1
|
Yoshizato K, Taira T, Sato-Matsubara M, Sekiguchi S, Yabunaka Y, Kira Y, Ohashi T, Daikoku A, Ofusa K, Kadono C, Oikawa D, Matsubara T, Nakagama Y, Kido Y, Tokunaga F, Ikeda K, Kaneko A, Kawada N. Cloaking the ACE2 receptor with salivary cationic proteins inhibits SARS-CoV-2 entry. J Biochem 2022; 172:205-216. [PMID: 35792074 PMCID: PMC9278198 DOI: 10.1093/jb/mvac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/27/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Saliva contributes to the innate immune system, which suggests that it can prevent SARS-CoV-2 entry. We studied the ability of healthy salivary proteins to bind to angiotensin-converting enzyme 2 (ACE2) using biolayer interferometry and pull-down assays. Their effects on binding between the receptor-binding domain of the SARS-CoV-2 spike protein S1 (S1) and ACE2 were determined using an enzyme-linked immunosorbent assay. Saliva bound to ACE2 and disrupted the binding of S1 to ACE2 and four ACE2-binding salivary proteins were identified, including cationic histone H2A and neutrophil elastase, which inhibited the S1-ACE2 interaction. Calf thymus histone (ct-histone) also inhibited binding as effectively as histone H2A. The results of a cell-based infection assay indicated that ct-histone suppressed SARS-CoV-2 pseudoviral invasion into ACE2-expressing host cells. Manufactured polypeptides, such as ε-poly-L-lysine, also disrupted S1-ACE2 binding, indicating the importance of the cationic properties of salivary proteins in ACE2 binding. Overall, we demonstrated that positively-charged salivary proteins are a barrier against SARS-CoV-2 entry by cloaking the negatively-charged surface of ACE2, and provided a view that the cationic polypeptides represent a preventative and therapeutic treatment against COVID-19.
Collapse
Affiliation(s)
- Katsutoshi Yoshizato
- Osaka Metropolitan University Donated Laboratory for Synthetic Biology, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
- Osaka Metropolitan University BioIntegrence Co., Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Toshio Taira
- Sapporo Division, Cosmo Bio Co., Ltd. , Otaru, Hokkaido 047-0261, Japan
| | - Misako Sato-Matsubara
- Osaka Metropolitan University Donated Laboratory for Synthetic Biology, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
- Osaka Metropolitan University Department of Hepatology, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Shizuko Sekiguchi
- Sapporo Division, Cosmo Bio Co., Ltd. , Otaru, Hokkaido 047-0261, Japan
| | - Yoriko Yabunaka
- Osaka Metropolitan University Department of Research Support Platform, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Yukimi Kira
- Osaka Metropolitan University Department of Research Support Platform, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Tetsu Ohashi
- Sapporo Division, Cosmo Bio Co., Ltd. , Otaru, Hokkaido 047-0261, Japan
| | - Atsuko Daikoku
- Osaka Metropolitan University Anatomy and Regenerative Biology, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Ken Ofusa
- Osaka Metropolitan University Laboratory of Foods and Life Sciences, IDEA Consultants, Inc., Osaka, Osaka 559-8519, Japan; 8 Department of Pathobiochemistry, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Chiho Kadono
- Osaka Metropolitan University Donated Laboratory for Synthetic Biology, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
- Osaka Metropolitan University Department of Hepatology, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Daisuke Oikawa
- Osaka Metropolitan University Department of Parasitology and Research Center for Infectious Disease Sciences, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Tsutomu Matsubara
- Osaka Metropolitan University Anatomy and Regenerative Biology, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Yu Nakagama
- Osaka Metropolitan University Department of Parasitology and Research Center for Infectious Disease Sciences, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Yasutoshi Kido
- Osaka Metropolitan University Department of Parasitology and Research Center for Infectious Disease Sciences, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Fuminori Tokunaga
- Osaka Metropolitan University Department of Parasitology and Research Center for Infectious Disease Sciences, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Kazuo Ikeda
- Osaka Metropolitan University Anatomy and Regenerative Biology, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Akira Kaneko
- Osaka Metropolitan University Department of Parasitology and Research Center for Infectious Disease Sciences, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| | - Norifumi Kawada
- Osaka Metropolitan University Department of Hepatology, Graduate School of Medicine, , Osaka, Osaka 545-8585, Japan
| |
Collapse
|
2
|
Anti-PDHA1 antibody is detected in a subset of patients with schizophrenia. Sci Rep 2020; 10:7906. [PMID: 32404964 PMCID: PMC7220915 DOI: 10.1038/s41598-020-63776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/06/2020] [Indexed: 11/30/2022] Open
Abstract
Autoantibodies have been implicated in schizophrenia aetiology. Here, novel autoantibodies were isolated from patients with schizophrenia. Autoantibody candidates were searched using two-dimensional gel electrophoresis and western blotting with rat brain proteins as antigens and two sera pools (25 schizophrenia patients versus 25 controls) as antibodies. Immunoreactive antigens were identified by mass spectrometry. Antibody prevalence were evaluated by western blotting using human recombinant proteins. Furthermore, brain magnetic resonance imaging data (regional brain volumes and diffusion tensor imaging measures) were compared. Two proteins of the mitochondrial respiration pathway were identified as candidate antigens. Three patients with schizophrenia, but no controls, expressed antibodies targeting one of the candidate antigens, i.e., pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (PDHA1, EC 1.2.4.1), which is related to mitochondrial energy production. Anti-PDHA1 antibody-positive patients (n = 3) had increased volumes in the left occipital fusiform gyrus compared to both controls (n = 23, p = 0.017) and antibody-negative patients (n = 16, p = 0.009), as well as in the left cuneus compared to antibody-negative patients (n = 16, p = 0.018). This is the first report of an anti-PDHA1 antibody in patients with schizophrenia. Compatible with recent findings of mitochondrial dysfunction in schizophrenia, this antibody may be involved in the pathogenesis of a specific subgroup of schizophrenia.
Collapse
|
3
|
Hashimoto A, Takeuchi S, Kajita R, Yamagata A, Kakui R, Tanaka T, Nakata K. Proteogenomic analysis of granulocyte macrophage colony- stimulating factor autoantibodies in the blood of a patient with autoimmune pulmonary alveolar proteinosis. Sci Rep 2020; 10:4923. [PMID: 32188922 PMCID: PMC7080758 DOI: 10.1038/s41598-020-61934-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/02/2020] [Indexed: 11/18/2022] Open
Abstract
Recently, attempts to reveal the structures of autoantibodies comprehensively using improved proteogenomics technology, have become popular. This technology identifies peptides in highly purified antibodies by using an Orbitrap device to compare spectra from liquid chromatography-tandem mass spectrometry against a cDNA database obtained through next-generation sequencing. In this study, we first analyzed granulocyte-macrophage colony-stimulating factor (GM-CSF) autoantibodies in a patient with autoimmune pulmonary alveolar proteinosis, using the trapped ion mobility spectrometry coupled with quadrupole time-of-flight (TIMS-TOF) instrument. The TIMS-TOF instrument identified peptides that partially matched sequences in up to 156 out of 162 cDNA clones. Complementarity-determining region 3 (CDR3) was fully and partially detected in nine and 132 clones, respectively. Moreover, we confirmed one unique framework region 4 (FR4) and at least three unique across CDR3 to FR4 peptides via de novo peptide sequencing. This new technology may thus permit the comprehensive identification of autoantibody structure.
Collapse
Affiliation(s)
| | - Shiho Takeuchi
- Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | | | | | - Takahiro Tanaka
- Niigata University Medical & Dental Hospital, Niigata, Japan
| | - Koh Nakata
- Niigata University Medical & Dental Hospital, Niigata, Japan.
| |
Collapse
|
4
|
Wei Q, Zhang T, Fan J, Jiang R, Chang Q, Hong J, Xu G. Pathological myopia-induced antioxidative proteins in the vitreous humor. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:193. [PMID: 32309340 PMCID: PMC7154397 DOI: 10.21037/atm.2020.01.63] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background This study aimed to investigate differentially expressed proteins in the vitreous humor (VH) of pathological myopia (PM) and normal eyes. Methods VH samples were collected from patients undergoing surgical treatment for rhegmatogenous retinal detachment (RRD), idiopathic epiretinal membrane (ERM), myopic retinoschisis (MRS) or macular hole (MH). A label-free quantitative proteomic analysis was performed to detect the differentially expressed proteins, and expression of three differentially expressed proteins was confirmed by ELISA. Results In PM patients (MH-PM, MRS-PM and RRD-PM), the expression of prostaglandin-H2 D-isomerase (PGDS) and glutathione peroxidase 3 (GPX3) was significantly lower than in controls (MH, ERM, and RRD). The versican core protein expression decreased in the PM group. The vitreous concentrations of PGDS and GPX3 in patients with axial length (AL) of 26.5–29.0 mm were higher than in patients with AL >29.0 mm or AL <26.5 mm. NRF-2 expression was the lowest in patients with AL >29.0 mm. Conclusions Our study provides new evidence on the molecular changes in the VH of PM patients, and these molecules have the potential to become new targets for the therapy of PM.
