Identification of methylated proteins by protein arginine N-methyltransferase 1, PRMT1, with a new expression cloning strategy

Immunohistochemical and western analyses of protein arginine N-methyltransferase 3 in the mouse brain

The distribution of protein arginine N-methyltransferase 3 (PRMT3) was investigated in the mouse brain using indirect immunofluorescence. PRMT3 was observed to be localized in the cell bodies and dendrites of neurons but not in the axons and glial cells, indicating that PRMT3 is involved in neuronal function. The distribution of the immunoreactive neurons in the brain was uneven, indicating that PRMT3 plays a role in specific neuronal systems such as the motor and limbic systems, as well as functions related to the cerebellum. The present ontogenetic analysis of PRMT1 and PRMT3 using Western blot methodology clearly revealed that PRMT3 develops during the perinatal stage and its expression is maintained even in adulthood. PRMT1, on the other hand, is expressed transiently during the early embryonic stage. These findings indicate that PRMT3 is related with neuronal function in both young and adult brains, while PRMT1 has roles in the immature brain, such as the formation of neural circuits.

Detection of dimethylarginines in protein hydrolysates by matrix-assisted laser desorption/ionization mass spectrometry

We report a method to detect the presence of dimethylarginines on proteins. Peptides with dimethylarginines were hydrolyzed in acid. The hydrolysates were subjected to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric analysis using a mixture of alpha-cyano-4-hydroxycinnamic acid and nitrocellulose as matrix. Both asymmetric omega-N(G),N(G)-dimethylarginine and symmetric omega-N(G),N(G')-dimethylarginine give a clear signal at m/z 203. Recombinant Sbp1p modified by Hmt1p in vivo were isolated by affinity chromatography followed by electrophoresis on a polyacrylamide gel and subjected to acid hydrolysis. MALDI-TOF analysis of the acid hydrolysates confirmed the presence of dimethylarginines. The detection limit of the method is estimated at approximately 1pmol of protein.

Genome-wide localization of histone 4 arginine 3 methylation in a differentiation primed myeloid leukemia cell line

Methylation of arginine residues in proteins is involved in modulation of various protein-protein interactions. At the chromatin level H4R3 methylation provides a signal integration step during myeloid differentiation. In order to globally characterize the role of arginine methylation in signal integration and developmental processes we decided to map genomic loci marked by protein arginine methyl transferase 1 (PRMT1) via histone H4 arginine 3 methylation. For this, we used the myeloid leukemia cell line, HL60, which is known to differentiate along the monocyte/macrophage or granulocyte lineage. We used chromatin immunoprecipitation with an antibody specific for the H4 arginine 3 methyl epitope followed by cloning to isolate genomic loci marked by this modification. After sequencing and in silico analysis we found that all of the genomic hits identified were intronic or within 5 kb of 5' ends of specific genes. The locations identified were enriched in conserved transcription factor binding sites of POU2F1, MEF-2 and FOXL1 factors. A significant number of the genes in the proximity of the identified genomic loci are involved in signaling pathways and developmental processes including immune response of myeloid cells.

Determination of a reference value for N(G), N(G)-dimethyl-L-arginine in 500 subjects

BACKGROUND

Asymmetric dimethylarginine (ADMA) acts as an endogenous inhibitor of NO-synthase. In the last years ADMA has emerged as a cardiovascular risk factor. The aim of this study was to determine a reference value for ADMA.

METHODS

Plasma samples of 500 healthy subjects in the 19-75 year age group were analyzed. Exclusion criteria from this study were smoking, any known significant disease, body-mass-index (BMI) above 30 kg m(-2), elevated plasma lipid levels, impaired renal function, hypertension, and intake of any medication. The ADMA levels were determined by ELISA, (DLD Diagnostics, Hamburg, Germany).

