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Results for “post translational modification”

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PubMed2003

O-GlcNAc turns twenty: functional implications for post-translational modification of nuclear and cytosolic proteins with a sugar.

O-linked beta-N-acetylglucosamine (O-GlcNAc) is a dynamic nucleocytoplasmic post-translational modification more analogous to phosphorylation than to classical complex O-glycosylation. A large number of nuclear and cytosolic proteins are modified by O-GlcNAc. Proteins modified by O-GlcNAc include transcription factors, signaling components, and metabolic enzymes. While the modification has been known for almost 20 years, functions for the monosaccharide modification are just now emerging. In this review, we will focus on the cycling enzymes and emerging roles for this post-translational modification in regulating signal transduction and transcription. Finally, we will discuss future directions and the working model of O-GlcNAc serving as a nutrient sensor.

Acetylglucosamine↗

PubMed1975

Post translational modifications of glucose-6-phosphate dehydrogenase in human leukemias.

The modifications of the electrofocusing pattern, the immunological reactivity and the kinetic properties of glucose 6 phosphate dehydrogenase have been studied in malignant blood cells of various leukemias and myeloproliferative disorders. 1. Granulocytic G-6PD forms with decreased isoelectric points have been found in all the acute myeloid leukemias and erythroleukemias, and in most of the chronic granulocytic leukemias and myelofibrosis. In contrast, granulocytic G-6PD from patients with polycythemia vera always was normal. On the same way leukemic lymphocyte or lymphoblast G-6PD was identical to that from normal lymphocytes. 2. The ratio of enzymatic activity to immunological reactivity (=molecular specific activity) was markedly decreased in the myeloblasts of two patients with acute myeloid leukemia, and in the erythroblast-rich cellular fraction of a patient with erythroleukemia. In these cells the decrease of molecular specific activity was parallel to the alteration of the electrofocusing pattern of G-6PD. 3. The enzymatic forms with decreased isoelectric point also exhibited an altered affinity for glucose 6 phosphate. These modifications are post translational alterations of the neosynthesized G-6PD, since this enzyme is a single molecule, coded by the same gene in all tissues; they seem to correspond to an accelerated molecular aging due to an increased concentration of "G-6PD modifying factors". The significance of such an increased concentration of these G-6PD modifying factors in malignant cells is discussed.

Glucosephosphate Dehydrogenase↗

PubMed1999

Phosphorylation of murine p53, but not human p53, by MAP kinase in vitro and in cultured cells highlights species-dependent variation in post-translational modification.

The p53 tumour suppressor protein is tightly regulated by protein-protein association, protein turnover and a variety of post-translational modifications. Multisite phosphorylation plays a major role in activating and in finely tuning p53 function. The proline rich domain of murine p53 is a substrate for phosphorylation, in vitro and in cultured cells, by the p42ERK2 and p44ERK1 mitogen-activated protein (MAP) kinases. However, to date there have been no reports of attempts to determine whether p53 from any other species is a substrate for MAP kinase. In this paper we confirm that murine p53 is targeted by recombinant MAP kinase and by MAP kinases in extracts of both murine and human cells. In contrast, human p53 is not a substrate for recombinant MAP kinase nor are there any detectable levels of protein kinase activity in stimulated human cell extracts which phosphorylate the proline rich domain of human p53 in vitro. Finally, although stimulation of murine fibroblasts with o-tetradecanolylphorbol 13-acetate (TPA), an indirect activator of the MAP kinase pathway, leads to site-specific phosphorylation of murine p53, similar treatment of human fibroblasts and epithelial cells showed no significant changes in the phosphorylation pattern. These data are consistent with accumulating evidence that significant species-dependent differences exist in the post-translational modification of p53.

Adenosine Triphosphate↗

PubMed1985

Changes in the post-translational modification of lysosomal enzymes during development of Dictyostelium.

The form of post-translational modification present on two lysosomal enzymes--acid phosphatase and alpha-mannosidase--changes as part of the developmental program of Dictyostelium discoideum. Prior to 8 h of development, all enzyme molecules are of a single modification type (early form enzyme). Starting at 8 h of development, enzyme molecules with a second type of modification (late-form enzymes) begin to appear in the cell. We separated the early and late forms of these enzymes from each other by chromatography on DEAE-cellulose. We found that the change in protein modification affects the enzymes' in vitro properties. The early and late forms of both of these enzymes differ in thermostability and susceptibility to proteolytic inactivation. We also found that the late form of alpha-mannosidase is preferentially secreted. We suggest that by synthesizing molecules with a second form of modification, the cell confers new characteristics to its lysosomal enzymes.

