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Tashima AK, de Castro LM, Fricker LD. Quantitative Peptidomics Using Reductive Methylation of Amines. Methods Mol Biol 2024; 2758:109-124. [PMID: 38549011 DOI: 10.1007/978-1-0716-3646-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
A number of different approaches have been used for quantitative peptidomics. In this protocol, we describe the method in which peptides are reacted with formaldehyde and sodium cyanoborohydride, which converts primary and secondary amines into tertiary amines. By using different combinations of regular reagents, deuterated reagents (2H), and reagents containing deuterium and 13C, it is possible to produce five isotopically distinct forms of the methylated peptides, which can be quantified by mass spectrometry. Peptides with free N-termini that are primary amines incorporate two methyl groups using this procedure, which differ by 2 Da for each of the five isotopic combinations. Peptides that contain unmodified lysine residues incorporate additional pairs of methyl groups, leading to larger mass differences between isotopic forms. The reagents are commercially available, relatively inexpensive, and chemically stable.
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Affiliation(s)
- Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.
| | - Leandro M de Castro
- Biodiversity of Coastal Environments Postgraduate Program, Bioscience Institute, São Paulo State University, São Vicente, SP, Brazil
| | - Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
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2
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Fricker LD. Quantitative Peptidomics: General Considerations. Methods Mol Biol 2024; 2758:89-108. [PMID: 38549010 DOI: 10.1007/978-1-0716-3646-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Peptidomics is the detection and identification of the peptides present in a sample, and quantitative peptidomics provides additional information about the amounts of these peptides. It is possible to perform absolute quantitation of peptide levels in which the biological sample is compared to synthetic standards of each peptide. More commonly, relative quantitation is performed to compare peptide levels between two or more samples. Relative quantitation can measure differences between all peptides that are detectable, which can exceed 1000 peptides in a complex sample. In this chapter, various techniques used for quantitative peptidomics are described along with discussion of the advantages and disadvantages of each approach. A guide to selecting the optimal quantitative approach is provided, based on the goals of the experiment and the resources that are available.
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Affiliation(s)
- Lloyd D Fricker
- Departments of Molecular Pharmacology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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3
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Abid MSR, Qiu H, Checco JW. Label-Free Quantitation of Endogenous Peptides. Methods Mol Biol 2024; 2758:125-150. [PMID: 38549012 PMCID: PMC11027169 DOI: 10.1007/978-1-0716-3646-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Liquid chromatography-mass spectrometry (LC-MS)-based peptidomics methods allow for the detection and identification of many peptides in a complex biological mixture in an untargeted manner. Quantitative peptidomics approaches allow for comparisons of peptide abundance between different samples, allowing one to draw conclusions about peptide differences as a function of experimental treatment or physiology. While stable isotope labeling is a powerful approach for quantitative proteomics and peptidomics, advances in mass spectrometry instrumentation and analysis tools have allowed label-free methods to gain popularity in recent years. In a general label-free quantitative peptidomics experiment, peak intensity information for each peptide is compared across multiple LC-MS runs. Here, we outline a general approach for label-free quantitative peptidomics experiments, including steps for sample preparation, LC-MS data acquisition, data processing, and statistical analysis. Special attention is paid to address run-to-run variability, which can lead to several major problems in label-free experiments. Overall, our method provides researchers with a framework for the development of their own quantitative peptidomics workflows applicable to quantitation of peptides from a wide variety of different biological sources.
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Affiliation(s)
| | - Haowen Qiu
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA.
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4
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SAKAGUCHI Y. Derivatization LC for the Sensitivity and Accuracy Bioanalysis. BUNSEKI KAGAKU 2022. [DOI: 10.2116/bunsekikagaku.71.307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fricker LD, Lemos Duarte M, Jeltyi A, Lueptow L, Fakira AK, Tashima AK, Hochgeschwender U, Wetsel WC, Devi LA. Mice heterozygous for a null mutation of Cpe show reduced expression of carboxypeptidase E mRNA and enzyme activity but normal physiology, behavior, and levels of neuropeptides. Brain Res 2022; 1789:147951. [PMID: 35618016 DOI: 10.1016/j.brainres.2022.147951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/02/2022]
Abstract
Carboxypeptidase E (CPE) is an essential enzyme that contributes to the biosynthesis of the vast majority of neuropeptides and peptide hormones. There are several reports claiming that small decreases in CPE activity cause physiological changes in animals and/or cultured cells, but these studies did not provide evidence that neuropeptide levels were affected by decreased CPE activity. In the present study, we tested if CPE is a rate-limiting enzyme in neuropeptide production using CpeNeo mice, which contain a neomycin cassette within the Cpe gene that eliminates enzyme expression. Homozygous CpeNeo/Neo mice show defects found in Cpefat/fat and/or Cpe global knockout (KO) mice, including greatly decreased levels of most neuropeptides, severely impaired fertility, depressive-like behavior, adult-onset obesity, and anxiety-like behavior. Removal of the neomycin cassette with Flp recombinase under a germline promoter restored expression of CPE activity and resulted in normal behavioral and physiological properties, including levels of neuropeptides. Mice heterozygous for the CpeNeo allele have greatly reduced levels of Cpe mRNA and CPE-like enzymatic activity. Despite the decreased levels of Cpe expression, heterozygous CpeNeo mice are behaviorally and physiologically identical to wild-type mice, with normal levels of most neuropeptides. These results indicate that CPE is not a rate-limiting enzyme in the production of most neuropeptides, casting doubt upon studies claiming small decreases in CPE activity contribute to obesity or other physiological effects.
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Affiliation(s)
- Lloyd D Fricker
- Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461.
| | - Mariana Lemos Duarte
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
| | - Andrei Jeltyi
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
| | - Lindsay Lueptow
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
| | - Amanda K Fakira
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
| | - Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP 04023-901, Brazil.
| | | | - William C Wetsel
- Departments of Psychiatry and Behavioral Sciences, Neurobiology, and Cell Biology, Duke University Medical Center, Durham, NC, 27710.
| | - Lakshmi A Devi
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029.
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6
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Lin Q, Li P, Fang M, Zhang D, Xia Y. Deep Profiling of Aminophospholipids Reveals a Dysregulated Desaturation Pattern in Breast Cancer Cell Lines. Anal Chem 2021; 94:820-828. [PMID: 34931817 DOI: 10.1021/acs.analchem.1c03494] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphatidylethanolamines (PEs), ether-PEs, and phosphatidylserines (PSs) are glycerophospholipids harboring a primary amino group in their headgroups. They are key components of mammalian cell membranes and play pivotal roles in cell signaling and apoptosis. In this study, a liquid chromatography-mass spectrometry (LC-MS) workflow for deep profiling of PEs, ether-PEs, and PSs has been developed by integrating two orthogonal derivatizations: (1) derivatization of the primary amino group by 4-trimethylammoniumbutyryl-N-hydroxysuccinimide (TMAB-NHS) for enhanced LC separation and MS detection and (2) the Paternò-Büchi (PB) reaction for carbon-carbon double bond (C═C) derivatization and localization. Significant improvement of the limit of identification down to the C═C location has been achieved for the standards of PSs (3 nM) and ether-PEs (20 nM). This workflow facilitates an identification of more than 200 molecular species of aminophospholipids in the porcine brain, two times more than those identified without TMAB-NHS derivatization. Importantly, we discovered that the n-10 isomers in C16:1 and C18:1 of aminophospholipids showed elevated contribution among other isomers, which correlated well with an increased transcription of the corresponding desaturase (FADS2) in the human breast cancer cell line (MDA-MB-231) relative to that in the normal cell line (HMEC). The abovementioned data suggest that lipid reprograming via forming different C═C location isomers might be an alternative mechanism in cancer cells.
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Affiliation(s)
- Qiaohong Lin
- Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 10084, China
| | - Pengyun Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Mengxuan Fang
- Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 10084, China.,School of Chemistry, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Donghui Zhang
- Department of Precision Instrument, Tsinghua University, Beijing 10084, China
| | - Yu Xia
- Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 10084, China
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Reichard CA, Naelitz BD, Wang Z, Jia X, Li J, Stampfer MJ, Klein EA, Hazen SL, Sharifi N. Gut Microbiome-Dependent Metabolic Pathways and Risk of Lethal Prostate Cancer: Prospective Analysis of a PLCO Cancer Screening Trial Cohort. Cancer Epidemiol Biomarkers Prev 2021; 31:192-199. [PMID: 34711629 DOI: 10.1158/1055-9965.epi-21-0766] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/01/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Diet and the gut microbiome have a complex interaction that generates metabolites with an unclear effect on lethal prostate cancer risk. Identification of modifiable risk factors for lethal prostate cancer is challenging given the long natural history of this disease and difficulty of prospectively identifying lethal cancers. METHODS Mass spectrometry was performed on baseline serum samples collected from 173 lethal prostate cancer cases and 519 controls enrolled in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening trial. Baseline serum levels of choline, carnitine, betaine, γ-butyrobetaine, crotonobetaine, phenylacetylglutamine, hippuric acid, and p-cresol sulfate were quantified and analyzed by quartile. Conditional multivariable logistic regression analysis associated analyte levels with lethal prostate cancer incidence after adjusting for body mass index and PSA. The Cochran-Armitage test evaluated analyte level trends across quartiles. RESULTS Relative to those in the first quartile, cases with the highest baseline levels of choline (Q4 OR: 2.19; 95% CI, 1.23-3.90; P-trend: 0.005) and betaine (Q4 OR: 1.86; 95% CI, 1.05-3.30; P-trend: 0.11) exhibited increased odds of developing lethal prostate cancer. Higher baseline serum levels of phenylacetylglutamine (Q4 OR: 2.55; 95% CI, 1.40-4.64; P-trend: 0.003), a gut microbiome metabolite of phenylalanine with adrenergic activity, were also associated with lethal prostate cancer. CONCLUSIONS Baseline serum levels of one-carbon methyl donors and adrenergic compounds resulting from human and gut microbiota-mediated metabolism are associated with increased lethal prostate cancer risk. IMPACT Dietary composition, circulating metabolite levels, and downstream signaling pathways may represent modifiable risk factors associated with incident lethal prostate cancer. Beta-adrenergic blockade represents an additional target for oncologic risk reduction.
