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Gupta A, Mardi P, Mishra PKK, Kumar A, Kumar R, Mahapatra A, Jena A, Behera PC. Evaluation of supplemented protein-L-isoaspartate-O-methyltransferase ( PIMT) gene of Carica papaya and Ricinus communis in stress survival of Escherichia coli BL21(DE3) cells. Prep Biochem Biotechnol 2024; 54:882-895. [PMID: 38170207 DOI: 10.1080/10826068.2023.2297692] [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: 01/05/2024]
Abstract
In growing plant population, effect of stress is a perturb issue affecting its physiological, biochemical, yield loss and developmental growth. Protein-L-isoaspartate-O-methyltransferase (PIMT) is a broadly distributed protein repair enzyme which actuate under stressful environment or aging. Stress can mediate damage converting protein bound aspartate (Asp) residues to isoaspartate (iso-Asp). This spontaneous and deleterious conversion occurs at an elevated state of stress and aging. Iso-Asp formation is associated with protein inactivation and compromised cellular survival. PIMT can convert iso-Asp back to Asp, thus repairing and contributing to cellular survival. The present work describes the isolation, cloning, sequencing and expression of PIMT genes of Carica papaya (Cp pimt) and Ricinus communis (Rc pimt) Using gene specific primers, both the pimts were amplified from their respective cDNAs and subsequently cloned in prokaryotic expression vector pProEXHTa. BL21(DE3) strain of E. coli cells were used as expression host. The expression kinetics of both the PIMTs were studied with various concentrations of IPTG and at different time points. Finally, the PIMT supplemented BL21(DE3) cells were evaluated against different stresses in comparison to their counterparts with the empty vector control.
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Affiliation(s)
- Akanksha Gupta
- Plant Biotechnology, Department of Genetics and Plant Breeding, Banaras Hindu University, Mirzapur, India
| | - Pragati Mardi
- Plant Biotechnology, Department of Genetics and Plant Breeding, Banaras Hindu University, Mirzapur, India
| | - Prasanta Kumar Koustasa Mishra
- Unit of Teaching Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, Banaras Hindu University, Mirzapur, India
| | - Anshuman Kumar
- Department of Animal Genetics and Breeding, Faculty of Veterinary and Animal Sciences, Banaras Hindu University, Mirzapur, India
| | - Rajesh Kumar
- Plant Biotechnology, Department of Genetics and Plant Breeding, Banaras Hindu University, Mirzapur, India
| | - Archana Mahapatra
- Department of Veterinary Anatomy, Faculty of Veterinary and Animal Sciences, Banaras Hindu University, Mirzapur, India
| | - Anupama Jena
- Fisheries and Animal Resource Development Department, Bhubaneswar, India
| | - Prakash Chandra Behera
- Department of Veterinary Biochemistry, College of Veterinary Science and Animal Husbandry, OUAT, Bhubaneshwar, India
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2
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Banreti A, Bhattacharya S, Wien F, Matsuo K, Réfrégiers M, Meinert C, Meierhenrich U, Hudry B, Thompson D, Noselli S. Biological effects of the loss of homochirality in a multicellular organism. Nat Commun 2022; 13:7059. [PMID: 36400783 PMCID: PMC9674851 DOI: 10.1038/s41467-022-34516-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022] Open
Abstract
Homochirality is a fundamental feature of all known forms of life, maintaining biomolecules (amino-acids, proteins, sugars, nucleic acids) in one specific chiral form. While this condition is central to biology, the mechanisms by which the adverse accumulation of non-L-α-amino-acids in proteins lead to pathophysiological consequences remain poorly understood. To address how heterochirality build-up impacts organism's health, we use chiral-selective in vivo assays to detect protein-bound non-L-α-amino acids (focusing on aspartate) and assess their functional significance in Drosophila. We find that altering the in vivo chiral balance creates a 'heterochirality syndrome' with impaired caspase activity, increased tumour formation, and premature death. Our work shows that preservation of homochirality is a key component of protein function that is essential to maintain homeostasis across the cell, tissue and organ level.
