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Results for “Protein Modification, Translational”

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PubMed2001

Expression of the mitogen-activated protein kinase kinase ZmMEK1 in the primary root of maize.

We have analyzed changes in the distribution and abundance of a mitogen-activated protein kinase kinase (MAPKK) enzyme (EC 2.7.1.37) known as ZmMEK1. in root apices of Zea mays L. under normal growth conditions, and after treatments that alter patterns of proliferation, as a means to assess the potential physiological role of the MAP kinase cascade in growth and development. The ZmMEK1 protein is most abundant within immature tissues such as the roots and leaves of seedlings, and is nearly undetectable in mature leaf tissue. Along the longitudinal axis of growing roots, ZmMEK1 mRNA and protein are abundant throughout the apical 12 mm. Two anti-ZmMEK1 antibody-reactive proteins can be resolved within the apical 4 mm of the root, spatially coinciding with the meristem and distal elongation zone. Phosphatase treatments suggest that both immunoreactive bands are forms of ZmMEK1 that differ in their state of phosphorylation. Expression of ZmMEK1, histone H4 and cyclin-dependent protein kinase (CDK) in roots after 7 days of exposure to low temperature and during a 48-hour recovery period was monitored during the coincident alterations in growth. Levels of ZmMEK1 mRNA and protein within these roots were indistinguishable from those of control roots. However, a slower-migrating form of ZmMEK1 temporally coincided with the observed increase in CDK levels during the transition into proliferative activity. We demonstrate that the ZmMEK1 MAPK activator is expressed and is differentially phosphorylated within the root meristem and distal elongation zone. We suggest that post-translational modifications of the protein regulate the function of ZmMEK1 within the root. Changes in ZmMEK1 phosphorylation state correlate with changes in proliferation in the root apex.

DNA-Binding Proteins↗

PubMed2006

Phosphoproteomic analysis of the human pituitary.

The pituitary is the central endocrine gland that regulates the functions of various target organs in the human body. Because of the pivotal regulatory role of the pituitary, it is essential to define on a global scale the components of the pituitary protein machinery, including a comprehensive characterization of the post-translational modifications of the pituitary proteins. Of particular interest is the examination of the phosphorylation status of the pituitary in health and disease. Towards the goal of global profiling of pituitary protein phosphorylation, we report here the application of the in-gel IEF-LC-MS/MS approach to the study of the pituitary phosphoproteome. The analytical strategy combined isoelectric focusing in immobilized pH gradient strips with immobilized metal ion affinity chromatography and mass spectrometry. With this method, a total of 50 phosphorylation sites were characterized in 26 proteins. Because the investigation involved primary tissue, the findings provide a direct glimpse into the phosphoprotein machinery operating within the human pituitary tissue microenvironment.

Adrenocorticotropic Hormone↗

PubMed2006

Genome-wide analysis of histone modifications by ChIP-on-chip.

Post-translational modifications to histone proteins regulate the packaging of genomic DNA into chromatin, gene activity and other functions of the genome. They are understood to play key roles in embryonic development and disease pathogenesis. Recent advances in technology have made it possible to analyze chromatin structure genome-wide in mammalian cells. Global patterns of histone modifications can be observed using a technique called ChIP-on-chip, which combines the specificity of chromatin immunoprecipitation with the unbiased, high-throughput capabilities of microarrays. The resulting maps provide insight into the functions of, and relationships between, different modifications. Here, we provide validated ChIP-on-chip methods for analyzing histone modification patterns at genome-scale in mammalian cells.

Animals↗

PubMedDate not supplied

Proteomics: a paradigm shift.

Proteome--the protein complement of a genome--has become the protein renaissance and a key research tool in the post-genomic era. The basic technology involves the routine usage of gel electrophoresis and spectrometry procedures for deciphering the primary protein sequence/structure as well as knowing certain unique post-translational modifications that a particular protein has undergone to perform a specific function in the cell. However, the recent advancements in protein analysis have ushered this science to provide deeper, bigger and more valuable perspectives regarding performance of subtle protein-protein interactions. Applications of this branch of molecular biology are as vast as the subject is and include clinical diagnostics, pharmaceutical and biotechnological industries. The 21st century hails the use of products, procedures and advancements of this science as finer touches required for the grooming of fast-paced technology.

Animals↗

PubMed2003

Evolving intricacies and implications of E2F1 regulation.