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Affiliation(s)
- Chad A Reichard
- Genitourinary Malignancies Research Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio.,Urology of Indiana, Indianapolis, Indiana
| | - Bryan D Naelitz
- Genitourinary Malignancies Research Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio
| | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland Ohio
| | - Xun Jia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland Ohio
| | - Jianbo Li
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio.,Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Meir J Stampfer
- Departments of Epidemiology and Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Eric A Klein
- Genitourinary Malignancies Research Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Stanley L Hazen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland Ohio.,Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland Ohio
| | - Nima Sharifi
- Genitourinary Malignancies Research Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio. .,Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
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Elucidation of an anaerobic pathway for metabolism of l-carnitine-derived γ-butyrobetaine to trimethylamine in human gut bacteria. Proc Natl Acad Sci U S A 2021; 118:2101498118. [PMID: 34362844 PMCID: PMC8364193 DOI: 10.1073/pnas.2101498118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Trimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient l-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent l-carnitine-metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the l-carnitine-derived metabolite γ-butyrobetaine (γbb) by the human gut bacterium Emergencia timonensis We identify a set of genes up-regulated by γbb and demonstrate that the enzymes encoded by the induced γbb utilization (bbu) gene cluster convert γbb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a putative flavin cofactor to catalyze a redox-neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess the bbu gene cluster, providing insights into the distribution of anaerobic γbb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from l-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of the bbu pathway provides the critical missing link in anaerobic metabolism of l-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.
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9
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Neuropeptidomic Analysis of a Genetically Defined Cell Type in Mouse Brain and Pituitary. Cell Chem Biol 2020; 28:105-112.e4. [PMID: 33217339 DOI: 10.1016/j.chembiol.2020.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/09/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
Neuropeptides and peptide hormones are important cell-cell signaling molecules that mediate many physiological processes. Unlike classic neurotransmitters, peptides undergo cell-type-specific post-translational modifications that affect their biological activity. To enable the identification of the peptide repertoire of a genetically defined cell type, we generated mice with a conditional disruption of the gene for carboxypeptidase E (Cpe), an essential neuropeptide-processing enzyme. The loss of Cpe leads to accumulation of neuropeptide precursors containing C-terminal basic residues, which serve as tags for affinity purification. The purified peptides are subsequently identified using quantitative peptidomics, thereby revealing the specific forms of neuropeptides in cells with the disrupted Cpe gene. To validate the method, we used mice expressing Cre recombinase under the proopiomelanocortin (Pomc) promoter and analyzed hypothalamic and pituitary extracts, detecting peptides derived from proopiomelanocortin (as expected) and also proSAAS in POMC neurons. This technique enables the analyses of specific forms of peptides in any Cre-expressing cell type.
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10
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Substrate Specificity and Structural Modeling of Human Carboxypeptidase Z: A Unique Protease with a Frizzled-Like Domain. Int J Mol Sci 2020; 21:ijms21228687. [PMID: 33217972 PMCID: PMC7698808 DOI: 10.3390/ijms21228687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/29/2022] Open
Abstract
Metallocarboxypeptidase Z (CPZ) is a secreted enzyme that is distinguished from all other members of the M14 metallocarboxypeptidase family by the presence of an N-terminal cysteine-rich Frizzled-like (Fz) domain that binds Wnt proteins. Here, we present a comprehensive analysis of the enzymatic properties and substrate specificity of human CPZ. To investigate the enzymatic properties, we employed dansylated peptide substrates. For substrate specificity profiling, we generated two different large peptide libraries and employed isotopic labeling and quantitative mass spectrometry to study the substrate preference of this enzyme. Our findings revealed that CPZ has a strict requirement for substrates with C-terminal Arg or Lys at the P1′ position. For the P1 position, CPZ was found to display specificity towards substrates with basic, small hydrophobic, or polar uncharged side chains. Deletion of the Fz domain did not affect CPZ activity as a carboxypeptidase. Finally, we modeled the structure of the Fz and catalytic domains of CPZ. Taken together, these studies provide the molecular elucidation of substrate recognition and specificity of the CPZ catalytic domain, as well as important insights into how the Fz domain binds Wnt proteins to modulate their functions.
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11
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Simizo A, Kitano ES, Sant'Anna SS, Grego KF, Tanaka-Azevedo AM, Tashima AK. Comparative gender peptidomics of Bothrops atrox venoms: are there differences between them? J Venom Anim Toxins Incl Trop Dis 2020; 26:e20200055. [PMID: 33088286 PMCID: PMC7546584 DOI: 10.1590/1678-9199-jvatitd-2020-0055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: Bothrops atrox is known to be the pit viper responsible for
most snakebites and human fatalities in the Amazon region. It can be found
in a wide geographical area including northern South America, the east of
Andes and the Amazon basin. Possibly, due to its wide distribution and
generalist feeding, intraspecific venom variation was reported by previous
proteomics studies. Sex-based and ontogenetic variations on venom
compositions of Bothrops snakes were also subject of
proteomic and peptidomic analysis. However, the venom peptidome of
B. atrox remains unknown. Methods: We conducted a mass spectrometry-based analysis of the venom peptides of
individual male and female specimens combining bottom-up and top-down
approaches. Results: We identified in B. atrox a total of 105 native peptides in
the mass range of 0.4 to 13.9 kDa. Quantitative analysis showed that
phospholipase A2 and bradykinin potentiating peptides were the
most abundant peptide families in both genders, whereas disintegrin levels
were significantly increased in the venoms of females. Known peptides
processed at non-canonical sites and new peptides as the Ba1a, which
contains the SVMP BATXSVMPII1 catalytic site, were also revealed in this
work. Conclusion: The venom peptidomes of male and female specimens of B.
atrox were analyzed by mass spectrometry-based approaches in
this work. The study points to differences in disintegrin levels in the
venoms of females that may result in distinct pathophysiology of
envenomation. Further research is required to explore the potential
biological implications of this finding.
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Affiliation(s)
- Adriana Simizo
- Department of Biochemistry, Federal University of São Paulo (Unifesp), São Paulo, SP, Brazil
| | - Eduardo S Kitano
- Laboratory of Immunology, Heart Institute, Medical School, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Sávio S Sant'Anna
- Laboratory of Herpetology, Butantan Institute, São Paulo, SP, Brazil
| | | | | | - Alexandre K Tashima
- Department of Biochemistry, Federal University of São Paulo (Unifesp), São Paulo, SP, Brazil.,Special Laboratory for Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, São Paulo, SP, Brazil
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Identification and characterization of RSIY-11, a novel seminal peptide derived from semenogelin-1, which acts as a neutral endopeptidase inhibitor modulating sperm motility. J Assist Reprod Genet 2019; 36:1891-1900. [PMID: 31346917 DOI: 10.1007/s10815-019-01524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/08/2019] [Indexed: 10/26/2022] Open
Abstract
PURPOSE Based on prior reports demonstrating that neutral endopeptidase (NEP) inhibitors increase sperm motility, the goal of our studies was to identify endogenous seminal peptides that inhibit NEP and investigate their potential effect on sperm motility. METHODS Peptidomic analysis was performed on human seminal fluid, identifying 22 novel peptides. One peptide, named RSIY-11, derived from semenogelin-1, was predicted through sequence analysis to be a substrate and/or potential inhibitor of NEP. Enzymatic analysis was conducted to determine the inhibitory constant (Ki) of RSIY-11 as an inhibitor of NEP. Total and progressive sperm motility was determined at baseline and 30 and 60 min following addition of RSIY-11 to seminal fluid in 59 patients undergoing an infertility workup at an urban medical center. Additionally, the effects of RSIY-11 on sperm motility were evaluated in 15 of the 59 patients that met criteria for asthenospermia. RESULTS RSIY-11 was shown to act as a competitive inhibitor of NEP with a Ki of 18.4 ± 1.6 μM. Addition of RSIY-11 at concentrations of 0.75 μM, 7.5 μM, and 75 μM significantly increased sperm motility at all time points investigated, with increases of 6.1%, 6.9%, and 9.2% at 60 min, respectively. Additionally, within the subgroup of patients with asthenospermia, RSIY-11 at concentrations of 0.75 μM, 7.5 μM, and 75 μM significantly increased sperm motility at all time points investigated, with increases of 7.6%, 8.8%, and 10.6% at 60 min, respectively. CONCLUSIONS RSIY-11 is a newly identified semenogelin-1-derived peptide present in seminal fluid. RSIY-11 acts as a potent competitive inhibitor of NEP, which when added to seminal fluid significantly increases sperm motility. RSIY-11 could play a potential role in the treatment for male factor infertility related to asthenospermia and improve intrauterine insemination outcomes.
