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Chen T, Nayak N, Majee SM, Lowenson J, Schäfermeyer KR, Eliopoulos AC, Lloyd TD, Dinkins R, Perry SE, Forsthoefel NR, Clarke SG, Vernon DM, Zhou ZS, Rejtar T, Downie AB. Substrates of the Arabidopsis thaliana protein isoaspartyl methyltransferase 1 identified using phage display and biopanning. J Biol Chem 2010; 285:37281-92. [PMID: 20870712 DOI: 10.1074/jbc.m110.157008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The role of protein isoaspartyl methyltransferase (PIMT) in repairing a wide assortment of damaged proteins in a host of organisms has been inferred from the affinity of the enzyme for isoaspartyl residues in a plethora of amino acid contexts. The identification of PIMT target proteins in plant seeds, where the enzyme is highly active and proteome long-lived, has been hindered by large amounts of isoaspartate-containing storage proteins. Mature seed phage display libraries circumvented this problem. Inclusion of the PIMT co-substrate, S-adenosylmethionine (AdoMet), during panning permitted PIMT to retain aged phage in greater numbers than controls lacking co-substrate or when PIMT protein binding was poisoned with S-adenosyl homocysteine. After four rounds, phage titer plateaued in AdoMet-containing pans, whereas titer declined in both controls. This strategy identified 17 in-frame PIMT target proteins, including a cupin-family protein similar to those identified previously using on-blot methylation. All recovered phage had at least one susceptible Asp or Asn residue. Five targets were recovered independently. Two in-frame targets were produced in Escherichia coli as recombinant proteins and shown by on-blot methylation to acquire isoAsp, becoming a PIMT target. Both gained isoAsp rapidly in solution upon thermal insult. Mutant analysis of plants deficient in any of three in-frame PIMT targets resulted in demonstrable phenotypes. An over-representation of clones encoding proteins involved in protein production suggests that the translational apparatus comprises a subgroup for which PIMT-mediated repair is vital for orthodox seed longevity. Impaired PIMT activity would hinder protein function in these targets, possibly resulting in poor seed performance.
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Affiliation(s)
- Tingsu Chen
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40546-0312, USA
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2
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Klee CB, Draetta GF, Hubbard MJ. Calcineurin. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 61:149-200. [PMID: 2833077 DOI: 10.1002/9780470123072.ch4] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- C B Klee
- Laboratory of Biochemistry, National Cancer Institute, Bethesda, Maryland 20892
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3
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O'Connor CM. 13 Protein L-isoaspartyl, D-aspartyl O-methyltransferases: Catalysts for protein repair. Enzymes 2006; 24:385-433. [PMID: 26718047 DOI: 10.1016/s1874-6047(06)80015-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Protein L-isoaspartyl, D-aspartyl O-methyltransferases (PIMTs) are ancient enzymes distributed through all phylogenetic domains. PIMTs catalyze the methylation of L-isoaspartyl, and to a lesser extent D-aspartyl, residues arising from the spontaneous deamidation and isomerization of protein asparaginyl and aspartyl residues. PIMTs catalyze the methylation of isoaspartyl residues in a large number of primary sequence configurations, which accounts for the broad specificity of the enzyme for protein substrates both in vitro and in vivo. PIMT-catalyzed methylation of isoaspartyl substrates initiates the repair of the polypeptide backbone in its damaged substrates by a spontaneous mechanism that involves a succinimidyl intermediate. The repair process catalyzed by PEVITs is not completely efficient, however, leaving open the possibility that unidentified enzymatic activities cooperate with PIMT in the repair process. Structurally, PIMTs are members of the class I family of AdoMet-dependent methyltransferases. PIMTs have a unique topological arrangement of strands in the central β sheet that provides a signature for this class of enzymes. The regulation and physiological significance of PIMT has been studied in several model organisms. PIMTs are constitutively synthesized by cells, but they can be upregulated in response to conditions that are potentially damaging to protein structures, or when proteins are stored for prolonged periods of time. Disruption of PIMT genes in bacteria and simple eukaryotes produces subtle phenotypes that are apparent only under stress. Loss of PIMT function in transgenic mice leads to fatalepilepsy, suggesting that PIMT function is particularly important to neurons in mammals.