E2F transcription factors may play a pivotal role in the transcriptional regulation of several cellular processes far beyond the originally described cell cycle and proliferation. Among the six E2F family members, only E2F1 is noted for its role in apoptosis. The pocket protein family members Rb, p107, and p130 act as the main regulators of E2F activity. Nonetheless, in recent years other protein-protein interactions have been described for E2Fs. The post-translational modifications resulting from such protein interactions may have significant implications in the stability, half-life, and functional activity of E2Fs. In human diseases the significance of E2Fs is still under appreciated and is primarily recognized only as a consequence of the impairment in retinoblastoma gene product (Rb). However, with increasing knowledge of other protein interactions, the derailment of E2F activity could be anticipated to stem from an abnormality of any node in the complex network governing their availability and activity. The present review is intended to provide a perspective on the diversity of biochemical mechanisms underlying abnormal E2F expression and activity, understanding of which may have significant clinical implications.

Animals↗

PubMed2006

Proteome-level display by 2-dimensional chromatography of extracellular matrix-dependent modulation of the phenotype of bladder cancer cells.

BACKGROUND: The extracellular matrix can have a profound effect upon the phenotype of cancer cells. Previous work has shown that growth of bladder cancer cells on a matrix derived from normal basement membrane suppresses many malignant features that are displayed when the cells are grown on a matrix that has been modified by malignant tumors. This work was undertaken to investigate proteome-level changes as determined by a new commercially available proteome display involving 2-dimensional chromatography for bladder cancer cells grown on different extracellular matrix preparations that modulate the expression of the malignant phenotype. RESULTS: Depending on the matrix, between 1300 and 2000 distinct peaks were detected by two-dimensional chromatographic fractionation of 2.1-4.4 mg of total cellular protein. The fractions eluting from the reversed-phase fractionation were suitable for mass spectrometric identification following only lyophilization and trypsin digestion and achieved approximately 10-fold higher sensitivity than was obtained with gel-based separations. Abundant proteins that were unique to cells grown on one of the matrices were identified by mass spectrometry. Following concentration, peaks of 0.03 AU provided unambiguous identification of protein components when 10% of the sample was analyzed, whereas peaks of 0.05 AU was approximately the lower limit of detection when the entire sample was separated on a gel and in-gel digestion was used. Although some fractions were homogeneous, others were not, and up to 3 proteins per fraction were identified. Strong evidence for post-translational modification of the unique proteins was noted. All 13 of the unique proteins from cells grown on Matrigel were related to MYC pathway. CONCLUSION: The system provides a viable alternative to 2-dimensional gel electrophoresis for proteomic display of biological systems. The findings suggest the importance of MYC to the malignant phenotype of bladder cancer cells.

Journal Article↗

PubMed1998

[Recent trends in protein structural studies].

Since the 1980's, structural studies of proteins have changed remarkably. It is currently possible to predict the entire amino acid sequence of a protein by the rapid and highly sensitive analysis of the nucleotide sequence of genomic DNA or cDNA encoding the protein. In the near future, the entire sequence of a protein may be predicted from a partial sequence just by searching a variety of databases now being constructed for many biological species. The predicted protein sequence, however, is the backbone structure of the precursor protein without post-translational modifications. Therefore, the major objectives of recent structural studies of proteins are directed to 1) rapid and sensitive confirmation of the predicted sequence and identification of those modifications present in mature proteins by newly developed mass spectrometry, 2) determination of the 3D structures of intact and mutant proteins isolated or expressed in cultured E. coli, yeast or animal cells using X-ray crystallography or NMR analysis, and 3) rapid prediction of the 3D structures of proteins utilizing protein databases. The "PROTEOME" project was proposed in 1998 to bring together all the data on the structure and function of mature proteins under international cooperation. The present paper summarizes such recent trends in protein structural studies.

Mass Spectrometry↗

PubMed2003

Farnesyltransferase inhibitors are potent lung cancer chemopreventive agents in A/J mice with a dominant-negative p53 and/or heterozygous deletion of Ink4a/Arf.

