METHYLATED AMINO ACID RESIDUES OF PROTEINS OF BRAIN AND OTHER ORGANS

—Methods for the determination of methyl-lysine, methyllarginine and methylhistidine residues of tissue proteins are described. They consist of preliminary purification of basic amino acids, enzymic removal of lysine, arginine and histidine followed by amino acid analysis. Recovery rates and specificities of the method were satisfactory. The contents of methylamino acids in proteins of mammalian organs were determined. The distribution of proteins containing the methylamino acids in human brain showed that the concentrations of methyl-lysine and N^G,N′^G-dimethylarginine were highest in the gray matter of the cerebellar cortex and relatively high in regions rich in gray matter, while those of N^G-mono- and N^G,N′^G-dimethylarginine were highest in the white matter. The following findings suggest that most of the N^G-mono- and N^G,N′^G-dimethylarginine was associated with the myelin basic protein. The distribution of the methylarginine residues of acid-soluble proteins in bovine brains coincided with the cerebroside pattern. The concentrations of the amino acids in acid-soluble proteins of rat brain increased concomitantly with the increase of cerebroside. The methylamino acid content in proteins increased during the purification of the myelin basic protein from the white matter of human and bovine brains. Proteins containing N^G,N^G-dimethyiarginine and di- and trimethyl-lysine are concentrated in cell nuclei. The first amino acid was found mainly in nucleoplasmic proteins and the other two were found in histones. The concentration of 3-methylhistidine residue, highest in muscular proteins, is low in cerebral proteins and is probably derived from proteins of walls of blood vessels in the brain.     

N-acetyl conjugates of basic amino acids newly identified in rat urine

Ninhydrin-negative conjugates of basic amino acids were isolated from rat urine and were characterized. The following conjugates of basic amino acids are the compounds newly identified in animal urine specimens, N^α-acetyl-N^π-methylhistidine, N^α-(N-acetyl-β-alanyl)histidine (N-acetylcarnosine), N^α-acetyl-N^G,N^′G-dimethylarginine, N^α-acetyl-N^G,N^G-dimethylarginine, and N^α-acetyl-N^?,N^?,N^?-trimethyllysine.     

Identification of NG, NG-dimethylarginine in a nuclear protein from the lower eukaryote physarum polycephalum homologous to the major proteins of mammalian 40S ribonucleoprotein particles

A nuclear protein apparently homologous to the two major proteins of 40S heterogeneous nuclear ribonucleoprotein particles from mammalian cells has been isolated from the lower eukaryote $\text{Physarum polycephalum}$, purified, and found to contain a substantial amount of the unusual amino acid N^G, N^G-dimethylarginine. The apparent homology is based on similar molecular weights, basic isoelectric points and amino acid compositions including the dimethylarginine and a high content of glycine. The implications of the presence of this protein in $\text{Physarum polycephalum}$ and the possible significance of the N^G, N^G-dimethylarginine are discussed.     

PARTIAL CHARACTERIZATION OF BASIC PROTEINS OF CHICKEN, TURTLE AND FROG CENTRAL NERVOUS SYSTEM MYELIN

Myelin basic proteins were isolated from CNS tissues of chicken, turtle and frog and compared with the corresponding protein of bovine origin. At acid pH all four proteins had comparable mobilities in polyacrylamide gels. Upon electrophoresis at alkaline pH the submammalian proteins, like the bovine protein, were separated into multiple components. The components of the chicken and frog proteins had exceptionally high and low mobilities, respectively, while those of the turtle protein had mobilities comparable to those of the bovine protein. The chicken and turtle proteins were similar to the bovine protein in amino acid composition except for containing considerably more serine and valine and having higher proportions of histidine to lysine. The frog protein differed further in having an unusually high content of tyrosine (approx 9 mol/mol protein), an unusually high arginine: glycine ratio (1.09) and practically no methylated arginine (0-0.036 mol/mol protein). Like those of mammalian origin, the submammalian proteins each contained a single tryptophan and two methionines. Arginine, serine and glycine together accounted for approximately 40 per cent of the residues in each protein. The chicken and turfle proteins each contained roughly equal amounts of N^G-monomethyl- and N^G, N^G-dimethylarginine, the two derivatives together comprising 0.5-0.6 mol/mol protein. No N^G, N^G-dimethylarginine was detected in any of the proteins examined. The microheterogeneity observed in the chicken and turtle proteins upon electrophoresis at alkaline pH was reproduced upon alkaline pH chromatography on carboxymethylcellulose. Chromatographic fractions of the chicken protein which differed electrophoretically at alkaline pH had virtualy identical amino acid compositions and apparent molecular weights and all contained comparable amounts of both N^G-monomethyl- and N^G, N^G-dimethylarginine. Treatment of the submammalian proteins with BNPS-skatole yielded two fragments comparable in size, charge and staining characteristics to those similarly produced from the bovine protein (residues 1-116 and 117-170). Fragments produced from the frog protein by treatment with BrCN were comparable in size and charge to those similarly produced from the bovine protein; those produced from the chicken and turtle proteins were much different. In immunodiffusion studies the submammalian and bovine proteins showed reactions of identity when tested against rabbit anti-chicken basic protein serum.     

