafficking protein. We show that, by binding to importin (IMP)α, a small fraction of ITSN1-s localizes in the cell nucleus at the steady state, where it preferentially associates with the nuclear envelope and interacts with lamin A/C. However, upon pharmacological ablation of chromosome region maintenance 1 (CRM-1)-dependent nuclear export pathway, the protein accumulates into the nucleus, thus revealing its moonlighting nature. Analysis of deletion mutants revealed that the coiled coil (CC) and Src homology (SH3) regions play the major role in its nucleocytoplasmic shuttling. While no evidence of nuclear localization signal (NLS) was detected in the CC region, a functional bipartite NLS was identified within the SH3D region of ITSN1-s (RKKNPGGWWEGELQARGKKRQIGW-1127), capable of conferring energy-dependent nuclear accumulation to reporter proteins and whose mutational ablation affects nuclear import of the whole SH3 region. Thus, ITSN1-s is an endocytic protein, which shuttles between the nucleus and the cytoplasm in a CRM-1- and IMPα-dependent fashion.
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Filareti M, Luotti S, Pasetto L, Pignataro M, Paolella K, Messina P, Pupillo E, Filosto M, Lunetta C, Mandrioli J, Fuda G, Calvo A, Chiò A, Corbo M, Bendotti C, Beghi E, Bonetto V. Decreased Levels of Foldase and Chaperone Proteins Are Associated with an Early-Onset Amyotrophic Lateral Sclerosis. Front Mol Neurosci 2017; 10:99. [PMID: 28428745 PMCID: PMC5382314 DOI: 10.3389/fnmol.2017.00099] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/23/2017] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by a progressive upper and lower motor neuron degeneration. One of the peculiar clinical characteristics of ALS is the wide distribution in age of onset, which is probably caused by different combinations of intrinsic and exogenous factors. We investigated whether these modifying factors are converging into common pathogenic pathways leading either to an early or a late disease onset. This would imply the identification of phenotypic biomarkers, that can distinguish the two populations of ALS patients, and of relevant pathways to consider in a therapeutic intervention. Toward this aim a differential proteomic analysis was performed in peripheral blood mononuclear cells (PBMC) from a group of 16 ALS patients with an age of onset ≤55 years and a group of 16 ALS patients with an age of onset ≥75 years, and matched healthy controls. We identified 43 differentially expressed proteins in the two groups of patients. Gene ontology analysis revealed that there was a significant enrichment in annotations associated with protein folding and response to stress. We next validated a selected number of proteins belonging to this functional group in 85 patients and 83 age- and sex-matched healthy controls using immunoassays. The results of the validation study confirmed that there was a decreased level of peptidyl-prolyl cis-trans isomerase A (also known as cyclophilin A), heat shock protein HSP 90-alpha, 78 kDa glucose-regulated protein (also known as BiP) and protein deglycase DJ-1 in PBMC of ALS patients with an early onset. Similar results were obtained in PBMC and spinal cord from two SOD1G93A mouse models with an early and late disease onset. This study suggests that a different ability to upregulate proteins involved in proteostasis, such as foldase and chaperone proteins, may be at the basis of a different susceptibility to ALS, putting forward the development of therapeutic approaches aiming at boosting the protein quality control system.