Mutations in the Kras2 gene are seen in both human and mouse lung adenocarcinomas. The protein product (p21ras) encoded by the Kras2 gene must be post-translationally modified at a terminal CAAX motif in order to be biologically active. In this study, we systematically investigated the chemopreventive efficacy of two different farnesyltransferase inhibitors (FTIs): one is a peptidomimetic (FTI-276) and the other is an imidazole (L778-123). Both FTIs are designed to inhibit the post-translational modification of p21ras proteins with a terminal CAAX motif. In a complete chemoprevention study, where the inhibitor was administered before carcinogen was given, and throughout the study, FTI-276 treatment significantly reduced both the tumor multiplicity by 41.7% (P<0.005), and the total tumor volume by 79.4% (P<0.0001). In the late treatment study, where mice were treated with an inhibitor 12 to 20 weeks after carcinogen administration, FTI-276 treatment resulted in a 60% reduction in tumor multiplicity and 58% reduction in tumor volume. Next, we examined the chemopreventive efficacy of a new FTI, L-778,123, on lung tumor development in A/J mice and transgenic mice with a dominant-negative p53 mutation and/or heterozygous deletion of Ink4a/Arf. Treatment of mice with L-778,123 for a period of 10 weeks from 20 weeks to 30 weeks post carcinogen initiation resulted in an approximately 50% decrease in tumor multiplicity in wild-type mice and mice with a dominant-negative p53 mutation and/or heterozygous deletion of the Ink4a/Arf tumor suppressor genes. Interestingly, tumor volume was decreased approximately 50% in wild-type mice and in mice with an Ink4a/Arf heterozygous deletion, while tumor volume was decreased approximately 75% in animals with a dominant-negative p53 and in mice with both a p53 mutation and heterozygous deletion of Ink4a/Arf. This result suggests that FTI exhibited a significantly (P<0.05) more efficacious chemopreventive effect in animals with alterations of p53 and Ink4a/Arf as contrasted with wild-type mice. Thus, FTIs are potent lung chemopreventive agents in both A/J mice and transgenic mice harboring a dominant-negative p53 and heterozygous deletion of Ink4a/Arf. In fact, L-778,123 is more effective in inhibiting primary lung progression in mice with a p53 mutation and/or an Ink4a/Arf deletion than in wild-type animals.

Adenocarcinoma↗

PubMed2005

High levels of protein expression using different mammalian CMV promoters in several cell lines.

With the recent completion of the human genome sequencing project, scientists are faced with the daunting challenge of deciphering the function of these newly found genes quickly and efficiently. Equally as important is to produce milligram quantities of the therapeutically relevant gene products as quickly as possible. Mammalian expression systems provide many advantages to aid in this task. Mammalian cell lines have the capacity for proper post-translational modifications including proper protein folding and glycosylation. In response to the needs described above, we investigated the protein expression levels driven by the human CMV in the presence or absence of intron A, the mouse and rat CMV promoters with intron A, and the MPSV promoter in plasmid expression vectors. We evaluated the different promoters using an in-house plasmid vector backbone. The protein expression levels of four genes of interest driven by these promoters were evaluated in HEK293EBNA and CHO-K1 cells. Stable and transient transfected cells were utilized. In general, the full-length human CMV, in the presence of intron A, gave the highest levels of protein expression in transient transfections in both cell lines. However, the MPSV promoter resulted in the highest levels of stable protein expression in CHO-K1 cells. Using the CMV driven constitutive promoters in the presence of intron A, we have been able to generate >10 microg/ml of recombinant protein using transient transfections.

Animals↗

PubMed1994

Mass-spectrographic analysis of a porcine amelogenin identifies a single phosphorylated locus.

The amelogenins of the extracellular matrix of developing dental enamel, comprise a family of tissue-specific proteins which are postulated to play a central role in the biomineralization of dental enamel [1]. The primary structures of amelogenins derived from cow, pig, human, mouse and rat have now been elucidated by the interpretation of cDNA sequences or by direct amino acid sequence determinations [2-6] demonstrating a high degree of sequence homology between species [1]. However, the nature of post-translational modification of these proteins is less clear. In particular, early reports of amelogenin phosphorylation [7-8] have proved to be difficult to confirm by direct chemical analyses [1]. Using mass spectrographic analysis, we recently [9], reported that the lower molecular weight (5-7 kDa) bovine and porcine amelogenin polypeptides (TRAP and LRAP) contained a single phospho-serine residue at position 16Ser and, since these polypeptides are derived by proteolytic processing from the higher molecular weight "parent" amelogenins (18-25 kDa), we concluded that these precursor molecules must also be phosphorylated, as has previously been suggested [10]. In contrast to these observations, an extensive amino acid sequencing study of porcine amelogenins has recently reported no evidence for such phosphorylation [1]. We now report that a new analysis of the major porcine ("20K") amelogenin provides positive evidence for porcine amelogenin phosphorylation.

Amelogenin↗

PubMedDate not supplied

Convergence of glucose- and fatty acid-induced abnormal myocardial excitation-contraction coupling and insulin signalling.

