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PubMed2005

Identification of post-translational modifications that occur during sperm maturation using difference in two-dimensional gel electrophoresis.

Difference in two-dimensional (2-D) gel electrophoresis (DIGE) is a novel method for analyzing up to three samples in one 2-D gel and using the information gained to study post-translational modifications of proteins. We describe the use of DIGE to isolate and characterize those proteins that undergo processing in spermatozoa as they transit the epididymal tract. We find up to 60 protein spots are significantly modified as sperm traverse the epididymis. In this article, we report eight unambiguous protein identifications and demonstrate that one protein, the beta-subunit of the mitochondrial F1-ATPase, is serine-phosphorylated as sperm undergo epididymal maturation. We suggest that phosphorylation of this particular protein in a cAMP-dependent manner may contribute to the mechanisms by which motility is conferred upon spermatozoa.

Adenosine Triphosphatases↗
PubMed2005

Functional dissection of sRNA translational regulators by nonhomologous random recombination and in vivo selection.

Small nontranslated RNAs (sRNAs) regulate a variety of biological processes. DsrA and OxyS are two E. coli sRNAs that regulate the translation of rpoS, which encodes a protein sigma factor. Due to their structural complexity, the functional dissection of sRNAs solely by designing and assaying mutants can be challenging. Here, we present a complementary approach to the study of functional RNAs, in which highly diversified RNA libraries are generated by nonhomologous random recombination (NRR) and processed efficiently by in vivo selections that link RNA activities to cell survival. When applied to DsrA and OxyS, this approach rapidly identified essential and nonessential regions of both sRNAs. Resulting hypotheses about DsrA and OxyS structure-function relationships were tested and further refined experimentally. Our findings demonstrate an efficient, unbiased approach to the functional dissection of nucleic acids.

Base Sequence↗
PubMed2001

Functions of poly(ADP-ribose) polymerase (PARP) in DNA repair, genomic integrity and cell death.

Poly(ADP-ribose) polymerase (PARP) is responsible for post-translational modification of proteins in the response to numerous endogenous and environmental genotoxic agents. PARP and poly(ADP-ribosyl)ation are proposed to be important for the regulation of many cellular processes such as DNA repair, cell death, chromatin functions and genomic stability. Activation of PARP is one of the early DNA damage responses, among other DNA sensing molecules, such as DNA-PK, ATM and p53. The generation and characterization of PARP deficient mouse models have been instrumental in defining the biological role of the molecule and its involvement in the pathogenesis of various diseases including diabetes, stroke, Parkinson disease, general inflammation as well as tumorigenesis, and have, therefore, provided information for the development of pharmaceutical strategies for the treatment of diseases.

Animals↗
PubMed2006

Molecular cloning of growth hormone from silver sea bream: effects of abiotic and biotic stress on transcriptional and translational expression.

The pituitary growth hormone (GH) gene of silver sea bream (Sparus sarba) was cloned and characterized and found to be 615 base pairs encoding a protein of 204 amino acids. Using a bacterial expression system, recombinant protein was prepared and rabbit polyclonal antibody was raised. Transcript and protein amounts of GH were measured in fish that were adapted to a range of salinities, acclimated to different temperatures, or undergoing a natural time course of Vibrio alginolyticus infection. Isoosmotic salinity (12 ppt) adaptation resulted in increased GH transcript and protein in comparison to freshwater (0 ppt) and seawater (33 ppt) adapted fish. It was also found that cold temperature (12 degrees C) acclimated sea bream had higher amounts of pituitary GH transcript and protein when compared to warm temperature (25 degrees C) acclimated fish. Finally, the amounts of GH transcript and protein were found to be rapidly downregulated from an early stage of disease. The results from the present study demonstrate how GH can be modulated during both abiotic and biotic stress in fish.

Adaptation, Physiological↗
PubMed2005

Phosphoproteomics in analyzing signaling pathways.