RESULTS

Mean ADMA plasma concentration of the total population was 0.69 micromol L(-1) (SD 0.20) and 95% of the measured values were in the range from 0.36 micromol L(-1) to 1.17 micromol L(-1). Women below 50 years of age had lower ADMA levels than men below 50 years of age [0.62 (0.17) micromol L(-1) vs. 0.69 (0.19) micromol L(-1); P = 0.001] and woman above 50 years of age had higher ADMA levels than men above 50 years of age [0.80 (0.22) micromol L(-1) vs. 0.73 (0.20) micromol L(-1); P = 0.036]. A regression analysis of ADMA levels and age was performed for each sex. The regression factor was r = 0.444 for women in a squared regression model (P < 0.001) and r = 0.212 for men in a linear regression model (P < 0.001).

CONCLUSION

The study was able to define a reference value for ADMA plasma levels with 0.36-1.17 micromol L(-1) and found sex dependent correlations between ADMA and age. Women showed a significant increase in ADMA plasma levels with onset of menopause.

Compartmentalization of hnRNP-K during cell cycle progression and its interaction with calponin in the cytoplasm

Coronary artery blockage, due to cardiovascular disease, is routinely treated by either balloon-angioplasty or bypass surgery. The limited success of these clinical interventions is due at least in part to smooth muscle cell (SMC) proliferation. Here we show that heterogeneous nuclear ribonucleoprotein complex K (hnRNP-K) protein levels increase in SMC with response to serum stimulation in vitro, in the aortas from an animal model of atherosclerosis, and in occluded human vein segments. hnRNP-K is a multi-functional protein that has been studied primarily in cancer cells and has been suggested to play a role in cell cycle progression. We show that in untransformed, cultured SMC, hnRNP-K protein sub-cellular localization modulates through the cell cycle in both the cytoplasm and nucleus. Using cycloheximide, we observed that cytoplasmic accumulation of hnRNP-K protein at later time points in the cell cycle occurred with a concomitant decrease in nuclear hnRNP-K protein, suggesting a translocation of nuclear hnRNP-K protein to the cytoplasm. Also, because we did not observe an increase in hnRNP-K protein at early time points in the cell cycle in the presence of cycloheximide, we propose that the early increase in cytoplasmic hnRNP-K protein following serum stimulation is due to new hnRNP-K protein synthesis. When present in the cytoplasm, hnRNP-K is part of a multi-protein complex that consists of at least two other proteins, calponin and ERK1/2. Our findings from this study are intriguing because they suggest that cytoplasmic hnRNP-K in SMC is part of a signaling complex that may be involved in growth-stimulated post-transcriptional regulation.

Arginine methylation an emerging regulator of protein function

Arginine methylation is now coming out of the shadows of protein phosphorylation and entering the mainstream, largely due to the identification of the family of enzymes that lay down this modification. In addition, modification-specific antibodies and proteomic approaches have facilitated the identification of an array of substrates for the protein arginine methyltransferases. This review describes recent insights into the molecular processes regulated by arginine methylation in normal and diseased cells.

o-Nitrobenzenesulfonamides in Nucleoside Synthesis: Efficient 5‘-Aziridination of Adenosine

5'-Aziridinoadenylates of the form 1 and a related nitrogen mustard variant have been constructed using a novel variation of the Mitsunobu reaction. Such molecules allow conversion of biological methyltransferases into nucleoside transferases, thus providing powerful tools for investigating S-adenosyl-l-methionine (SAM)-dependent methylation. We present here a highly effective synthesis of such molecules that is amenable to aziridine diversification as well as elaboration of the base moiety so as to afford "bumped" cofactor mimics compatible with "hole"-bearing mutant proteins.

Transcriptional down-regulation through nuclear exclusion of EWS methylated by PRMT1

The EWS gene is known to be chromosomally translocated and fused to various members of the DNA-binding transcription factors in Ewing's sarcoma and primitive neuroectodermal tumor. The product of this gene encodes the N-terminal transcriptional activation domain and the C-terminal RNA-binding domain containing an RNA-recognition motif and three arginine-glycine-glycine rich (RGG) motifs. Recently, we demonstrated EWS as a coactivator for hepatocyte nuclear factor 4 (HNF4)-mediated transcription. However, regulatory factors controlling EWS function are poorly characterized. In this study, we found that a protein arginine methyltransferase, PRMT1, physically interacts with EWS, whose cellular localization depends upon its RGG motifs targeted for methylation. Overexpression of PRMT1 down-regulates coactivator activity of EWS for HNF4-mediated transcription, because of the cytoplasmic retention of EWS from the nucleus. These results suggest that PRMT1 plays a post-translationally important role in regulating the transcriptional activity.