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13
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Teixeira CMM, Correa CN, Iwai LK, Ferro ES, Castro LMD. Characterization of Intracellular Peptides from Zebrafish (Danio rerio) Brain. Zebrafish 2019; 16:240-251. [DOI: 10.1089/zeb.2018.1718] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | - Leo Kei Iwai
- Special Laboratory of Applied Toxinology, Center of Toxins, Immune Response and Cell Signaling, Butantan Institute, São Paulo, Brazil
| | - Emer Suavinho Ferro
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo, Brazil
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Effect of Protein Denaturation and Enzyme Inhibitors on Proteasomal-Mediated Production of Peptides in Human Embryonic Kidney Cells. Biomolecules 2019; 9:biom9060207. [PMID: 31142026 PMCID: PMC6627375 DOI: 10.3390/biom9060207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/30/2019] [Accepted: 05/16/2019] [Indexed: 12/13/2022] Open
Abstract
Peptides produced by the proteasome have been proposed to function as signaling molecules that regulate a number of biological processes. In the current study, we used quantitative peptidomics to test whether conditions that affect protein stability, synthesis, or turnover cause changes in the levels of peptides in Human Embryonic Kidney 293T (HEK293T) cells. Mild heat shock (42 °C for 1 h) or treatment with the deubiquitinase inhibitor b-AP15 led to higher levels of ubiquitinated proteins but did not significantly increase the levels of intracellular peptides. Treatment with cycloheximide, an inhibitor of protein translation, did not substantially alter the levels of intracellular peptides identified herein. Cells treated with a combination of epoxomicin and bortezomib showed large increases in the levels of most peptides, relative to the levels in cells treated with either compound alone. Taken together with previous studies, these results support a mechanism in which the proteasome cleaves proteins into peptides that are readily detected in our assays (i.e., 6–37 amino acids) and then further degrades many of these peptides into smaller fragments.
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15
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Koeth RA, Lam-Galvez BR, Kirsop J, Wang Z, Levison BS, Gu X, Copeland MF, Bartlett D, Cody DB, Dai HJ, Culley MK, Li XS, Fu X, Wu Y, Li L, DiDonato JA, Tang WHW, Garcia-Garcia JC, Hazen SL. l-Carnitine in omnivorous diets induces an atherogenic gut microbial pathway in humans. J Clin Invest 2018; 129:373-387. [PMID: 30530985 DOI: 10.1172/jci94601] [Citation(s) in RCA: 191] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/30/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND l-Carnitine, an abundant nutrient in red meat, accelerates atherosclerosis in mice via gut microbiota-dependent formation of trimethylamine (TMA) and trimethylamine N-oxide (TMAO) via a multistep pathway involving an atherogenic intermediate, γ-butyrobetaine (γBB). The contribution of γBB in gut microbiota-dependent l-carnitine metabolism in humans is unknown. METHODS Omnivores and vegans/vegetarians ingested deuterium-labeled l-carnitine (d3-l-carnitine) or γBB (d9-γBB), and both plasma metabolites and fecal polymicrobial transformations were examined at baseline, following oral antibiotics, or following chronic (≥2 months) l-carnitine supplementation. Human fecal commensals capable of performing each step of the l-carnitine→γBB→TMA transformation were identified. RESULTS Studies with oral d3-l-carnitine or d9-γBB before versus after antibiotic exposure revealed gut microbiota contribution to the initial 2 steps in a metaorganismal l-carnitine→γBB→TMA→TMAO pathway in subjects. Moreover, a striking increase in d3-TMAO generation was observed in omnivores over vegans/vegetarians (>20-fold; P = 0.001) following oral d3-l-carnitine ingestion, whereas fasting endogenous plasma l-carnitine and γBB levels were similar in vegans/vegetarians (n = 32) versus omnivores (n = 40). Fecal metabolic transformation studies, and oral isotope tracer studies before versus after chronic l-carnitine supplementation, revealed that omnivores and vegans/vegetarians alike rapidly converted carnitine to γBB, whereas the second gut microbial transformation, γBB→TMA, was diet inducible (l-carnitine, omnivorous). Extensive anaerobic subculturing of human feces identified no single commensal capable of l-carnitine→TMA transformation, multiple community members that converted l-carnitine to γBB, and only 1 Clostridiales bacterium, Emergencia timonensis, that converted γBB to TMA. In coculture, E. timonensis promoted the complete l-carnitine→TMA transformation. CONCLUSION In humans, dietary l-carnitine is converted into the atherosclerosis- and thrombosis-promoting metabolite TMAO via 2 sequential gut microbiota-dependent transformations: (a) initial rapid generation of the atherogenic intermediate γBB, followed by (b) transformation into TMA via low-abundance microbiota in omnivores, and to a markedly lower extent, in vegans/vegetarians. Gut microbiota γBB→TMA/TMAO transformation is induced by omnivorous dietary patterns and chronic l-carnitine exposure. TRIAL REGISTRATION ClinicalTrials.gov NCT01731236. FUNDING NIH and Office of Dietary Supplements grants HL103866, HL126827, and DK106000, and the Leducq Foundation.
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Affiliation(s)
- Robert A Koeth
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and.,Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Jennifer Kirsop
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Zeneng Wang
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Bruce S Levison
- Department of Cellular and Molecular Medicine, Lerner Research Institute
| | - Xiaodong Gu
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | | | - David Bartlett
- Department of Cellular and Molecular Medicine, Lerner Research Institute
| | | | - Hong J Dai
- Global Biosciences, The Procter & Gamble Company, Cincinnati, Ohio, USA
| | - Miranda K Culley
- Department of Cellular and Molecular Medicine, Lerner Research Institute
| | - Xinmin S Li
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Xiaoming Fu
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Yuping Wu
- Department of Mathematics, Cleveland State University, Cleveland, Ohio, USA
| | - Lin Li
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - Joseph A DiDonato
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and
| | - W H Wilson Tang
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and.,Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Stanley L Hazen
- Department of Cellular and Molecular Medicine, Lerner Research Institute.,Center for Microbiome and Human Health, and.,Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
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Li Y, Wang X, Wang F, You L, Xu P, Cao Y, Chen L, Wen J, Guo X, Cui X, Ji C. Identification of intracellular peptides associated with thermogenesis in human brown adipocytes. J Cell Physiol 2018; 234:7104-7114. [PMID: 30387133 DOI: 10.1002/jcp.27465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/29/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Yun Li
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Xing Wang
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Fei Wang
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Lianghui You
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Pengfei Xu
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Yan Cao
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Ling Chen
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Juan Wen
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Xirong Guo
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Xianwei Cui
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
| | - Chenbo Ji
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital) Nanjing China
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17
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Tashima AK, Fricker LD. Quantitative Peptidomics with Five-plex Reductive Methylation labels. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:866-878. [PMID: 29235040 DOI: 10.1007/s13361-017-1852-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/16/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines. Up to five different isotopic forms can be generated, depending on the isotopic forms of formaldehyde and cyanoborohydride reagents, allowing for five-plex quantitation. However, the mass difference between each of these forms is only 1 Da per methyl group incorporated into the peptide, and for many peptides there is substantial overlap from the natural abundance of 13C and other isotopes. In this study, we calculated the contribution from the natural isotopes for 26 native peptides and derived equations to correct the peak intensities. These equations were applied to data from a study using human embryonic kidney HEK293T cells in which five replicates were treated with 100 nM vinblastine for 3 h and compared with five replicates of cells treated with control medium. The correction equations brought the replicates to the expected 1:1 ratios and revealed significant decreases in levels of 21 peptides upon vinblastine treatment. These equations enable accurate quantitation of small changes in peptide levels using the reductive methylation labeling approach. Graphical abstract ᅟ.
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Affiliation(s)
- Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, 04023-901, Brazil.
| | - Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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18
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Dasgupta S, Castro LM, Tashima AK, Fricker L. Quantitative Peptidomics Using Reductive Methylation of Amines. Methods Mol Biol 2018; 1719:161-174. [PMID: 29476510 DOI: 10.1007/978-1-4939-7537-2_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A number of different approaches have been used for quantitative peptidomics. In this protocol we describe the method in which peptides are reacted with formaldehyde and sodium cyanoborohydride, which converts primary and secondary amines into tertiary amines. By using different combinations of regular reagents, deuterated reagents (2H), and reagents containing deuterium and 13C, it is possible to produce five isotopically distinct forms of the methylated peptides which can be quantified by mass spectrometry. Peptides with free N-termini that are primary amines incorporate two methyl groups using this procedure, which differ by 2 Da for each of the five isotopic combinations. Peptides that contain unmodified lysine residues incorporate additional pairs of methyl groups, leading to larger mass differences between isotopic forms. The reagents are commercially available, relatively inexpensive, and chemically stable.
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Affiliation(s)
- Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Leandro M Castro
- Bioscience Institute, São Paulo State University, São Vicente, SP, Brazil
| | - Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Lloyd Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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Abstract
Peptidomics is the detection and identification of the peptides present in a sample, while quantitative peptidomics provides additional information about the amounts of these peptides. Comparison of peptide levels among two or more samples is termed relative quantitation. It is also possible to perform absolute quantitation of peptide levels in which the biological sample is compared to synthetic standards, which requires a separate standard for each peptide. In contrast, relative quantitation can compare levels of all peptides that are detectable in a sample, which can exceed 1000 peptides in a complex sample. In this chapter, various techniques used for quantitative peptidomics are described along with discussion of the advantages and disadvantages of each approach. A guide to selecting the optimal quantitative approach is provided, based on the goals of the experiment and the resources that are available.