Acid Phosphatase↗

PubMed2003

O-GlcNAc: a regulatory post-translational modification.

Beta-N-acetylglucosamine (O-GlcNAc) is a regulatory post-translational modification of nuclear and cytosolic proteins. The enzymes for its addition and removal have recently been cloned and partially characterized. While only about 80 mammalian proteins have been identified to date that carry this modification, it is clear that this represents just a small percentage of the modified proteins. O-GlcNAc has all the properties of a regulatory modification including being dynamic and inducible. The modification appears to modulate transcriptional and signal transduction events. There are also accruing data that O-GlcNAc plays a role in apoptosis and neurodegeneration. A working model is emerging that O-GlcNAc serves as a metabolic sensor that attenuates a cell's response to extracellular stimuli based on the energy state of the cell. In this review, we will focus on the enzymes that add/remove O-GlcNAc, the functional impact of O-GlcNAc modification, and the current working model for O-GlcNAc as a nutrient sensor.

Acetylglucosamine↗

PubMed2005

AutoMotif server: prediction of single residue post-translational modifications in proteins.

UNLABELLED: The AutoMotif Server allows for identification of post-translational modification (PTM) sites in proteins based only on local sequence information. The local sequence preferences of short segments around PTM residues are described here as linear functional motifs (LFMs). Sequence models for all types of PTMs are trained by support vector machine on short-sequence fragments of proteins in the current release of Swiss-Prot database (phosphorylation by various protein kinases, sulfation, acetylation, methylation, amidation, etc.). The accuracy of the identification is estimated using the standard leave-one-out procedure. The sensitivities for all types of short LFMs are in the range of 70%. AVAILABILITY: The AutoMotif Server is available free for academic use at http://automotif.bioinfo.pl/

Algorithms↗

PubMed2006

Post-Translational Modifications of the P2X(4) purinergic receptor subtype in the human placenta are altered in preeclampsia.

P2X(4) receptors are activated by extracellular ATP to raise intracellular calcium, thus altering cell signalling. ATP release occurs under pathophysiological, stress and adverse cell conditions; these are all increased in preeclampsia. Although P2X(4) is abundantly expressed in normal placenta neither the differences in the amount of protein nor its post-translational modifications have been studied in placentae from pregnancies complicated by preeclampsia. Thus we examined P2X(4) protein expression, localization and post-translational modifications in normotensive controls, term and preterm preeclamptic placentae. Densitometric analysis of Western blots showed a significant increase in P2X(4) protein expression in both term (p=0.002) and preterm preeclamptic (p=0.0008) placental samples compared to normotensive controls however the tissue localization of this receptor subtype was unaltered across the groups. Our data showed that P2X(4) is a nitrated protein in the placenta and this nitration is upregulated in preterm preeclamptic placenta compared to normotensive controls (p=0.03). We also demonstrated that P2X(4) is heavily glycosylated in the placenta by deglycosylation with PNGase F which reduced the protein product size by 23 kDa. We propose that P2X(4) acts within the syncytiotrophoblast to alter intracellular calcium and subsequent signalling pathways thereby restoring placental cell homeostasis following ATP-induced changes during pathophysiological conditions such as preeclampsia. We also propose that the post-translational modifications of nitration and glycosylation are required for the normal functioning of P2X(4).

Adult↗

PubMedDate not supplied

[Computational search for potential post-translational modification sites in human RNA polymerase III subunits].

The transcription of small stable non-translated RNA genes (class III genes), directed by RNA polymerase III, is strictly regulated in accordance to physiological state of the cell (growth rate, cell cycle stage, apoptosis, etc.) Post-translational modifications of the polymerase may play the important role in class III gene transcription regulation. Using computational programs searching for potential post-translational modifications sites in proteins (MotifScan, NetPhos 2.0, and Yin-Yan 1.2), possible sites of phosphorylation were identified in all 17 subunits of human RNA polymerase III, and possible sites of reciprocal phosphorylation and glycosilation ("yin-yan" sites) - in 13 subunits. Among the identified sites -17 sites of phosphorylation in seven subunits are conservative in human, Saccharomyces cerevisiae and Schizosaccharomyces pombe, including two "yin-yan" sites in two subunits. The data obtained can be used for experimental identification of RNA polymerase III modification sites in vivo in cells being in different physiological states.