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Affiliation(s)
- Clare M O'Connor
- Biology Department Boston College 140 Commonwealth Avenue Chestnut Hill, MA 02467, USA
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4
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Cho JY, Kim SS, Kwon MH, Kim SH, Lee HW, Hong S. Protein carboxylmethylation in porcine spleen is mainly mediated by class I protein carboxyl O-methyltransferase. Arch Pharm Res 2004; 27:206-16. [PMID: 15022724 DOI: 10.1007/bf02980108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The functional role of protein carboxylmethylation (PCM) has not yet been clearly elucidated in the tissue level. The biochemical feature of PCM in porcine spleen was therefore studied by investigating the methyl accepting capacity (MAC) of natural endogenous substrate proteins for protein carboxyl O-methyltransferase (PCMT) in various conditions. Strong acidic and alkaline-conditioned (at pH 11.0) analyses of the MAC indicated that approximately 65% of total protein methylation seemed to be mediated by spleen PCMT. The hydrolytic kinetics of the PCM products, such as carboxylmethylesters (CMEs), under mild alkaline conditions revealed that there may be three different kinds of CMEs [displaying half-times (T1/2) of 1.1 min (82.7% of total CMEs), 13.9 min (4.6%), and 478.0 min (12.7%)], assuming that the majority of CME is base-labile and may be catalyzed by class I PCMT. In agreement with these results, several natural endogenous substrate proteins (14, 31 and 86 kDa) were identified strikingly by acidic-conditioned electrophoresis, and their MAC was lost upon alkaline conditions. On the other hand, other proteins (23 and 62 kDa) weakly appeared under alkaline conditions, indicating that PCM mediated by class II or III PCMT may be a minor reaction. The MAC of an isolated endogenous substrate protein (23-kDa) was also detected upon acidic-conditioned electrophoresis. Therefore, our data suggest that most spleen PCM may be catalyzed by class I PCMT, which participates in repairing aged proteins.
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Affiliation(s)
- Jae Youl Cho
- Department of Genetic Engineering, Faculty of Life Science and Technology, Sungkyunkwan University, Suwon 440-746, Korea
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5
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Solstad T, Carvalho RN, Andersen OA, Waidelich D, Flatmark T. Deamidation of labile asparagine residues in the autoregulatory sequence of human phenylalanine hydroxylase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:929-38. [PMID: 12603326 DOI: 10.1046/j.1432-1033.2003.03455.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two dimensional electrophoresis has revealed a microheterogeneity in the recombinant human phenylalanine hydroxylase (hPAH) protomer, that is the result of spontaneous nonenzymatic deamidations of labile asparagine (Asn) residues [Solstad, T. and Flatmark, T. (2000) Eur. J. Biochem.267, 6302-6310]. Using of a computer algorithm, the relative deamidation rates of all Asn residues in hPAH have been predicted, and we here verify that Asn32, followed by a glycine residue, as well as Asn28 and Asn30 in a loop region of the N-terminal autoregulatory sequence (residues 19-33) of wt-hPAH, are among the susceptible residues. First, on MALDI-TOF mass spectrometry of the 24 h expressed enzyme, the E. coli 28-residue peptide, L15-K42 (containing three Asn residues), was recovered with four monoisotopic mass numbers (i.e., m/z of 3106.455, 3107.470, 3108.474 and 3109.476, of decreasing intensity) that differed by 1 Da. Secondly, by reverse-phase chromatography, isoaspartyl (isoAsp) was demonstrated in this 28-residue peptide by its methylation by protein-l-isoaspartic acid O-methyltransferase (PIMT; EC 2.1.1.77). Thirdly, on incubation at pH 7.0 and 37 degrees C of the phosphorylated form (at Ser16) of this 28-residue peptide, a time-dependent mobility shift from tR approximately 34 min to approximately 31 min (i.e., to a more hydrophilic position) was observed on reverse-phase chromatography, and the recovery of the tR approximately 34 min species decreased with a biphasic time-course with t0.5-values of 1.9 and 6.2 days. The fastest rate is compatible with the rate determined for the sequence-controlled deamidation of Asn32 (in a pentapeptide without 3D structural interference), i.e., a deamidation half-time of approximately 1.5 days in 150 mm Tris/HCl, pH 7.0 at 37 degrees C. Asn32 is located in a cluster of three Asn residues (Asn28, Asn30 and Asn32) of a loop structure stabilized by a hydrogen-bond network. Deamidation of Asn32 introduces a negative charge and a partial beta-isomerization (isoAsp), which is predicted to result in a change in the backbone conformation of the loop structure and a repositioning of the autoregulatory sequence and thus affect its regulatory properties. The functional implications of this deamidation was further studied by site-directed mutagenesis, and the mutant form (Asn32-->Asp) revealed a 1.7-fold increase in the catalytic efficiency, an increased affinity and positive cooperativity of L-Phe binding as well as substrate inhibition.