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Affiliation(s)
- Lloyd Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA.
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20
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Boonen K, De Haes W, Van Houtven J, Verdonck R, Baggerman G, Valkenborg D, Schoofs L. Quantitative Peptidomics with Isotopic and Isobaric Tags. Methods Mol Biol 2018; 1719:141-159. [PMID: 29476509 DOI: 10.1007/978-1-4939-7537-2_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In differential peptidomics, peptide profiles are compared between biological samples and the resulting expression levels are correlated to a phenotype of interest. This, in turn, allows us insight into how peptides may affect the phenotype of interest. In quantitative differential peptidomics, both label-based and label-free techniques are often employed. Label-based techniques have several advantages over label-free methods, primarily that labels allow for various samples to be pooled prior to liquid chromatography-mass spectrometry (LC-MS) analysis, reducing between-run variation. Here, we detail a method for performing quantitative peptidomics using stable amine-binding isotopic and isobaric tags.
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Affiliation(s)
- Kurt Boonen
- Research Group of Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Wouter De Haes
- Research Group of Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium
- Research Group of Molecular and Functional Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Joris Van Houtven
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven, Belgium
| | - Rik Verdonck
- Research Group of Molecular Developmental Physiology and Signal Transduction, Department of Biology, KU Leuven, Leuven, Belgium
| | - Geert Baggerman
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Dirk Valkenborg
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Liliane Schoofs
- Research Group of Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium.
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21
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Garcia-Pardo J, Tanco S, Díaz L, Dasgupta S, Fernandez-Recio J, Lorenzo J, Aviles FX, Fricker LD. Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains. PLoS One 2017; 12:e0187778. [PMID: 29131831 PMCID: PMC5683605 DOI: 10.1371/journal.pone.0187778] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/25/2017] [Indexed: 11/18/2022] Open
Abstract
Metallocarboxypeptidase D (CPD) is a membrane-bound component of the trans-Golgi network that cycles to the cell surface through exocytic and endocytic pathways. Unlike other members of the metallocarboxypeptidase family, CPD is a multicatalytic enzyme with three carboxypeptidase-like domains, although only the first two domains are predicted to be enzymatically active. To investigate the enzymatic properties of each domain in human CPD, a critical active site Glu in domain I and/or II was mutated to Gln and the protein expressed, purified, and assayed with a wide variety of peptide substrates. CPD with all three domains intact displays >50% activity from pH 5.0 to 7.5 with a maximum at pH 6.5, as does CPD with mutation of domain I. In contrast, the domain II mutant displayed >50% activity from pH 6.5–7.5. CPD with mutations in both domains I and II was completely inactive towards all substrates and at all pH values. A quantitative peptidomics approach was used to compare the activities of CPD domains I and II towards a large number of peptides. CPD cleaved C-terminal Lys or Arg from a subset of the peptides. Most of the identified substrates of domain I contained C-terminal Arg, whereas comparable numbers of Lys- and Arg-containing peptides were substrates of domain II. We also report that some peptides with C-terminal basic residues were not cleaved by either domain I or II, showing the importance of the P1 position for CPD activity. Finally, the preference of domain I for C-terminal Arg was validated through molecular docking experiments. Together with the differences in pH optima, the different substrate specificities of CPD domains I and II allow the enzyme to perform distinct functions in the various locations within the cell.
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Affiliation(s)
- Javier Garcia-Pardo
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Sebastian Tanco
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lucía Díaz
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona, Spain
| | - Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Juan Fernandez-Recio
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona, Spain
| | - Julia Lorenzo
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Francesc X. Aviles
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- * E-mail: (LDF); (FXA)
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (LDF); (FXA)
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22
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Berezniuk I, Rodriguiz RM, Zee ML, Marcus DJ, Pintar J, Morgan DJ, Wetsel WC, Fricker LD. ProSAAS-derived peptides are regulated by cocaine and are required for sensitization to the locomotor effects of cocaine. J Neurochem 2017; 143:268-281. [PMID: 28881029 DOI: 10.1111/jnc.14209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/08/2017] [Accepted: 08/21/2017] [Indexed: 12/11/2022]
Abstract
To identify neuropeptides that are regulated by cocaine, we used a quantitative peptidomic technique to examine the relative levels of neuropeptides in several regions of mouse brain following daily intraperitoneal administration of 10 mg/kg cocaine or saline for 7 days. A total of 102 distinct peptides were identified in one or more of the following brain regions: nucleus accumbens, caudate putamen, frontal cortex, and ventral tegmental area. None of the peptides detected in the caudate putamen or frontal cortex were altered by cocaine administration. Three peptides in the nucleus accumbens and seven peptides in the ventral tegmental area were significantly decreased in cocaine-treated mice. Five of these ten peptides are derived from proSAAS, a secretory pathway protein and neuropeptide precursor. To investigate whether proSAAS peptides contribute to the physiological effects of psychostimulants, we examined acute responses to cocaine and amphetamine in the open field with wild-type (WT) and proSAAS knockout (KO) mice. Locomotion was stimulated more robustly in the WT compared to mutant mice for both psychostimulants. Behavioral sensitization to amphetamine was not maintained in proSAAS KO mice and these mutants failed to sensitize to cocaine. To determine whether the rewarding effects of cocaine were altered, mice were tested in conditioned place preference (CPP). Both WT and proSAAS KO mice showed dose-dependent CPP to cocaine that was not distinguished by genotype. Taken together, these results suggest that proSAAS-derived peptides contribute differentially to the behavioral sensitization to psychostimulants, while the rewarding effects of cocaine appear intact in mice lacking proSAAS.
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Affiliation(s)
- Iryna Berezniuk
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ramona M Rodriguiz
- Department of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, North Carolina, USA
| | - Michael L Zee
- Department of Anesthesiology and Perioperative Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - David J Marcus
- Department of Anesthesiology and Perioperative Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - John Pintar
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Daniel J Morgan
- Department of Anesthesiology and Perioperative Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - William C Wetsel
- Department of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, North Carolina, USA.,Departments of Neurobiology and Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Lloyd D Fricker
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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23
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Topolyan AP, Strizhevskaya DA, Slyundina MS, Belyaeva MA, Ivanova OM, Korshun VA, Ustinov AV, Mikhura IV, Formanovsky AA, Borisov RS. Tris(2,6-dimethoxyphenyl)methyl carbenium ion as a charge derivatization agent for the analysis of primary amines by MALDI mass spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1134/s106193481614015x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Monte ER, Rossato C, Llanos RP, Russo LC, de Castro LM, Gozzo FC, de Araujo CB, Peron JPS, Sant'Anna OA, Ferro ES, Rioli V. Interferon-gamma activity is potentiated by an intracellular peptide derived from the human 19S ATPase regulatory subunit 4 of the proteasome. J Proteomics 2017; 151:74-82. [DOI: 10.1016/j.jprot.2016.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/20/2016] [Accepted: 08/04/2016] [Indexed: 11/24/2022]
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25
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Sakaguchi Y, Kinumi T, Takatsu A. Quantification of peptides using N-terminal isotope coding and C-terminal derivatization for sensitive analysis by micro liquid chromatography-tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1111-1119. [PMID: 27591418 DOI: 10.1002/jms.3845] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/24/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
Stable isotope-coding coupled with mass spectrometry is a popular method for quantitative proteomics and peptide quantification. However, the efficiency of the derivatization reaction at a particular functional group, especially in complex structures, can affect accuracy. Here, we present a dual functional-group derivatization of bioactive peptides followed by micro liquid chromatography-tandem mass spectrometry (LC-MS/MS). By separating the sensitivity-enhancement and isotope-coding derivatization reactions, suitable chemistries can be chosen. The peptide amino groups were reductively alkylated with acetaldehyde or acetaldehyde-d4 to afford N-alkylated products with different masses. This process is simple, quick and high-yield, and accurate comparative analysis can be achieved for the mass-differentiated peptides. Then, the carboxyl groups were derivatized with 1-(2-pyrimidinyl)piperazine to increase MS/MS sensitivity. Angiotensins I-IV, bradykinin and neurotensin were analyzed after online solid phase extraction by micro LC-MS/MS. In all instances, a greater than 17-fold increase in sensitivity was achieved, compared with the analyses of the underivatized peptides. Furthermore, the values obtained from the present method were in agreement with the result from isotope dilution quantification using isotopically labeled angiotensin I [Asp-Arg-(Val-d8 )-Tyr-Ile-His-Pro-(Phe-d8 )-His-Leu]. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Yohei Sakaguchi
- Bio-medical Standards Group, Research Institute for Material and Chemical Measurement, National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), C-3, 1-1-1, Umezomo, Tsukuba, Ibaraki, 305-8563, Japan
| | - Tomoya Kinumi
- Bio-medical Standards Group, Research Institute for Material and Chemical Measurement, National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), C-3, 1-1-1, Umezomo, Tsukuba, Ibaraki, 305-8563, Japan
| | - Akiko Takatsu
- Bio-medical Standards Group, Research Institute for Material and Chemical Measurement, National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), C-3, 1-1-1, Umezomo, Tsukuba, Ibaraki, 305-8563, Japan
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26
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Dasgupta S, Yang C, Castro LM, Tashima AK, Ferro ES, Moir RD, Willis IM, Fricker LD. Analysis of the Yeast Peptidome and Comparison with the Human Peptidome. PLoS One 2016; 11:e0163312. [PMID: 27685651 PMCID: PMC5042401 DOI: 10.1371/journal.pone.0163312] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/07/2016] [Indexed: 12/22/2022] Open
Abstract
Peptides function as signaling molecules in species as diverse as humans and yeast. Mass spectrometry-based peptidomics techniques provide a relatively unbiased method to assess the peptidome of biological samples. In the present study, we used a quantitative peptidomic technique to characterize the peptidome of the yeast Saccharomyces cerevisiae and compare it to the peptidomes of mammalian cell lines and tissues. Altogether, 297 yeast peptides derived from 75 proteins were identified. The yeast peptides are similar to those of the human peptidome in average size and amino acid composition. Inhibition of proteasome activity with either bortezomib or epoxomicin led to decreased levels of some yeast peptides, suggesting that these peptides are generated by the proteasome. Approximately 30% of the yeast peptides correspond to the N- or C-terminus of the protein; the human peptidome is also highly represented in N- or C-terminal protein fragments. Most yeast and humans peptides are derived from a subset of abundant proteins, many with functions involving cellular metabolism or protein synthesis and folding. Of the 75 yeast proteins that give rise to peptides, 24 have orthologs that give rise to human and/or mouse peptides and for some, the same region of the proteins are found in the human, mouse, and yeast peptidomes. Taken together, these results support the hypothesis that intracellular peptides may have specific and conserved biological functions.