Elevation of asymmetric dimethylarginine in patients with unstable angina and recurrent cardiovascular events

AIMS

We investigated the role of asymmetric dimethylarginine (ADMA) for clinical outcome of patients with unstable angina.

METHODS AND RESULTS

Forty-five patients with stable angina, 36 patients with unstable angina, and 40 healthy controls were included in this study. Coronary artery disease (CAD) patients were prospectively followed for 1 year. ADMA levels were measured at baseline and after 6 weeks using a validated ELISA. Baseline ADMA concentration in controls was significantly lower than in patients with CAD (0.59+/-0.23 vs. 0.76+/-0.17 micromol/L; P<0.001). Patients with unstable angina had significantly higher baseline ADMA levels than patients with stable angina (0.82+/-0.18 vs. 0.73+/-0.15 micromol/L; P=0.01). There was a significant reduction of ADMA levels at 6 weeks after percutaneous coronary intervention (PCI) in patients with unstable angina who experienced no recurrent cardiovascular event (from 0.81+/-0.14 to 0.73+/-0.19 micromol/L; P<0.05). In contrast, patients with unstable angina who had an event showed no significant decrease in ADMA at 6 weeks. Actuarial survival analysis showed a significantly higher event rate in patients with persistently elevated ADMA plasma concentrations.

CONCLUSION

ADMA is significantly elevated in patients with unstable angina. A reduced ADMA level at 6 weeks after PCI may indicate a decreased risk of recurrent cardiovascular events.

Protein interfaces in signaling regulated by arginine methylation

Posttranslational modifications are well-known effectors of signal transduction. Arginine methylation is a covalent modification that results in the addition of methyl groups to the nitrogen atoms of the arginine side chains. A probable role of arginine methylation in signal transduction is emerging with the identification of new arginine-methylated proteins. However, the functional consequences of arginine methylation and its mode of regulation remain unknown. The identification of the protein arginine methyltransferase family and the development of methylarginine-specific antibodies have raised renewed interest in this modification during the last decade. Arginine methylation was mainly observed on abundant proteins such as RNA-binding proteins and histones, but recent advances have revealed a plethora of arginine-methylated proteins implicated in a variety of cellular processes, including signaling by interferon and cytokines, and in T cell signaling. We discuss these recent advances and the role of arginine methylation in signal transduction.

Identification and phylogenetic analyses of the protein arginine methyltransferase gene family in fish and ascidians

Protein arginine methyltransferases (PRMT) involved in the regulations of signal transduction, protein subcellular localization, and transcription have been mostly studied in mammals and yeast. In this study orthologues of eight human PRMT genes (PRMT1-7 and HRMT1L3) were identified in both puffer fish Fugu rubripes and zebrafish Danio rerio. The fish PRMT genes appear to be conserved with their mammalian orthologues at the levels of amino acid sequences as well as genomic structures. All vertebrate PRMT genes contain 10-16 coding exons except PRMT6 that contains only one coding exon. Western blot analyses of zebrafish tissue extracts confirmed the expression of some PRMT proteins in zebra fish. We further identified six PRMT members (PRMT1, 3-7) in an invertebrate chordate Ciona intestinalis. Genomic structures of the PRMT orthologues are no more conserved in the ascidians, as PRMT3 and PRMT5 contain only one coding exon while PRMT6 contains six exons. PRMT2 and HRMT1L3 that are missing in Ciona appear to be vertebrate-specific. HRMT1L3 is a PRMT1 paralogue with highly conserved sequences and exact exon junctions, whereas the PRMT2 orthologues are very diverged. Different PRMT orthologues are likely to evolve at different rates and the PRMT1 orthologues appear to be most conserved through evolution. Furthermore, phylogenetic analyses using the core regions of various PRMT genes show that PRMT5 with the type II PRMT activity is separated in one branch. All other PRMT genes including PRMT1, 2, 3, 4, 6, 7 and HRMT1L3 clustered in the other branch, probably represent the genes for the type I activity.