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Affiliation(s)
- Therese Solstad
- Department of Biochemistry and Molecular Biology, Proteomic Unit, University of Bergen, Arstadveien 19, N-5009 Bergen, Norway
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6
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Iida T, Santa T, Toriba A, Imai K. Amino acid sequence and D/L-configuration determination methods for D-amino acid-containing peptides in living organisms. Biomed Chromatogr 2001; 15:319-27. [PMID: 11507713 DOI: 10.1002/bmc.80] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
D-amino acid-containing peptides with biological activities have been isolated from invertebrates and amphibians, and partial racemization of amino acid residues in mammalian peptides associated with aging and diseases have been discussed. Here, we review the amino acid configuration determination methods in these peptides and recent progress of simultaneous determination method for sequence and configuration of amino acid residues. The applicability of C-terminus sequence analysis and mass spectrometry to configuration determination of amino acids is also discussed.
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Affiliation(s)
- T Iida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, Japan
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7
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Abstract
Mature human erythrocytes are highly differentiated cells which have lost the ability to biosynthesize proteins de novo. During cell aging in circulation, erythrocyte proteins undergo spontaneous postbiosynthetic modifications, regarded as "protein fatigue" damage, which include formation of isomerized and/or racemized aspartyl residues. These damaged proteins cannot be replaced by new molecules; nevertheless, data support the notion that they can be repaired to a significant extent, through an enzymatic transmethylation reaction. This repair reaction has therefore been used as a means to monitor the increase of altered aspartyl residues in erythrocyte membrane proteins during cell aging. The relationship between protein repair and aspartyl racemization in red blood cell stress and disease is discussed.
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Affiliation(s)
- D Ingrosso
- Institute of Biochemistry of Macromolecules, S.U.N. School of Medicine and Surgery, Naples, Italy
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8
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Xie H, Clarke S. Protein phosphatase 2A is reversibly modified by methyl esterification at its C-terminal leucine residue in bovine brain. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)42124-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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9
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Xie H, Clarke S. Methyl esterification of C-terminal leucine residues in cytosolic 36-kDa polypeptides of bovine brain. A novel eucaryotic protein carboxyl methylation reaction. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)38660-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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10
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Ladino CA, O'Connor CM. Methylation of atypical protein aspartyl residues during the stress response of HeLa cells. J Cell Physiol 1992; 153:297-304. [PMID: 1429850 DOI: 10.1002/jcp.1041530209] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A protein carboxyl methyltransferase (PCMT), which specifically modifies atypical protein L-isoaspartyl and D-aspartyl residues, is widely distributed in eucaryotic cells, but the factors that regulate its activity in vivo have not been identified. It has been proposed that the PCMT initiates the repair of structurally damaged proteins. To test the possibility that the concentration of structurally abnormal cellular proteins affects PCMT activity, protein carboxyl methylation reactions were studied in HeLa cells exposed to various stresses that increase the extent of protein unfolding in cells. Protein carboxyl methylation rates increased 70-80% during incubations at 42 degrees C and remained elevated for periods of up to 8 hr. This sustained increase was greater than that predicted from thermal effects on the enzyme alone and may reflect the exposure of atypical aspartyl sites as proteins unfold as well as increased rates of protein deamidation and isomerization at elevated temperatures. Methylation rates showed no increases following 12 hr incubations with the amino acid analogs L-azetidine-2-carboxylic acid or L-canavanine. Northern blot analysis of RNA preparations from control and stressed cells revealed three major transcripts for the PCMT in HeLa cells, which are 1.6, 2.6, and 4.5 kb in length. The concentrations of all three transcripts decreased by approximately 20% from control levels during heat shock. No changes in PCMT transcript concentrations were observed during incubation with the amino acid analogs. By contrast, large increases in the concentrations of hsp70 and ubiquitin transcripts were observed following either heat or chemical stresses. The results demonstrate that the PCMT is a constitutive component of cells whose function is required under normal conditions as well as during stress conditions, which accelerate structural damage to cellular proteins.
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Affiliation(s)
- C A Ladino
- Worcester Foundation for Experimental Biology, Shrewsbury, Massachusetts 01545
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11
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Ubbink JB, Vermaak WJ, van der Merwe A, Becker PJ. The effect of blood sample aging and food consumption on plasma total homocysteine levels. Clin Chim Acta 1992; 207:119-28. [PMID: 1591859 DOI: 10.1016/0009-8981(92)90155-j] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The stability of homocysteine in whole blood and plasma was investigated. Total homocysteine concentrations in whole blood increased rapidly to values in excess of 180% of the basal concentration if whole blood was left at ambient temperature. Sodium fluoride partially inhibited homocysteine accumulation, while refrigeration inhibited homocysteine accumulation for at least 4 h. Since intracellular concentrations of homocysteine were low, the results indicate continued metabolism of L-methionine to homocysteine after the blood sample had been obtained. In contrast to whole blood, homocysteine was stable in plasma, even at room temperature. Food consumption (normal breakfast) resulted in significantly lower plasma homocysteine concentrations, which returned to pre-prandial concentrations 8 h later. The results indicate that both blood sampling and food intake should be rigorously standardized in epidemiological studies to elucidate the possible role of elevated circulating homocysteine concentrations in premature vascular disease.