Collapse
Affiliation(s)
- Qiaoling Wei
- Ophthalmology Department, EYE & ENT Hospital of Fudan University, Shanghai 200031, China.,Key Laboratory of Visual Impairment and Restoration of Fudan University, Shanghai 200031, China
| | - Ting Zhang
- Ophthalmology Department, EYE & ENT Hospital of Fudan University, Shanghai 200031, China.,Key Laboratory of Visual Impairment and Restoration of Fudan University, Shanghai 200031, China
| | - Jiawen Fan
- Ophthalmology Department, EYE & ENT Hospital of Fudan University, Shanghai 200031, China.,Key Laboratory of Visual Impairment and Restoration of Fudan University, Shanghai 200031, China
| | - Rui Jiang
- Ophthalmology Department, EYE & ENT Hospital of Fudan University, Shanghai 200031, China.,Key Laboratory of Visual Impairment and Restoration of Fudan University, Shanghai 200031, China
| | - Qing Chang
- Ophthalmology Department, EYE & ENT Hospital of Fudan University, Shanghai 200031, China.,Key Laboratory of Visual Impairment and Restoration of Fudan University, Shanghai 200031, China
| | - Jin Hong
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200031, China
| | - Gezhi Xu
- Ophthalmology Department, EYE & ENT Hospital of Fudan University, Shanghai 200031, China.,Key Laboratory of Visual Impairment and Restoration of Fudan University, Shanghai 200031, China
| |
Collapse
|
5
|
Kashiwazaki D, Uchino H, Kuroda S. Downregulation of Apolipoprotein-E and Apolipoprotein-J in Moyamoya Disease-A Proteome Analysis of Cerebrospinal Fluid. J Stroke Cerebrovasc Dis 2017; 26:2981-2987. [PMID: 28843803 DOI: 10.1016/j.jstrokecerebrovasdis.2017.07.028] [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] [Received: 06/22/2017] [Revised: 07/18/2017] [Accepted: 07/25/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND AND PURPOSE Genetic factors are closely involved in the etiology of moyamoya disease (MMD). However, its postgenomic mechanisms are still unknown. This study was aimed to identify specific biomarkers in the cerebrospinal fluid (CSF) of patients with MMD, using quantitative proteome technique. METHODS This study included 10 patients with MMD and 4 controls. The CSF was collected without blood contamination during surgery. A comparative 2-dimensional gel electrophoresis study (2D-PAGE) was performed. Protein spots that showed significant differences between moyamoya patients and controls were selected for further analysis by mass spectrometry. RESULTS On 2D-PAGE, 2 proteins were significantly upregulated, and 2 other proteins were downregulated in the CSF of MMD. Further mass spectrometry analysis revealed that haptoglobin and α-1-B-glycoprotein (A1BG) were upregulated. On the other hand, apolipoprotein-E (apoE), apoE precursor, and apolipoprotein-J (apoJ) were significantly downregulated in the CSF of MMD. The observed probability-based MOWSE score was 72 for haptoglobin (P <.05), 521 for A1BG (P <.05), 62 for apoE (P <.05), 72 for apoE precursor (P <.05), and 112 for apoJ (P <.05). CONCLUSION Although the role of A1BG in the central nervous system is still unknown, the overexpressed haptoglobin may indicate the inflammation and/or angiogenesis in MMD. The downregulation of apoE and apoJ strongly suggests a critical role of lipid metabolism in the development and progression of MMD. These proteins may be novel biomarkers in shedding light on the pathogenesis of MMD, although further studies would be warranted.
Collapse
Affiliation(s)
- Daina Kashiwazaki
- Department of Neurosurgery, Graduate School of Medicine and Pharmaceutical Science, University of Toyama University, Toyama, Japan.
| | - Haruto Uchino
- Department of Neurosurgery, Graduate School of Medicine and Pharmaceutical Science, University of Toyama University, Toyama, Japan
| | - Satoshi Kuroda
- Department of Neurosurgery, Graduate School of Medicine and Pharmaceutical Science, University of Toyama University, Toyama, Japan
| |
Collapse
|
6
|
Kuo HK, Chen YH, Huang F, Wu YC, Shiea J, Wu PC. The upregulation of zinc finger protein 670 and prostaglandin D2 synthase in proliferative vitreoretinopathy. Graefes Arch Clin Exp Ophthalmol 2015; 254:205-13. [DOI: 10.1007/s00417-015-3022-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 01/13/2023] Open
|
7
|
Tateno C, Yamamoto T, Utoh R, Yamasaki C, Ishida Y, Myoken Y, Oofusa K, Okada M, Tsutsui N, Yoshizato K. Chimeric Mice with Hepatocyte-humanized Liver as an Appropriate Model to Study Human Peroxisome Proliferator–activated Receptor-α. Toxicol Pathol 2014; 43:233-48. [DOI: 10.1177/0192623314544378] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Peroxisome proliferator (PP)–activated receptor-α (PPARα) agonists exhibit species-specific effects on livers of the rodent and human (h), which has been considered to reside in the difference of PPARα gene structures. However, the contribution of h-hepatocytes (heps) to the species-specificity remains to be clarified. In this study, the effects of fenofibrate were investigated using a hepatocyte-humanized chimeric mouse (m) model whose livers were replaced with h-heps at >70%. Fenofibrate induced hepatocellular hypertrophy, cell proliferation, and peroxisome proliferation in livers of severe combined immunodeficiency (SCID) mice, but not in the h-hep of chimeric mouse livers. Fenofibrate increased the expression of the enzymes of β- and ω-hydroxylation and deoxygenation of lipids at both gene and protein levels in SCID mouse livers, but not in the h-heps of chimeric mouse livers, supporting the studies with h-PPARα-transgenic mice, a hitherto reliable model for studying the regulation of h-PPARα in the h-liver in most respects, except the induction of the peroxisome proliferation. This study indicates the importance of not only h-PPARα gene but also h-heps themselves to correctly predict effects of fibrates on h-livers, and, therefore, suggests that the chimeric mouse is a currently available, consistent, and reliable model to obtain pharmaceutical data concerning the effects of fibrates on h-livers.
Collapse
Affiliation(s)
- Chise Tateno
- Yoshizato Project, Cooperative Link of Unique Science and Technology for Economy Revitalization (CLUSTER), Hiroshima Prefectural Institute of Industrial Science and Technology, Higashihiroshima, Japan
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- PhoenixBio Co., Ltd., Higashihiroshima, Japan
| | - Toshinobu Yamamoto
- Safety Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Kisarazu, Japan
| | - Rie Utoh
- Yoshizato Project, Cooperative Link of Unique Science and Technology for Economy Revitalization (CLUSTER), Hiroshima Prefectural Institute of Industrial Science and Technology, Higashihiroshima, Japan
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Tokyo, Japan
| | - Chihiro Yamasaki
- Yoshizato Project, Cooperative Link of Unique Science and Technology for Economy Revitalization (CLUSTER), Hiroshima Prefectural Institute of Industrial Science and Technology, Higashihiroshima, Japan
- PhoenixBio Co., Ltd., Higashihiroshima, Japan
| | - Yuji Ishida
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- PhoenixBio Co., Ltd., Higashihiroshima, Japan
| | - Yuka Myoken
- Prophoenix Co., Ltd., Developmental Biology Laboratory, Higashihiroshima, Japan
| | - Ken Oofusa
- Prophoenix Co., Ltd., Developmental Biology Laboratory, Higashihiroshima, Japan
- Prophoenix Division, Idea Consultants, Osaka, Japan
| | - Miyoko Okada
- Safety Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Kisarazu, Japan
| | - Naohisa Tsutsui
- Safety Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Kisarazu, Japan
| | - Katsutoshi Yoshizato
- Yoshizato Project, Cooperative Link of Unique Science and Technology for Economy Revitalization (CLUSTER), Hiroshima Prefectural Institute of Industrial Science and Technology, Higashihiroshima, Japan
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- PhoenixBio Co., Ltd., Higashihiroshima, Japan
- Hiroshima University 21st Century COE Program for Advanced Radiation Casualty Medicine, Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| |
Collapse
|
8
|
Shen Y, Smith RD. Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics. Expert Rev Proteomics 2014; 2:431-47. [PMID: 16000088 DOI: 10.1586/14789450.2.3.431] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent developments in combined separations with mass spectrometry for sensitive and high-throughput proteomic analyses are reviewed herein. These developments primarily involve high-efficiency (separation peak capacities of approximately 10(3)) nanoscale liquid chromatography (flow rates extending down to approximately 20 nl/min at optimal liquid mobile-phase separation linear velocities through narrow packed capillaries) in combination with advanced mass spectrometry and in particular, high-sensitivity and high-resolution Fourier transform ion cyclotron resonance mass spectrometry. Such approaches enable analysis of low nanogram level proteomic samples (i.e., nanoscale proteomics) with individual protein identification sensitivity at the low zeptomole level. The resultant protein measurement dynamic range can approach 10(6) for nanogram-sized proteomic samples, while more abundant proteins can be detected from subpicogram-sized (total) proteome samples. These qualities provide the foundation for proteomics studies of single or small populations of cells. The instrumental robustness required for automation and providing high-quality routine performance nanoscale proteomic analyses is also discussed.
Collapse
Affiliation(s)
- Yufeng Shen
- Biological Science Division & Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99352, USA.
| | | |
Collapse
|
9
|
Wang X, Liang J, Liu R, Dong Z, Yu S. The expression of succinate semialdehyde dehydrogenase in the caudal part of the spinal trigeminal nucleus is down-regulated after electrical stimulation of the dura mater surrounding the superior sagittal sinus in conscious rats. Neuroscience 2013; 248:145-53. [DOI: 10.1016/j.neuroscience.2013.05.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 05/01/2013] [Accepted: 05/13/2013] [Indexed: 01/13/2023]
|
10
|
Kweon HK, Andrews PC. Quantitative analysis of global phosphorylation changes with high-resolution tandem mass spectrometry and stable isotopic labeling. Methods 2013; 61:251-9. [PMID: 23611819 PMCID: PMC3700606 DOI: 10.1016/j.ymeth.2013.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 03/05/2013] [Accepted: 04/13/2013] [Indexed: 11/23/2022] Open
Abstract
Quantitative measurement of specific protein phosphorylation sites is a primary interest of biologists, as site-specific phosphorylation information provides insights into cell signaling networks and cellular dynamics at a system level. Over the last decade, selective phosphopeptide enrichment methods including IMAC and metal oxides (TiO₂ and ZrO₂) have been developed and greatly facilitate large scale phosphoproteome analysis of various cells, tissues and living organisms, in combination with modern mass spectrometers featuring high mass accuracy and high mass resolution. Various quantification strategies have been applied to detecting relative changes in expression of proteins, peptides, and specific modifications between samples. The combination of mass spectrometry-based phosphoproteome analysis with quantification strategies provides a straightforward and unbiased method to identify and quantify site-specific phosphorylation. We describe common strategies for mass spectrometric analysis of stable isotope labeled samples, as well as two widely applied phosphopeptide enrichment methods based on IMAC(NTA-Fe³⁺) and metal oxide (ZrO₂). Instrumental configurations for on-line LC-tandem mass spectrometric analysis and parameters of conventional bioinformatic analysis of large data sets are also considered for confident identification, localization, and reliable quantification of site-specific phosphorylation.
