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Results for “Protein Modification, Translational”

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PubMed2002

A survey of the plant mitochondrial proteome in relation to development.

To expand the functional analysis of plant mitochondria, we have undertaken the building of the proteome of pea mitochondria purified from leaves (green and etiolated), roots and seeds. In the first stage, we focused our proteomic exploration on the soluble protein complement of the green leaf mitochondria. We used traditional two-dimensional polyacrylamide gel electrophoresis, in combination with size exclusion chromatography as a third dimension, to identify the major proteins and further resolve their macromolecular complexity. The two-dimensional map of soluble proteins of green leaf mitochondria revealed 433 spots (with Coomassie blue staining) and around 73% of the proteins (in mass) were identified using three different approaches: Edman degradation, matrix-assisted laser desorption/ionization mass spectrometry and electrospray ionization tandem mass spectrometry. Quite a lot of the polypeptides were present in multiforms which indicated the presence of isoforms or the occurrence of post-translational modifications. Among these proteins, we uncovered an abundant family that was identified as aldehyde dehydrogenases, representing approximately 7.5% of the soluble proteins. The comparative analysis of soluble mitochondrial proteomes led to the identification of a number of proteins which were specifically present in root or in seed mitochondria, thus revealing the impact of tissue differentiation at the mitochondrial level.

Cell Fractionation↗

PubMed2002

The effects of phosphorylation on adaptor protein function.

Adaptor proteins are specialized protein binding partners that serve to link signaling proteins to each other, as a mechanism to propagate a cellular signal. Ultimately, these signals are required for a specific biological response. Thus, it is important that the cell develop mechanisms to regulate these signaling cascades. One way these cascades can be regulated is through post translational modifications of adaptor proteins which would regulate their ability to forge protein-protein interactions. In this review, we summarize the effects of serine/threonine and tyrosine phosphorylation on adaptor protein function, with a specific focus upon those adaptor proteins in which phosphorylation has been demonstrated to regulate a signaling cascade or biological response.

Animals↗

PubMed1997

Arterial gene therapy: a molecular biological perspective for the treatment of arterial ischemia.

Since most cells do not naturally incorporate foreign DNA, strategies for arterial gene transfer have generally relied on agents designed to augment cellular DNA uptake such as liposomes, viral vectors, and protein conjugates. However, even when DNA has been successfully introduced into a cell, the likelihood of gene expression remains uncertain because the transgene has to escape lysosomal degradation, be transferred to the nucleus for transcription of mRNA, and be exported to the cytoplasm for translation and/or post-translation modification of the protein product. Transfection efficiency represents the final index of this regulatory sequence. The extent to which this compromises human gene therapy for cardiovascular disease depends in part on the presence or absence of a signal sequence permitting active secretion of the gene product. The implication of these issues is discussed with regard to restenosis and angiogenesis.

Animals↗

PubMed2001

Proteomics: unraveling the complexity of heart disease and striving to change cardiology.

Heart disease encompasses a broad spectrum of pathological conditions, involving many different etiologies. Abnormal changes to the proteome, the complete cellular protein complement, are responsible for the various disease phenotypes. The proteome is dynamic, however, and is constantly changing due to a combination of factors, including temporal and functional regulation of gene expression, differrential mRNA splicing and subsequent protein post-translational modifications. This dynamic response is compounded during the development of acute responses of the heart (such as myocardial preconditioning, stunning and infarction), just as it is during the development and onset of chronic heart disease (eg, heart failure). Proteomic analyses enable the identification and characterization of these disease-induced protein changes using a multitude of experimental techniques. This review provides an overview of proteomic technology with emphasis on the unique problems associated with the analysis of the heart, summarizes the latest proteomic studies, assesses what information analogous genomic studies can provide for the design and execution of proteomics, and finally discusses the implications of proteomics for the identification and development of diagnostics and therapeutic targets specifically for heart disease. The future holds great promise for the availability of a panel of cardiac serum biomarkers able to delineate different stages of each heart disease, thus allowing the design of clinical interventions potentially using stage-specific therapeutics. All of this is feasible only with detailed information about the unique and selective protein modifications that occur during the development of heart disease.

Cardiology↗

PubMed2000

High performance liquid chromatography-electrospray mass spectrometry for the simultaneous resolution and identification of intrinsic thylakoid membrane proteins.