1. Myocardial insulin resistance and abnormal Ca(2+) regulation are hallmarks of hypertrophic and diabetic hearts, but deprivation of energetic substrates does not tell the whole story. Is there a link between the aetiology of these dysfunctions? 2. Diabetic cardiomyopathy is defined as phenotypic changes in the heart muscle cell independent of associated coronary vascular disease. The cellular consequences of diabetes on excitation-contraction (E-C) coupling and insulin signalling are presented in various models of diabetes in order to set the stage for exploring the pathogenesis of heart disease. 3. Excess glucose or fatty acids can lead to augmented flux through the hexosamine biosynthesis pathway (HBP). The formation of uridine 5 cent-diphosphate-hexosamines has been shown to be involved in abnormal E-C coupling and myocardial insulin resistance. 4. There is growing evidence that O-linked glycosylation (downstream of HBP) may regulate the function of cytosolic and nuclear proteins in a dynamic manner, similar to phosphorylation and perhaps involving reciprocal or synergistic modification of serine/threonine sites. 5. This review focuses on the question of whether there is a role for HBP and dynamic O-linked glycosylation in the development of myocardial insulin resistance and abnormal E-C coupling. The emerging concept that O-linked glycosylation is a regulatory, post-translational modification of cytosolic/nuclear proteins that interacts with phosphorylation in the heart is explored.

Animals↗

PubMed2006

Vincristine regulates the phosphorylation of the antiapoptotic protein HSP27 in breast cancer cells.

Vincristine is an antitumor drug that inhibits microtubule polymerization, causes G2/M arrest and induces apoptosis. 2D-PAGE and MALDI-TOF-MS analysis of vincristine effects on MCF7 cells, revealed a vincristine upregulated form and a vincristine downregulated form of the antiapoptotic protein HSP27. These findings linked to the lack of vincristine effect over HSP27 mRNA, suggest a protein post-translational modification. Further assays indicated the presence of a phosphorylated peptide, containing serine 82, only in the vincristine upregulated form. Serine 82 phosphorylation was confirmed using specific antibodies. Thus, phosphorylation of HSP27 may play a role in the cellular response to vincristine.

Amino Acid Sequence↗

PubMed2002

MEF2-mediated recruitment of class II HDAC at the EBV immediate early gene BZLF1 links latency and chromatin remodeling.

In B lymphocytes induced to proliferate in vitro by the Epstein-Barr virus (EBV), extra-chromosomal viral episomes packaged in chromatin persist in the nucleus, and there is no productive cycle. A switch from this latency to the productive cycle is observed after induced expression of the EBV BZLF1 gene product, the transcription factor EB1. We present evidence that, during latency, proteins of the myocyte enhancer binding factor 2 (MEF2) family are bound to the BZLF1 promoter and recruit class II histone deacetylases. Furthermore, we propose that latency is determined primarily by a specific and local recruitment of class II histone deacetylase (HDAC) by MEF2D to the BZLF1 gene promoter. The switch from latency to the productive cycle could be due in part to post-translational modification of MEF2 proteins and changes in the local acetylation state of the chromatin.

B-Lymphocytes↗

PubMed1995

Characterization of an 80-kD membrane glycoprotein (gp80) of human keratinocytes: a marker for commitment to terminal differentiation in vivo and in vitro.

We have characterized an 80-kD cell-surface glycoprotein (gp80) identified by monoclonal antibody BT 15, the expression of which is closely associated with a commitment to terminal squamous or follicular differentiation of keratinocytes in normal adult and fetal human epidermis. Maximum expression was found in the suprabasal layers, but basal cells located at the epidermal sulci were also clearly positive, in contrast to the virtually negative basal cells at the epidermal ridges. This protein was also present in benign hyperproliferative disorders of the epidermis (i.e., common warts, keratoacanthoma, psoriasis, and seborrhoic keratoses) with monoclonal antibody BT 15 preferentially staining suprabasal cells and some basal cells at the epidermal sulci. Gp80 was completely lacking in most basal cell carcinomas; the only exceptions were two cases of partially cornifying tumors that were strongly stained around keratotic pearls. In squamous cell carcinomas, gp80 was expressed in keratinized areas of the tumors. In organotypic keratinocyte cultures that resemble the in vivo situation, gp80 was strongly expressed in the suprabasal layers. However, unlike known markers for terminal differentiation, gp80 was weakly expressed by basal cells. Synthesis rates of gp80 were high in keratinocyte cell suspensions freshly prepared from skin, and decreased in primary cultures and first and second subcultures (ratio 10:4:2:1). Elevated concentrations of the Ca++ that increased stratification of cultured keratinocytes resulted in a two- to threefold increase of gp80 synthesis. GP80 was not synthesized at detectable levels by the immortal keratinocyte cell line HaCaT; however, it was expressed in HaCaT cultures treated with mitomycin C, indicating an association with cessation of growth. Pulse-chase experiments revealed that gp80 is synthesized from a 55-kD precursor molecule, the maturation of which was prevented by treating cells with tunicamycin. Glycosidase digestion of BT 15 immunoprecipitates from untreated cells indicated that the predominant post-translational modification of the protein is N-linked glycosylation. Our data indicate that gp80 is a glycoprotein that is expressed by growth-arrested human keratinocytes or as part of the terminal differentiation program.