A surprisingly fewer than expected number of genes in the human genome suggests that sophistication of its biologic system is, in part, due to complex regulation of protein activities. The activities of most cellular proteins are regulated by post-translational modifications. One of the most important post-translational modifications is reversible protein phosphorylation, which decorates more than 30% of the proteome and regulates signal transduction pathways under normal conditions as well as in disorders such as diabetes, neurodegenerative diseases, autoimmune diseases and several forms of cancers. This review examines the recent developments in mass spectrometry-based methods for phosphoproteome analysis and its applications for the study of signal transduction pathways. The basic principles of non-mass spectrometry-based methods, such as chemical genetics and flow cytometry-based approaches, are also discussed as well as their specific advantages to signaling studies. Finally, signaling pathways are discussed in the light of large-scale protein interaction studies. The proteomic methods addressed in this review are emerging as some of the essential components in systems biology, which seeks to describe signaling networks through integration of diverse types of data and, in the future, to allow computational simulations of complex biologic pathways in health and disease.

Chromatography, Affinity↗
PubMed2001

[Aging at the molecular level exemplified by proteins].

During their life span, human proteins may undergo post-translational modifications that can be interpreted as manifestations of protein aging. The most frequently discussed modifications in that context are oxidation, glycation, deamidation, isomerization and racemization. Their pathophysiological relevance depends on the availability of repair mechanisms and on the protein turnover. Proteins with high turnover will be exchanged before molecular modifications become relevant. The most affected proteins are long-living and permanent proteins. Such proteins can be identified by the determination of their D-aspartic content (as a measure of an in vivo racemization and isomerization of aspartyl and asparaginyl residues). Using this method it could be demonstrated that numerous proteins in diverse human tissues are long-living or permanent and cannot escape post-translational modification by turnover. The human organism is confronted with an accumulation of "abnormal", post-translationally modified proteins during aging, especially in the extracellular space, but also at a cellular level. The exact pathophysiological dimension of post-translational modifications as manifestations of protein aging has to be further elucidated. However, they have been already discussed as relevant factors in the pathogenesis of diseases of old age.

Aged↗
PubMed2026

Protein arginine methyltransferases as metabolic regulators: many roles beyond cancer.

Metabolic syndrome (MetS) comprises a cluster of interconnected metabolic abnormalities that collectively elevate the risk of cardiovascular disease and mortality. With its global prevalence escalating, understanding the molecular underpinnings of MetS has become increasingly imperative. Protein arginine methyltransferases (PRMTs), classically studied for their epigenetic functions and oncogenic properties, are now recognized as pivotal regulators of metabolic homeostasis. Emerging research reveals that these enzymes coordinate crucial aspects of cellular metabolism through multiple mechanisms, including methylation of metabolic transcription factors, modulation of nutrient-sensing pathways, and direct regulation of enzymatic activities in glucose and lipid metabolism. This review summarizes current knowledge on the metabolic roles of PRMTs, specifying their roles in the development and function of major metabolic tissues and their associations with various metabolic disorders. We further review how PRMTs influence metabolic processes by modifying key transcriptional networks and signaling cascades through methylation of different substrates. By integrating these insights, we establish PRMTs as central players in metabolic regulation and assess their potential as therapeutic targets for metabolic diseases beyond their established roles in cancer biology, thereby providing a framework for future research and clinical development.

glucose metabolism↗
PubMed2004

Endogenous protein kinase-C activity and phosphorylated proteins in messenger ribonucleoprotein complexes of developing embryos of alfalfa.