Cardiovascular biology of the asymmetric dimethylarginine:dimethylarginine dimethylaminohydrolase pathway

An increasing number of reports indicate that endogenously produced inhibitors of nitric oxide synthase, particularly asymmetric dimethylarginine (ADMA), regulate nitric oxide generation in disease states. This article describes the biology of ADMA and the implications for cardiovascular physiology and pathophysiology.

A subtractive approach to characterize genes with regionalized expression in the gliogenic ventral neuroepithelium: identification of chick Sulfatase 1 as a new oligodendrocyte lineage gene

To address the question of the origin of glial cells and the mechanisms leading to their specification, we have sought to identify novel genes expressed in glial progenitors. We adopted suppression subtractive hybridization (SSH) to establish a chick cDNA library enriched for genes specifically expressed at 6 days of incubation (E6) in the ventral neuroepithelium, a tissue previously shown to contain glial progenitors. Screens were then undertaken to select differentially expressed cDNAs, and out of 82 unique SSH clones, 21 were confirmed to display a regionalized expression along the dorsoventral axis of the E6 ventral neuroepithelium. Among these, we identified a transcript coding for the chick orthologue of Sulf1, a recently identified cell surface sulfatase, as a new, early marker of oligodendrocyte (OL) precursors in the chick embryonic spinal cord. This study provides groundwork for the further identification of genes involved in glial specification.

Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides

PRMT1 is the predominant type I protein arginine methyltransferase in mammals and highly conserved among all eukaryotes. It is essential for early postimplantation development in mouse. Here we describe the crystal structure of rat PRMT1 in complex with the reaction product AdoHcy and a 19 residue substrate peptide containing three arginines. The results reveal a two-domain structure-an AdoMet binding domain and a barrel-like domain-with the active site pocket located between the two domains. Mutagenesis studies confirmed that two active site glutamates are essential for enzymatic activity, and that dimerization of PRMT1 is essential for AdoMet binding. Three peptide binding channels are identified: two are between the two domains, and the third is on the surface perpendicular to the strands forming the beta barrel.

Targeted recruitment of a histone H4-specific methyltransferase by the transcription factor YY1

Methylation of specific residues within the N-terminal histone tails plays a critical role in regulating eukaryotic gene expression. Although great advances have been made toward identifying histone methyltransferases (HMTs) and elucidating the consequences of histone methylation, little is known about the recruitment of HMTs to regulatory regions of chromatin. Here we report that the sequence-specific DNA-binding transcription factor Yin Yang 1 (YY1) binds to and recruits the histone H4 (Arg 3)-specific methyltransferase, PRMT1, to a YY1-activated promoter. Our data confirm that histone methylation does not occur randomly but rather is a targeted event and provides one mechanism by which HMTs can be recruited to chromatin to activate gene expression.

Contributions of mass spectrometry in the study of nucleic acid-binding proteins and of nucleic acid-protein interactions

Nucleic-acid-protein (NA-P) interactions play essential roles in a variety of biological processes-gene expression regulation, DNA repair, chromatin structure regulation, transcription regulation, RNA processing, and translation-to cite only a few. Such biological processes involve a broad spectrum of NA-P interactions as well as protein-protein (P-P) interactions. These interactions are dynamic, in terms of the chemical composition of the complexes involved and in terms of their mere existence, which may be restricted to a given cell-cycle phase. In this review, the contributions of mass spectrometry (MS) to the deciphering of these intricate networked interactions are described along with the numerous applications in which it has proven useful. Such applications include, for example, the identification of the partners involved in NA-P or P-P complexes, the identification of post-translational modifications that (may) regulate such complexes' activities, or even the precise molecular mapping of the interaction sites in the NA-P complex. From a biological standpoint, we felt that it was worth the reader's time to be as informative as possible about the functional significance of the analytical methods reviewed herein. From a technical standpoint, because mass spectrometry without proper sample preparation would serve no purpose, each application described in this review is detailed by duly emphasizing the sample preparation-whenever this step is considered innovative-that led to significant analytical achievements.