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Affiliation(s)
- J B Ubbink
- Department of Chemical Pathology, Faculty of Medicine, University of Pretoria, South Africa
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12
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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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13
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Ladino CA, O'Connor CM. Identification of a site for carboxyl methylation in human alpha-globin. Biochem Biophys Res Commun 1991; 180:742-7. [PMID: 1953748 DOI: 10.1016/s0006-291x(05)81128-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The human erythrocyte protein carboxyl methyltransferase modifies unusual protein D-aspartyl and L-isoaspartyl residues which arise spontaneously from internal rearrangements accompanying asparaginyl deamidation and aspartyl isomerization. A site of methylation associated with alpha-globin in intact cells has been identified by peptide mapping of radiolabeled globin isolated from human erythrocytes previously incubated with L-[methyl-3H]methionine. The site is located in a Staphylococcus V8 peptide containing residues 1-30 of alpha-globin. Two potential sources of methylation sites are present in this sequence at Asp-t and Asn-9.
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Affiliation(s)
- C A Ladino
- Worcester Foundation for Experimental Biology, Shrewsbury, MA 01545
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14
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Structural elements affecting the recognition of L-isoaspartyl residues by the L-isoaspartyl/D-aspartyl protein methyltransferase. Implications for the repair hypothesis. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)55010-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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15
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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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16
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Galletti P, Manna C, Ingrosso D, Iardino P, Zappia V. Hypotheses on the physiological role of enzymatic protein methyl esterification using human erythrocytes as a model system. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1991; 307:149-60. [PMID: 1805583 DOI: 10.1007/978-1-4684-5985-2_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- P Galletti
- Department of Biochemistry of Macromolecules, 1st Medical School, University of Napoli, Italy
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17
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Ota IM, Clarke S. Multiple sites of methyl esterification of calmodulin in intact human erythrocytes. Arch Biochem Biophys 1990; 279:320-7. [PMID: 2190534 DOI: 10.1016/0003-9861(90)90498-n] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aspartyl and asparaginyl residues are susceptible to spontaneous chemical degradation reactions that result in the formation of isomerized and racemized aspartyl residues. At least a subset of these abnormal residues are recognized by a widely distributed protein D-aspartyl/L-isoaspartyl methyltransferase (EC 2.1.1.77) that can participate in their conversion to normal L-aspartyl residues. We have used this methyltransferase as a probe to identify modified aspartyl and asparaginyl residues in peptides and proteins. In purified calmodulin from bovine brain, major sites of methylation were found to originate from the Asp-2 residue near the amino terminus and the Asp-78 residue in the alpha-helix that connects the two globular calcium-binding domains. When purified calmodulin was incubated at physiological temperature and pH in the absence of calcium, additional methylation sites were found in three of the four calcium-binding sites. In this work we have analyzed the methyl esterification of human calmodulin catalyzed by this enzyme in intact erythrocytes. On the basis of results from peptide mapping studies, Asp-2, Asp-78/80, and residues in calcium-binding domains III and IV appear to be methylated. Methylation of sites in the calcium-binding regions appears to reflect the low concentration of free calcium in human erythrocytes. We also found that calmodulin isolated from erythrocytes and methylated in vitro contains major methylation sites at Asp-2 and Asp-78/80 but not in the calcium-binding sites. Comparison of the number of available methylation sites of calmodulin in intact cells and in material aged in vitro supports the hypothesis that repair processes can occur in erythrocytes.