Developing somatic and zygotic embryos of alfalfa (Medicago sativa L.) exhibited endogenous protein kinase activity and protein acceptors of phosphate groups using both cell-free translational extracts and oligo(dT)-cellulose-column-purified mRNPs. The cell-free-translation extracts from pre-cotyledonary-stage somatic embryos had approximately 50- and 100-fold more protein kinase activity than cotyledonary-stage somatic and zygotic embryos. Several polypeptides were phosphorylated; some of them were unique to the early stage and some to the late-stage developing embryos. A 65 kDa protein was phosphorylated heavily in pre-cotyledonary-stage somatic embryos. This phosphorylated protein was comprised of three main components, two of which were phosphorylated heavily. Heat-shock treated-embryos lost their exitant kinase activity and at the same time another form of protein kinase activity was activated which phosphorylated a novel 28 kDa protein. Endogenous protein kinase activity was also observed within the mRNPs of polysomal and non-polysomal fractions of developing embryos, and this phosphorylated only 65, 43 and 30 kDa proteins within these fractions. A 30 kDa protein from the pre-cotyledonary-stage somatic embryos showed a higher affinity for accepting phosphate groups than the proteins from cotyledonary-stage somatic or zygotic embryos. The activity of protein kinase was largely c-AMP-independent, but was dependent on Ca2+, phospholipid and phorbol ester. The enzyme belongs to the protein kinase-C family; the 65 kDa protein cross-reacts with antibodies made against protein kinase-C (alpha- and beta-isoforms) and it may be an autophosphorylated protein.

Cotyledon↗
PubMed2004

Aminoacyl-tRNA synthesis by pre-translational amino acid modification.

Aminoacyl-tRNAs (aa-tRNAs) are essential substrates for ribosomal translation, and are generally synthesized by aminoacyl-tRNA synthetases (aaRSs). It was expected earlier that every organism would contain a complete set of twenty aaRSs, one for each canonical amino acid. However, analysis of the many known genome sequences and biochemical studies revealed that most organisms lack asparaginyl- and glutaminyl-tRNA synthetases, and thus are unable to attach asparagine and glutamine directly onto their corresponding tRNA. Instead, a pretranslational amino acid modification is required to convert Asp-tRNA(Asn) and Glu-tRNA(Gln) to the correctly charged Asn-tRNA(Asn) and Gln-tRNA(Gln), respectively. This transamidation pathway of amide aa-tRNA synthesis is common in most bacteria and archaea. Unexpected results from biochemical, genetic and genomic studies showed that a large variety of different bacteria rely on tRNA-dependent transamidation for the formation of the amino acid asparagine. Pretranslational modifications are not restricted to asparagine and glutamine but are also found in the biosynthesis of some other aa-tRNAs, such as the initiator tRNA fmet-tRNA(Met)(i) and Sec-tRNA(Sec) specifying selenocysteine, the 21(st) cotranslationally inserted amino acid. tRNA-dependent amino acid modification is also involved in the generation of aminolevulinic acid, the first precursor for porphyrin biosynthesis in many organisms.

Amino Acids↗
PubMed2006

Diagnostic strategy for the detection of dystrophin gene mutations in asian patients and carriers using immortalized cell lines.

Duchenne muscular dystrophy and Becker muscular dystrophy are X-linked recessive diseases of muscle degeneration caused by mutations in the dystrophin gene. More than half of our local Asian patients have point mutations that cannot be detected by conventional multiplex polymerase chain reaction deletion screening. This study aimed to develop mutational screening and carrier detection for Duchenne and Becker muscular dystrophy using protein truncation analysis from Epstein-Barr virus-transformed lymphocyte cell lines. Messenger ribonucleic acid was extracted from fresh lymphocytes and Epstein-Barr virus-transformed lymphocyte cell lines of 14 patients. Reverse transcriptase polymerase chain reaction was performed in 11 overlapping segments, followed by in vitro protein translation and truncation analysis. DNA sequencing was carried out for the corresponding complementary DNA regions, which showed aberrant truncated protein products. Carrier studies using this method were also performed for two families. Half of the patients had frame-shifting deletions, and the remaining seven patients showed point mutations, of which four were novel. These mutations were detected in messenger ribonucleic acid extracted from both fresh lymphocytes and Epstein-Barr virus-transformed lymphocyte cell lines. Carrier status was confirmed in one family and was found to be negative in the other family studied. Protein truncation analysis is an efficient method of screening truncating point mutations from immortalized lymphocyte cell lines from patients. This approach not only serves to prove the pathogenicity of both deletion- and nondeletion-type mutations; it is also effective for carrier detection. The use of such cell lines obviates the need for repeated blood and muscle sampling in patients and offers a perpetual source of messenger ribonucleic acid that can be used long after the patient's demise.