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Affiliation(s)
- Agnes Banreti
- grid.461605.0Université Côte d’Azur, CNRS, Inserm, Institut de Biologie Valrose, 06108 Nice, France
| | - Shayon Bhattacharya
- grid.10049.3c0000 0004 1936 9692Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Frank Wien
- grid.426328.9DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Koichi Matsuo
- grid.257022.00000 0000 8711 3200HiSOR Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
| | - Matthieu Réfrégiers
- grid.417870.d0000 0004 0614 8532Centre de Biophysique Moléculaire, CNRS; UPR4301, 45071 Orléans, France
| | - Cornelia Meinert
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, Institut de Chimie de Nice, CNRS; UMR 7272, 06108 Nice, France
| | - Uwe Meierhenrich
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, Institut de Chimie de Nice, CNRS; UMR 7272, 06108 Nice, France
| | - Bruno Hudry
- grid.461605.0Université Côte d’Azur, CNRS, Inserm, Institut de Biologie Valrose, 06108 Nice, France
| | - Damien Thompson
- grid.10049.3c0000 0004 1936 9692Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Stéphane Noselli
- grid.461605.0Université Côte d’Azur, CNRS, Inserm, Institut de Biologie Valrose, 06108 Nice, France
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3
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Hubbard EE, Heil LR, Merrihew GE, Chhatwal JP, Farlow MR, McLean CA, Ghetti B, Newell KL, Frosch MP, Bateman RJ, Larson EB, Keene CD, Perrin RJ, Montine TJ, MacCoss MJ, Julian RR. Does Data-Independent Acquisition Data Contain Hidden Gems? A Case Study Related to Alzheimer's Disease. J Proteome Res 2022; 21:118-131. [PMID: 34818016 PMCID: PMC8741752 DOI: 10.1021/acs.jproteome.1c00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the potential benefits of using data-independent acquisition (DIA) proteomics protocols is that information not originally targeted by the study may be present and discovered by subsequent analysis. Herein, we reanalyzed DIA data originally recorded for global proteomic analysis to look for isomerized peptides, which occur as a result of spontaneous chemical modifications to long-lived proteins. Examination of a large set of human brain samples revealed a striking relationship between Alzheimer's disease (AD) status and isomerization of aspartic acid in a peptide from tau. Relative to controls, a surprising increase in isomer abundance was found in both autosomal dominant and sporadic AD samples. To explore potential mechanisms that might account for these observations, quantitative analysis of proteins related to isomerization repair and autophagy was performed. Differences consistent with reduced autophagic flux in AD-related samples relative to controls were found for numerous proteins, including most notably p62, a recognized indicator of autophagic inhibition. These results suggest, but do not conclusively demonstrate, that lower autophagic flux may be strongly associated with loss of function in AD brains. This study illustrates that DIA data may contain unforeseen results of interest and may be particularly useful for pilot studies investigating new research directions. In this case, a promising target for future investigations into the therapy and prevention of AD has been identified.
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Affiliation(s)
- Evan E. Hubbard
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Lilian R. Heil
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, United States
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, United States
| | - Jasmeer P. Chhatwal
- Harvard Medical School, Massachusetts General Hospital, Department of Neurology, 15 Parkman St, Suite 835, Boston MA 02114
| | - Martin R. Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, 46202
| | | | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Kathy L. Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Matthew P. Frosch
- C.S. Kubik Laboratory for Neuropathology, and Massachusetts Alzheimer Disease Research Center, Massachusetts General Hospital, Boston, MA 02114
| | - Randall J. Bateman
- Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, Box 8111, St. Louis, 63110, Missouri, USA
| | - Eric B. Larson
- Kaiser Permanente Washington Health Research Institute and Department of Medicine, University of Washington, Seattle WA
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, United States
| | - Richard J. Perrin
- Department of Pathology and Immunology, Department of Neurology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Thomas J. Montine
- Department of Pathology, Stanford University, Stanford, CA, 94305, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States,corresponding author:
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4
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Sadakane Y, Senda S, Deguchi T, Tanaka A, Tsuruta H, Morimoto S. Effect of amino acids present at the carboxyl end of succinimidyl residue on the rate constants for succinimidyl hydrolysis in small peptides. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140496. [PMID: 32673742 DOI: 10.1016/j.bbapap.2020.140496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 12/19/2022]
Abstract
Structural alterations of aspartyl and asparaginyl residues in various proteins can lead to their malfunction, which may result in severe health disorders. The formation and hydrolysis of succinimidyl intermediates are crucial in specific protein modifications. Nonetheless, only few studies investigating the hydrolysis of succinimidyl intermediates have been published. In this study, we established a method to prepare peptides bearing succinimidyl residues using recombinant protein l-isoaspartyl methyltransferase and ultrafiltration units. Using succinimidyl peptides, we examined the effect of amino acid residues on succinimidyl hydrolysis at the carboxyl end of succinimidyl residues and determined the rate constant of hydrolysis for each peptide. The rate constant of succinimidyl hydrolysis in the peptide bearing a Ser residue at the carboxyl side (0.50 ± 0.02 /h) was 3.0 times higher than that for the peptide bearing an Ala residue (0.17 ± 0.01 /h), whereas it was just 1.2 times higher for the peptide bearing a Gly residue (0.20 ± 0.01 /h). The rate constant of succinimidyl formation in the peptide bearing a Ser residue [(2.44 ± 0.11) × 10-3 /d] was only 1.2 times higher than that for the peptide bearing an Ala residue ([1.87 ± 0.09) × 10-3 /d], whereas 5.5 times higher for the peptide bearing a Gly residue [(10.2 ± 0.2) × 10-3 /d]. These results show that the Gly and Ser residues at the carboxyl end of the succinimidyl residue have opposing roles in succinimidyl formation and hydrolysis. Catalysis of Ser residue's hydroxyl group plays a crucial role in succinimidyl hydrolysis.