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Affiliation(s)
- Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, United States of America
| | - Leandro M. Castro
- Biomedical Science Institute, Campus on the São Paulo Coast, São Paulo State University, São Vicente, 11330–900, SP, Brazil
| | - Alexandre K. Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, 04023–901, SP, Brazil
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo, 05508–000, SP, Brazil
| | - Robyn D. Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
| | - Ian M. Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
- * E-mail:
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Verdonck R, De Haes W, Cardoen D, Menschaert G, Huhn T, Landuyt B, Baggerman G, Boonen K, Wenseleers T, Schoofs L. Fast and Reliable Quantitative Peptidomics with labelpepmatch. J Proteome Res 2016; 15:1080-9. [DOI: 10.1021/acs.jproteome.5b00845] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Gerben Menschaert
- Research
Group of Bio-informatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Thomas Huhn
- Chemistry
Department, University of Konstanz, Konstanz, Germany
| | | | - Geert Baggerman
- CFP/CeProMa, Antwerp University, Antwerp, Belgium
- Applied Bio & Molecular Systems, Vito, Mol, Belgium
| | - Kurt Boonen
- Biology
Department, KU Leuven, Leuven, Belgium
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Dasgupta S, Fishman MA, Mahallati H, Castro LM, Tashima AK, Ferro ES, Fricker LD. Reduced Levels of Proteasome Products in a Mouse Striatal Cell Model of Huntington's Disease. PLoS One 2015; 10:e0145333. [PMID: 26691307 PMCID: PMC4686214 DOI: 10.1371/journal.pone.0145333] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022] Open
Abstract
Huntington's disease is the result of a long polyglutamine tract in the gene encoding huntingtin protein, which in turn causes a large number of cellular changes and ultimately results in neurodegeneration of striatal neurons. Although many theories have been proposed, the precise mechanism by which the polyglutamine expansion causes cellular changes is not certain. Some evidence supports the hypothesis that the long polyglutamine tract inhibits the proteasome, a multiprotein complex involved in protein degradation. However, other studies report normal proteasome function in cells expressing long polyglutamine tracts. The controversy may be due to the methods used to examine proteasome activity in each of the previous studies. In the present study, we measured proteasome function by examining levels of endogenous peptides that are products of proteasome cleavage. Peptide levels were compared among mouse striatal cell lines expressing either 7 glutamines (STHdhQ7/Q7) or 111 glutamines in the huntingtin protein, either heterozygous (STHdhQ7/Q111) or homozygous (STHdhQ111/Q111). Both of the cell lines expressing huntingtin with 111 glutamines showed a large reduction in nearly all of the peptides detected in the cells, relative to levels of these peptides in cells homozygous for 7 glutamines. Treatment of STHdhQ7/Q7 cells with proteasome inhibitors epoxomicin or bortezomib also caused a large reduction in most of these peptides, suggesting that they are products of proteasome-mediated cleavage of cellular proteins. Taken together, these results support the hypothesis that proteasome function is impaired by the expression of huntingtin protein containing long polyglutamine tracts.
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Affiliation(s)
- Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
| | - Michael A. Fishman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
| | - Hana Mahallati
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
| | - Leandro M. Castro
- São Paulo State University (UNESP), Experimental Campus on the São Paulo Coast, São Vicente, 11330–900, SP, Brazil
| | - Alexandre K. Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, 04023–901, SP, Brazil
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo, 05508–000, SP, Brazil
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
- * E-mail:
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Fricker LD. Limitations of Mass Spectrometry-Based Peptidomic Approaches. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1981-91. [PMID: 26305799 PMCID: PMC6597174 DOI: 10.1007/s13361-015-1231-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/02/2015] [Accepted: 07/03/2015] [Indexed: 05/23/2023]
Abstract
Mass spectrometry-based peptidomic approaches are powerful techniques to detect and identify the peptide content of biological samples. The present study investigated the limitations of peptidomic approaches using trimethylammonium butyrate isotopic tags to quantify relative peptide levels and Mascot searches to identify peptides. Data were combined from previous studies on human cell lines or mouse tissues. The combined databases contain 2155 unique peptides ranging in mass from 444 to 8765 Da, with the vast majority between 1 and 3 kDa. The amino acid composition of the identified peptides generally reflected the frequency in the Eukaryotic proteome with the exception of Cys, which was not present in any of the identified peptides in the free-SH form but was detected at low frequency as a disulfide with Cys residues, a disulfide with glutathione, or as S-cyanocysteine. To test if the low detection rate of peptides smaller than 500 Da, larger than 3 kDa, or containing Cys was a limitation of the peptidomics procedure, tryptic peptides of known proteins were processed for peptidomics using the same approach used for human cell lines and mouse tissues. The identified tryptic peptides ranged from 516 to 2418 Da, whereas the theoretical digest ranged from 217 to 7559 Da. Peptides with Cys were rarely detected and, if present, the Cys was usually modified S-cyanocysteine. Additionally, peptides with mono- and di-iodo Tyr and His were identified. Taken together, there are limitations of peptidomic techniques, and awareness of these limitations is important to properly use and interpret results. Graphical Abstract ᅟ.
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Affiliation(s)
- Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, 10461, USA.
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Buchberger A, Yu Q, Li L. Advances in Mass Spectrometric Tools for Probing Neuropeptides. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:485-509. [PMID: 26070718 PMCID: PMC6314846 DOI: 10.1146/annurev-anchem-071114-040210] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Neuropeptides are important mediators in the functionality of the brain and other neurological organs. Because neuropeptides exist in a wide range of concentrations, appropriate characterization methods are needed to provide dynamic, chemical, and spatial information. Mass spectrometry and compatible tools have been a popular choice in analyzing neuropeptides. There have been several advances and challenges, both of which are the focus of this review. Discussions range from sample collection to bioinformatic tools, although avenues such as quantitation and imaging are included. Further development of the presented methods for neuropeptidomic mass spectrometric analysis is inevitable, which will lead to a further understanding of the complex interplay of neuropeptides and other signaling molecules in the nervous system.
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Affiliation(s)
- Amanda Buchberger
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1322;
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222;
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1322;
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222;
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Proteolytic Processing of Neuropeptides. ANALYSIS OF POST-TRANSLATIONAL MODIFICATIONS AND PROTEOLYSIS IN NEUROSCIENCE 2015. [DOI: 10.1007/7657_2015_87] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Koeth RA, Levison BS, Culley MK, Buffa JA, Wang Z, Gregory JC, Org E, Wu Y, Li L, Smith JD, Tang WHW, DiDonato JA, Lusis AJ, Hazen SL. γ-Butyrobetaine is a proatherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO. Cell Metab 2014; 20:799-812. [PMID: 25440057 PMCID: PMC4255476 DOI: 10.1016/j.cmet.2014.10.006] [Citation(s) in RCA: 374] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 09/05/2014] [Accepted: 10/13/2014] [Indexed: 01/30/2023]
Abstract
L-carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein, we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ∼1,000-fold higher than the formation of TMA. Moreover, we show that γBB is the major gut microbial metabolite formed from dietary L-carnitine in mice, is converted into TMA and TMAO in a gut microbiota-dependent manner (like dietary L-carnitine), and accelerates atherosclerosis. Gut microbial composition and functional metabolic studies reveal that distinct taxa are associated with the production of γBB or TMA/TMAO from dietary L-carnitine. Moreover, despite their close structural similarity, chronic dietary exposure to L-carnitine or γBB promotes development of functionally distinct microbial communities optimized for the metabolism of L-carnitine or γBB, respectively.
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Affiliation(s)
- Robert A Koeth
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bruce S Levison
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Miranda K Culley
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jennifer A Buffa
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zeneng Wang
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jill C Gregory
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Elin Org
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Yuping Wu
- Department of Mathematics, Cleveland State University, Cleveland, OH 44115, USA
| | - Lin Li
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jonathan D Smith
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - W H Wilson Tang
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Joseph A DiDonato
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Aldons J Lusis
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Stanley L Hazen
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA.