Collapse
Affiliation(s)
- Hye Kyong Kweon
- Department of Biological Chemistry, University of Michigan, USA.
| | | |
Collapse
|
11
|
Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | | | | |
Collapse
|
12
|
Wenger CD, Coon JJ. A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. J Proteome Res 2013; 12:1377-86. [PMID: 23323968 DOI: 10.1021/pr301024c] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The acquisition of high-resolution tandem mass spectra (MS/MS) is becoming more prevalent in proteomics, but most researchers employ peptide identification algorithms that were designed prior to this development. Here, we demonstrate new software, Morpheus, designed specifically for high-mass accuracy data, based on a simple score that is little more than the number of matching products. For a diverse collection of data sets from a variety of organisms (E. coli, yeast, human) acquired on a variety of instruments (quadrupole-time-of-flight, ion trap-orbitrap, and quadrupole-orbitrap) in different laboratories, Morpheus gives more spectrum, peptide, and protein identifications at a 1% false discovery rate (FDR) than Mascot, Open Mass Spectrometry Search Algorithm (OMSSA), and Sequest. Additionally, Morpheus is 1.5 to 4.6 times faster, depending on the data set, than the next fastest algorithm, OMSSA. Morpheus was developed in C# .NET and is available free and open source under a permissive license.
Collapse
Affiliation(s)
- Craig D Wenger
- Agilent Laboratories, Agilent Technologies, Santa Clara, California 95051, United States.
| | | |
Collapse
|
13
|
|
14
|
Tretyakova N, Goggin M, Sangaraju D, Janis G. Quantitation of DNA adducts by stable isotope dilution mass spectrometry. Chem Res Toxicol 2012; 25:2007-35. [PMID: 22827593 DOI: 10.1021/tx3002548] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exposure to endogenous and exogenous chemicals can lead to the formation of structurally modified DNA bases (DNA adducts). If not repaired, these nucleobase lesions can cause polymerase errors during DNA replication, leading to heritable mutations and potentially contributing to the development of cancer. Because of their critical role in cancer initiation, DNA adducts represent mechanism-based biomarkers of carcinogen exposure, and their quantitation is particularly useful for cancer risk assessment. DNA adducts are also valuable in mechanistic studies linking tumorigenic effects of environmental and industrial carcinogens to specific electrophilic species generated from their metabolism. While multiple experimental methodologies have been developed for DNA adduct analysis in biological samples, including immunoassay, HPLC, and ³²P-postlabeling, isotope dilution high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) generally has superior selectivity, sensitivity, accuracy, and reproducibility. As typical DNA adduct concentrations in biological samples are between 0.01-10 adducts per 10⁸ normal nucleotides, ultrasensitive HPLC-ESI-MS/MS methodologies are required for their analysis. Recent developments in analytical separations and biological mass spectrometry, especially nanoflow HPLC, nanospray ionization MS, chip-MS, and high resolution MS, have pushed the limits of analytical HPLC-ESI-MS/MS methodologies for DNA adducts, allowing researchers to accurately measure their concentrations in biological samples from patients treated with DNA alkylating drugs and in populations exposed to carcinogens from urban air, drinking water, cooked food, alcohol, and cigarette smoke.
Collapse
Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, USA.
| | | | | | | |
Collapse
|
15
|
Affiliation(s)
- Carol L Nilsson
- Department of Pharmacology & Toxicology, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas 77555-0617, United States.
| |
Collapse
|
16
|
Jedrychowski MP, Huttlin EL, Haas W, Sowa ME, Rad R, Gygi SP. Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol Cell Proteomics 2011; 10:M111.009910. [PMID: 21917720 DOI: 10.1074/mcp.m111.009910] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation modulates a myriad of biological functions, and its regulation is vital for proper cellular activity. Mass spectrometry is the enabling tool for phosphopeptide analysis, where recent instrumentation advances in both speed and sensitivity in linear ion trap and orbitrap technologies may yield more comprehensive phosphoproteomic analyses in less time. Protein phosphorylation analysis by MS relies on structural information derived through controlled peptide fragmentation. Compared with traditional, ion-trap-based collision-induced dissociation (CID), a more recent type of fragmentation termed HCD (higher energy collisional dissociation) provides beam type CID tandem MS with detection of fragment ions at high resolution in the orbitrap mass analyzer. Here we compared HCD to traditional CID for large-scale phosphorylation analyses of murine brain under three separate experimental conditions. These included a same-precursor analysis where CID and HCD scans were performed back-to-back, separate analyses of a phosphotyrosine peptide immunoprecipitation experiment, and separate whole phosphoproteome analyses. HCD generally provided higher search engine scores with more peptides identified, thus out-performing CID for back-to-back experiments for most metrics tested. However, for phosphotyrosine IPs and in a full phosphoproteome study of mouse brain, the greater acquisition speed of CID-only analyses provided larger data sets. We reconciled our results with those in direct contradiction from Nagaraj N, D'Souza RCJ et al. (J. Proteome Res. 9:6786, 2010). We conclude, for large-scale phosphoproteomics, CID fragmentation with rapid detection in the ion trap still produced substantially richer data sets, but the back-to-back experiments demonstrated the promise of HCD and orbitrap detection for the future.
Collapse
|
17
|
Hsieh LS, Ma GJ, Yang CC, Lee PD. Cloning, expression, site-directed mutagenesis and immunolocalization of phenylalanine ammonia-lyase in Bambusa oldhamii. PHYTOCHEMISTRY 2010; 71:1999-2009. [PMID: 21035152 DOI: 10.1016/j.phytochem.2010.09.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 08/30/2010] [Accepted: 09/27/2010] [Indexed: 05/30/2023]
Abstract
Phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) from green bamboo was isolated and cloned from the shell of Bambusa oldhamii. The K(m) of bamboo shell PAL for L-Phe was 476 μM, and the molecular mass of native PAL was estimated as 275 kDa and the molecular mass of a subunit was about 76 kDa, indicating that PAL from bamboo also exists as a tetramer. The optimum temperature for PAL activity was 50°C and the optimal pH 9.0. The identity of the purified bamboo shell PAL was confirmed using Q-TOF tandem MS/MS de novo sequencing. Four PAL genes, designated as BoPAL1 to BoPAL4, were cloned from B. oldhamii. The open reading frames of BoPAL3 and BoPAL4 were 2142 and 2106 bp in size, respectively: BoPAL2-4 contained one intron and two exons, but no intron was found in BoPAL1. BoPAL4 expressed in Escherichia coli possessed both PAL and tyrosine ammonia-lyase activities. While recombinant wild-type PAL proteins had similar biochemical properties to the native bamboo shell PAL, both site-directed mutagenesis of BoPAL1 F133H and BoPAL2 F134H, respectively, showed decreased k(cat)/K(m) values toward L-Phe, whereas BoPAL2 F134H showed a slightly increased k(cat)/K(m) value toward L-Tyr. These data suggest other residues largely control Phe/Tyr substrate specificity. An antibody raised against the purified shell PAL was generated for histochemical studies. In bamboo shell and branch shoots, PAL was localized primarily in sclerenchyma cells.
Collapse
Affiliation(s)
- Lu-Sheng Hsieh
- Institute of Microbiology and Biochemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei, Taiwan
| | | | | | | |
Collapse
|
18
|
Yamazaki H, Kuribayashi S, Inoue T, Tateno C, Nishikura Y, Oofusa K, Harada D, Naito S, Horie T, Ohta S. Approach for in Vivo Protein Binding of 5-n-Butyl-pyrazolo[1,5-a]pyrimidine Bioactivated in Chimeric Mice with Humanized Liver by Two-Dimensional Electrophoresis with Accelerator Mass Spectrometry. Chem Res Toxicol 2009; 23:152-8. [DOI: 10.1021/tx900323a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hiroshi Yamazaki
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| | - Shunji Kuribayashi
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| | - Tae Inoue
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| | - Chise Tateno
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| | - Yasufumi Nishikura
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| | - Ken Oofusa
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| | - Daisuke Harada
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| | - Shinsaku Naito
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| | - Toru Horie
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| | - Shigeru Ohta
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan, Preclinical Assessment Department, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima 772-8601, Japan, PhoenixBio, Co., Higashi-Hiroshima, Hiroshima 739-0046, Japan, Graduate School of Biomedical Sciences, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan, and Towa Environment Science Co., Suminoe-ku, Osaka 559-0034, Japan
| |
Collapse
|
19
|
Ito K, Funayama S, Hitomi Y, Nomura S, Katsura K, Saito M, Hayashi T, Kaneko N, Nohno K, Igarashi A. Proteome analysis of gelatin-bound salivary proteins in patients with primary Sjögren's Syndrome. Clin Chim Acta 2009; 403:269-71. [DOI: 10.1016/j.cca.2009.03.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 03/10/2009] [Accepted: 03/11/2009] [Indexed: 12/27/2022]
|
20
|
Kawase T, Okuda K, Kogami H, Nakayama H, Nagata M, Nakata K, Yoshie H. Characterization of human cultured periosteal sheets expressing bone-forming potential:in vitroandin vivoanimal studies. J Tissue Eng Regen Med 2009; 3:218-29. [DOI: 10.1002/term.156] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
21
|
Abstract
Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.