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Affiliation(s)
- Yutaka Sadakane
- School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670, Japan.
| | - Sayumi Senda
- School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670, Japan
| | - Taku Deguchi
- School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670, Japan
| | - Atsuki Tanaka
- School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670, Japan
| | - Hiromasa Tsuruta
- School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670, Japan
| | - Shota Morimoto
- School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670, Japan
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5
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Jiang Y, Schneck JL, Grimes M, Taylor AN, Hou W, Thrall SH, Sweitzer SM. Methyltransferases prefer monomer over core-trimmed nucleosomes as in vitro substrates. Anal Biochem 2011; 415:84-6. [PMID: 21459076 DOI: 10.1016/j.ab.2011.03.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 03/28/2011] [Accepted: 03/29/2011] [Indexed: 11/23/2022]
Abstract
Epigenetics is an area of increasing interest for drug discovery, driving the need for assays that use nucleosome substrates. Our studies showed that SUV39H1, a histone lysine methyltransferase, and Dnmt3b/Dnmt3L, a DNA methyltransferase, both exhibited approximately five times more activity on monomer nucleosomes than on DNA-core-trimmed nucleosomes in a scintillation proximity assay (SPA). The methyltransferases recognize and have a preference for nucleosomes with longer DNA strands. Our findings suggest that the use of monomer nucleosomes as substrates using SPA technology could lead to more robust screening assays and potentially more specific small molecule inhibitors of epigenetic enzymes.
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Affiliation(s)
- Yong Jiang
- Department of Biological Reagents and Assay Development, GlaxoSmithKline, Collegeville, PA 19426, USA
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6
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Cantor JR, Stone EM, Chantranupong L, Georgiou G. The human asparaginase-like protein 1 hASRGL1 is an Ntn hydrolase with beta-aspartyl peptidase activity. Biochemistry 2009; 48:11026-31. [PMID: 19839645 PMCID: PMC2782781 DOI: 10.1021/bi901397h] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein we report the bacterial expression, purification, and enzymatic characterization of the human asparaginase-like protein 1 (hASRGL1). We present evidence that hASRGL1 exhibits beta-aspartyl peptidase activity consistent with enzymes designated as plant-type asparaginases, which had thus far been found in only plants and bacteria. Similar to nonmammalian plant-type asparaginases, hASRGL1 is shown to be an Ntn hydrolase for which Thr168 serves as the essential N-terminal nucleophile for intramolecular processing and catalysis, corroborated in part by abolishment of both activities through the Thr168Ala point mutation. In light of the activity profile reported here, ASRGL1s may act synergistically with protein l-isoaspartyl methyl transferase to relieve accumulation of potentially toxic isoaspartyl peptides in mammalian brain and other tissues.
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Affiliation(s)
- Jason R. Cantor
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
| | - Everett M. Stone
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
| | | | - George Georgiou
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
- Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712, USA
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7
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8
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Glickman JF, Schmid A, Ferrand S. Scintillation Proximity Assays in High-Throughput Screening. Assay Drug Dev Technol 2008; 6:433-55. [DOI: 10.1089/adt.2008.135] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Andres Schmid
- Novartis Institutes for BioMedical Research, Basel, Switzerland
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9
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McCudden CR, Kraus VB. Biochemistry of amino acid racemization and clinical application to musculoskeletal disease. Clin Biochem 2006; 39:1112-30. [PMID: 17046734 DOI: 10.1016/j.clinbiochem.2006.07.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 06/27/2006] [Accepted: 07/13/2006] [Indexed: 11/30/2022]
Abstract
During aging, proteins are subject to numerous forms of damage. Several types of non-enzymatic post-translational modifications have been described in aging proteins, including oxidation, nitration, glycation, and racemization. Racemization of amino acids is the spontaneous conversion of L-enantiomers to the D-form, which is dependent on temperature, pH, and time. Because of the time-dependent nature of racemization, it can be used to determine the relative age and turnover rates of long-lived proteins. There are many such long-lived proteins within the body; they are found in the brain, eye, and heart, but are particularly abundant in proteins found in musculoskeletal tissues such as bone and cartilage. During disease, musculoskeletal tissues have pathologically altered turnover rates. Because turnover rates can be estimated from levels of racemization, racemized musculoskeletal protein fragments may serve as useful biomarkers of disease. This review discusses the biochemistry of amino acid racemization in proteins and its clinical application to musculoskeletal disease.