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Affiliation(s)
- I M Ota
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90024-1569
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18
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19
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Romanik EA, O'Connor CM. Methylation of Microinjected Isoaspartyl Peptides in Xenopus oocytes. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)71640-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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20
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Degradation of structurally characterized proteins injected into HeLa cells. Tests of hypotheses. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)77713-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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21
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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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22
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O'Connor CM, Yutzey KE. Enhanced carboxyl methylation of membrane-associated hemoglobin in human erythrocytes. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)57315-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Clarke S. Propensity for spontaneous succinimide formation from aspartyl and asparaginyl residues in cellular proteins. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1987; 30:808-21. [PMID: 3440704 DOI: 10.1111/j.1399-3011.1987.tb03390.x] [Citation(s) in RCA: 271] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
One mechanism for the spontaneous degradation of polypeptides is the intramolecular attack of the peptide bond nitrogen on the side chain carbonyl carbon atom of aspartic acid and asparagine residues. This reaction results in the formation of succinimide derivatives and has been shown to be largely responsible for the racemization, isomerization, and deamidation of these residues in several peptides under physiological conditions (Geiger, T. & Clarke, S. J. Biol. Chem. 262, 785-794 (1987]. To determine if similar reactions might occur in proteins, I examined the sequence and conformation about aspartic acid and asparagine residues in a sample of stable, well-characterized proteins. There did not appear to be any large bias against dipeptide sequences that readily form succinimides in small peptides. However, it was found that aspartyl and asparaginyl residues generally exist in native proteins in conformations where the peptide bond nitrogen atom cannot approach the side chain carbonyl carbon to form a succinimide ring. These orientations also represent energy minimum states, and it appears that this factor may account for a low rate of spontaneous damage to proteins by succinimide-linked reactions. The presence of aspartic acid and asparagine residues in other conformations, such as those in partially denatured, conformationally flexible regions, may lead to more rapid succinimide formation and contribute to the degradation of the molecule. The possible role of isoimide intermediates, formed by the attack of the peptide oxygen atom on the side chain carboxyl group, in protein racemization, isomerization, and deamidation is also considered.
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Affiliation(s)
- S Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles
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24
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Abstract
To test whether cellular protein kinases exist that phosphorylate D-amino acid residues, a method was developed for separating O-phospho-D-serine from O-phospho-L-serine and O-phospho-L-tyrosine from O-phospho-D-tyrosine. This was accomplished by converting these amino acids to the L-leucyl dipeptide derivatives followed by separation of the diastereomers by anion-exchange high-performance liquid chromatography. The enantiomeric content of these D- and L-residues were measured in hydrolysates of 32P-labeled proteins produced by the protein kinases of human erythrocytes and the tyrosyl protein kinase of the Abelson leukemia virus. We found no measurable D-phosphoserine in erythrocyte membrane proteins under conditions where a 1% content of this residue relative to L-phosphoserine would have been detected. These values can be used to place an upper hypothetical limit on the fraction of erythrocyte protein kinase activity that is specific for serine residues in the D-configuration. In separate experiments, we examined the specificity of the tyrosyl protein kinases. We found that all of the phosphotyrosine that we isolated from the erythrocyte band 3 NH2-terminal fragment and from the autophosphorylation of the Abelson virus tyrosyl kinase was in the L-configuration.
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Affiliation(s)
- P N McFadden
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90024
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25
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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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26
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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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27
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Nguyen MH, Harbour D, Gagnon C. Secretory proteins from adrenal medullary cells are carboxyl-methylated in vivo and released under their methylated form by acetylcholine. J Neurochem 1987; 49:38-44. [PMID: 3585340 DOI: 10.1111/j.1471-4159.1987.tb03391.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The carboxyl methylation of secretory proteins in vivo was investigated in bovine adrenal medullary cells in culture. Chromogranin A, the major intragranular secretory protein in adrenal medullary cells, and other secretory proteins were found to be carboxyl-methylated within secretory vesicles. The in vivo labeling pattern using [methyl-3H]methionine and the in vitro labeling pattern using S-adenosyl-[methyl-14C]methionine of intravesicular secretory proteins were similar. The detection of methylated chromogranin A in mature secretory vesicles required 3-6 h, a time consistent with the synthesis and storage of secretory proteins in this tissue. Carboxyl-methylated chromogranin A was secreted from medullary cells by exocytosis via activation of nicotinic cholinergic receptor and recovered still under the methylated form in the incubation medium. Since protein-carboxyl-methylase is cytosolic, these results suggest that methylation of secretory proteins is a cotranslational phenomenon.
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Methylation at specific altered aspartyl and asparaginyl residues in glucagon by the erythrocyte protein carboxyl methyltransferase. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)47445-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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29
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Nuske JH. Protein methylase II in five taxa from three phyla. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1987; 86:37-47. [PMID: 3030627 DOI: 10.1016/0305-0491(87)90172-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein methylase II (protein O-methyltransferase, EC 2.1.1.24) was found in Dictyostelium discoideum amoebae, Astacus leptodactylus axonal, Locusta migratoroides neuronal, Torpedo marmorata electroplaque and Bos bovis stratial tissue and compared in both the soluble and particulate fractions. The intrinsic decay data of the methyl groups transferred onto proteins from Dictyostelium and Torpedo tissues were virtually identical. The short term kinetics of the methyl group transfer of all fractions and of all taxa investigated were non-linear and multiphasic. The particulate fractions displayed transient peaks at 1 min, 3 min, or both after the start of the reaction. The methyl group transfer was stimulated by the neurotoxins veratridine (VTx) and inhibited by veratridine plus tetrodotoxin (TTx) (axonal membrane vesicles of Astacus), stimulated transiently and in a biphasic manner by carbamoylcholine and phospholipase A2 (AChR-rich membrane vesicles of Torpedo), and stimulated transiently and biphasically by the adequate chemotactic stimulus cAMP (aggregation competent amoebae of Dictyostelium).