Computational Biology↗

PubMed2000

Post-translational modification of alphaB-crystallin of normal human lens.

The current study reports several post-translational modifications of alphaB-crystallin in normal human lenses. The isoforms of post-translational modified alphaB-crystallin were isolated from the normal human lenses of >70-age group by ion exchange chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The isoform modifications were determined in detail by fast atom bombardment mass spectroscopy and amino acid sequence analysis. As the criterion of non-modified alphaB-crystallin, alphaB-crystallin from 1-d-old infant lenses were used. The modifications found in this study involve oxidation of the N-terminal methionine-1 residue, phosphorylation of the serine-59 residue, and truncation of four amino acids from the C-terminal position of the crystallin. The oxidation of methionine-1 was found in the early stage of human life in 1-d-old lens, although other modification of alphaB-crystallin were usually only found in old lenses (>70-age group).

Amino Acid Sequence↗

PubMed1997

Phosducin and betagamma-transducin interaction I: effects of post-translational modifications.

The interaction between phosducin and betagamma-transducin plays regulatory roles in light adaptation of photoreceptors. Both phosducin and betagamma-transducin undergo post-translational modifications, with phosducin modified by phosphorylation and the gamma subunit of betagamma-transducin by farnesylation and carboxylmethylation. In this study we exploited the electrophoretic mobilities of these native proteins to develop a micro binding assay and examined the effects of post-translational modifications on binding affinities. It was found that decarboxylmethylation of gamma-transducin increased the mobility of betagamma-transducin during native gel electrophoresis, but decreased the apparent affinity for phosducin by about 2-fold. Phosphorylation of phosducin by protein kinase A increased the mobility but decreased the apparent affinity for betagamma-transducin by at least 3-fold.

Animals↗

PubMed2004

Characterization and location of post-translational modifications on chromogranin B from bovine adrenal medullary chromaffin granules.

Bovine chromoganin B (CGB)/secretogranin I, an acidic protein with a sequence of 626 residues and an isoelectric point of 5.2 is a major member of the chromogranin/secretogranin (CG/Sg) family. The difference between the theoretical molecular mass (76 kDa) and the value estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis results from post-translational modifications (glycosylation, phosphorylation and sulfation) and from the abundance of acidic residues (D 4.6%, and E 16.5%). Although the sequence of CGB is known, the structural analyses of the post-translational modifications have so far not been carried out. In the present study, using a combination of proteomic techniques including two-dimensional gel electrophoresis, Western blot, high-performance liquid chromatography purification, enzymatic digestion, sequencing, carbohydrate analysis, matrix-assisted laser desorption/ionization-time of flight and liquid chromatography mass spectrometry analysis, we have located 18 post-translational modifications on bovine CGB, isolated from adrenal medulla chromaffin granules. Furthermore, we have identified at the molecular level the presence of a mutation M/V on position 577 of natural CGB. All together these data reflect the complex structure of this protein marker of the neuroendocrine system.

Adrenal Medulla↗

PubMed2025

Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach.

MOTIVATION: Bottom-up mass spectrometry-based proteomics studies changes in protein abundance and structure across conditions. Since the currency of these experiments are peptides, i.e. subsets of protein sequences that carry the quantitative information, conclusions at a different level must be computationally inferred. The inference is particularly challenging in situations where the peptides are shared by multiple proteins or post-translational modifications. While many approaches infer the underlying abundances from unique peptides, there is a need to distinguish the quantitative patterns when peptides are shared. RESULTS: We propose a statistical approach for estimating protein abundances, as well as site occupancies of post-translational modifications, based on quantitative information from shared peptides. The approach treats the quantitative patterns of shared peptides as convex combinations of abundances of individual proteins or modification sites, and estimates the abundance of each source in a sample together with the weights of the combination. In simulation-based evaluations, the proposed approach improved the precision of estimated fold changes between conditions. We further demonstrated the practical utility of the approach in experiments with diverse biological objectives, ranging from protein degradation and thermal proteome stability, to changes in protein post-translational modifications. AVAILABILITY AND IMPLEMENTATION: The approach is implemented in an open-source R package MSstatsWeightedSummary. The package is currently available at https://github.com/Vitek-Lab/MSstatsWeightedSummary (doi: 10.5281/zenodo.14662989). Code required to reproduce the results presented in this article can be found in a repository https://github.com/mstaniak/MWS_reproduction (doi: 10.5281/zenodo.14656053).