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Affiliation(s)
- Christopher R McCudden
- Division of Rheumatology, Department of Medicine, Box 3416, Duke University, Medical Center, Durham, NC 27710, USA
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10
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Jang H, Mason JB, Choi SW. Genetic and epigenetic interactions between folate and aging in carcinogenesis. J Nutr 2005; 135:2967S-2971S. [PMID: 16317156 DOI: 10.1093/jn/135.12.2967s] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Folate is among the most strongly implicated dietary components to convey protection against colon cancer, and diminished folate status is associated with an enhanced risk of colon cancer. Age is also regarded as one of the most important risk factors for colonic carcinogenesis. It is therefore of considerable interest to determine whether the process of aging influences folate metabolism in the colon and whether folate supplementation might prevent the procarcinogenic effects associated with aging. Recent studies in our laboratory demonstrated that the colonic mucosa of elder rats is more susceptible to folate depletion than that of young rats. Depletion of folate results in a shift in the forms of folate in the colon as well as increased uracil incorporation into DNA, a purported mechanism for colonic carcinogenesis. However, modest folate supplementation eliminates evidence of inadequate folate status in the colons of elder rats, suggesting that the relation between age and folate status in the colon might be one mechanism by which aging modulates colorectal cancer risk. Interactions between folate and aging also affect a spectrum of epigenetic and genetic phenomena such as uracil misincorporation, DNA methylation, protein methylation, mitochondrial deletion, and critical gene expression, which could be related to carcinogenesis. Aging and inadequate dietary folate may interact and collectively induce derangements in folate metabolism, thereby provoking subsequent molecular aberrations, which may enhance carcinogenesis. However, folate supplementation appears to reverse these adverse effects of aging, which is potentially of substantial import because the latter is an unmodifiable risk factor.
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Affiliation(s)
- Hyeran Jang
- Vitamins and Carcinogenesis Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA
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11
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Young GW, Hoofring SA, Mamula MJ, Doyle HA, Bunick GJ, Hu Y, Aswad DW. Protein L-Isoaspartyl Methyltransferase Catalyzes in Vivo Racemization of Aspartate-25 in Mammalian Histone H2B. J Biol Chem 2005; 280:26094-8. [PMID: 15908425 DOI: 10.1074/jbc.m503624200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein L-isoaspartyl methyltransferase (PIMT) has been implicated in the repair or metabolism of proteins containing atypical L-isoaspartyl peptide bonds. The repair hypothesis is supported by previous studies demonstrating in vitro repair of isoaspartyl peptides via formation of a succinimide intermediate. Utilization of this mechanism in vivo predicts that PIMT modification sites should exhibit significant racemization as a side reaction to the main repair pathway. We therefore studied the D/L ratio of aspartic acid at specific sites in histone H2B, a known target of PIMT in vivo. Using H2B from canine brain, we found that Asp25 (the major PIMT target site in H2B) was significantly racemized, exhibiting d/l ratios as high as 0.12, whereas Asp51, a comparison site, exhibited negligible racemization (D/L < or = 0.01). Racemization of Asp25 was independent of animal age over the range of 2-15 years. Using H2B from 2-3-week mouse brain, we found a similar D/L ratio (0.14) at Asp25 in wild type mice, but substantially less racemization (D/L = 0.035) at Asp25 in PIMT-deficient mice. These findings suggest that PIMT functions in the repair, rather than the metabolic turnover, of isoaspartyl proteins in vivo. Because PIMT has numerous substrates in cells, these findings also suggest that D-aspartate may be more common in cellular proteins than hitherto imagined and that its occurrence, in some proteins at least, is independent of animal age.
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Affiliation(s)
- Glen W Young
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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12
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Thapar N, Griffith SC, Yeates TO, Clarke S. Protein repair methyltransferase from the hyperthermophilic archaeon Pyrococcus furiosus. Unusual methyl-accepting affinity for D-aspartyl and N-succinyl-containing peptides. J Biol Chem 2002; 277:1058-65. [PMID: 11694513 DOI: 10.1074/jbc.m108261200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Protein l-isoaspartate-(d-aspartate) O-methyltransferases (EC ), present in a wide variety of prokaryotic and eukaryotic organisms, can initiate the conversion of abnormal l-isoaspartyl residues that arise spontaneously with age to normal l-aspartyl residues. In addition, the mammalian enzyme can recognize spontaneously racemized d-aspartyl residues for conversion to l-aspartyl residues, although no such activity has been seen to date for enzymes from lower animals or prokaryotes. In this work, we characterize the enzyme from the hyperthermophilic archaebacterium Pyrococcus furiosus. Remarkably, this methyltransferase catalyzes both l-isoaspartyl and d-aspartyl methylation reactions in synthetic peptides with affinities that can be significantly higher than those of the human enzyme, previously the most catalytically efficient species known. Analysis of the common features of l-isoaspartyl and d-aspartyl residues suggested that the basic substrate recognition element for this enzyme may be mimicked by an N-terminal succinyl peptide. We tested this hypothesis with a number of synthetic peptides using both the P. furiosus and the human enzyme. We found that peptides devoid of aspartyl residues but containing the N-succinyl group were in fact methyl esterified by both enzymes. The recent structure determined for the l-isoaspartyl methyltransferase from P. furiosus complexed with an l-isoaspartyl peptide supports this mode of methyl-acceptor recognition. The combination of the thermophilicity and the high affinity binding of methyl-accepting substrates makes the P. furiosus enzyme useful both as a reagent for detecting isomerized and racemized residues in damaged proteins and for possible human therapeutic use in repairing damaged proteins in extracellular environments where the cytosolic enzyme is not normally found.