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30
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Meydan N, Egozi Y, Kloog Y. Enzymatic protein carboxyl methylation in rat posterior pituitary: neurophysins in rapid-turnover pool determine methyl accepting capacity. J Neurochem 1987; 48:208-16. [PMID: 3794701 DOI: 10.1111/j.1471-4159.1987.tb13149.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In vitro stimulation of intact rat posterior pituitary by either veratridine or K+ depolarization results in the concomitant release of neurophysins and in a decrease (70-80%) in their carboxyl methylation as measured either with L-[methyl-3H]methionine in the intact lobes after stimulation or in their homogenates with [methyl-3H]S-adenosyl-L-methionine and purified protein carboxyl methyltransferase. A similar reduction in neurophysin methylation (60%) was observed when the arrival of newly synthesized neurophysins at the posterior pituitary was blocked by colchicine. Experimental data indicate that the reduction in neurophysin content of the lobes after 12 h of colchicine treatment (less than 7%) or after in vitro stimulation (about 10%) cannot account for the marked reduction in neurophysin methylation. The results suggest that the granule pool characterized by rapid turnover of neurophysins probably represents the major source of methyl acceptor proteins in the lobe. In spite of the marked reduction in neurophysin methyl accepting capacity observed after stimulation, there was no parallel increase in methyl accepting capacity of the released neurophysins. We propose that a neurophysin subfraction that might be associated with the membrane of releasable granules participates in the methylation reaction in situ.
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31
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Age-dependent accumulation of protein residues which can be hydrolyzed to D-aspartic acid in human erythrocytes. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67121-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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32
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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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Barber JR, Morimoto BH, Brunauer LS, Clarke S. Metabolism of S-adenosyl-L-methionine in intact human erythrocytes. BIOCHIMICA ET BIOPHYSICA ACTA 1986; 886:361-72. [PMID: 3011117 DOI: 10.1016/0167-4889(86)90171-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Freshly isolated human erythrocytes contain S-adenosyl-L-methionine (AdoMet) at a concentration of about 3.5 mumol/l cells. When such cells are incubated in a medium containing 30 microM L-methionine, 18 mM D-glucose and 118 mM sodium phosphate (pH 7.4), intracellular AdoMet levels continuously decrease to a value of about 0.1 microM after 24 h. This occurs in spite of the fact that the cellular concentrations of the substrates for the AdoMet synthetase reaction, ATP and L-methionine, remain relatively constant. In a search for incubation conditions that lead to stable levels of AdoMet in incubated cells, we have developed a sodium-Hepes-buffered medium which includes 1 mM adenine and a stoichiometric excess of MgCl2 over its ligand, phosphate. The inclusion of magnesium ion (and a reduction in phosphate) appears to increase intracellular free Mg2+, which is required for full activity of the erythrocyte AdoMet synthetase. Even in the presence of MgCl2, however, the AdoMet pool level can drop 4-6-fold within the first 2 h of incubation. We present evidence that suggests that this initial fall in the cellular AdoMet level may be due to the activation of AdoMet-dependent protein carboxyl methyltransferase, an enzyme which accounts for a large fraction of the total cellular AdoMet utilization. Adenine, or related compounds in the medium may prevent this activation, although the mechanism of this action is not clear at present.
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34
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McFadden PN, Clarke S. Protein carboxyl methyltransferase and methyl acceptor proteins in aging and cataractous tissue of the human eye lens. Mech Ageing Dev 1986; 34:91-105. [PMID: 3713272 DOI: 10.1016/0047-6374(86)90107-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have studied the enzymatic modification of proteins in human eye lens tissue where these molecules can be long-lived and can be exposed to non-enzymatic degradation processes for periods of time up to the age of the individual. We have detected a protein carboxyl methyltransferase that is similar to enzymes from other mammalian tissues which appear to catalyze the methyl esterification of altered aspartyl residues, including D-aspartyl and beta-isomerized L-aspartyl residues, but which have no activity on normal L-aspartyl sites. Upon gel filtration of human lens extracts, we find protein substrates for the lens methyltransferase in each of the major soluble classes of protein. In comparing individual lenses of various ages, protein carboxyl methyltransferase activity was present in tissue from all normal and yellow cataractous lenses tested, but was present only at very low apparent levels in brunescent lens tissue. We find that the methyltransferase is much more highly saturated by endogenous methyl acceptor substrates in lens extracts from older individuals, suggesting that the prolonged in vivo aging of lens protein leads to the accumulation and perhaps metabolism of altered aspartyl residues.