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Dasgupta S, Castro LM, Dulman R, Yang C, Schmidt M, Ferro ES, Fricker LD. Proteasome inhibitors alter levels of intracellular peptides in HEK293T and SH-SY5Y cells. PLoS One 2014; 9:e103604. [PMID: 25079948 PMCID: PMC4117522 DOI: 10.1371/journal.pone.0103604] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/03/2014] [Indexed: 12/17/2022] Open
Abstract
The proteasome cleaves intracellular proteins into peptides. Earlier studies found that treatment of human embryonic kidney 293T (HEK293T) cells with epoxomicin (an irreversible proteasome inhibitor) generally caused a decrease in levels of intracellular peptides. However, bortezomib (an antitumor drug and proteasome inhibitor) caused an unexpected increase in the levels of most intracellular peptides in HEK293T and SH-SY5Y cells. To address this apparent paradox, quantitative peptidomics was used to study the effect of a variety of other proteasome inhibitors on peptide levels in HEK293T and SH-SY5Y cells. Inhibitors tested included carfilzomib, MG132, MG262, MLN2238, AM114, and clasto-Lactacystin β-lactone. Only MG262 caused a substantial elevation in peptide levels that was comparable to the effect of bortezomib, although carfilzomib and MLN2238 elevated the levels of some peptides. To explore off-target effects, the proteosome inhibitors were tested with various cellular peptidases. Bortezomib did not inhibit tripeptidyl peptidase 2 and only weakly inhibited cellular aminopeptidase activity, as did some of the other proteasome inhibitors. However, potent inhibitors of tripeptidyl peptidase 2 (butabindide) and cellular aminopeptidases (bestatin) did not substantially alter the peptidome, indicating that the increase in peptide levels due to proteasome inhibitors is not a result of peptidase inhibition. Although we cannot exclude other possibilities, we presume that the paradoxical increase in peptide levels upon treatment with bortezomib and other inhibitors is the result of allosteric effects of these compounds on the proteasome. Because intracellular peptides are likely to be functional, it is possible that some of the physiologic effects of bortezomib and carfilzomib arise from the perturbation of peptide levels inside the cell.
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Affiliation(s)
- Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Leandro M. Castro
- Department of Pharmacology, Support Center for Research in Proteolysis and Cell Signaling, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Russell Dulman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Ciyu Yang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Marion Schmidt
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Emer S. Ferro
- Department of Pharmacology, Support Center for Research in Proteolysis and Cell Signaling, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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Schrader M, Schulz-Knappe P, Fricker LD. Historical perspective of peptidomics. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.02.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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de Araujo CB, Russo LC, Castro LM, Forti FL, do Monte ER, Rioli V, Gozzo FC, Colquhoun A, Ferro ES. A novel intracellular peptide derived from g1/s cyclin d2 induces cell death. J Biol Chem 2014; 289:16711-26. [PMID: 24764300 DOI: 10.1074/jbc.m113.537118] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intracellular peptides are constantly produced by the ubiquitin-proteasome system, and many are probably functional. Here, the peptide WELVVLGKL (pep5) from G1/S-specific cyclin D2 showed a 2-fold increase during the S phase of HeLa cell cycle. pep5 (25-100 μm) induced cell death in several tumor cells only when it was fused to a cell-penetrating peptide (pep5-cpp), suggesting its intracellular function. In vivo, pep5-cpp reduced the volume of the rat C6 glioblastoma by almost 50%. The tryptophan at the N terminus of pep5 is essential for its cell death activity, and N terminus acetylation reduced the potency of pep5-cpp. WELVVL is the minimal active sequence of pep5, whereas Leu-Ala substitutions totally abolished pep5 cell death activity. Findings from the initial characterization of the cell death/signaling mechanism of pep5 include caspase 3/7 and 9 activation, inhibition of Akt2 phosphorylation, activation of p38α and -γ, and inhibition of proteasome activity. Further pharmacological analyses suggest that pep5 can trigger cell death by distinctive pathways, which can be blocked by IM-54 or a combination of necrostatin-1 and q-VD-OPh. These data further support the biological and pharmacological potential of intracellular peptides.
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Affiliation(s)
| | - Lilian C Russo
- the Department of Biochemistry, Support Center for Research in Proteolysis and Cell Signaling (NAPPS), Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil
| | | | - Fábio L Forti
- the Department of Biochemistry, Support Center for Research in Proteolysis and Cell Signaling (NAPPS), Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil
| | | | - Vanessa Rioli
- the Special Laboratory of Applied Toxinology (LETA), Center of Toxins, Immune Response, and Cell Signaling (CETICS), Butantan Institute, 05503-000, São Paulo, SP, Brazil, and
| | - Fabio C Gozzo
- the Institute of Chemistry, State University of Campinas, 13083-862, Campinas, SP, Brazil
| | - Alison Colquhoun
- Cell Biology and Development, Support Center for Research in Proteolysis and Cell Signaling (NAPPS), Biomedical Science Institute, University of São Paulo, São Paulo, 05508-000, SP, Brazil
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Peptidomic analysis of the neurolysin-knockout mouse brain. J Proteomics 2014; 111:238-48. [PMID: 24727097 DOI: 10.1016/j.jprot.2014.03.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 03/20/2014] [Accepted: 03/31/2014] [Indexed: 12/12/2022]
Abstract
UNLABELLED A large number of intracellular peptides are constantly produced following protein degradation by the proteasome. A few of these peptides function in cell signaling and regulate protein-protein interactions. Neurolysin (Nln) is a structurally defined and biochemically well-characterized endooligopeptidase, and its subcellular distribution and biological activity in the vertebrate brain have been previously investigated. However, the contribution of Nln to peptide metabolism in vivo is poorly understood. In this study, we used quantitative mass spectrometry to investigate the brain peptidome of Nln-knockout mice. An additional in vitro digestion assay with recombinant Nln was also performed to confirm the identification of the substrates and/or products of Nln. Altogether, the data presented suggest that Nln is a key enzyme in the in vivo degradation of only a few peptides derived from proenkephalin, such as Met-enkephalin and octapeptide. Nln was found to have only a minor contribution to the intracellular peptide metabolism in the entire mouse brain. However, further studies appear necessary to investigate the contribution of Nln to the peptide metabolism in specific areas of the murine brain. BIOLOGICAL SIGNIFICANCE Neurolysin was first identified in the synaptic membranes of the rat brain in the middle 80's by Frederic Checler and colleagues. Neurolysin was well characterized biochemically, and its brain distribution has been confirmed by immunohistochemical methods. The neurolysin contribution to the central and peripheral neurotensin-mediated functions in vivo has been delineated through inhibitor-based pharmacological approaches, but its genuine contribution to the physiological inactivation of neuropeptides remains to be firmly established. As a result, the main significance of this work is the first characterization of the brain peptidome of the neurolysin-knockout mouse. This article is part of a Special Issue entitled: Proteomics, mass spectrometry and peptidomics, Cancun 2013. Guest Editors: César López-Camarillo, Victoria Pando-Robles and Bronwyn Jane Barkla.
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Ribeiro NM, Toniolo EF, Castro LM, Russo LC, Rioli V, Ferro ES, Dale CS. AGH is a new hemoglobin alpha-chain fragment with antinociceptive activity. Peptides 2013; 48:10-20. [PMID: 23911313 DOI: 10.1016/j.peptides.2013.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 07/14/2013] [Accepted: 07/15/2013] [Indexed: 01/24/2023]
Abstract
Limited proteolysis of certain proteins leads to the release of endogenous bioactive peptides. Hemoglobin-derived peptides such as hemorphins and hemopressins are examples of intracellular protein-derived peptides that have antinociceptive effects by modulating G-protein coupled receptors activities. In the present study, a previously characterized substrate capture assay that uses a catalytically inactive form of the thimet oligopeptidase was combined with isotopic labeling and mass spectrometry in order to identify new bioactive peptides. Indeed, we have identified the peptide AGHLDDLPGALSAL (AGH), a fragment of the hemoglobin alpha-chain, which specifically bind to the inactive thimet oligopeptidase in the substrate capture assay. Previous peptidomics studies have identified the AGH as well as many other natural peptides derived from hemoglobin alpha-chain containing this sequence, further suggesting that AGH is a natural endogenous peptide. Pharmacological assays suggest that AGH inhibits peripheral inflammatory hyperalgesic responses through indirect activation of mu opioid receptors, without having a central nervous system activity. Therefore, we have successfully used the substrate capture assay to identify a new endogenous bioactive peptide derived from hemoglobin alpha-chain.
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Affiliation(s)
- Natalia M Ribeiro
- Department of Cell Biology and Development, Biomedical Sciences Institute (ICB), University of São Paulo (USP), Av. Prof. Lineu Prestes, 1524, S435, São Paulo, SP 05508-00, Brazil.