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Affiliation(s)
- Nitika Thapar
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
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13
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Wolosker H, D'Aniello A, Snyder SH. D-aspartate disposition in neuronal and endocrine tissues: ontogeny, biosynthesis and release. Neuroscience 2001; 100:183-9. [PMID: 10996468 DOI: 10.1016/s0306-4522(00)00321-3] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
High levels of D-aspartate occur in the brain and endocrine glands, such as pineal, adrenal and pituitary. In the brain, D-aspartate levels are highest in embryonic and early postnatal stages. Notably high levels occur in the early postnatal cortical plate and subventricular zone of the cerebral cortical cultures, implying a role in development. In embryonic neuronal primary culture cells, we detected high levels of endogenous D-aspartate and demonstrated biosynthesis of [14C]D-aspartate using [14C]L-aspartate as precursor. Synthesis of D-aspartate in cell cultures is inhibited by amino-oxyacetic acid, an inhibitor of pyridoxal phosphate-dependent enzymes. In the rat adrenal medulla, D-aspartate is depleted by treatment of the animals with intraperitoneal nicotine injections. In adrenal slices, D-aspartate is released by depolarization with KCl or acetylcholine, implying physiological release by activation of the cholinergic innervation of the adrenal. Our characterization of D-aspartate ontogeny, biosynthesis and depolarization-induced release implies specific physiological roles for this amino acid.
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Affiliation(s)
- H Wolosker
- Departamento de Bioquimica, ICB/CCS, Universidade Federal do Rio de Janeiro, RJ 21941-590, Rio de Janeiro, Brazil
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14
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Tarcsa E, Szymanska G, Lecker S, O'Connor CM, Goldberg AL. Ca2+-free calmodulin and calmodulin damaged by in vitro aging are selectively degraded by 26 S proteasomes without ubiquitination. J Biol Chem 2000; 275:20295-301. [PMID: 10791958 DOI: 10.1074/jbc.m001555200] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-proteasome pathway is believed to selectively degrade post-synthetically damaged proteins in eukaryotic cells. To study this process we used calmodulin (CaM) as a substrate because of its importance in cell regulation and because it acquires isoaspartyl residues in its Ca(2+)-binding regions both in vivo and after in vitro "aging" (incubation for 2 weeks without Ca(2+)). When microinjected into Xenopus oocytes, in vitro aged CaM was degraded much faster than native CaM by a proteasome-dependent process. Similarly, in HeLa cell extracts aged CaM was degraded at a higher rate, even though it was not conjugated to ubiquitin more rapidly than the native species. Ca(2+) stimulated the ubiquitination of both species, but inhibited their degradation. Thus, for CaM, ubiquitination and proteolysis appear to be dissociated. Accordingly, purified muscle 26 S proteasomes could degrade aged CaM and native Ca(2+)-free (apo) CaM without ubiquitination. Addition of Ca(2+) dramatically reduced degradation of the native molecules but only slightly reduced the breakdown of the aged species. Thus, upon Ca(2+) binding, native CaM assumes a non-degradable conformation, which most of the age-damaged species cannot assume. Thus, flexible conformations, as may arise from age-induced damage or the absence of ligands, can promote degradation directly by the proteasome without ubiquitination.
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Affiliation(s)
- E Tarcsa
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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15
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Niewmierzycka A, Clarke S. Do damaged proteins accumulate in Caenorhabditis elegans L-isoaspartate methyltransferase (pcm-1) deletion mutants? Arch Biochem Biophys 1999; 364:209-18. [PMID: 10190976 DOI: 10.1006/abbi.1999.1114] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The protein l-isoaspartate (d-aspartate) O-methyltransferase (E.C. 2. 1.1.77) can initiate the conversion of isomerized and racemized aspartyl residues to their normal l-aspartyl forms and has therefore been hypothesized to function as a repair enzyme, responsible for helping to limit the accumulation of damaged proteins in aging organisms. In this study, the effect of a disruption in the pcm-1 gene encoding the l-isoaspartyl methyltransferase was investigated in the nematode Caenorhabditis elegans. It was found that damaged proteins recognized by this enzyme accumulated to significant levels during long-term incubation of both pcm-1+ and pcm-1- nematodes in a specialized larval stage called the dauer. The l-isoaspartyl methyltransferase-deficient mutants accumulated about twice the level of damaged proteins as the control nematodes during dauer aging. The mutants also accumulated higher levels of damage when both strains were incubated at 30 degrees C for up to 3 days. However, when nonviable nematodes were removed in a Percoll separation, similar levels of damage were measured between the two strains following both dauer aging and 30 degrees C incubation. Both strains were able to effectively eliminate damaged proteins recognized by the methyltransferase after recovery from dauer. Characterization of the methyl-accepting polypeptide substrates which accumulate in aged dauers revealed that although substrates of all molecular weights are present, the majority of substrates are peptides not precipitated by acetone. These results suggest that protein degradation, rather than repair, may be the major mechanism by which C. elegans eliminates damaged proteins containing l-isoaspartyl residues.