In higher plants, both photosystem I (PSI) and II (PSII) consist of membrane-embedded proteins that contain more than one transmembrane alpha helix. PSI is a multiprotein complex consisting of a core complex of thirteen proteins surrounded by four different types of light harvesting antenna proteins. Up to now, the protein components of both photosystems have been characterized by SDS-PAGE and/or immunoblotting and, therefore, identification made only on the basis of electrophoretic mobility, which is sometimes not sufficient to discriminate between individual membrane proteins. This is also complicated by the fact that some proteins, such as the antenna proteins, have almost identical molecular mass and amino acid sequence, making it difficult to identify and ascertain the relative stoichiometry of the proteins. In this paper, we report the complete resolution of the antenna proteins and most of the core components of PSI from spinach, together with the identification of proteins by molecular mass, successfully deduced by the combined use of HPLC coupled on-line with a mass spectrometer equipped with an electrospray ion source (ESI-MS). The proposed RP-HPLC-ESI-MS method holds several advantages over SDS-PAGE, including better protein separation, especially for antenna proteins, mass accuracy, speed, efficiency, and the potential to reveal isomeric forms. Moreover, the molecular masses determined by HPLC-ESI-MS are in good agreement with the molecular masses of the individual components calculated on the basis of their nucleotide-derived amino acid sequences, indicating an absence of post-translational modifications in these proteins. It follows that if the method proposed is useful for these highly hydrophobic proteins, it may be of general use for any membrane proteins, where the presence of detergent for solubilization may compromise their characterization.

Chromatography, High Pressure Liquid↗

PubMed1995

The cytochrome subunit is necessary for covalent FAD attachment to the flavoprotein subunit of p-cresol methylhydroxylase.

When p-cresol methylhydroxylase (PCMH) is expressed in its natural host Pseudomonas putida, or when the genes of the alpha and beta subunits of the enzyme are expressed together in the heterologous host Escherichia coli, flavin-adenine dinucleotide (FAD) is covalently attached to Tyr384 of the alpha subunit and the correct alpha 2 beta 2 form of the enzyme is assembled. The apoflavoprotein has been expressed in E. coli in the absence of the beta cytochrome c subunit and purified. While noncovalent FAD binding to apoflavoprotein in the absence of the cytochrome subunit could not be directly demonstrated, circumstantial evidence suggests that this indeed occurs. Covalent flavinylation requires one molecule each of FAD and cytochrome for each flavoprotein subunit. The flavinylation process leads to the 2-electron-reduced form of covalently bound FAD, and the resulting alpha 2 beta 2 enzyme is identical to wild-type PCMH. This work presents clear evidence that covalent flavinylation occurs by a self-catalytic mechanism; an external enzyme or chaperon is not required, nor is prior chemical activation of FAD or of the protein. This work is the first to define the basic chemistry of covalent flavinylation of an enzyme to produce the normal, active species, and confirms a long standing, postulated chemical mechanism of this process. It also demonstrates, for the first time, the absolute requirement for a partner subunit in the post-translational modification of a protein. It is proposed that the covalent FAD bond to Tyr384 and the phenolic portion of this Tyr are part of the essential electron transfer path from FAD to heme.

Amino Acid Sequence↗

PubMed2004

Resolution of G(s)alpha and G(q)alpha/G(11)alpha proteins in membrane domains by two-dimensional electrophoresis: the effect of long-term agonist stimulation.

Low-density membrane-domain fractions were prepared from S49 lymphoma cells and clone e2m11 of HEK293 cells expressing a large number of thyrotropin-releasing hormone receptor (TRH-R) and G(11)alpha by flotation on sucrose density gradients. The intact cell structure was broken by detergent-extraction, alkaline-treatment or drastic homogenization. Three types of low-density membranes were resolved by two-dimensional electrophoresis and analyzed for G(s)alpha (S49) or G(q)alpha/G11) (e2m11) content. Four individual immunoblot signals of Gsalpha protein were identified in S49 lymphoma cells indicating complete resolution of the long G(s)alpha L+/-ser and short G(s)alpha S+/-ser variants of G(s)alpha. All these were diminished by prolonged agonist (isoprenaline) stimulation. In e2m11-HEK cells, five different immunoblot signals were detected indicating post-translational modification of G proteins of G(q)alpha/G(11)alpha family. The two major spots corresponding to exogenously (over)expressed G(11)alpha and endogenous G(q)alpha were reduced; the minor spots diminished by hormonal stimulation. Parallel analysis by silver staining of the total protein content indicated that no major changes in protein composition occurred under these conditions. Our data thus indicate that agonist-stimulation of target cells results in down-regulation of all different members of G(s) and G(q)/G(11) families. This agonist-specific effect may be demonstrated in crude membrane as well as domain/raft preparations and it is not accompanied by changes in overall protein composition.

Cell Line, Tumor↗

PubMed1997

Structural heterogeneity, post-translational modifications, and biological activities of SV-IV, a major protein secreted from the rat seminal vesicle epithelium.