Collapse
Affiliation(s)
- Alison Lovegrove
- Department of Plant Sciences, Rothamsted Research, Centre for Crop Genetic Improvement, Harpenden, Hertfordshire, UK
| | | | | |
Collapse
|
22
|
Nabuchi Y, Murao N, Asoh Y, Takayama M. Probing the Unfolding and Refolding Processes of Carbonic Anhydrase 2 Using Electrospray Ionization Mass Spectrometry Combined with pH Jump. Anal Chem 2007; 79:8342-9. [PMID: 17900145 DOI: 10.1021/ac071130u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel method for proving the time course of the unfolding and refolding processes of metalloprotein bovine carbonic anhydrase 2 (CA2) is demonstrated using electrospray ionization mass spectrometry (ESI MS) combined with pH jumps between 3.6 and 4.4. The shift in mass accompanied by the release or coordination of a zinc ion and the change in the charge state distribution were measured to evaluate the folding process. The time course of the ESI mass spectra revealed the existence of four types of ions in the experimental system, i.e., lower charged apo-CA2 and holo-CA2 ions and higher charged apo-CA2 and holo-CA2 ions. The deconvolution spectrum of the ion peak ensemble for each type of ion was processed and time course plots of the relative intensities of the four ions were prepared in order to analyze the folding processes. These analyses revealed the coexistence of two folding states of the lower and higher charged apo-CA2 under the condition of pH 3.6. The lower and higher charged apoproteins spontaneously refolded to the lower charged holoprotein by a pH jump from 3.6 to 4.4 without the addition of an extra zinc ion. The higher charged holoprotein observed during both the unfolding and refolding processes was considered to be an intermediate of the change in folding. The present study indicates that ESI MS combined with pH jump would be a powerful method to probe the unfolding and refolding of proteins. This method simultaneously measures mass spectra and analyzes the folding processes as a function of time using deconvolution spectra constructed by selecting a suitable m/z range for the analysis from the peaks of charge state distributions.
Collapse
Affiliation(s)
- Yoshiaki Nabuchi
- Fuji Gotemba Research Laboratories, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka 412-8513, Japan.
| | | | | | | |
Collapse
|
23
|
Hu WS, Lin YH, Shih CC. A proteomic approach to study Salmonella enterica serovar Typhimurium putative transporter YjeH associated with ceftriaxone resistance. Biochem Biophys Res Commun 2007; 361:694-9. [PMID: 17669360 DOI: 10.1016/j.bbrc.2007.07.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2007] [Accepted: 07/18/2007] [Indexed: 10/23/2022]
Abstract
Mutant 6B7 of Salmonella enterica serovar Typhimurium has a transposon inserted in the putative transporter gene yjeH and shows a more-than-fourfold reduction in resistance to ceftriaxone. In this report we have used proteomic analysis to compare outer membrane protein profiles between this mutant and its parental strain R200. Five identified proteins were found to be altered. Of these proteins, the level of expression of the porin OmpD was increased and those of the putative outer membrane proteins STM1530 and STM3031, a subunit of the proton-pumping oxidoreductase NuoB and the heat shock protein MopA were decreased in 6B7 strain. Although the function of the yjeH gene remains unknown, a complementation assay suggested that the OmpD, STM1530, STM3031, NuoB, and MopA proteins are associated with ceftriaxone resistance and the expression of these proteins is influenced by the putative transporter gene yjeH in S. enterica serovar Typhimurium.
Collapse
Affiliation(s)
- Wensi S Hu
- Institute of Biotechnology in Medicine, School of Medical Technology and Engineering, National Yang-Ming University, 155, Li-Nong St., Sec. 2, Peitou, Taipei, Taiwan.
| | | | | |
Collapse
|
24
|
Hu WS, Yao SM, Fung CP, Hsieh YP, Liu CP, Lin JF. An OXA-66/OXA-51-like carbapenemase and possibly an efflux pump are associated with resistance to imipenem in Acinetobacter baumannii. Antimicrob Agents Chemother 2007; 51:3844-52. [PMID: 17724156 PMCID: PMC2151406 DOI: 10.1128/aac.01512-06] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We investigated the mechanisms involved in imipenem resistance in 23 clinical strains of Acinetobacter baumannii. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis showed the presence of a 30-kDa protein in imipenem-intermediate A. baumannii (IIAB) and imipenem-resistant A. baumannii (IRAB) strains; this protein was almost undetectable in imipenem-susceptible A. baumannii (ISAB) strains. The 30-kDa protein was identified as an OXA-51-like carbapenemase using two-dimensional gel electrophoresis and mass spectrometry. Similar to other recent findings, bla(OXA-51-like) genes were found to exist in all 23 clinical strains; however, the transcript levels of bla(OXA-51-like) in the IIAB and IRAB were higher than in the ISAB strains using reverse transcriptase PCR (RT-PCR) and real-time RT-PCR assays. This change was due to the presence of an insertion sequence, ISAba1, upstream of bla(OXA-51-like) in the IIAB and IRAB strains that was not present in the ISAB strains. The introduction of bla(OXA-66) (a bla(OXA-51)(-like) gene), identified in ISAB ab1254 and IRAB ab1266, into Escherichia coli TOP10 cells resulted in 3.95-fold and 7.90-fold elevations in resistance to imipenem, respectively. Furthermore, when ISAB ab8 and ISAB ab1254 and their in vitro-selected imipenem-resistant mutants ISAB ab8(r) and ISAB ab1254(r) were compared, the results showed no change in the bla(OXA-66)/bla(OXA-51-like) gene sequences, in expression of the gene, and in the outer membrane protein profiles. However, there was a four- to eightfold reduction in imipenem resistance upon adding carbonyl cyanide m-chlorophenylhydrazone. Taken together, these results suggest that the OXA-66/OXA-51-like carbapenemase contributes to intrinsic resistance to imipenem; however, drug export by an efflux pump may be more important and/or occur more frequently in imipenem-resistant A. baumannii. Furthermore, this is the first report of a Taiwanese strain of an OXA-66/OXA-51-like carbapenemase that confers imipenem resistance in A. baumannii.
Collapse
Affiliation(s)
- Wensi S Hu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, 155 Li-Nong St., Sec. 2, Peitou, Taipei 112, Taiwan.
| | | | | | | | | | | |
Collapse
|
25
|
Kusaka T, Ueno M, Miki T, Kanenishi K, Nagai Y, Huang CL, Okamoto Y, Ogawa T, Onodera M, Itoh S, Akiguchi I, Sakamoto H. Accumulation of triosephosphate isomerase, with sequence homology to Beta amyloid peptides, in vessel walls of the newborn piglet hippocampus. Microsc Res Tech 2007; 70:648-55. [PMID: 17393492 DOI: 10.1002/jemt.20448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We investigated whether beta-amyloid (Abeta)-like immunoreactivity was seen in the brains of newborn piglets. The immunoreactivity for Abeta(1-42) and Abeta(1-40) proteins, but not Abeta precursor protein, was present in CD68-positive perivascular cells of the hippocampus and in parts of the meninges. It was colocalized with immunoreactivity for receptor for advanced glycation end product and tumor necrosis factor-alpha. The protein with a molecular mass of 27 kDa, which was recognized by the Abeta antibodies, was identified as triosephosphate isomerase (TPI) with sequence homology to Abeta peptides by N-terminal amino acid sequencing, mass fingerprint analysis using matrix-associated laser desorption/ionization mass spectrometry, and Western blotting. Western blotting assay also revealed that detectable expression of Abeta proteins were not seen in the piglet brains. These findings indicate that TPI with sequence homology to Abeta peptides accumulates in perivascular cells of the microglia/macrophage lineage located around arterial vessels of the newborn piglet hippocampus.
Collapse
Affiliation(s)
- Takashi Kusaka
- Maternal and Perinatal Center, Faculty of Medicine, Kagawa University, Miki-cho 1750-1, Kita-gun, Kagawa, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Gerashchenko BI, Yamagata A, Oofusa K, Yoshizato K, de Toledo SM, Howell RW. Proteome analysis of proliferative response of bystander cells adjacent to cells exposed to ionizing radiation. Proteomics 2007; 7:2000-8. [PMID: 17514680 PMCID: PMC2921897 DOI: 10.1002/pmic.200600948] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Indexed: 12/30/2022]
Abstract
Recently (Cytometry 2003, 56A, 71-80), we reported that direct cell-to-cell contact is required for stimulating proliferation of bystander rat liver cells (WB-F344) cocultured with irradiated cells, and neither functional gap junction intercellular communication nor long-range extracellular factors appear to be involved in this proliferative bystander response (PBR). The molecular basis for this response is unknown. Confluent monolayers of WB-F344 cells were exposed to 5-Gray (Gy) of gamma-rays. Irradiated cells were mixed with unirradiated cells and co-cultured for 24 h. Cells were harvested and protein expression was examined using 2-DE. Protein expression was also determined in cultures of unirradiated and 5-Gy irradiated cells. Proteins were identified by MS. Nucleophosmin (NPM)-1, a multifunctional nucleolar protein, was more highly expressed in bystander cells than in either unirradiated or 5-Gy irradiated cells. Enolase-alpha, a glycolytic enzyme, was present in acidic and basic variants in unirradiated cells. In bystander and 5-Gy irradiated cells, the basic variant was weakly expressed, whereas the acidic variant was overwhelmingly present. These data indicate that the presence of irradiated cells can affect NPM-1 and enolase-alpha in adjacent bystander cells. These proteins appear to participate in molecular events related to the PBR and suggest that this response may involve cellular defense, proliferation, and metabolism.
Collapse
Affiliation(s)
- Bogdan I Gerashchenko
- Department of Radiology, MSB F-451, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, NJ, USA.
| | | | | | | | | | | |
Collapse
|
27
|
Li SQ, Qi HW, Wu CG, Zhang XJ, Yang SG, Zhao X, Wu Z, Wang Y, Que HP, Liu SJ. Comparative proteomic study of acute pulmonary embolism in a rat model. Proteomics 2007; 7:2287-99. [PMID: 17594686 DOI: 10.1002/pmic.200500665] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Pulmonary embolism (PE) is a common, potentially fatal disease, whose blood clots originate from the deep venous system of the lower extremities. PE is of clinical importance because of the considerable mortality and morbidity. In this study, at first we established a rat PE model by injecting 3-4 emboli into the left jugular vein. Before collecting the lung tissues, we perfused them with saline through the right jugular vein and at the same time cut off the right carotid to remove the blood. Then we separated and identified differentially expressed proteins in lung tissues at different time points using the techniques of 2-DE and MS. After image analysis of 2-DE gels, 46 protein spots of interest were excised from the gels and identified by MALDI-TOF-MS. Thirty-two protein spots of them found their corresponding protein candidates in the database. These proteins are associated with distinct aspects of PE such as the contractive function of smooth muscles, metabolism of energy, collagen and toxicant, cellular differentiation, apoptosis and injury, blood pressure adjustment, maintaining of acid-base balance, and so on. Ten of the identified proteins were validated by semiquantitative RT-PCR, and three of them were further validated by Western blot analysis. The differential expression patterns of these proteins suggest the distinct roles they may play in different stages of the rat PE model, and information from this study may be helpful to uncover the pathophysiologic molecular mechanisms involved in PE.