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Affiliation(s)
- A Niewmierzycka
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California, 90095-1569, USA
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16
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Abstract
Protein L-isoaspartyl methyltransferase (PIMT) is suggested to play a role in the repair of aged protein spontaneously incorporated with isoaspartyl residues. We generated PIMT-deficient mice by targeted disruption of the PIMT gene to elucidate the biological role of the gene in vivo. PIMT-deficient mice died from progressive epileptic seizures with grand mal and myoclonus between 4 and 12 weeks of age. An anticonvulsive drug, dipropylacetic acid (DPA), improved their survival but failed to cure the fatal outcome. L-Isoaspartatate, the putative substrate for PIMT, was increased ninefold in the brains of PIMT-deficient mice. The brains of PIMT-deficient mice started to enlarge after 4 weeks of age when the apical dendrites of pyramidal neurons in cerebral cortices showed aberrant arborizations with disorganized microtubules. We conclude that methylation of modified proteins with isoaspartyl residues is essential for the maintenance of a mature CNS and that a deficiency in PIMT results in fatal progressive epilepsy in mice.
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Yamamoto A, Takagi H, Kitamura D, Tatsuoka H, Nakano H, Kawano H, Kuroyanagi H, Yahagi Y, Kobayashi S, Koizumi K, Sakai T, Saito K, Chiba T, Kawamura K, Suzuki K, Watanabe T, Mori H, Shirasawa T. Deficiency in protein L-isoaspartyl methyltransferase results in a fatal progressive epilepsy. J Neurosci 1998; 18:2063-74. [PMID: 9482793 PMCID: PMC6792936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Protein L-isoaspartyl methyltransferase (PIMT) is suggested to play a role in the repair of aged protein spontaneously incorporated with isoaspartyl residues. We generated PIMT-deficient mice by targeted disruption of the PIMT gene to elucidate the biological role of the gene in vivo. PIMT-deficient mice died from progressive epileptic seizures with grand mal and myoclonus between 4 and 12 weeks of age. An anticonvulsive drug, dipropylacetic acid (DPA), improved their survival but failed to cure the fatal outcome. L-Isoaspartatate, the putative substrate for PIMT, was increased ninefold in the brains of PIMT-deficient mice. The brains of PIMT-deficient mice started to enlarge after 4 weeks of age when the apical dendrites of pyramidal neurons in cerebral cortices showed aberrant arborizations with disorganized microtubules. We conclude that methylation of modified proteins with isoaspartyl residues is essential for the maintenance of a mature CNS and that a deficiency in PIMT results in fatal progressive epilepsy in mice.
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Affiliation(s)
- A Yamamoto
- Department of Neurophysiology, Tokyo Metropolitan Institute of Gerontology, Tokyo-173, Japan
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18
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Kagan RM, Niewmierzycka A, Clarke S. Targeted gene disruption of the Caenorhabditis elegans L-isoaspartyl protein repair methyltransferase impairs survival of dauer stage nematodes. Arch Biochem Biophys 1997; 348:320-8. [PMID: 9434744 DOI: 10.1006/abbi.1997.0362] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The methylation of abnormal L-isoaspartyl residues by protein L-isoaspartate (D-aspartate) O-methyltransferase (EC 2.1.1.77) can lead to their conversion to L-aspartyl residues. For polypeptides damaged by spontaneous reactions that generate L-isoaspartyl residues, these steps represent a protein repair pathway that can limit the accumulation of potentially detrimental proteins in the aging process. We report here the construction and the characterization of an animal model deficient in this methyltransferase. We utilized Tc1-transposon-mediated mutagenesis in the nematode Caenorhabditis elegans to construct a homozygous excision mutant lacking exons 2-5 of the pcm-1 gene encoding this enzyme. Nematodes carrying this deletion exhibited no detectable L-isoaspartyl methyltransferase activity. These worms demonstrated normal morphology and behavior and adult mutant nematodes exhibited a normal lifespan. However, the survival of dauer-phase mutants was diminished by 3.5-fold relative to wild-type dauers after 50 days in the dauer phase. The fitness of the pcm-1 deletion nematodes was reduced by about 16% relative to that of wild-type nematodes as measured by the ability of these mutants to compete reproductively against a wild-type population. We found that the absence of the functional methyltransferase gene leads to a modest accumulation of altered protein substrates in aged dauer worms. However, in the viable fraction of these dauer worms, no differences were seen in the levels of altered substrate proteins in the parent and methyltransferase-deficient worms, suggesting that the enzyme in wild-type cells does not efficiently catalyze the repair of spontaneously damaged proteins.