Asian People↗
PubMed2006

Human protein reference database--2006 update.

Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein-protein interactions (>30 000) and PTMs (>8000) for human proteins. We have also introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer (http://www.genprot.org), developed by us that allows integration of genomic and proteomic information. With the continued support and active participation by the biomedical community, we expect HPRD to become a unique source of curated information for the human proteome and spur biomedical discoveries based on integration of genomic, transcriptomic and proteomic data.

Databases, Protein↗
PubMed1990

Post-translational modification of low molecular mass GTP-binding proteins by isoprenoid.

Several proteins in mammalian cells are modified post-translationally by the isoprenoid, farnesol. Incubation of cultured cells with [3H]mevalonate, an isoprenoid precursor, results in the labeling of multiple polypeptides, the most prominent of which migrate in the range of 21-26 kDa on sodium dodecyl sulfate-polyacrylamide gels. In Rat-6 fibroblasts transformed by H-ras, one of the farnesylated proteins was identified as p21ras by two-dimensional immunoblotting. However, this protein accounted for only a small proportion of the [3H]mevalonate-derived radioactivity incorporated into 21-26-kDa proteins. Murine erythroleukemia cells, which did not express immunodetectable quantities of p21ras, contained several 21-26-kDa farnesylated proteins distributed in both the cytosolic and particulate fractions. At least eight of these proteins were capable of binding [alpha-32P]GTP on nitrocellulose membranes. Pulse-chase studies showed that the isoprenoid modification did not necessarily result in the translocation of the cytosolic proteins to the cell membrane. A prominent group of carboxyl-methylated proteins in murine erythroleukemia cells overlapped with the 21-26-kDa farnesylated proteins on one-dimensional sodium dodecyl sulfate gels. Methylation of this group of proteins was selectively abolished when cells were treated with lovastatin, an inhibitor of isoprenoid synthesis. Addition of exogenous mevalonate to the lovastatin-treated cells fully restored carboxyl methylation. These studies suggest that the 21-26-kDa farnesylated proteins in mammalian cells are members of a recently discovered family of low molecular mass GTP-binding proteins which, although ras-related, appear to be distinct structurally and possibly functionally from the products of the ras genes. The observed isoprenoid-dependent carboxyl methylation of a group of 21-26-kDa proteins suggests that the low molecular mass GTP-binding proteins may undergo a series of post-translational C-terminal cysteine modifications (i.e. farnesylation, carboxyl methylation) analogous to those recently elucidated for p21ras.

Animals↗
PubMed2006

Identification of new gene expression regulators specifically expressed during plant seed maturation.

A cDNA-AFLP approach on Linum usitatissimum (flax) was used to identify genes specifically expressed during the seed maturation process. Among the 20,000 cDNA-AFLP tags produced, 486 were selected for their seed-specific expression during maturation. When compared with the publicly available databases, half of them presented some significant similarity with known plant sequences. The results obtained confirmed the accuracy of the approach as numerous genes previously described as being expressed exclusively in plant seeds were identified in this screen. The focus was on sequences similar to plant regulators involved in the control of gene expression, either at the transcriptional, post-transcriptional, or post-translational levels. Using a real-time RT-PCR approach, seed-specific expression kinetics were confirmed for 13 of these regulators that were never characterized for being expressed during seed maturation. Among these, a flax gene of the non-LEC1-like HAP3 family and a flax MYB factor were shown to be expressed in specialized tissues of flax embryo using an in situ hybridization approach. By expression kinetic comparison between these flax genes and their Arabidopsis counterparts, it was found that the new HAP3 gene should be related to a ubiquitous seed maturation mechanism, while a new MYB factor appears to be related to a more seed-specific maturation mechanism. These results demonstrate the utility of the flax database in not only identifying new genes expressed during seed maturation but also in being able to highlight the distinction between conserved and non-conserved seed maturation mechanisms.

Arabidopsis↗
PubMed1992

Structure of the EF corner favors deamidation of asparaginyl residues in hemoglobin: the example of Hb La Roche-sur-Yon [beta 81 (EF5) Leu----His].