Collapse
Affiliation(s)
- Sheng-qing Li
- Department of Respiratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Wiley PR, Tosi P, Evrard A, Lovegrove A, Jones HD, Shewry PR. Promoter analysis and immunolocalisation show that puroindoline genes are exclusively expressed in starchy endosperm cells of wheat grain. PLANT MOLECULAR BIOLOGY 2007; 64:125-36. [PMID: 17294254 DOI: 10.1007/s11103-007-9139-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 01/20/2007] [Indexed: 05/13/2023]
Abstract
The purolindolines are small cysteine-rich proteins which are present in the grain of wheat. They have a major impact on the utilisation of the grain as they are the major determinants of grain texture, which affects both milling and baking properties. Bread and durum wheats were transformed with constructs comprising the promoter regions of the Puroindoline a (Pina) and Puroindoline b (Pinb) genes fused to the uidA (GUS) reporter gene. Nine lines showing 3:1 segregation for the transgene and comprising all transgene/species combinations were selected for detailed analysis of transgene expression during grain development. This showed that transgene expression occurred only in the starchy endosperm cells and was not observed in any other seed or vegetative tissues. The location of the puroindoline proteins in these cells was confirmed by tissue printing of developing grain, using a highly specific monoclonal antibody for detection and an antibody to the aleurone-localised 8S globulin as a control. This provides clear evidence that puroindolines are only synthesised and accumulated in the starchy endosperm cells of the wheat grain.
Collapse
Affiliation(s)
- Paul R Wiley
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | | | | | | | | | | |
Collapse
|
29
|
Kawakami M, Nakamura T, Okamura N, Komoto C, Markova S, Kobayashi H, Hashimoto N, Okumura K, Sakaeda T. Knock-down of Sorcin Induces Up-regulation of MDR1 in HeLa Cells. Biol Pharm Bull 2007; 30:1065-73. [PMID: 17541155 DOI: 10.1248/bpb.30.1065] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In our previous study, the MDR1/Pglycoprotein-overexpressing multidrug resistant subline, Hvr100-6, was established from the human cervical carcinoma cell line HeLa-Ohio (HeLa) by stepwise exposure to an anti-microtubule agent, vinblastine sulfate, a typical substrate of MDR1. Their gene and protein expression profiles were analyzed herein, and 148 genes were identified to be differentially expressed by cDNA microarray analysis. The up-regulation of sorcin, a soluble resistance-related calcium-binding protein of 22 kDa, was confirmed in Hvr100-6 cells by the proteome analysis. To clarify the relationship between MDR1 and sorcin, HeLa cells were treated with small interfering RNAs (siRNAs) targeted for theirs mRNAs. The siRNA for MDR1 mRNA resulted in its decrease by 86% and 61% on the days 1 and 2 after the treatment, whereas the expression level of sorcin mRNA was not changed. On the other hand, the siRNA for sorcin mRNA suppressed its expression by 80-90% on days 1-3 after the treatment. Interestingly; suppression of sorcin induced a more than 3-fold increase in the expression level for MDR1 mRNA. An efflux function of MDR1 evaluated with using rhodamine 123 as a probe showed a tendency to be increased in HeLa cells treated with siRNA for sorcin, compared with that in the cells treated with scramble siRNA. The activity and the expression of caspase-3 in the sorcin knock-down HeLa cells were relatively higher than those in the cells treated with scramble siRNA. Thus, we demonstrated that sorcin might be a partial suppressor of MDR1 expression. Furthermore, the present study suggested that sorcin repressed apoptosis via dysfunction of caspase-3.
Collapse
Affiliation(s)
- Megumi Kawakami
- Department of Hospital Pharmacy, School of Medicine, Kobe University, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Li SQ, Yun J, Xue FB, Bai CQ, Yang SG, Que HP, Zhao X, Wu Z, Wang Y, Liu SJ. Comparative Proteome Analysis of Serum from Acute Pulmonary Embolism Rat Model for Biomarker Discovery. J Proteome Res 2006; 6:150-9. [PMID: 17203959 DOI: 10.1021/pr0603102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pulmonary embolism (PE) is a common, potentially fatal disease and its diagnosis is challenging because clinical signs and symptoms are nonspecific. In this study, to investigate protein alterations of a rat PE model, total serum proteins collected at different time points were separated by two-dimensional electrophoresis (2-DE) and identified using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Bioinformatics analysis of 24 differentially expressed proteins showed that 20 had corresponding protein candidates in the database. According to their properties and obvious alterations after PE, changes of serum concentrations of Hp, Fn, DBP, RBP, and TTR were selected to be reidentified by western blot analysis. Semiquantitative RT-PCR showed DBP, RBP, and TTR to be down-regulated at mRNA levels in livers but not in lung tissues. The low serum concentrations of DBP, RBP, and TTR resulted in the up-regulation of 25(OH)D3, vitamin A, and FT4 (ligands of DBP, RBP, and TTR) after acute PE in rat models. The serum levels of Hp and Fn were detected in patients with DVT/PE and controls to explore their diagnostic prospects in acute PE because the mRNA levels of Hp and Fn were found to be up-regulated both in lung tissues and in livers after acute PE. Our data suggested that the concentration of serum Fn in controls was 79.42 +/- 31.57 microg/L, whereas that of PE/DVT patients was 554.43 +/- 136.18 microg/L (P < 0.001), and that the concentration of serum Hp in controls was 824.37 +/- 235.24 mg/L, whereas that of PE/DVT patients was 2063.48 +/- 425.38 mg/L (P < 0.001). The experimental PE rat model selected in this study was more similar to the clinical process than the other existing PE animal models, and the findings indicated instant changes of serum proteins within 48 h after acute PE. The exploration of these differentially expressed proteins or their combination with existent markers such as D-dimer may greatly improve the accuracy of the diagnosis of acute PE, but diagnostic tests are still needed to evaluate the sensitivity and specificity of these markers and also the number of false positives and false negatives.
Collapse
Affiliation(s)
- Sheng-qing Li
- Department of Respiratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi an 710032, PR China.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Kubo M, Nishitsuji H, Kurihara K, Hayashi T, Masuda T, Kannagi M. Suppression of human immunodeficiency virus type 1 replication by arginine deiminase of Mycoplasma arginini. J Gen Virol 2006; 87:1589-1593. [PMID: 16690923 DOI: 10.1099/vir.0.81549-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It was found previously that human immunodeficiency virus type 1 (HIV-1)-irrelevant CD8+ cytotoxic T lymphocytes (CTLs) from uninfected donors suppressed HIV-1 replication in a cell-contact-dependent manner. However, one of these CTL lines (CTL-3) also significantly suppressed HIV-1 replication through its supernatant. Here, the suppressive fraction from CTL-3 supernatant was purified and analysed by mass spectrometry. A protein band specific for the suppressive fraction was identified as arginine deiminase from Mycoplasma arginini, which catalyses the hydrolysis of arginine to citrulline. Addition of L-arginine or the use of antibiotics against mycoplasma restored supernatant-mediated but not cell-contact-dependent suppression of HIV-1 replication by CTL-3, clearly indicating that arginine deiminase of M. arginini in the supernatants suppressed HIV-1 replication, which is independent of CD8+ T-cell-mediated HIV-1 suppression via cell contact. Arginine deiminase is known to be a chemotherapeutic agent against arginine-requiring tumours and these results suggest that it also has potential application in antiviral therapy.
Collapse
Affiliation(s)
- Makoto Kubo
- Japanese Foundation for AIDS Prevention, Tokyo 105-0001, Japan
- Department of Immunotherapeutics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Hironori Nishitsuji
- Department of Immunotherapeutics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Kiyoshi Kurihara
- Department of Immunotherapeutics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takaya Hayashi
- Department of Immunotherapeutics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takao Masuda
- Department of Immunotherapeutics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Mari Kannagi
- Department of Immunotherapeutics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| |
Collapse
|
32
|
Yokoyama T, Yamane K, Minamoto A, Tsukamoto H, Yamashita H, Izumi S, Hoppe G, Sears JE, Mishima HK. High glucose concentration induces elevated expression of anti-oxidant and proteolytic enzymes in cultured human retinal pigment epithelial cells. Exp Eye Res 2006; 83:602-9. [PMID: 16697369 DOI: 10.1016/j.exer.2006.02.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 02/20/2006] [Accepted: 02/21/2006] [Indexed: 11/24/2022]
Abstract
We investigated the differential protein expression patterns of retinal pigment epithelial (RPE) cells exposed to increased glucose concentrations. Cultured human RPE cells (ARPE-19) were exposed for 4 days with normal blood glucose concentration (5.5 mM D-glucose), followed by exposure to either normal (5.5 mM) or high (33 mM) concentrations of D-glucose for 48h. Protein extracts of glucose-treated RPE cells were then subjected to comparative proteome analysis based on 2-D gel electrophoresis. Protein spots were visualized by silver staining. The differentially expressed proteins were excised and digested in-gel with trypsin, then analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The expression levels of cathepsin B, glutathione peroxidase and heat shock protein 27 were increased, and that of protein disulfide isomerase decreased in high glucose treated RPE compared to normal glucose. The isoelectric point of copper/zinc-containing superoxide dismutase (Cu/Zn-SOD) shifted toward acidic region in response to high glucose. Cu/Zn-SOD activity in high glucose group was significantly lower than that in normal glucose group (P<0.05, Mann-Whitney U-test). Systematic survey of protein expression has revealed that RPE cells respond to acute, pathologically high glucose levels by the elevated expression of anti-oxidant and proteolytic enzymes.