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Berezniuk I, Sironi JJ, Wardman J, Pasek RC, Berbari NF, Yoder BK, Fricker LD. Quantitative peptidomics of Purkinje cell degeneration mice. PLoS One 2013; 8:e60981. [PMID: 23593366 PMCID: PMC3620535 DOI: 10.1371/journal.pone.0060981] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 03/06/2013] [Indexed: 11/19/2022] Open
Abstract
Cytosolic carboxypeptidase 1 (CCP1) is a metallopeptidase that removes C-terminal and side-chain glutamates from tubulin. The Purkinje cell degeneration (pcd) mouse lacks CCP1 due to a mutation. Previously, elevated levels of peptides derived from cytosolic and mitochondrial proteins were found in adult pcd mouse brain, raising the possibility that CCP1 functions in the degradation of intracellular peptides. To test this hypothesis, we used a quantitative peptidomics technique to compare peptide levels in wild-type and pcd mice, examining adult heart, spleen, and brain, and presymptomatic 3 week-old amygdala and cerebellum. Contrary to adult mouse brain, young pcd brain and adult heart and spleen did not show a large increase in levels of intracellular peptides. Unexpectedly, levels of peptides derived from secretory pathway proteins were altered in adult pcd mouse brain. The pattern of changes for the intracellular and secretory pathway peptides in pcd mice was generally similar to the pattern observed in mice lacking primary cilia. Collectively, these results suggest that intracellular peptide accumulation in adult pcd mouse brain is a secondary effect and is not due to a role of CCP1 in peptide turnover.
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Affiliation(s)
- Iryna Berezniuk
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Juan J. Sironi
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jonathan Wardman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Raymond C. Pasek
- Department of Cell, Development, and Integrative Biology, University of Alabama at Birmingham Medical School, Birmingham, Alabama, United States of America
| | - Nicolas F. Berbari
- Department of Cell, Development, and Integrative Biology, University of Alabama at Birmingham Medical School, Birmingham, Alabama, United States of America
| | - Bradley K. Yoder
- Department of Cell, Development, and Integrative Biology, University of Alabama at Birmingham Medical School, Birmingham, Alabama, United States of America
| | - Lloyd D. Fricker
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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Gelman JS, Dasgupta S, Berezniuk I, Fricker LD. Analysis of peptides secreted from cultured mouse brain tissue. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2408-17. [PMID: 23402728 DOI: 10.1016/j.bbapap.2013.01.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/25/2013] [Accepted: 01/29/2013] [Indexed: 01/02/2023]
Abstract
Peptides represent a major class of cell-cell signaling molecules. Most peptidomic studies have focused on peptides present in brain or other tissues. For a peptide to function in intercellular signaling, it must be secreted. The present study was undertaken to identify the major peptides secreted from mouse brain slices that were cultured in oxygenated buffer for 3-4h. Approximately 75% of the peptides identified in extracts of cultured slices matched the previously reported peptide content of heat-inactivated mouse brain tissue, whereas only 2% matched the peptide content of unheated brain tissue; the latter showed a large number of postmortem changes. As found with extracts of heat-inactivated mouse brain, the extracts of cultured brain slices represented secretory pathway peptides as well as peptides derived from intracellular proteins such as those present in the cytosol and mitochondria. A subset of the peptides detected in the extracts of the cultured slices was detected in the culture media. The vast majority of secreted peptides arose from intracellular proteins and not secretory pathway proteins. The peptide RVD-hemopressin, a CB1 cannabinoid receptor agonist, was detected in culture media, which is consistent with a role for RVD-hemopressin as a non-classical neuropeptide. Taken together with previous studies, the present results show that short-term culture of mouse brain slices is an appropriate system to study peptide secretion, especially the non-conventional pathway(s) by which peptides produced from intracellular proteins are secreted. This article is part of a Special Issue entitled: An Updated Secretome.
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Affiliation(s)
- Julia S Gelman
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Lee JE, Zamdborg L, Southey BR, Atkins N, Mitchell JW, Li M, Gillette MU, Kelleher NL, Sweedler JV. Quantitative peptidomics for discovery of circadian-related peptides from the rat suprachiasmatic nucleus. J Proteome Res 2013; 12:585-93. [PMID: 23256577 DOI: 10.1021/pr300605p] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In mammals the suprachiasmatic nucleus (SCN), the master circadian clock, is sensitive to light input via the optic chiasm and synchronizes many daily biological rhythms. Here we explore variations in the expression levels of neuropeptides present in the SCN of rats using a label-free quantification approach that is based on integrating peak intensities between daytime, Zeitgeber time (ZT) 6, and nighttime, ZT 18. From nine analyses comparing the levels between these two time points, 10 endogenous peptides derived from eight prohormones exhibited significant differences in their expression levels (adjusted p-value <0.05). Of these, seven peptides derived from six prohormones, including GRP, PACAP, and CART, exhibited ≥ 30% increases at ZT 18, and the VGRPEWWMDYQ peptide derived from proenkephalin A showed a >50% increase at nighttime. Several endogenous peptides showing statistically significant changes in this study have not been previously reported to alter their levels as a function of time of day, nor have they been implicated in prior functional SCN studies. This information on peptide expression changes serves as a resource for discovering unknown peptide regulators that affect circadian rhythms in the SCN.
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Affiliation(s)
- Ji Eun Lee
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, USA
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41
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Gelman JS, Sironi J, Berezniuk I, Dasgupta S, Castro LM, Gozzo FC, Ferro ES, Fricker LD. Alterations of the intracellular peptidome in response to the proteasome inhibitor bortezomib. PLoS One 2013; 8:e53263. [PMID: 23308178 PMCID: PMC3538785 DOI: 10.1371/journal.pone.0053263] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/27/2012] [Indexed: 01/07/2023] Open
Abstract
Bortezomib is an antitumor drug that competitively inhibits proteasome beta-1 and beta-5 subunits. While the impact of bortezomib on protein stability is known, the effect of this drug on intracellular peptides has not been previously explored. A quantitative peptidomics technique was used to examine the effect of treating human embryonic kidney 293T (HEK293T) cells with 5-500 nM bortezomib for various lengths of time (30 minutes to 16 hours), and human neuroblastoma SH-SY5Y cells with 500 nM bortezomib for 1 hour. Although bortezomib treatment decreased the levels of some intracellular peptides, the majority of peptides were increased by 50-500 nM bortezomib. Peptides requiring cleavage at acidic and hydrophobic sites, which involve beta-1 and -5 proteasome subunits, were among those elevated by bortezomib. In contrast, the proteasome inhibitor epoxomicin caused a decrease in the levels of many of these peptides. Although bortezomib can induce autophagy under certain conditions, the rapid bortezomib-mediated increase in peptide levels did not correlate with the induction of autophagy. Taken together, the present data indicate that bortezomib alters the balance of intracellular peptides, which may contribute to the biological effects of this drug.
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Affiliation(s)
- Julia S. Gelman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Juan Sironi
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Iryna Berezniuk
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Leandro M. Castro
- Department of Cell Biology and Development, University of São Paulo, São Paulo, Brazil
| | - Fabio C. Gozzo
- Chemistry Institute, State University of Campinas, São Paulo, Brazil
| | - Emer S. Ferro
- Department of Cell Biology and Development, University of São Paulo, São Paulo, Brazil
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
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42
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Targeted single-cell microchemical analysis: MS-based peptidomics of individual paraformaldehyde-fixed and immunolabeled neurons. ACTA ACUST UNITED AC 2012; 19:1010-9. [PMID: 22921068 DOI: 10.1016/j.chembiol.2012.05.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/20/2012] [Accepted: 05/30/2012] [Indexed: 12/11/2022]
Abstract
Pinpointing a specific cell from within a relatively uniform cell population to determine its chemical content presents a challenging bioanalytical task. Immunocytochemistry is the classical method used to localize specific molecules and, hence, selected cells. Mass spectrometry also probes endogenous molecules such as neuropeptides within a cell. Here, these two approaches are hyphenated to allow microchemical analysis of immunocytochemical-selected peptidergic neurons. This two-step strategy utilizes antibody-based localization of cells containing selected biomarkers to isolate the cell(s) of interest, followed by peptidomic analysis via mass spectrometry. Applicable to a broad range of analyte and cell types, the strategy was used to successfully profile neuropeptides from individual immunostained insect neurons stored for up to 2 weeks as well as from tissues preserved for 42 weeks.
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43
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McAlister GC, Huttlin EL, Haas W, Ting L, Jedrychowski MP, Rogers JC, Kuhn K, Pike I, Grothe RA, Blethrow JD, Gygi SP. Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal Chem 2012; 84:7469-78. [PMID: 22880955 DOI: 10.1021/ac301572t] [Citation(s) in RCA: 439] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Quantitative mass spectrometry methods offer near-comprehensive proteome coverage; however, these methods still suffer with regards to sample throughput. Multiplex quantitation via isobaric chemical tags (e.g., TMT and iTRAQ) provides an avenue for mass spectrometry-based proteome quantitation experiments to move away from simple binary comparisons and toward greater parallelization. Herein, we demonstrate a straightforward method for immediately expanding the throughput of the TMT isobaric reagents from 6-plex to 8-plex. This method is based upon our ability to resolve the isotopic shift that results from substituting a (15)N for a (13)C. In an accommodation to the preferred fragmentation pathways of ETD, the TMT-127 and -129 reagents were recently modified such that a (13)C was exchanged for a (15)N. As a result of this substitution, the new TMT reporter ions are 6.32 mDa lighter. Even though the mass difference between these reporter ion isotopologues is incredibly small, modern high-resolution and mass accuracy analyzers can resolve these ions. On the basis of our ability to resolve and accurately measure the relative intensity of these isobaric reporter ions, we demonstrate that we are able to quantify across eight samples simultaneously by combining the (13)C- and (15)N-containing reporter ions. Considering the structure of the TMT reporter ion, we believe this work serves as a blueprint for expanding the multiplexing capacity of the TMT reagents to at least 10-plex and possibly up to 18-plex.