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Affiliation(s)
- Melania Filareti
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy.,Department of Neurorehabilitation Sciences, Casa Cura PoliclinicoMilan, Italy
| | - Silvia Luotti
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Laura Pasetto
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Mauro Pignataro
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Katia Paolella
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Paolo Messina
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Elisabetta Pupillo
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Massimiliano Filosto
- Center for Neuromuscular Diseases and Neuropathies, Unit of Neurology, ASST Spedali Civili and University of BresciaBrescia, Italy
| | | | - Jessica Mandrioli
- Department of Neuroscience, Azienda Ospedaliero Universitaria di Modena, Ospedale Civile S. Agostino-EstenseModena, Italy
| | - Giuseppe Fuda
- ALS Center, Department of Neuroscience Rita Levi Montalcini, University of TorinoTorino, Italy
| | - Andrea Calvo
- ALS Center, Department of Neuroscience Rita Levi Montalcini, University of TorinoTorino, Italy
| | - Adriano Chiò
- ALS Center, Department of Neuroscience Rita Levi Montalcini, University of TorinoTorino, Italy
| | - Massimo Corbo
- Department of Neurorehabilitation Sciences, Casa Cura PoliclinicoMilan, Italy
| | - Caterina Bendotti
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Ettore Beghi
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Valentina Bonetto
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
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Gupta DB, Rai Y, Gayali S, Chakraborty S, Chakraborty N. Plant Organellar Proteomics in Response to Dehydration: Turning Protein Repertoire into Insights. FRONTIERS IN PLANT SCIENCE 2016; 7:460. [PMID: 27148291 PMCID: PMC4829595 DOI: 10.3389/fpls.2016.00460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/24/2016] [Indexed: 05/29/2023]
Abstract
Stress adaptation or tolerance in plants is a complex phenomenon involving changes in physiological and metabolic processes. Plants must develop elaborate networks of defense mechanisms, and adapt to and survive for sustainable agriculture. Water-deficit or dehydration is the most critical environmental factor that plants are exposed to during their life cycle, which influences geographical distribution and productivity of many crop species. The cellular responses to dehydration are orchestrated by a series of multidirectional relays of biochemical events at organelle level. The new challenge is to dissect the underlying mechanisms controlling the perception of stress signals and their transmission to cellular machinery for activation of adaptive responses. The completeness of current descriptions of spatial distribution of proteins, the relevance of subcellular locations in diverse functional processes, and the changes of protein abundance in response to dehydration hold the key to understanding how plants cope with such stress conditions. During past decades, organellar proteomics has proved to be useful not only for deciphering reprograming of plant responses to dehydration, but also to dissect stress-responsive pathways. This review summarizes a range of organellar proteomics investigations under dehydration to gain a holistic view of plant responses to water-deficit conditions, which may facilitate future efforts to develop genetically engineered crops for better adaptation.
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Affiliation(s)
- Deepti B. Gupta
- Department of Biotechnology, TERI UniversityNew Delhi, India
| | - Yogita Rai
- Department of Biotechnology, TERI UniversityNew Delhi, India
| | - Saurabh Gayali
- National Institute of Plant Genome Research, Jawaharlal Nehru University CampusNew Delhi, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University CampusNew Delhi, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University CampusNew Delhi, India
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Jankowska U, Latosinska A, Skupien-Rabian B, Swiderska B, Dziedzicka-Wasylewska M, Kedracka-Krok S. Optimized procedure of extraction, purification and proteomic analysis of nuclear proteins from mouse brain. J Neurosci Methods 2015; 261:1-9. [PMID: 26698226 DOI: 10.1016/j.jneumeth.2015.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND The cell nucleus is a highly dynamic subcellular compartment performing crucial processes for functioning and administration of the cell. Proteomic analysis of isolated nuclear fraction enables in-depth insight into these processes leading to better understanding of physiological and pathological state of the brain. There is no universal method for nuclear proteome investigation and each biological material needs individual optimization. An additional difficulty is the large amount of nucleic acids, which impairs isoelectrofocusing of proteins and shotgun mass spectrometry analysis of complex peptide samples. NEW METHOD We performed the first comprehensive optimization of intact nuclei isolation from mouse brain in combination with nuclear protein purification prior to two-dimensional gel electrophoresis (2DE) and gel-free proteomic analysis. RESULTS Application of sonication, digestion with nuclease and protein precipitation with acetone allowed to obtain high quality 2DE gels. Shotgun mass spectrometry analysis of isolated proteins proved an enrichment in nuclear proteins. The 66.4% of 265 identified proteins had assigned nucleus localization in UniProt database. Gene Ontology analysis using DAVID platform revealed the highest fold enrichment in spliceosome (24.5), nuclear periphery (12.4) and nuclear matrix (11.3). COMPARISON WITH EXISTING METHODS The proposed procedure is tailored to mouse brain tissue nuclear subproteome investigation. The quality of isolated nuclei, the effectiveness of the protein purification, efficiency of protein recovery after precipitation and overall method reproducibility was taken into detailed consideration. CONCLUSIONS The elaborated procedure could be further applied for in-depth proteomic analysis of molecular processes occurring in the mouse brain nucleus.