Collapse
Affiliation(s)
- Tomoko Yokoyama
- Department of Ophthalmology and Visual Science, Graduate School of Biomedical Sciences, Hiroshima University 1-2-3, Kasumi, Minami-ku, Hiroshima 734-8551, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Ding Q, Wu Z, Guo Y, Zhao C, Jia Y, Kong F, Chen B, Wang H, Xiong S, Que H, Jing S, Liu S. Proteome analysis of up-regulated proteins in the rat spinal cord induced by transection injury. Proteomics 2006; 6:505-18. [PMID: 16372269 DOI: 10.1002/pmic.200500296] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The inability of the CNS to regenerate in adult mammals propels us to reveal associated proteins involved in the injured CNS. In this paper, either thoracic laminectomy (as sham control) or thoracic spinal cord transection was performed on male adult rats. Five days after surgery, the whole spinal cord tissue was dissected and fractionated into water-soluble (dissolved in Tris buffer) and water-insoluble (dissolved in a solution containing chaotropes and surfactants) portions for 2-DE. Protein identification was performed by MS and further confirmed by Western blot. As a result, over 30 protein spots in the injured spinal cord were shown to be up-regulated no less than 1.5-fold. These identified proteins possibly play various roles during the injury and repair process and may be functionally categorized as several different groups, such as stress-responsive and metabolic changes, lipid and protein degeneration, neural survival and regeneration. In particular, over-expression of 11-zinc finger protein and glypican may be responsible for the inhibition of axonal growth and regeneration. Moreover, three unknown proteins with novel sequences were found to be up-regulated by spinal cord injury. Further characterization of these molecules may help us come closer to understanding the mechanisms that underlie the inability of the adult CNS to regenerate.
Collapse
Affiliation(s)
- Qinxue Ding
- Department of Neurobiology, Institute of Basic Medical Sciences, Beijing, PR China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Saito M, Kimoto M, Araki T, Shimada Y, Fujii R, Oofusa K, Hide M, Usui T, Yoshizato K. Proteome Analysis of Gelatin-Bound Urinary Proteins from Patients with Bladder Cancers. Eur Urol 2005; 48:865-71. [PMID: 15964125 DOI: 10.1016/j.eururo.2005.04.028] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Accepted: 04/26/2005] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Proteome analysis with protein separation by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometric measurement is utilized for comprehensive identification of proteins in various biological samples. However, this technique has not been widely applied for the analysis of body fluid for clinical assessments, because large amounts of proteins in fluid such as albumin and globulin hinder the detection of small amounts of proteins with high clinical values. The aim of the present study is to develop a method of proteomic analysis for urine of patients with bladder cancers. MATERIALS AND METHODS Urine samples collected from 40 patients with bladder cancers, 32 healthy volunteers, and 7 old volunteers with benign prostate hypertrophy were treated with gelatin-beads as a group-specific affinity carrier. The gelatin-bound proteins were subjected to the proteome analysis. RESULTS Various amounts of matrix metalloproteinase-2 (MMP-2), -9 (MMP-9), fibronectin (FN), and their fragments were identified on 2-D PAGE gels from cancer-bearing patients, but not from normal individuals. Importantly, not only total amounts of these proteins, but also patterns of their distributions on the gels were well matched with the extent of invasion diagnosed with histopathological examinations. Thus, the score including such qualitative patterning of these proteins predicts pathological stages of the cancer. CONCLUSION The proteomic analysis with gelatin-affinity purification of urine samples is useful not only for the diagnosis of bladder cancers, but also for estimating the extent of tumor invasion.
Collapse
|
35
|
Shieh IF, Lee CY, Shiea J. Eliminating the Interferences from TRIS Buffer and SDS in Protein Analysis by Fused-Droplet Electrospray Ionization Mass Spectrometry. J Proteome Res 2005; 4:606-12. [PMID: 15822941 DOI: 10.1021/pr049765m] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multiply charged protein ions were detected from the solutions containing a high concentration of tris(hydroxymethyl) aminomethane buffer (TRIS) and sodium dodecyl sulfate (SDS) using fused-droplet electrospray ionization mass spectrometry (FD-ESI/MS). The sample aerosols were generated at ambient temperature with a pneumatic nebulizer commonly used to produce sample aerosols in an atmospheric pressure chemical ionization (APCI) source. The aerosols were carried by nitrogen gas to the tip of a capillary where charged methanol droplets had been continuously generated by electrospraying an acidic methanol solution. The neutral sample aerosols then fused with the charged methanol droplets and electrospray ionization proceeded from the newly formed fused droplets to generate multiply charged protein ions. Because of its low solubility in methanol, TRIS molecules (concentration as high as 1 M) were efficiently excluded from the newly formed droplets and the protein ion signals were detected and observed in the mass spectra. To remove the interferences from SDS, equal moles of positively charged cetyltrimethylammonium bromide (CTAB) was added into the SDS containing sample solution to form the dodecyl sulfate-cetyltrimethylammonium ion pair (DS-CTA). The DS-CTA ion pair has a low polarity and solubility in methanol and is excluded from the fused droplet. Protein ions were still detected from the solution containing 10(-2) M of SDS.
Collapse
Affiliation(s)
- I-Fan Shieh
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | | | | |
Collapse
|
36
|
Tabata T, Katoh M, Tokudome S, Nakajima M, Yokoi T. Identification of the cytosolic carboxylesterase catalyzing the 5'-deoxy-5-fluorocytidine formation from capecitabine in human liver. Drug Metab Dispos 2004; 32:1103-10. [PMID: 15269188 DOI: 10.1124/dmd.104.000554] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Capecitabine, a prodrug of 5-fluorouracil, is first metabolized to 5'-deoxy-5-fluorocytidine (5'-DFCR) by carboxylesterase (CES), which is mainly expressed in microsomes. Recently, we clarified that 5'-DFCR formation was catalyzed by the enzyme in cytosol as well as microsomes in human liver. In the present study, the cytosolic enzyme involved in 5'-DFCR formation from capecitabine was identified. This enzyme was purified in the cytosolic preparation by ammonium sulfate precipitation, Sephacryl S-300 gel filtration, Mono P chromatofocusing, and Superdex 200 gel filtration. The purified enzyme was identified by the amino acid sequence analysis to be CES1A1 or a CES1A1 precursor. Based on the result of the N-terminal amino acid sequence analysis, the purified enzyme has no putative signal peptide, indicating that it was CES1A1. The apparent Km and Vmax values of 5'-DFCR formation were 19.2 mM and 88.3 nmol/min/mg protein, respectively. The 5'-DFCR formation catalyzed by the purified enzyme was inhibited by both diisopropylfluorophosphate and bis(p-nitrophenyl)phosphate in a concentration-dependent manner. 7-Ethyl-10-hydroxycamptothecin (SN-38) formation from irinotecan also occurred in the purified enzyme, cytosol, and microsomes. In conclusion, the cytosolic enzyme involved in 5'-DFCR formation from capecitabine would be CES1A1. It is suggested that the cytosolic CES has significant hydrolysis activity and plays an important role as the microsomal CES in drug metabolism. It is worthy to investigate the metabolic enzyme in cytosol involved in the activation of ester-type prodrugs such as capecitabine.
Collapse
Affiliation(s)
- Toshiki Tabata
- Drug Metabolism and Toxicology, Division of Pharmaceutical Sciences, Graduate School of Medical Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | | | | | | | | |
Collapse
|
37
|
Zhang X, Huang C, Tang X, Zhuang Y, Hew CL. Identification of structural proteins from shrimp white spot syndrome virus (WSSV) by 2DE-MS. Proteins 2004; 55:229-35. [PMID: 15048816 DOI: 10.1002/prot.10640] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
White spot syndrome virus (WSSV) is a major shrimp pathogen that also infects many other species of crustaceans. Its 305-kb double-stranded DNA genome has the capacity to encode 181 presumptive proteins. In an attempt to identify the viral proteins from the 181 theoretical proteins, proteins of the purified WSSV were separated by two-dimensional electrophoresis (2-DE). More than 60 protein spots were revealed, as detected by silver staining, from which 12 viral proteins were identified by mass spectrometry. In total, 25 WSSV proteins, including those reported in one of our earlier studies (Huang et al., Mol Cell Proteomics 2002;1:223-231), were revealed by this proteomic approach, and their corresponding genes were further confirmed by reverse transcription-polymerase chain reaction (RT-PCR). Two of them were characterized to be WSSV envelope proteins using immuno-electron microscopy. Our study showed that the proteomic approach is a powerful method for discovering the viral structural proteins and their corresponding genes.