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35
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Maeda N, Kon K, Sekiya M, Shiga T. Increase of ATP level in human erythrocytes induced by S-adenosyl-L-methionine. Biochem Pharmacol 1986; 35:625-9. [PMID: 3947393 DOI: 10.1016/0006-2952(86)90358-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The effect of S-adenosyl-L-methionine (SAM) on the ATP level, the morphology and the deformability of human erythrocytes was investigated and compared with that of adenosine. (i) Upon incubation with SAM, the ATP level increased considerably in fresh cells (in both young and old cells in similar extent) and in stored (partially ATP-depleted) cells. But the incubation with adenosine increased ATP level to a lesser extent. (ii) The incubation of stored cells with SAM hardly affected (or rather decreased) the IMP level, while that with adenosine remarkably increased IMP (and ITP). (iii) The morphology and the deformability of stored erythrocytes were well conserved in spite of the treatment with SAM, as compared with the treatment with adenosine. The echinocytic transformation was induced in old cells to some extent by SAM, while did not in young cells.
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36
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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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37
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Barber JR, Clarke S. Demethylation of protein carboxyl methyl esters: a nonenzymatic process in human erythrocytes? Biochemistry 1985; 24:4867-71. [PMID: 4074664 DOI: 10.1021/bi00339a021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have compared the demethylation rate of protein carboxyl methyl esters from isolated human erythrocyte membranes with the corresponding rate of metabolic turnover of these same methyl groups in the intact erythrocyte. Surprisingly, the apparent spontaneous demethylation of these membrane protein methyl esters was significantly faster at physiological pH than the corresponding rate determined by pulse-chase analysis of intact cells incubated with L-[methyl-3H]methionine. Readdition of erythrocyte lysate to purified membranes did not increase the rate of demethylation, as might be expected if there were cytosolic or membrane-bound protein methylesterase activity, but resulted instead in an apparent stabilization of these methyl esters. Thus, the metabolic lability of these protein methyl esters in intact cells may be quantitatively explained by spontaneous, rather than enzymatic, demethylation reactions. A model is presented in which a rapid but nonenzymatic intramolecular demethylation reaction results in the formation of a polypeptide imide or anhydride intermediate. The metabolic fate of these hypothetical intermediates is unknown but may lead to the repair or degradation of protein D-aspartyl and L-isoaspartyl residues, which appear to be the substrates for the initial transmethylation reaction.
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O'Connor CM, Clarke S. Analysis of erythrocyte protein methyl esters by two-dimensional gel electrophoresis under acidic separating conditions. Anal Biochem 1985; 148:79-86. [PMID: 4037310 DOI: 10.1016/0003-2697(85)90630-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A two-dimensional polyacrylamide gel electrophoresis system which is suitable for the analysis of protein methylation reactions in cells incubated with L-[methyl-3H]methionine is described. The procedure separates proteins under primarily acidic conditions by isoelectric focusing in the first dimension and by sodium dodecyl sulfate electrophoresis at pH 2.4 in the second dimension. The low pH is essential for preserving protein [3H]methyl esters, but it limits the effective separating range of this system to proteins with isoelectric points between 4 and 8. With this system, we have shown that most, if not all, erythrocyte membrane and cytosolic proteins can act as substoichiometric methyl acceptors for an intracellular S-adenosylmethionine-dependent carboxyl methyltransferase and that protein carboxyl methylation reactions may be the major methyl transfer reaction in erythrocytes. These results are most consistent with the generation of protein substrate sites for the carboxyl methyltransferase by spontaneous deamidation and racemization reactions.