Biomarkers↗

PubMed2026

Integrative proteomics and bioinformatics pipelines for PTM profiling.

Post-translational modifications (PTMs) regulate protein function across all life forms and allow plants to respond rapidly to biotic and abiotic stress. Over 450 PTM types have been described across organisms, of which 23-33 have been experimentally confirmed in plants, including phosphorylation, acetylation, methylation, glycosylation, ubiquitination, and sumoylation. These modifications are highly dynamic and often reversible, and frequently act in combination, or "crosstalk," to fine-tune cellular processes. Advances in high-resolution mass spectrometry and large-scale genome sequencing continue to expand the catalogue of known PTM sites, while machine learning and deep learning approaches increasingly support prediction of PTM site localization and function. Unlike broader surveys of plant PTMs, this review focuses specifically on O-phosphorylation and Lys-N(ε)-acetylation, the two best-characterized and most extensively crosstalking PTMs in plants, and integrates four perspectives: the historical development of proteomic and bioinformatics approaches to these modifications; current mass spectrometry-based workflows and enrichment strategies; the bioinformatics tools and databases available for their analysis; and the technical and species-related challenges, particularly in non-model plants, that currently limit their study. We close by outlining priority directions for future research, including multi-omics integration, AI-based prediction, and the translation of PTM knowledge into crop stress resilience and breeding applications.

Protein Processing, Post-Translational↗

PubMed1999

Potential involvement of post-translational modifications as a mechanism modulating selective proteolysis after fertilization.

The role of proteolysis during fertilization has been investigated only to a very limited extent as compared with its role on the control of cell cycle progression. In this report, we discuss briefly the proteases involved in fertilization, their relevance in the egg-sperm interaction and in the chromatin remodeling that occurs before the reestablishment of the diploid condition of the zygote. We further emphasize how the post-translational modifications of target proteins modulate these proteolytic events. J. Cell. Biochem. Suppls. 32/33:149-157, 1999.

Animals↗

PubMed2006

Peptide-based phosphoproteomics with immobilized metal ion chromatography.

The identification of protein phosphorylation sites has always been a challenging task, traditionally involving large amounts of radioactive phosphorus and high-performance liquid chromatography separation and Edman sequencing of phosphopeptides. The rapid development of mass spectrometric methods has advanced protein research significantly, and the identification of in vivo post-translational modifications of even rare proteins is now possible. Even with the new generation of machines, however, phosphopeptides do not lend themselves easily to mass spectrometric analysis. In complex mixtures of peptides, phosphopeptides are often difficult to detect because of suppression effects during ionization. This problem can be largely solved by affinity purification/enrichment of the phosphopeptides, and immobilized metal ion affinity chromatography (IMAC) on chelated Fe3+ or other metal ions has emerged as the simplest and most useful method. IMAC has been useful to identify several in vivo phosphorylation sites of individual proteins, but is easier to apply to complex mixtures. We describe a complete protocol as it has been used for Arabidopsis plasma membranes, and note where it can be adapted for soluble protein mixtures.

Arabidopsis↗

PubMed2002

Differential protein expression, DNA binding and interaction with SV40 large tumour antigen implicate the p63-family of proteins in replicative senescence.

P53 activity plays a key role in mammalian cells when they undergo replicative senescence at their Hayflick limit. To determine whether p63 proteins, members of the family of p53-related genes, are also involved in this process, we examined their expression in serially passaged rat embryo fibroblasts. Upon senescence, two truncated DeltaNp63 proteins decreased in abundance whereas two TAp63 isoforms accumulated. 2-D gel analysis showed that the DeltaNp63 proteins underwent post-translational modifications in both proliferating and senescent cells. Direct binding of DeltaNp63 proteins to a p53 consensus motif was greater in proliferating cells than senescent cells. In contrast p63alpha isoforms bound to DNA in a p53 dependent manner and this was higher in senescent cells than proliferating cells. An interaction of p63alpha proteins with SV40 large tumour antigen was also detected and ectopic expression of DeltaNp63alpha can extend the lifespan of rat embryo fibroblasts. Taken together the results indicate that p63 proteins may play a role in replicative senescence either by competition for p53 DNA binding sites or by direct interaction with p53 protein bound to DNA.

Animals↗