Collapse
MESH Headings
- Animals
- Decapoda/virology
- Electrophoresis, Gel, Two-Dimensional
- Escherichia coli/genetics
- Gene Expression Regulation, Viral
- Genes, Viral/genetics
- Genome, Viral
- Mass Spectrometry
- Open Reading Frames
- Proteomics/methods
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sequence Homology
- Silver Staining
- Syndrome
- Transcription, Genetic/genetics
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/isolation & purification
- Viruses/chemistry
- Viruses/genetics
Collapse
Affiliation(s)
- Xiaobo Zhang
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | | | | | | |
Collapse
|
38
|
Yamane K, Minamoto A, Yamashita H, Takamura H, Miyamoto-Myoken Y, Yoshizato K, Nabetani T, Tsugita A, Mishima HK. Proteome analysis of human vitreous proteins. Mol Cell Proteomics 2003; 2:1177-87. [PMID: 12975481 DOI: 10.1074/mcp.m300038-mcp200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
PURPOSE Various protein contents such as enzymes, growth factors, and structural components are responsible for biological activities in organs. We have created a map of vitreous proteins and developed a proteome analysis of human vitreous samples to understand the underlying molecular mechanism and to provide clues to new therapeutic approaches in eyes with proliferative diabetic retinopathy (PDR). METHODS Vitreous and serum samples were obtained from subjects with idiopathic macular hole (MH, 26 cases) and PDR (33 cases). The expressed proteins in the samples were separated by two-dimensional (2-D) polyacrylamide gel electrophoresis. Protein spots were visualized by silver staining, and their expression patterns were analyzed. Some protein spots of concern were excised from the 2-D gels, digested in situ with trypsin, and analyzed by mass spectrometry. RESULTS More than 400 spots were detected on 2-D gels of MH cases, of which 78 spots were successfully analyzed. The spots corresponded to peptide fragments of 18 proteins, including pigment epithelium-derived factor, prostaglandin-D2 synthase, and interphotoreceptor retinoid-binding protein. These were not identified in the corresponding serum samples. These proteins were also expressed in PDR samples, with no distinct tendency to increase or decrease compared with the MH samples. More than 600 spots were detected on 2-D gels of PDR cases, of which 141 spots were successfully analyzed. The spots corresponded to peptide fragments of 38 proteins. Enolase and catalase were identified among four detected spots. Neither was found in MH vitreous or in PDR serum samples. CONCLUSION A map of protein expression was made in human vitreous from eyes with MH and PDR. In the PDR eyes, the increased protein expression observed was due to barrier dysfunction and/or production in the eye. Proteome analysis was useful in systematic screening of various protein expression in human vitreous samples.
Collapse
Affiliation(s)
- Ken Yamane
- Department of Ophthalmology and Visual Science, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Proteome analysis by two-dimensional gel electrophoresis and mass spectrometry: strengths and limitations. Trends Analyt Chem 2003. [DOI: 10.1016/s0165-9936(03)00508-9] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
40
|
Shipkova M, Armstrong VW, Oellerich M, Wieland E. Acyl glucuronide drug metabolites: toxicological and analytical implications. Ther Drug Monit 2003; 25:1-16. [PMID: 12548138 DOI: 10.1097/00007691-200302000-00001] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Although glucuronidation is generally considered a detoxification route of drug metabolism, the chemical reactivity of acyl glucuronides has been linked with the toxic properties of drugs that contain carboxylic acid moieties. It is now well documented that such metabolites can reach appreciable concentrations in blood. Furthermore, they are labile, undergo hydrolysis and pH-dependent intramolecular acyl migration to isomeric conjugates of glucuronic acid, and may react irreversibly with plasma proteins, tissue proteins, and with nucleic acids. This stable binding causes chemical alterations that are thought to contribute to drug toxicity either through changes in the functional properties of the modified molecules or through antigen formation with subsequent hypersensitivity and other immune reactions. Whereas in vitro data on the toxicity of acyl glucuronides have steadily accumulated, direct evidence for their toxicity in vivo is scarce. Acyl glucuronides display limited stability, which is dependent on pH, temperature, nature of the aglycon, and so on. Therefore, careful sample collection, handling, and storage procedures are critical to ensure generation of reliable pharmacologic and toxicologic data during clinical studies. Acyl glucuronides can be directly quantified in biologic specimens using chromatographic procedures. Their adducts with plasma or cell proteins can be determined after electrophoretic separation, followed by blotting. ELISA techniques have been used to assess the presence of antibodies against acyl glucuronide-protein adducts. This review summarizes the most recent evidence concerning biologic and toxicologic effects of acyl glucuronide metabolites of various drugs and discusses their relevance for drug monitoring. A critical evaluation of the available methodology is included.
Collapse
Affiliation(s)
- Maria Shipkova
- Department of Clinical Chemistry, Georg-August-University, Göttingen, Germany.
| | | | | | | |
Collapse
|
41
|
Wall DB, Berger SJ, Finch JW, Cohen SA, Richardson K, Chapman R, Drabble D, Brown J, Gostick D. Continuous sample deposition from reversed-phase liquid chromatography to tracks on a matrix-assisted laser desorption/ionization precoated target for the analysis of protein digests. Electrophoresis 2002; 23:3193-204. [PMID: 12298091 DOI: 10.1002/1522-2683(200209)23:18<3193::aid-elps3193>3.0.co;2-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Peptide mass fingerprinting by matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry (MS) is one of the standard high-throughput methods for protein identification today. Traditionally this method has been based on spotting peptide mixtures onto MALDI targets. While this method works well for more abundant proteins, low-abundance proteins mixed with high-abundance proteins tend to go undetected due to ion suppression effects, instrumental dynamic range limitations and chemical noise interference. We present an alternative approach where liquid chromatography (LC) effluent is continuously collected as linear tracks on a MALDI target. In this manner the chromatographic separation is spatially preserved on the target, which enables generation of off-line LC-MS and LC-MS/MS data by MALDI. LC-MALDI sample collection provides improved sensitivity and dynamic range, spatial resolution of peptides along the sample track, and permits peptide mass mapping of low-abundance proteins in mixtures containing high-abundance proteins. In this work, standard and ribosomal protein digests are resolved and captured using LC-MALDI sample collection and analyzed by MALDI-TOF-MS.
Collapse
|
42
|
Shen Y, Zhao R, Berger SJ, Anderson GA, Rodriguez N, Smith RD. High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal Chem 2002; 74:4235-49. [PMID: 12199598 DOI: 10.1021/ac0202280] [Citation(s) in RCA: 220] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe high-efficiency (peak capacities of approximately 10(3)) nanoscale (using column inner diameters down to 15 microm) liquid chromatography (nanoLC)/low flow rate electrospray (nanoESI) mass spectrometry (MS) for the sensitive analysis of complex global cellular protein enzymatic digests (i.e., proteomics). Using a liquid slurry packing method with carefully selected packing solvents, 87-cm-length capillaries having inner diameters of 14.9-74.5 microm were successfully packed with 3-microm C18-bonded porous (300-A pores) silica particles at a pressure of 18,000 psi. With a mobile-phase delivery pressure of 10,000 psi, these packed capillaries provided mobile-phase flow rates as low as approximately 20 nL/min at LC linear velocities of approximately 0.2 cm/s, which is near optimal for separation efficiency. To maintain chromatographic efficiency, unions with internal channel diameters as small as 10 microm were specially produced for connecting packed capillaries to replaceable nanoESI emitters having orifice diameters of 2-10 microm (depending on the packed capillary dimensions). Coupled on-line with a hybrid-quadrupole time-of-flight MS through the nanoESI interface, the nanoLC separations provided peak capacities of approximately 10(3) for proteome proteolytic polypeptide mixtures when a positive feedback switching valve was used for quantitatively introducing samples. Over a relatively large range of sample loadings (e.g., 5-100 ng, and 50-500 ng of cellular proteolytic peptides for 14.9- and 29.7-microm-i.d. packed capillaries, respectively), the nanoLC/nanoESI MS response for low-abundance components of the complex mixtures was found to increase linearly with sample loading. The nanoLC/nanoESI-MS sensitivity also increased linearly with decreasing flow rate (or approximately inversely proportional to the square of the capillary inner diameter) in the flow range of 20-400 nL/min. Thus, except at the lower loadings, decreasing the separation capillary inner diameter has an effect equivalent to increasing sample loading, which is important for sample-limited proteomic applications. No significant effects on recovery of eluting polypeptides were observed using porous C18 particles with surface pores of 300-A versus nonporous particles. Tandem MS analyses were also demonstrated using the high-efficiency nanoLC separations. Chromatographic elution time, MS response intensity, and mass measurement accuracy was examined between runs with a single column (with a single nanoESI emitter), between different columns (same and different inner diameters with different nanoESI emitters), and for different samples (various concentrations of cellular proteolytic peptides) and demonstrated robust and reproducible sensitive analyses for complex proteomic samples.
Collapse
Affiliation(s)
- Yufeng Shen
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | | | | | | | | | | |
Collapse
|
43
|
Leymarie N, Berg EA, McComb ME, O'Connor PB, Grogan J, Oppenheim FG, Costello CE. Tandem mass spectrometry for structural characterization of proline-rich proteins: application to salivary PRP-3. Anal Chem 2002; 74:4124-32. [PMID: 12199583 DOI: 10.1021/ac0255835] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proline-rich proteins (PRPs), including collagens, complement 1q, and salivary PRPs, are unusually difficult to sequence by mass spectrometry, due to the high efficiency of cleavage at the amide bond on the N-terminal of proline residues and the consequently low relative abundance of fragment arising from cleavages at other amide bonds. To fully characterize these proteins by mass spectrometry, specialized approaches to fragmentation are needed for the peptides with high proline content. Our work reported herein focused on the analysis of the set of peptides derived by tryptic cleavage of the salivary protein PRP-3. Two methods of fragmentation were compared: Collision-induced dissociation (CID) and electron capture dissociation (ECD). The data obtained demonstrated that ECD spectra of peptides containing more than 30% proline residues are simpler and easier to interpret than are CID spectra of those peptides. Factors that limit the two methods of fragmentation include the complexity of information contained in the CID spectra and the low efficiency of ECD processes. A complementary approach using both decomposition methods provides more complete and interpretable sequence information and yielded >93% sequence coverage for the 11-kDa PRP-3 isolated from human saliva.