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Affiliation(s)
- R M Kagan
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90095-1569, USA
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19
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Weber DJ, McFadden PN. Detection and characterization of a protein isoaspartyl methyltransferase which becomes trapped in the extracellular space during blood vessel injury. JOURNAL OF PROTEIN CHEMISTRY 1997; 16:257-67. [PMID: 9188065 DOI: 10.1023/a:1026300924908] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Injury to rat blood vessels in vivo was found to release intracellular pools of protein D-aspartyl/L-isoaspartyl carboxyl methyltransferase (PIMT) into the extracellular milieu, where it becomes trapped. This trapped cohort of PIMT is able to utilize radiolabeled S-adenosyl-L-methionine (AdoMet) introduced into the circulation to methylate blood vessel proteins containing altered aspartyl residues. As further shown in this study, methylated substrates are detected only at the specific site of injury. In vitro studies more fully characterized this endogenous PIMT activity in thoracic aorta and inferior vena cava. Methylation kinetics, immunoblotting, and the lability of methylated substrates at mild alkaline pH were used to demonstrate that both types of blood vessel contain an endogenous protein D-aspartyl/L-isoaspartyl carboxyl methyltransferase (PIMT). At least 50% of the PIMT activity is resistant to nonionic detergent extraction, suggesting that the enzyme activity becomes trapped within or behind the extracellular matrix (ECM). Quantities of lactate dehydrogenase (LDH), another soluble enzyme of presumed intracellular origin, were found to be similarly trapped in the extracellular space of blood vessels.
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Affiliation(s)
- D J Weber
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331, USA
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20
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Tuong A, Maftouh M, Ponthus C, Whitechurch O, Roitsch C, Picard C. Characterization of the deamidated forms of recombinant hirudin. Biochemistry 1992; 31:8291-9. [PMID: 1525166 DOI: 10.1021/bi00150a024] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recombinant hirudin variant rHV2-Lys 47 (MW = 6906.5) was intentionally deamidated by incubation in pH 9 phosphate buffer at 37 degrees C. Anion-exchange HPLC analysis showed that 11 forms could be generated. These were isolated and purified by combined anion-exchange and reversed-phase HPLC. Acid-catalyzed carboxyl methylation was used to introduce a mass shift of +15 amu per deamidated residue present in the molecule before analysis by liquid secondary ion mass spectrometry (LSIMS). Methylation enhanced, in particular, the abundance of the sequence ions in the LSIMS spectra. This permitted the determination of both the number (three) and the localization of the deamidated residues: Asn 52, Asn 53, and a residue located in the N-terminal 1-39 domain. Complementary sequencing techniques proved that the latter residue was Asn 33. Altogether four mono-, three di-, and four tri-deamidated forms were identified. The heterogeneity of the forms having identical deamidation positions but being chromatographically separable is thought to arise from the generation of alpha- and beta-aspartyl iso forms during the nonenzymatic deamidation process.
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Affiliation(s)
- A Tuong
- Sanofi Recherche, Toulouse, France
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21
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Recognition of D-aspartyl residues in polypeptides by the erythrocyte L-isoaspartyl/D-aspartyl protein methyltransferase. Implications for the repair hypothesis. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42652-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Fu J, Ding L, Clarke S. Purification, gene cloning, and sequence analysis of an L-isoaspartyl protein carboxyl methyltransferase from Escherichia coli. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)98723-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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23
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Ingrosso D, Clarke S. Human erythrocyte D-aspartyl/L-isoaspartyl methyltransferases: enzymes that recognize age-damaged proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1991; 307:263-76. [PMID: 1805590 DOI: 10.1007/978-1-4684-5985-2_24] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- D Ingrosso
- Istituto di Biochimica delle Macromolecole, I Facoltà di Medicina e Chirurgia, Università di Napoli, Italy
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24
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Henzel WJ, Stults JT, Hsu CA, Aswad DW. The Primary Structure of a Protein Carboxyl Methyltransferase from Bovine Brain That Selectively Methylates L-Isoaspartyl Sites. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)71564-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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26
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Sellinger OZ, Kramer CM. The carboxylmethylation of membrane-bound proteins in the aging rat brain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1988; 231:269-80. [PMID: 3414435 DOI: 10.1007/978-1-4684-9042-8_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- O Z Sellinger
- Laboratory of Neurochemistry, Mental Health Research Institute, University of Michigan Medical Center, Ann Arbor
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Clarke S. Perspectives on the biological function and enzymology of protein carboxyl methylation reactions in eucaryotic and procaryotic cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1988; 231:213-28. [PMID: 3046247 DOI: 10.1007/978-1-4684-9042-8_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- S Clarke
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA 90024-1569