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Affiliation(s)
- Urszula Jankowska
- Department of Structural Biology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agnieszka Latosinska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Bozena Skupien-Rabian
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Bianka Swiderska
- Department of Structural Biology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Marta Dziedzicka-Wasylewska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Structural Biology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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Brennan P, Shore AM, Clement M, Hewamana S, Jones CM, Giles P, Fegan C, Pepper C, Brewis IA. Quantitative nuclear proteomics reveals new phenotypes altered in lymphoblastoid cells. Proteomics Clin Appl 2015; 3:359-69. [PMID: 26238753 DOI: 10.1002/prca.200800137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Indexed: 12/23/2022]
Abstract
B-lymphocytes are essential for the production of antibodies to fight pathogens and are the cells of origin in 95% of human lymphomas. During their activation, and immortalisation by Epstein-Barr virus (EBV) which contributes to human cancers, B-lymphocytes undergo dramatic changes in cell size and protein content. This study was initiated to compare the proteome of two B-cell lines, from the same individual, that reflect different patterns of activation, one is EBV negative and the other is EBV positive. Using isobaric tags, LC-MALDI TOF-TOF and subcellular fractionation, we quantified 499 proteins from B-cells. From a detergent lysed protein extract, we identified 34 proteins that were differentially expressed in EBV-immortalised B-cells. By analysing a nuclear extract, we identified a further 29 differentially expressed proteins with only four proteins shared between the two extracts, illustrating the benefit of subcellular fractionation. This analysis has identified proteins involved in the cytoskeletal phenotype of activated B-cells and the increased antigen recognition in EBV-immortalised cells. Importantly, we have also identified new regulators of transcription and changes in ribonuclear proteins that may contribute to the increased cell size and immortalisation of lymphoblastoid cells.
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Affiliation(s)
- Paul Brennan
- Department of Medical Biochemistry and Immunology, School of Medicine, Cardiff University, Heath Park, Cardiff, UK.
| | - Angharad M Shore
- Department of Medical Biochemistry and Immunology, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Mathew Clement
- Department of Medical Biochemistry and Immunology, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Saman Hewamana
- Department of Medical Biochemistry and Immunology, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Catrin M Jones
- Department of Medical Biochemistry and Immunology, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Peter Giles
- Department of Pathology, Cardiff University, Heath Park, Cardiff, UK
| | - Christopher Fegan
- Department of Haematology, Cardiff University, Heath Park, Cardiff, UK
| | | | - Ian A Brewis
- Department of Medical Biochemistry and Immunology, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
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Li Q, Jain MR, Chen W, Li H. A multidimensional approach to an in-depth proteomics analysis of transcriptional regulators in neuroblastoma cells. J Neurosci Methods 2013; 216:118-27. [PMID: 23558336 DOI: 10.1016/j.jneumeth.2013.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/21/2013] [Accepted: 03/24/2013] [Indexed: 12/13/2022]
Abstract
The dynamic regulation of transcriptional events is fundamental to many aspects of neuronal cell functions. However, proteomics methods have not been routinely used in global neuroproteomics analyses of transcriptional regulators because they are much less abundant than the "house-keeping" proteins in cells and tissues. Recent improvements in both biochemical preparations of nuclear proteins and detection sensitivities of proteomics technologies have made the global analysis of nuclear transcriptional regulators possible. We report here an optimised neuroproteomic method for the analysis of transcriptional regulators in the nuclear extracts of SHSY-5Y neuroblastoma cells by combining an improved nuclear protein extraction procedure with multidimensional peptide separation approaches. We found that rigorous removal of cytoplasmic proteins and solubilisation of DNA-associated proteins improved the number of nuclear proteins identified. Furthermore, we discovered that multidimensional peptide separations by either strong cation exchange (SCX) chromatography or electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) analysis detected more than 1800 nuclear proteins, which constitutes one of the largest datasets of nuclear proteins reported for a neuronal cell. Thus, in-depth analysis of transcriptional regulators for studying neurological diseases are increasingly feasible.