Collapse
Affiliation(s)
- Nancy Leymarie
- Department of Biochemistry, Boston University School of Medicine, Massachusetts 02118, USA
| | | | | | | | | | | | | |
Collapse
|
44
|
Helsper JPFG, Gilissen LJWJ, van Ree R, America AHP, Cordewener JHG, Bosch D. Quadrupole time-of-flight mass spectrometry: a method to study the actual expression of allergen isoforms identified by PCR cloning. J Allergy Clin Immunol 2002; 110:131-8. [PMID: 12110832 DOI: 10.1067/mai.2002.125599] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Over the past 2 decades, molecular biology has shown that most major allergens exist in multiple isoforms. Very little is known about the relevance of allergen isoforms at the level of expressed protein (ie, actual allergen exposure). OBJECTIVE The aim of this study was to evaluate the applicability of state-of-the-art quadrupole time-of-flight mass spectrometry (Q-TOF MSMS) to the identification and quantification of allergen isoforms at the protein level. METHODS Q-TOF MSMS is a mass spectrometric approach for sequencing peptides and proteins. In our study it was applied to recombinant (r)Mal d 1, rBet v 1a and rBet v 1d, and natural (n)Mal d 1 from fruits of Malus domestica, cultivar Granny Smith. RESULTS Q-TOF MSMS allowed sequencing of about 70% of all amino acids in Mal d 1 and about 60% of those in Bet v 1. Mixing experiments with rBet v 1 isoforms and with rMal d 1 and nMal d 1 revealed that the technique allows identification of isoforms in mixtures down to a level of at least 5%. Recombinant Mal d 1 was identified as a Mal d 1a representative, whereas Granny Smith apples were shown to contain Mal d 1b-like allergen isoforms. In this apple cultivar hitherto unreported modifications of Mal d 1b were identified. Q-TOF MSMS allowed semiquantitative measurement of allergen at the femtomole to picomole level. CONCLUSION Q-TOF MSMS is a powerful tool to find out whether an allergen isoform, detected at the cDNA level, is really expressed in quantities relevant for the allergic patient.
Collapse
|
45
|
Zal F, Chausson F, Leize E, Van Dorsselaer A, Lallier FH, Green BN. Quadrupole time-of-flight mass spectrometry of the native hemocyanin of the deep-sea crab Bythograea thermydron. Biomacromolecules 2002; 3:229-31. [PMID: 11888305 DOI: 10.1021/bm0101668] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since electrospray ionization mass spectrometry (ESI-MS) has demonstrated capabilities for observing intact, weak interactions, there has been increasing interest in studying by this method noncovalently bound complexes. In this communication, we report for the first time the structure obtained by a commercial ESI quadrupole time-of-flight spectrometer on a native hemocyanin of deep-sea crab Bythograea thermydron with a molecular mass of 1.3 MDa. ESI-MS analysis of the native hemocyanin revealed the formation of a 18-mer noncovalent assembly with a measured molecular mass of 1354940 +/- 480 Da. ESI-MS data also revealed that this huge structure is an equilibrium with several assemblages, dodecamer (measured molecular weight = 902570 +/- 110 Da), hexamer (measured molecular weight = 450310 +/- 260 Da), and monomeric structures (measured molecular weight = 74999 +/- 85 Da).
Collapse
Affiliation(s)
- Franck Zal
- Equipe Ecophysiologie, UMR 7127 CNRS/UPMC, Station Biologique, BP 74, 29682 Roscoff Cedex, France.
| | | | | | | | | | | |
Collapse
|
46
|
Abstract
The emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Moreover, only through the study of proteins can posttranslational modifications be determined, which can profoundly affect protein function. Proteomics has been enabled by the accumulation of both DNA and protein sequence databases, improvements in mass spectrometry, and the development of computer algorithms for database searching. In this review, we describe why proteomics is important, how it is conducted, and how it can be applied to complement other existing technologies. We conclude that currently, the most practical application of proteomics is the analysis of target proteins as opposed to entire proteomes. This type of proteomics, referred to as functional proteomics, is always driven by a specific biological question. In this way, protein identification and characterization has a meaningful outcome. We discuss some of the advantages of a functional proteomics approach and provide examples of how different methodologies can be utilized to address a wide variety of biological problems.
Collapse
Affiliation(s)
- Paul R Graves
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, USA
| | | |
Collapse
|
47
|
Wabnitz PA, Loo JA. Drug screening of pharmaceutical discovery compounds by micro-size exclusion chromatography/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2002; 16:85-91. [PMID: 11754252 DOI: 10.1002/rcm.546] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Micro-size exclusion chromatography coupled with capillary liquid chromatography (capLC) and mass spectrometry (MS) provides a rapid and simple approach to the preliminary screening of active ligands toward a specific target macromolecule. In this study, the effectiveness of this technique is demonstrated by a number of small molecule ligands with known binding affinities towards the protein target. All ligands were incubated together with a target protein under native conditions. Separation was then achieved by microcentrifugation where the high molecular weight (MW) compounds were selectively passed through the size-exclusion material. The retained low MW compounds were then recovered and analyzed by capLC/MS. The absence of the ligand indicated strong affinity towards the target, while ligand detection indicated inactivity. This assay demonstrated the drugs that were acting as strong inhibitors of Co-PDF from those showing to be comparatively inactive. The relative binding rank order of the drugs towards Co-PDF was also determined. The results were validated by a corresponding set of control experiments in which the target molecules were excluded from the process. In principle, high-throughput micro-size exclusion chromatography, coupled with capLC/MS, offers a powerful technique as a preliminary screen in determining both the strong binding affinity and the relative affinity rank ordering of ligands towards a specific target macromolecule, and is complementary with other analytical drug screening techniques.
Collapse
Affiliation(s)
- Paul A Wabnitz
- Department of Pharmacokinetics, Dynamics and Metabolism. Pfizer Global Research & Development, Ann Arbor Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA.
| | | |
Collapse
|
48
|
Hille JM, Freed AL, Wätzig H. Possibilities to improve automation, speed and precision of proteome analysis: a comparison of two-dimensional electrophoresis and alternatives. Electrophoresis 2001; 22:4035-52. [PMID: 11824628 DOI: 10.1002/1522-2683(200111)22:19<4035::aid-elps4035>3.0.co;2-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Proteome analysis requires fast methods with high separation efficiencies in order to screen the various cell and tissue types for their proteome expression and monitor the effect of environmental conditions and time on this expression. The established two-dimensional gel electrophoresis (2-DE) is by far too slow for a consequential screening. Moreover, it is not precise enough to observe changes in protein concentrations. There are various approaches that promise faster, automated proteome analysis. This article concentrates on capillary (CT isoelectric focusing coupled to mass spectrometry (CIEF-MSn) and preparative IEF followed by size-exclusion chromatography, hyphenated with MS (PIEF-SEC-MS). These two approaches provide a similar separation pattern as the established 2-DE technique and therefore allow for the continued use of data based on this traditional approach. Their performances have been discussed and compared to 2-DE, evaluating 169 recent articles. Data on analysis time, automation, the detection limit, quantitation, peak capacity, mass and pI accuracy, as well as on the required sample amount are compared in a table.
Collapse
Affiliation(s)
- J M Hille
- Institute of Pharmaceutical Chemistry, University of Braunschweig, Germany
| | | | | |
Collapse
|
49
|
Li L, Masselon CD, Anderson GA, Pasa-Tolić L, Lee SW, Shen Y, Zhao R, Lipton MS, Conrads TP, Tolić N, Smith RD. High-throughput peptide identification from protein digests using data-dependent multiplexed tandem FTICR mass spectrometry coupled with capillary liquid chromatography. Anal Chem 2001; 73:3312-22. [PMID: 11476231 DOI: 10.1021/ac010192w] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tandem mass spectrometry (MS/MS) plays an important role in the unambiguous identification and structural elucidation of biomolecules. In contrast to conventional MS/MS approaches for protein identification where an individual polypeptide is sequentially selected and dissociated, a multiplexed-MS/MS approach increases throughput by selecting several peptides for simultaneous dissociation using either infrared multiphoton dissociation (IRMPD) or multiple frequency sustained off-resonance irradiation (SORI) collisionally induced dissociation (CID). The high mass measurement accuracy and resolution of FTICR combined with knowledge of peptide dissociation pathways allows the fragments arising from several different parent ions to be assigned. Herein we report the application of multiplexed-MS/MS coupled with on-line separations for the identification of peptides present in complex mixtures (i.e., whole cell lysate digests). Software was developed to enable "on-the-fly" data-dependent peak selection of a subset of polypeptides from each FTICR MS acquisition. In the subsequent MS/MS acquisitions, several coeluting peptides were fragmented simultaneously using either IRMPD or SORI-CID techniques. The utility of this approach has been demonstrated using a bovine serum albumin tryptic digest separated by capillary LC where multiple peptides were readily identified in single MS/MS acquisitions. We also present initial results from multiplexed-MS/MS analysis of a D. radiodurans whole cell digest to illustrate the utility of this approach for high-throughput analysis of a bacterial proteome.
Collapse
Affiliation(s)
- L Li
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Kawada N, Kristensen DB, Asahina K, Nakatani K, Minamiyama Y, Seki S, Yoshizato K. Characterization of a stellate cell activation-associated protein (STAP) with peroxidase activity found in rat hepatic stellate cells. J Biol Chem 2001; 276:25318-23. [PMID: 11320098 DOI: 10.1074/jbc.m102630200] [Citation(s) in RCA: 260] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A proteome approach for the molecular analysis of the activation of rat stellate cell, a liver-specific pericyte, led to the discovery of a novel protein named STAP (stellate cell activation-associated protein). We cloned STAP cDNA. STAP is a cytoplasmic protein with molecular weight of 21,496 and shows about 40% amino acid sequence homology with myoglobin. STAP was dramatically induced in in vivo activated stellate cells isolated from fibrotic liver and in stellate cells undergoing in vitro activation during primary culture. This induction was seen together with that of other activation-associated molecules, such as smooth muscle alpha-actin, PDGF receptor-beta, and neural cell adhesion molecule. The expression of STAP protein and mRNA was augmented time dependently in thioacetamide-induced fibrotic liver. Immunoelectron microscopy and proteome analysis detected STAP in stellate cells but not in other hepatic constituent cells. Biochemical characterization of recombinant rat STAP revealed that STAP is a heme protein exhibiting peroxidase activity toward hydrogen peroxide and linoleic acid hydroperoxide. These results indicate that STAP is a novel endogenous peroxidase catabolizing hydrogen peroxide and lipid hydroperoxides, both of which have been reported to trigger stellate cell activation and consequently promote progression of liver fibrosis. STAP could thus play a role as an antifibrotic scavenger of peroxides in the liver.
Collapse
Affiliation(s)
- N Kawada
- Department of Hepatology, Graduate School of Medicine, Osaka City University Medical School, Osaka 545-8585, Japan
| | | | | | | | | | | | | |
Collapse
|