Protein Processing, Post-Translational↗

PubMed2003

Post-translational modifications of three members of the human MAP1LC3 family and detection of a novel type of modification for MAP1LC3B.

The molecular machinery required for autophagy is highly conserved in all eukaryotes as seen by the high degree of conservation of proteins involved in the formation of the autophagosome membranes. Recently, both yeast Apg8p and its rat homologue Map1lc3 were identified as essential constituents of autophagosome membrane as a processed form. In addition, both the yeast and human proteins exist in two modified forms produced by a series of post-translational modifications including a critical C-terminal cleavage after a conserved Gly residue, and the smaller processed form is associated with the autophagosome membranes. Herein, we report the identification and characterization of three human orthologs of the rat Map1LC3, named MAP1LC3A, MAP1LC3B, and MAP1LC3C. We show that the three isoforms of human MAP1LC3 exhibit distinct expression patterns in different human tissues. Importantly, we found that the three isoforms of MAP1LC3 differ in their post-translation modifications. Although MAP1LC3A and MAP1LC3C are produced by the proteolytic cleavage after the conserved C-terminal Gly residue, like their rat counterpart, MAP1LC3B does not undergo C-terminal cleavage and exists in a single modified form. The essential site for the distinct post-translation modification of MAP1LC3B is Lys-122 rather than the conserved Gly-120. Subcellular localization by cell fractionation and immunofluorescence revealed that three human isoforms are associated with membranes involved in the autophagic pathway. These results revealed different regulation of the three human isoforms of MAP1LC3 and implicate that the three isoforms may have different physiological functions.

Amino Acid Sequence↗

PubMed1998

The post-translational modification in cytochrome c oxidase is required to establish a functional environment of the catalytic site.

Mutation of tyrosine-288 to a phenylalanine in cytochrome c oxidase from Rhodobacter sphaeroides drastically alters its properties. Tyr-288 lies in the CuB-cytochrome a3 binuclear catalytic site and forms a hydrogen bond with the hydroxy group on the farnesyl side chain of the heme. In addition, through a post-translational modification, Y288 is covalently linked to one of the histidine ligands that is coordinated to CuB. In the Y288F mutant enzyme, the "as-isolated" preparation is a mixture of reduced cytochrome a and oxidized cytochrome a3. The cytochrome a3 heme, which is largely six-coordinate low-spin in both oxidation states of the mutant, cannot be reduced by cytochrome c, but only by dithionite, possibly due to a large decrease in its reduction potential. It is postulated that the Y288F mutation prevents the post-translational modification from occurring. As a consequence, the catalytic site becomes disrupted. Thus, one role of the post-translational modification is to stabilize the functional catalytic site by maintaining the correct ligands on CuB, thereby preventing nonfunctional ligands from coordinating to the heme.

Binding Sites↗

PubMed2003

Post-translational modifications of alpha-tubulin in Zea mays L are highly tissue specific.

To further understand post-translational modifications (PTMs) of plant alpha-tubulin, post-translationally modified alpha-tubulin isoforms from selected tissues of Zea mays L. were examined using two-dimensional electrophoresis and immunoblotting. Except for polyglycylated tubulin, tyrosinated, detyrosinated, acetylated and polyglutamylated alpha-tubulin isoforms were all present in maize tissues. Tyrosinated alpha-tubulin was the predominant variant in all cases, with isoforms alpha1-alpha4 (alpha5) being the most common components. Leaves exhibited a striking difference in PTM patterns of alpha-tubulin isoforms compared to other tissues examined. In leaves, several major specific isoforms were highly modified by detyrosination, acetylation and polyglutamylation. In pollen and anthers, only the most abundant isoform alpha3 was acetylated to an appreciable extent, and no acetylated isoform was found in roots. Similarly, in pollen, anthers and roots, only alpha3 was appreciably polyglutamylated. Additionally, a detyrosinated isoform alpha6 was present in anthers and in leaves, while the tyrosinated isoform alpha6 seemed to be pollen specific. These results indicate that certain types of PTM of plant alpha-tubulin preferentially occur in a tissue-specific way.