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Affiliation(s)
- Qing Li
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School Cancer Center, 205 S. Orange Avenue, F-1226, Newark, NJ 07103, USA
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Lelong C, Chevallet M, Diemer H, Luche S, Van Dorsselaer A, Rabilloud T. Improved proteomic analysis of nuclear proteins, as exemplified by the comparison of two myeloid cell lines nuclear proteomes. J Proteomics 2012; 77:577-602. [DOI: 10.1016/j.jprot.2012.09.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 09/18/2012] [Accepted: 09/22/2012] [Indexed: 02/04/2023]
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Wasbrough ER, Dorus S, Hester S, Howard-Murkin J, Lilley K, Wilkin E, Polpitiya A, Petritis K, Karr TL. The Drosophila melanogaster sperm proteome-II (DmSP-II). J Proteomics 2010; 73:2171-85. [DOI: 10.1016/j.jprot.2010.09.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 09/07/2010] [Accepted: 09/07/2010] [Indexed: 01/07/2023]
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Seymour LM, Deutscher AT, Jenkins C, Kuit TA, Falconer L, Minion FC, Crossett B, Padula M, Dixon NE, Djordjevic SP, Walker MJ. A processed multidomain mycoplasma hyopneumoniae adhesin binds fibronectin, plasminogen, and swine respiratory cilia. J Biol Chem 2010; 285:33971-8. [PMID: 20813843 DOI: 10.1074/jbc.m110.104463] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Porcine enzootic pneumonia is a chronic respiratory disease that affects swine. The etiological agent of the disease, Mycoplasma hyopneumoniae, is a bacterium that adheres to cilia of the swine respiratory tract, resulting in loss of cilia and epithelial cell damage. A M. hyopneumoniae protein P116, encoded by mhp108, was investigated as a potential adhesin. Examination of P116 expression using proteomic analyses observed P116 as a full-length protein and also as fragments, ranging from 17 to 70 kDa in size. A variety of pathogenic bacterial species have been shown to bind the extracellular matrix component fibronectin as an adherence mechanism. M. hyopneumoniae cells were found to bind fibronectin in a dose-dependent and saturable manner. Surface plasmon resonance was used to show that a recombinant C-terminal domain of P116 bound fibronectin at physiologically relevant concentrations (K(D) 24 ± 6 nm). Plasmin(ogen)-binding proteins are also expressed by many bacterial pathogens, facilitating extracellular matrix degradation. M. hyopneumoniae cells were found to also bind plasminogen in a dose-dependent and saturable manner; the C-terminal domain of P116 binds to plasminogen (K(D) 44 ± 5 nm). Plasminogen binding was abolished when the C-terminal lysine of P116 was deleted, implicating this residue as part of the plasminogen binding site. P116 fragments adhere to the PK15 porcine kidney epithelial-like cell line and swine respiratory cilia. Collectively these data suggest that P116 is an important adhesin and virulence factor of M. hyopneumoniae.