The primary structure of purified SV-IV, a major secretory protein synthesized by the rat seminal vesicle (SV) epithelium, was analysed by electrospray mass spectrometry (ES-MS). The protein was found to be highly heterogeneous. The various components were separated and identified by reversed phase high-performance liquid chromatography (HPLC) on line with ES-MS. Structural characterization of the SV-IV cyanogen bromide digests revealed the occurrence of a Val/Met substitution in about 50% of the purified protein molecules. We suggest that this mutation is the expression of a genetic polymorphism. Other minor components, corresponding to structural changes (fragmentation, deletion, and phosphorylation) of SV-IV and probably due to post-translational modifications of the native protein, were also detected. In particular, by using protein tyrosine phosphatase hydrolysis combined with ES-MS, we demonstrated that, in the phosphorylated species of SV-IV, a single phosphate group was covalently bound to the Tyr-36 residue. The significance of these findings in relation to the regulation of important biological processes, such as immune response, blood coagulation, inflammatory reaction, and mammalian reproduction, are discussed.

Amino Acid Sequence↗

PubMed2005

Recent advancements in differential proteomics based on stable isotope coding.

Stable isotope coding continues to be a powerful approach in comparative proteomics. This review focuses on recent developments in stable isotope coding-based strategies targeted towards protein expression, protein interactions with other biomolecules, post-translational modifications and absolute quantification. The focus of the bulk of proteomics studies is still on protein expression. An important recent application of isotope coding has been in organelle proteomics. The review ends with the conclusion that isotope coding remains an integral part of quantitative proteomics. There is, however, a need to develop coding strategies which can differentiate changes in protein expression and post-translational modification, address issues of protein dynamic range and facilitate real-time detection of proteins which show a statistically significant change after stimulus.

Amino Acids↗

PubMed1994

Post-translational modification of p53.

The p53 tumor suppressor protein is extensively post-translationally modified, mostly by phosphorylation. The phosphorylation sites are clustered into two distinct domains within the p53 polypeptide and the protein kinases and phosphatases which modify many of these sites have been identified. In addition, signaling pathways which modulate the phosphorylation state of p53, leading perhaps to changes in its activity, are being actively investigated. Similarly, the transforming proteins of DNA tumor viruses modulate p53 phosphorylation and may therefore be useful tools for probing these regulatory mechanisms. Given the very potent effects of p53 on cell growth and the extent of phosphorylation of this protein, p53 may well be controlled tightly and coordinately by more than one signaling mechanism.

Amino Acid Sequence↗

PubMed2005

Transient transfection of CHO-K1-S using serum-free medium in suspension: a rapid mammalian protein expression system.

With the recent completion of the human genome sequencing project, scientists now face the daunting challenge of deciphering the function of these newly found genes quickly and efficiently. For biotechnology, it is equally important to identify the therapeutically relevant genes 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 these needs, a CHO-K1 cell line that grows in suspension and in serum-free media was initially established and designated CHO-K1-S. An antibody gene of interest was chosen as the target for optimization rather than a reporter gene system. A comparison of various lipid transfection reagents was made using recombinant protein expression as the endpoint readout. Various other parameters including lipid:DNA ratios, cell density, and transfections in shaker versus spinner flasks were tested using the CHO-K1-S cell line. As a result, a rapid and reliable transient transfection protocol was developed. Using this procedure, we have produced milligram/per liter quantities of bioactive recombinant proteins from several genes of interest.

Animals↗

PubMed2006

Quantitative proteomic analysis of post-translational modifications of human histones.

Histone proteins are subject to a range of post-transcriptional modifications in living cells. The combinatorial nature of these modifications constitutes the "histone code" that dictates chromatin structure and function during development, growth, differentiation, and homeostasis of cells. Deciphering of the histone code is hampered by the lack of analytical methods for monitoring the combinatorial complexity of reversible multisite modifications of histones, including acetylation and methylation. To address this problem, we used LC-MSMS technology and Virtual Expert Mass Spectrometrist software for qualitative and quantitative proteomic analysis of histones extracted from human small cell lung cancer cells. A total of 32 acetylations, methylations, and ubiquitinations were located in the human histones H2A, H2B, H3, and H4, including seven novel modifications. An LC-MSMS-based method was applied in a quantitative proteomic study of the dose-response effect of the histone deacetylase inhibitor (HDACi) PXD101 on histone acetylation in human cell cultures. Triplicate LC-MSMS runs at six different HDACi concentrations demonstrated that PXD101 affects acetylation of histones H2A, H2B, H3, and H4 in a site-specific and dose-dependent manner. This unbiased analysis revealed that a relative increase in acetylated peptide from the histone variants H2A, H2B, and H4 was accompanied by a relative decrease of dimethylated Lys(57) from histone H2B. The dose-response results obtained by quantitative proteomics of histones from HDACi-treated cells were consistent with Western blot analysis of histone acetylation, cytotoxicity, and dose-dependent expression profiles of p21 and cyclin A2. This demonstrates that mass spectrometry-based quantitative proteomic analysis of post-translational modifications is a viable approach for functional analysis of candidate drugs, such as HDAC inhibitors.