Electrophoresis, Polyacrylamide Gel↗

PubMed2001

Post-translational modifications and activation of p53 by genotoxic stresses.

In unstressed cells, the tumor suppressor protein p53 is present in a latent state and is maintained at low levels through targeted degradation. A variety of genotoxic stresses initiate signaling pathways that transiently stabilize the p53 protein, cause it to accumulate in the nucleus, and activate it as a transcription factor. Activation leads either to growth arrest at the G1/S or G2/M transitions of the cell cycle or to apoptosis. Recent studies point to roles for multiple post-translational modifications in mediating these events in response to genotoxic stresses through several potentially interacting but distinct pathways. The approximately 100 amino-acid N-terminal and approximately 90 amino-acid C-terminal domains are highly modified by post-translational modifications. The N-terminus is heavily phosphorylated while the C-terminus contains phosphorylated, acetylated and sumoylated residues. Antibodies that recognize p53 only when it has been modified at specific sites have been developed, and studies with these reagents show that most known post-translational modifications are induced when cells are exposed to genotoxic stresses. These recent results, coupled with biochemical and genetic studies, suggest that N-terminal phosphorylations are important for stabilizing p53 and are crucial for acetylation of C-terminal sites, which in combination lead to the full p53-mediated response to genotoxic stresses. Modifications to the C-terminus inhibit the ability of this domain to negatively regulate sequence-specific DNA binding; additionally, they modulate the stability, the oligomerization state, the nuclear import/export process and the degree of ubiquitination of p53.

Animals↗

PubMed1994

The post-translational modification of ras p21 is important for Raf-1 activation.

Raf-1, a serine/threonine kinase, is required for the mitogenic action of ras p21. It has been recently demonstrated that ras p21 directly associates with Raf-1. The C-terminal region of ras p21 is modified by farnesylation and carboxyl methylation. This modification is necessary for ras p21 function. To elucidate the role of post-translational modification of ras p21 in Raf-1 activation, we examined ras p21-dependent Raf-1 activity in baculovirus/Sf9 cells overexpressing Raf-1 and ras p21. Coexpression of Raf-1 with v-ras p21 in Sf9 cells stimulated the autophosphorylating activity of Raf-1. The activity of Raf-1, as assessed by its ability to activate extracellular signal-regulated kinase kinase (MEK) in vitro, was also increased when Raf-1 was coexpressed with v-ras p21. However, neither the autophosphorylating activity of Raf-1 nor its ability to activate MEK was stimulated by v-ras p21 mutants which are not post-translationally modified. Raf-1 formed a complex with v-ras p21 and the v-ras p21 mutants in Sf9 cells. These results indicate that the post-translational modification of ras p21 is necessary for Raf-1 activation but that the association of Raf-1 with ras p21 is not sufficient to activate Raf-1.

Animals↗

PubMedDate not supplied

Capillary affinity electrophoresis for the screening of post-translational modification of proteins with carbohydrates.

Glycosylation is one of the most important post-translational events for proteins, affecting their functions in health and disease, and plays significant roles in various information traffics for intracellular and intercellular biological events (Hancock, W. S. J. Proteome Res. 2002, 1, 297). We have attempted to obtain the information on the numbers and amounts of carbohydrate chains. Interaction between carbohydrate chains and proteins that recognize them is a target to understand the biological roles of glycosylation. To date, there have been a few strategies for simultaneous analysis of the interactions between complex mixtures of carbohydrates and proteins. Here, we report an approach to categorize carbohydrate chains using a few glycoprotein samples as models for the studies on the analysis of post-translational modification of proteins with carbohydrates. A combination of some specific lectins was used as carbohydrate-binding proteins. The method is based on high-resolution separation of fluorescent-labeled carbohydrates by capillary electrophoresis with laser-induced fluorescent detection in the presence of carbohydrate-binding proteins at different concentrations. The present technique affords (1) simultaneous determination of carbohydrate chains, (2) binding specificity of the constituent carbohydrate chains to specific proteins, and (3) kinetic data such as the association constant of each carbohydrate. We found that the lectins employed in the present study could discriminate subtle difference in linkages and resolved the carbohydrate mixtures. The results will be useful, for example, to understand the biological events expressed with carbohydrate changes on the cell surface.

Agglutinins↗