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Affiliation(s)
- Lisa M Seymour
- Schools of Biological Sciences, University of Wollongong, New South Wales 2522, Australia
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Zhao P, Zhang L, Zhong W, Ying X, Huang H, Yao B, Yuan Z, Fu J, Wang Y, Zhou Z. Antigen-subtracted 2-DE/MS strategy, a novel proteomic analysis platform. Arch Toxicol 2010; 85:35-41. [DOI: 10.1007/s00204-010-0539-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 03/23/2010] [Indexed: 10/19/2022]
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Qin H, Wang Y. Exploring DNA-binding proteins with in vivo chemical cross-linking and mass spectrometry. J Proteome Res 2009; 8:1983-91. [PMID: 19714816 DOI: 10.1021/pr8009319] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA-binding proteins are very important constituents of proteomes of all species and play crucial roles in transcription, DNA replication, recombination, repair, and other activities associated with DNA. Although a number of DNA-binding proteins have been identified, many proteins involved in gene regulation and DNA repair are likely still unknown because of their dynamic and/or weak interactions with DNA. In this report, we described an approach for the comprehensive identification of DNA-binding proteins with in vivo formaldehyde cross-linking and LC-MS/MS. DNA-binding proteins could be purified via the isolation of DNA-protein complexes and released from the complexes by reversing the cross-linking. By using this method, we were able to identify more than one hundred DNA-binding proteins, such as proteins involved in transcription, gene regulation, DNA replication and repair, and a large number of proteins that are potentially associated with DNA and DNA-binding proteins. This method should be generally applicable to the investigation of other nucleic acid-binding proteins, and hold great potential in the comprehensive study of gene regulation, DNA damage response and repair, as well as many other critical biological processes at proteomic level.
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Affiliation(s)
- Haibo Qin
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA
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Rabilloud T, Vaezzadeh AR, Potier N, Lelong C, Leize-Wagner E, Chevallet M. Power and limitations of electrophoretic separations in proteomics strategies. MASS SPECTROMETRY REVIEWS 2009; 28:816-843. [PMID: 19072760 DOI: 10.1002/mas.20204] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.
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15
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Behr B, Rath D, Mueller P, Hildebrandt T, Goeritz F, Braun B, Leahy T, de Graaf S, Maxwell W, Hermes R. Feasibility of sex-sorting sperm from the white and the black rhinoceros (Ceratotherium simum, Diceros bicornis). Theriogenology 2009; 72:353-64. [DOI: 10.1016/j.theriogenology.2009.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 03/13/2009] [Accepted: 03/15/2009] [Indexed: 10/20/2022]
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16
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Aki T, Yanagisawa S. Application of Rice Nuclear Proteome Analysis to the Identification of Evolutionarily Conserved and Glucose-Responsive Nuclear Proteins. J Proteome Res 2009; 8:3912-24. [DOI: 10.1021/pr900187e] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Toshihiko Aki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Shuichi Yanagisawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
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Henrich S, Gez S, Crossett B, Mulligan SP, Christopherson RI. Fludarabine induces differential expression of proteins in human leukemia and lymphoma cells. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:634-40. [PMID: 18600519 DOI: 10.1080/15257770802142287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The purine analog fludarabine (FdAMP) is widely used for chemotherapy of B-lymphoid malignancies, and multiple mechanisms of action leading to apoptosis have been proposed. We examined changes at the protein level induced in the Raji cell line (Burkitt's lymphoma) by fludarabine nucleoside (FdA). Raji cells are sensitive to FdA. Raji cells treated with FdA (3 micro M, 24 hours), accumulate multiple phosphorylated forms of p53 in the nucleus that in turn degrade to phosphorylated forms of p40. Using CD antibody microarrays to determine surface expression profiles for Raji cells treated with FdA, we found up-regulation of the following CD antigens: CD20, CD54, CD80, CD86, and CD95. FdA thus induces changes in the genetic program of the cells that might be exploited to obtain synergy with therapeutic antibodies.
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Affiliation(s)
- S Henrich
- School of Molecular and Microbial Biosciences, University of Sydney, New South Wales, Australia
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