Some abnormal hemoglobins constitute models which allow one to evaluate the structural requirements for post-translational modifications in proteins, such as deamidation. Hb La Roche-sur-Yon [beta 81 (EF5) Leu----His] is an unstable hemoglobin variant displaying a moderately increased oxygen affinity. About half of the abnormal hemoglobin, in addition to the substitution at position beta 81, carries a deamidation of the neighboring asparagine residue, beta 80 (EF4). The histidine at position beta 81 cannot fit into the small hydrophobic pocket which normally accomodates the leucine residue. This structural change opens the heme pocket and modifies the general conformation of the EF segment, thus explaining the increase in oxygen affinity and the achievement of a three-dimensional structure favoring asparagine deamidation. Histidine beta 81 could also act as a catalyst in the deamidation reaction. Deamidation has already been reported for two other variants of the EF corner, Hb Providence [beta 82 (EF6) Lys----Asn] and Hb J Singapore [alpha 79 (EF8) Ala----Gly]. In all these cases it seems that a histidine may catalyze the deamidation of the asparagine residues and that disturbing the folding of the EF corner will provide an extra flexibility favoring the reaction.

Adolescent↗
PubMed2002

Transglutaminases: nature's biological glues.

Transglutaminases (Tgases) are a widely distributed group of enzymes that catalyse the post-translational modification of proteins by the formation of isopeptide bonds. This occurs either through protein cross-linking via epsilon-(gamma-glutamyl)lysine bonds or through incorporation of primary amines at selected peptide-bound glutamine residues. The cross-linked products, often of high molecular mass, are highly resistant to mechanical challenge and proteolytic degradation, and their accumulation is found in a number of tissues and processes where such properties are important, including skin, hair, blood clotting and wound healing. However, deregulation of enzyme activity generally associated with major disruptions in cellular homoeostatic mechanisms has resulted in these enzymes contributing to a number of human diseases, including chronic neurodegeneration, neoplastic diseases, autoimmune diseases, diseases involving progressive tissue fibrosis and diseases related to the epidermis of the skin. In the present review we detail the structural and regulatory features important in mammalian Tgases, with particular focus on the ubiquitous type 2 tissue enzyme. Physiological roles and substrates are discussed with a view to increasing and understanding the pathogenesis of the diseases associated with transglutaminases. Moreover the ability of these enzymes to modify proteins and act as biological glues has not gone unnoticed by the commercial sector. As a consequence, we have included some of the present and future biotechnological applications of this increasingly important group of enzymes.

Animals↗
PubMed2006

Rab GTPases containing a CAAX motif are processed post-geranylgeranylation by proteolysis and methylation.

Post-translational modification by protein prenylation is required for membrane targeting and biological function of monomeric GTPases. Ras and Rho proteins possess a C-terminal CAAX motif (C is cysteine, A is usually an aliphatic residue, and X is any amino acid), in which the cysteine is prenylated, followed by proteolytic cleavage of the AAX peptide and carboxyl methylation by the Rce1 CAAX protease and Icmt methyltransferase, respectively. Rab GTPases usually undergo double geranylgeranylation within CC or CXC motifs. However, very little is known about processing and membrane targeting of Rabs that naturally contain a CAAX motif. We show here that a variety of Rab-CAAX proteins undergo carboxyl methylation, both in vitro and in vivo, with one exception. Rab38(CAKS) is not methylated in vivo, presumably because of the inhibitory action of the lysine residue within the AAX motif for cleavage by Rce1. Unlike farnesylated Ras proteins, we observed no targeting defects of overexpressed Rab-CAAX proteins in cells deficient in Rce1 or Icmt, as reported for geranylgeranylated Rho proteins. However, endogenous geranylgeranylated non-methylated Rab-CAAX and Rab-CXC proteins were significantly redistributed to the cytosol at steady-state levels and redistribution correlates with higher affinity of RabGDI for non-methylated Rabs in Icmt-deficient cells. Our data suggest a role for methylation in Rab function by regulating the cycle of Rab membrane recruitment and retrieval. Our findings also imply that those Rabs that undergo post-prenylation processing follow an indirect targeting pathway requiring initial endoplasmic reticulum membrane association prior to specific organelle targeting.