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Affiliation(s)
- Graeme C McAlister
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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44
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Russo LC, Asega AF, Castro LM, Negraes PD, Cruz L, Gozzo FC, Ulrich H, Camargo ACM, Rioli V, Ferro ES. Natural intracellular peptides can modulate the interactions of mouse brain proteins and thimet oligopeptidase with 14-3-3ε and calmodulin. Proteomics 2012; 12:2641-55. [DOI: 10.1002/pmic.201200032] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 05/31/2012] [Accepted: 06/03/2012] [Indexed: 02/03/2023]
Affiliation(s)
- Lilian C. Russo
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
| | - Amanda F. Asega
- Laboratory of Applied Toxinology (LETA); Butantan Institute; SP Brazil
| | - Leandro M. Castro
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
| | - Priscilla D. Negraes
- Biochemistry Department; Chemistry Institute; University of São Paulo; São Paulo Brazil
| | - Lilian Cruz
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
| | - Fabio C. Gozzo
- Chemistry Institute; Campinas State University; Campinas SP Brazil
| | - Henning Ulrich
- Biochemistry Department; Chemistry Institute; University of São Paulo; São Paulo Brazil
| | | | - Vanessa Rioli
- Laboratory of Applied Toxinology (LETA); Butantan Institute; SP Brazil
| | - Emer S. Ferro
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
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45
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Berti DA, Russo LC, Castro LM, Cruz L, Gozzo FC, Heimann JC, Lima FB, Oliveira AC, Andreotti S, Prada PO, Heimann AS, Ferro ES. Identification of intracellular peptides in rat adipose tissue: Insights into insulin resistance. Proteomics 2012; 12:2668-81. [DOI: 10.1002/pmic.201200051] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 01/07/2023]
Affiliation(s)
- Denise A. Berti
- Department of Cell Biology and Development; University of São Paulo; São Paulo Brazil
| | - Lilian C. Russo
- Department of Cell Biology and Development; University of São Paulo; São Paulo Brazil
| | - Leandro M. Castro
- Department of Cell Biology and Development; University of São Paulo; São Paulo Brazil
| | - Lilian Cruz
- Department of Cell Biology and Development; University of São Paulo; São Paulo Brazil
| | - Fábio C. Gozzo
- Chemistry Institute; Campinas State University; Campinas São Paulo Brazil
| | - Joel C. Heimann
- Department of Internal Medicine; School of Medicine; University of São Paulo; São Paulo Brazil
| | - Fabio B. Lima
- Department of Physiology and Biophysics; Institute of Biomedical Sciences; University of São Paulo; São Paulo Brazil
| | - Ariclécio C. Oliveira
- Department of Physiology and Biophysics; Institute of Biomedical Sciences; University of São Paulo; São Paulo Brazil
| | - Sandra Andreotti
- Department of Physiology and Biophysics; Institute of Biomedical Sciences; University of São Paulo; São Paulo Brazil
| | - Patrícia O. Prada
- Chemistry Institute; Campinas State University; Campinas São Paulo Brazil
| | | | - Emer S. Ferro
- Department of Cell Biology and Development; University of São Paulo; São Paulo Brazil
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Russo LC, Castro LM, Gozzo FC, Ferro ES. Inhibition of thimet oligopeptidase by siRNA alters specific intracellular peptides and potentiates isoproterenol signal transduction. FEBS Lett 2012; 586:3287-92. [DOI: 10.1016/j.febslet.2012.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/14/2012] [Accepted: 07/02/2012] [Indexed: 12/11/2022]
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Wardman J, Fricker LD. Quantitative peptidomics of mice lacking peptide-processing enzymes. Methods Mol Biol 2012; 768:307-23. [PMID: 21805251 DOI: 10.1007/978-1-61779-204-5_17] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptidomics is defined as the analysis of peptides present in a tissue extract, usually using mass spectrometry-based approaches. Unlike radioimmunoassay-based detection techniques, peptidomics measures the precise form of each peptide, including post-translational modifications, and can readily distinguish between longer and shorter forms of the same peptide. Also, peptidomics is not limited to known peptides and can detect hundreds of peptides in a single experiment. Quantitative peptidomics enables comparisons between two or more groups of samples and is perfect for studies examining the effect of gene knockouts on tissue levels of peptides. We describe the method for quantitative peptidomics using isotopic labels based on trimethylammonium butyrate, which can be synthesized in five different isotopic forms; this permits multivariate analysis of five different groups of tissue extracts in a single liquid chromatography/mass spectrometry run.
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Affiliation(s)
- Jonathan Wardman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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48
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van der Maaden K, Sliedregt K, Kros A, Jiskoot W, Bouwstra J. Fluorescent nanoparticle adhesion assay: a novel method for surface pKa determination of self-assembled monolayers on silicon surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:3403-3411. [PMID: 22224905 DOI: 10.1021/la203560k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Since the computer industry enables us to generate smaller and smaller structures, silicon surface chemistry is becoming increasingly important for (bio-)analytical and biological applications. For controlling the binding of charged biomacromolecules such as DNA and proteins on modified silicon surfaces, the surface pK(a) is an important factor. Here we present a fluorescent nanoparticle adhesion assay as a novel method to determine the surface pK(a) of silicon surfaces modified with weak acids or bases. This method is based upon electrostatic interactions between the modified silicon surface and fluorescent nanoparticles with an opposite charge. Silicon slides were modified with 3-aminopropyltriethoxysilane (APTES) and were further derivatized with succinic anhydride. Layer thickness of these surfaces was determined by ellipsometry. After incubating the surfaces with an amine-reactive fluorescent dye, fluorescence microscopy revealed that the silicon surfaces were successfully modified with amine- and carboxyl-groups. Two surface pK(a) values were found for APTES surfaces by the fluorescent nanoparticle adhesion assay. The first surface pK(a) (6.55 ± 0.73) was comparable with the surface pK(a) obtained by contact angle titration (7.3 ± 0.8), and the second surface pK(a) (9.94 ± 0.19) was only found by using the fluorescent nanoparticle adhesion assay. The surface pK(a) of the carboxyl-modified surface by the fluorescent nanoparticle adhesion assay (4.37 ± 0.59) did not significantly differ from that found by contact angle titration (5.7 ± 1.4). In conclusion, we have developed a novel method to determine the surface pK(a) of modified silicon surfaces: the fluorescent nanoparticle adhesion assay. This method may provide a useful tool for designing pH-dependent electrostatic protein and particle binding/release and to design surfaces with a pH-dependent surface charge for (bio-)analytical lab-on-a-chip devices or drug delivery purposes.
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Affiliation(s)
- Koen van der Maaden
- Division of Drug Delivery Technology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 2300 RA, Leiden, The Netherlands
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49
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Fricker LD, Gelman JS, Castro LM, Gozzo FC, Ferro ES. Peptidomic analysis of HEK293T cells: effect of the proteasome inhibitor epoxomicin on intracellular peptides. J Proteome Res 2012; 11:1981-90. [PMID: 22304392 DOI: 10.1021/pr2012076] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Peptides derived from cytosolic, mitochondrial, and nuclear proteins have been detected in extracts of animal tissues and cell lines. To test whether the proteasome is involved in their formation, HEK293T cells were treated with epoxomicin (0.2 or 2 μM) for 1 h and quantitative peptidomics analysis was performed. Altogether, 147 unique peptides were identified by mass spectrometry sequence analysis. Epoxomicin treatment decreased the levels of the majority of intracellular peptides, consistent with inhibition of the proteasome beta-2 and beta-5 subunits. Treatment with the higher concentration of epoxomicin elevated the levels of some peptides. Most of the elevated peptides resulted from cleavages at acidic residues, suggesting that epoxomicin increased the processing of proteins through the beta-1 subunit. Interestingly, some of the peptides that were elevated by the epoxomicin treatment had hydrophobic residues in P1 cleavage sites. Taken together, these findings suggest that, while the proteasome is the major source of intracellular peptides, other peptide-generating mechanisms exist. Because intracellular peptides are likely to perform intracellular functions, studies using proteasome inhibitors need to be interpreted with caution, as it is possible that the effects of these inhibitors are due to a change in the peptide levels rather than inhibition of protein degradation.
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Affiliation(s)
- Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine , Bronx, New York 10461, United States
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50
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Quantitative peptidomics to measure neuropeptide levels in animal models relevant to psychiatric disorders. Methods Mol Biol 2012; 829:487-503. [PMID: 22231834 PMCID: PMC4327865 DOI: 10.1007/978-1-61779-458-2_31] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Neuropeptides play many important roles in cell-cell signaling and are involved in the control of anxiety, depression, pain, reward pathways, and many other processes that are relevant to psychiatric disorders. Mass spectrometry-based peptidomics techniques can identify the precise forms of peptides that are present in a given tissue. Utilizing this technique, peptides with any posttranslational modifications can be identified, and the exact sequence of the peptides can be determined. Unlike radioimmunoassays, which are limited by specific antibodies and often cannot discriminate between different lengths of peptides from the same precursor, peptidomics reveals the precise sequence and allows for the identification of both known and novel peptides. The use of isotopic labels allows for quantitative peptidomics, which results in the ability to compare peptide levels between differently treated samples. These tags can be synthesized in five different isotopic forms, permitting multivariate analysis of up to five different groups of tissue extracts in a single liquid chromatography/mass spectrometry run; this is ideal for measuring changes in neuropeptides in animals subjected to drug treatments, or in comparing animal models of psychiatric disorders.
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