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39
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Billingsley ML, Kim S, Kuhn DM. Immunohistochemical localization of protein-O-carboxylmethyltransferase in rat brain neurons. Neuroscience 1985; 15:159-71. [PMID: 3892360 DOI: 10.1016/0306-4522(85)90130-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The distribution of the enzyme protein-O-carboxylmethyltransferase (EC 2.1.1.24) has been investigated in the rat brain using both immunohistochemical and biochemical techniques. The enzyme, which carboxylmethylates free aspartic and glutamic acid residues of protein substrates, was localized in neurons, but not other cell types throughout the brain. The highest immunoreactivity was detected throughout the cortex, followed by the hippocampus, the corpus striatum, the thalamus and the amygdala. Immunoreactive cells were detected in other brain regions but were not as prominent as those regions listed above. The distribution of immunoreactivity in the hippocampus was most striking, with considerable labelling of the pyramidal and granule cells in all regions. Numerous pyramidal cells were labelled in the cerebral cortex, with some ascending processes exhibiting immunoreactivity. The corpus striatum was uniformly labelled, suggesting that the enzyme was not localized to any specific neurotransmitter system. The antisera employed in this study was generated against purified bovine brain protein-O-carboxylmethyltransferase and Western immunoblot analysis showed cross reactivity against both rat brain and human erythrocyte forms of the enzyme. Enzyme activity and methyl acceptor protein capacity were examined in 1.5 mm coronal sections of rat brain. The regions with highest enzyme activities were found in cross-sections containing cortex and corpus striatum or cortex and hippocampus. The lowest enzyme activities were noted in slices of brainstem and cerebellum, areas exhibiting low amounts of immunoreactive protein-O-carboxylmethyltransferase. Methyl acceptor protein capacity was highest in slices of cortex and corpus striatum, cortex and hippocampus and was lowest in slices of brainstem and cerebellum. These results demonstrate that protein-O-carboxylmethyltransferase has an unique neuronal pattern of distribution in the rodent central nervous system, and suggest that the carboxylmethylation of proteins may be of functional significance in these neurons.
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40
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Billingsley ML, Lovenberg W. Protein carboxylmethylation and nervous system function. Neurochem Int 1985; 7:575-87. [DOI: 10.1016/0197-0186(85)90054-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/1984] [Accepted: 11/26/1984] [Indexed: 12/22/2022]
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Williams-Ashman HG, Hatch R, Harvey SE. Protein O-carboxylmethylation in relation to male gamete production and function. ADVANCES IN ENZYME REGULATION 1985; 23:389-416. [PMID: 3907306 DOI: 10.1016/0065-2571(85)90058-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein O-carboxylmethyltransferase (PCM) activity of differentiating male germ cells in the testis and of spermatozoa is strikingly high. PCM catalyzes the methylesterification by S-adenosylmethionine of dicarboxylic amino acid residues in proteins. PCM appears to be the only type of protein methyltransferase present in mature spermatozoa. Mammalian sperms contain considerable amounts of S-adenosylmethionine and can apparently synthesize this nucleoside from L-methionine and ATP. Spermatozoa are rich in S-adenosylhomocysteine hydrolase. The characteristics of this enzyme in testicular germ cells and in sperms are very similar to those in other mammalian tissues; the very sub-stoichiometric extent of methylation of various pure protein substrates, and the rapid spontaneous hydrolysis of the protein methyl ester products at physiological and especially higher pH values, are particularly remarkable. From studies on processes related to protein O-carboxylmethylation in rat spermatozoa from different regions of the epididymis, and in ejaculated spermatozoa from normal and infertile men, unequivocal evidence could not be obtained for hypotheses of other investigators that PCM-catalyzed reactions are of regulatory importance for the acquisition of a potentiality for motility in sperms during their transit and maturation in the epididymis, or for the locomotion of ejaculated sperms. The findings are discussed in the light of the recent hypothesis of S. Clarke that PCM catalyzes methylesterification of D-aspartyl residues that accumulate in certain proteins as a result of slow spontaneous racemization of L-aspartyl residues, and that the methyl esterification of D-aspartyl residues may be related to disposal or repair of proteins damaged in this fashion.
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42
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Steinbrecher UP, Fisher M, Witztum JL, Curtiss LK. Immunogenicity of homologous low density lipoprotein after methylation, ethylation, acetylation, or carbamylation: generation of antibodies specific for derivatized lysine. J Lipid Res 1984. [DOI: 10.1016/s0022-2275(20)37720-8] [Citation(s) in RCA: 131] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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43
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Murray ED, Clarke S. Synthetic peptide substrates for the erythrocyte protein carboxyl methyltransferase. Detection of a new site of methylation at isomerized L-aspartyl residues. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)90571-5] [Citation(s) in RCA: 101] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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44
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Barber JR, Clarke S. Inhibition of protein carboxyl methylation by S-adenosyl-L-homocysteine in intact erythrocytes. Physiological consequences. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)39845-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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45
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Clarke S, McFadden PN, O'Connor CM, Lou LL. Isolation of D-aspartic acid beta-methyl ester from erythrocyte carboxyl methylated proteins. Methods Enzymol 1984; 106:330-44. [PMID: 6387377 DOI: 10.1016/0076-6879(84)06033-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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