Acetylation↗

PubMed2003

Identification of post-translational modifications resulting from LHbeta polymorphisms by matrix-assisted laser desorption time-of-flight mass spectrometric analysis of pituitary LHbeta core fragment.

Metabolism of the human chorionic gonadotrophin (hCG)- and LHbeta-subunits (hCGbeta, LHbeta) terminates with the urinary excretion of core fragment (hCGbetacf, LHbetacf) molecules that retain antigenic shape and constituent N-linked carbohydrate moieties. We have previously demonstrated the resolved mass spectra of hCGbetacf, from which the carbohydrate moieties present at two N-linked glycosylation sites were identified. LHbetacf was subjected to the same mass spectrometric analysis. As LHbeta shares 82% homology with hCGbeta but possesses only one glycosylation consensus site a simpler spectral fingerprint of LHbetacf glycoforms was expected. LHbetacf was reduced with dithiothreitol and analysed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Glycoforms were predicted by subtracting the peptide mass from the m/z values of the observed peaks and then sequentially subtracting the masses of the monosaccharide residues of hCGbeta N-linked carbohydrates reported in the literature. The mass spectra of LHbetacf revealed a broad single peak ranging from m/z 8700 to 10 700. Following reduction, this peak was replaced by a set of partially resolved peaks between m/z 4130 and 5205 corresponding to glycosylated forms of the peptide LHbeta6-40. A peak at m/z 4252.2 corresponded to the non-glycosylated peptide LHbeta55-93. Remaining peaks indicated that the pooled sample comprised a wide set of glycoforms, contained LHbetacf with two N-linked carbohydrate moieties and indicated evidence of further glycosylation due to amino acid substitution in polymorphic variants. This is evidence that a single nucleotide polymorphism alters the post-translational modification of a protein and hence its structural phenotype.

Carbohydrate Conformation↗

PubMed1994

Myristoylated alanine-rich C kinase substrate (MARCKS), a major protein kinase C substrate, is an in vivo substrate of proline-directed protein kinase(s). A mass spectroscopic analysis of the post-translational modifications.

Myristoylated alanine-rich C kinase substrate (MARCKS), a major in vivo substrate protein of protein kinase C, isolated from calf brain contains various species phosphorylated to different degrees. To establish the in vivo phosphorylation sites, the protein was digested with lysyl endoprotease, and the digests were analyzed by the capillary high performance liquid chromatography interfaced on-line to an electrospray mass spectrometer. Six out of 17 peptides were found to be phosphorylated. Of the 7 phosphorylated serine residues identified by Edman degradation, only 1 was within the known phosphorylation domain by protein kinase C. All the other phosphorylated serine residues originated from the N-terminal half of the molecule and were immediately followed by proline. Therefore, MARCKS, a major in vivo substrate of protein kinase C, is also an in vivo substrate of proline-directed protein kinase(s) such as mitogen-activated protein kinase or Cdk5 kinase.

Amino Acid Sequence↗

PubMed1992

Desmosome assembly in MDCK epithelial cells does not require the presence of functional microtubules.

Desmosomes, complex multisubunit structures that assemble at sites of cell-cell contact, are important components of the epithelial junctional complex. Desmosome assembly requires the coordinated interaction at the plasma membrane of at least 8 cytoplasmic and integral membrane proteins organized into two structurally and functionally distinct domains, the cytoplasmic plaque and membrane core. Previous studies (Pasdar et al., J. Cell Biol., 113:645-655) provided evidence that cytokeratin filaments and microtubules may regulate transfer and assembly of cytoplasmic plaque and membrane core proteins, respectively. To determine directly the role of microtubules in these processes, Madin-Darby canine kidney (MDCK) cells were treated with nocodazole or colchicine to disrupt the microtubular network. Biochemical analysis of the different components of the cytoplasmic plaque and membrane core domains revealed little or no effect of nocodazole or colchicine on the kinetics of synthesis, post-translational modifications, transfer of proteins to the plasma membrane or their metabolic stability in the presence or absence of cell-cell contact. Likewise, immunofluorescence analysis of desmosome formation demonstrated an apparently normal desmosome assembly in the presence of nocodazole or colchicine upon induction of cell-cell contact. These results indicate that an intact microtubular network is not necessary for the processing or transport of the desmosomal membrane core glycoproteins to the plasma membrane in the absence or presence of cell-cell contact. Furthermore, the integration of the cytoplasmic plaque and membrane core domains induced by cell-cell contact at the plasma membranes of adjacent cells does not require the presence of functional microtubules.

Animals↗

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↗