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Kinetic and electrophoretic analysis of transmethylation reactions in intact Xenopus laevis oocytes. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61127-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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29
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O'Connor C. Regulation and subcellular distribution of a protein methyltransferase and its damaged aspartyl substrate sites in developing Xenopus oocytes. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61126-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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30
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Acheson A, Thoenen H. Both short- and long-term effects of nerve growth factor on tyrosine hydroxylase in calf adrenal chromaffin cells are blocked by S-adenosylhomocysteine hydrolase inhibitors. J Neurochem 1987; 48:1416-24. [PMID: 2881981 DOI: 10.1111/j.1471-4159.1987.tb05680.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have previously shown that primary cultures of calf chromaffin cells respond to nerve growth factor (NGF) treatment with a selective induction of tyrosine hydroxylase (TH), which takes 48 h to be manifested. In the present study, we report that short exposure of calf chromaffin cells to NGF (5-60 min) results in TH activation, which involves a change in the Vmax of the enzyme with no change in the number of enzyme molecules, similar to an effect that has been previously reported in PC12 cells. This activation is markedly potentiated when the chromaffin cells are plated on a laminin substrate, such that after 5 min of NGF exposure, there is an approximately fourfold increase in the TH activity. Both short-term activation and long-term TH induction brought about by NGF treatment are blocked by 5'-deoxy-5'-methylthioadenosine and other drugs that act as S-adenosylhomocysteine (SAH) hydrolase inhibitors to block methylation by end-product inhibition. These drugs did not inhibit cyclic AMP-mediated TH activation or increases in the levels of TH. However, measurements of the degree of blockade of methylation in cells treated with these drugs, taken together with conceptual information regarding the nonregulatory nature of methylation in eukaryotic cells, were not consistent with inhibition of methylation as the crucial effect of the drugs to block the effects of NGF. Nonetheless, since SAH hydrolase inhibitors selectively inhibited NGF-mediated effects, and not comparable effects triggered by other stimuli, these compounds provide useful tools in future studies of the biochemical signalling mechanism of NGF.
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Thoenen H, Bandtlow C, Heumann R. The physiological function of nerve growth factor in the central nervous system: comparison with the periphery. Rev Physiol Biochem Pharmacol 1987; 109:145-78. [PMID: 3317757 DOI: 10.1007/bfb0031026] [Citation(s) in RCA: 393] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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McFadden PN, Clarke S. Chemical conversion of aspartyl peptides to isoaspartyl peptides. A method for generating new methyl-accepting substrates for the erythrocyte D-aspartyl/L-isoaspartyl protein methyltransferase. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67272-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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33
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Brunauer LS, Clarke S. Methylation of calmodulin at carboxylic acid residues in erythrocytes. A non-regulatory covalent modification? Biochem J 1986; 236:811-20. [PMID: 3790092 PMCID: PMC1146914 DOI: 10.1042/bj2360811] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The physiological role of protein carboxy-group methylation reactions in human erythrocytes was studied with calmodulin as an endogenous methyl-group acceptor. The steady-state degree of calmodulin carboxy-group methylation is substoichiometric both in intact cells and in a lysed-cell system (about 0.0003 mol of methyl groups/mol of polypeptide). Purified erythrocyte calmodulin is a substrate for a partially purified erythrocyte carboxy-group methyltransferase and can be methylated to the extent of about 0.0007-0.001 mol of methyl groups/mol of polypeptide. This erythrocyte protein methyltransferase displays an apparent specificity for atypical racemized and/or isomerized D-aspartate and L-isoaspartate residues [McFadden & Clarke (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 2460-2464; Murray & Clarke (1984) J. Biol. Chem. 259, 10722-10732]. Exposure of calmodulin to elevated temperatures before methylation results in racemization of aspartate and/or asparagine residues, and may result in isoaspartate formation as well. The methylatability of these samples also increases as a function of time of heating, independent of the pH (over the range pH 5-9) or Ca2+ concentration; the most significant increase occurs during the initial 60 min, when calmodulin retains a fraction of its biological activity. These results are consistent with the hypothesis that methylation of calmodulin may occur at these uncommon aspartate residues, but are not consistent with a regulatory role for the methylation reaction.
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Murray ED, Clarke S. Metabolism of a synthetic L-isoaspartyl-containing hexapeptide in erythrocyte extracts. Enzymatic methyl esterification is followed by nonenzymatic succinimide formation. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)42470-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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35
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Johnson BA, Freitag NE, Aswad DW. Protein carboxyl methyltransferase selectively modifies an atypical form of calmodulin. Evidence for methylation at deamidated asparagine residues. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39120-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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