Alkyl and Aryl Transferases↗
PubMed1997

Post-translational modifications in cartilage oligomeric matrix protein. Characterization of the N-linked oligosaccharides by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Analysis of the carboxymethylated subunit of human cartilage oligomeric matrix protein (COMP) by matrix-assisted laser desorption time-of-flight mass spectrometry indicated a protonated molecular mass of 86949 +/- 149 Da, compared with 83547.0 Da calculated from the sequence. Treatment with N-glycanase caused a reduction in mass of 3571 +/- 219 Da, but there was no loss of mass after treatment with O-glycanase or neuraminidase. Peptides containing two putative sites of N-glycosylation were purified and characterized. Analysis of the masses of these after N-glycanase treatment indicated that one was substituted at Asn-101 with an oligosaccharide of mass 1847. 2 +/- 6.6 Da, and the other was unsubstituted at Asn-124. The remaining site of attachment, at Asn-721, was, therefore, also substituted with an oligosaccharide of mass 1724 +/- 226 Da. Analysis of the total monosaccharide content by chemical methods indicated that there were no additional oligosaccharide substituents. The MALDI-TOF mass spectra of COMP from bovine fetal and adult cartilage were compared, indicating a more heterogeneous pattern of substitution at Asn-101 in the fetal form. Since COMP is distributed throughout the pericellular and territorial environments in developing cartilage but occupies the interterritorial zone in mature cartilage, these changes in glycosylation may allow for different intermolecular interactions.

Amino Acid Sequence↗
PubMed2006

Helicobacter pylori induces mono-(adenosine 5'-diphosphate)-ribosylation in human gastric adenocarcinoma.

Mono-(adenosine 5'-diphosphate) (ADP)-ribosylation, which transfers an ADP-ribose from nicotinamide adenine dinucleotide (NAD) to an acceptor protein, is an important post-translational modification of cellular proteins. Several bacterial toxins are known to possess the mono-ADP-ribosyltransferase activity to catalyze this reaction as a possible pathogenic factor. Therefore, the aim of this study was to examine whether H. pylori may also induce mono-ADP-ribosylation in a human gastric mucosal protein in association with gastric cancer development. Tumorous and adjacent non-tumorous mucosal tissue specimens were obtained from the surgically removed stomachs of 5 patients with gastric adenocarcinoma, and then were homogenized into cytosolic and membranous fractions. Each homogenate or an H. pylori extract was assayed for mono-ADP-ribosylation with [adenylate-(32)P]-NAD and 3-aminobenzamide, a potent inhibitor of poly-ADP-ribosylation. The radiolabeled proteins were separated by sodium dodecylsulfate-polyacrylamide gel electrophoresis followed by radio-image analysis. In the extracts from H. pylori, a strain-dependent, endogenous radiolabeling of 70-kDa protein was detected. An assay of the membranous fractions from 5 gastric adenocarcinomas with the extract of OMH4, a clinical H. pylori isolate, revealed notable radiolabelings of 55- and 45-kDa proteins, which were not found without the OMH4 extract. In contrast, the radiolabelings were minimal in the membranous fractions from respective non-tumorous mucosae, and they were not detected in any of the examined cytosolic fractions. All three radiolabelings of 70-, 55-, and 45-kDa proteins were dependent on NAD, but not on ADP-ribose. Snake venom phosphodiesterase digestion of the 3 radiolabeled proteins released only AMP. We thus found that H. pylori had an enzymatic mono-ADP-ribosyltransferase activity which enabled it to modify the 55- and 45-kDa membranous proteins of human gastric adenocarcinoma, as well as the 70-kDa protein of H. pylori itself. The possible roles underlying our observations on carcinogenesis or development of human gastric carcinoma are yet to be elucidated.

ADP Ribose Transferases↗