The influence of dietary calcium and phosphorus on intestinal calcium transport in rats given vitamin D metabolites.

A new method for the simple analysis of methylated amino acids based on autoradiography is introduced. With this technique a survey of protein methylation in a prokaryote, Escherichia coli, and a eukaryote, fibroblasts in culture, was carried out in an attempt to identify, quantitate, and determine the subcellular localization of all the methylated amino acids found in the proteins of these organisms.In mammalian cells using an established mouse fibroblast line (3T3), we have found that nuclei-free and mitochondria-free cytoplasm contain readily detectable amounts of four identifiable methylated amino acids: N^?,N^?-dimethyllysine, N^?,N^?,N^?-trimethyllysine, N^G,N^G-dimethylarginine (or N^G-methylarginine), and N^G,N′^G-dimethylarginine. The crude nuclear pellet also contains these methylated amino acids, but in addition contains N^?-methyllysine and a new as yet unidentified methylated compound. Histones purified from these nuclei contain essentially the same array of methylated compounds.The ribosomal subunits of the mammalian cells contained only small amounts of the methylated amino acids; the 40S subunit contained a substantial amount of just one, N^G,N^G-dimethylarginine (or N^G-methylarginine), and smaller amounts of N^G,N′^G-dimethylarginine, and an as yet unidentified methylated compound. The 60S subunit contained even smaller amounts of methylated amino acids, 50% of which was N^?,N^?,N^?-trimethyllysine and smaller amounts of N^?-methyllysine, N^?,N^?-dimethyllysine, and N^G,N^G-dimethylarginine. These subunits also contained an as yet unidentified methylated compoundThese results were in marked contrast to those that we obtained with the prokaryote, Escherichia coli. Only the proteins of the 50S ribosomal subunit of the bacteria contained methylated amino acids. Of those present 50% was N^?,N^?,N^?-trimethyllysine, with the remainder distributed about equally between N^?-methyllysine and three unknowns, one of which is apparently the same as that found in the 60S subunit of the mouse fibroblasts. All of the N^?-methyllysine was apparently in the small acidic proteins, L7 and L12.     

Methylation of ribosomal proteins in HeLa cells.

Methylated amino acids from both 40 and 60S subunit proteins of HeLa cytoplasmic ribosome were analyzed. It was observed that methylation of ribosomal proteins occurs in both subunits with N^G,N^G-dimethylarginine as the major methylated amino acid. The presence of N^G,N^G-dimethylarginine has been identified by high-voltage paper electrophoresis, by paper chromatography, and by amino acid analysis. In addition, both ribosomal subunits contain methylated lysines with ?-N-trimethyllysine being the predominant one, followed by ?-N-dimethyllysine. Little, if any ?-N-monomethyllysine was detected in either subunit. The cytoplasmic 60S ribosomal subunit contains much more ?-N-trimethyllysine compared to the 40S ribosomal subunit. The possible biological significance of methylation was discussed.     

Spliceosome Sm proteins D1, D3, and B/B' are asymmetrically dimethylated at arginine residues in the nucleus

We report a novel modification of spliceosome proteins Sm D1, Sm D3, and Sm B/B′. L292 mouse fibroblasts were labeled in vivo with [³H]methionine. Sm D1, Sm D3, and Sm B/B′ were purified from either nuclear extracts, cytosolic extracts or a cytosolic 6S complex by immunoprecipitation of the Sm protein-containing complexes and then separation by electrophoresis on a polyacrylamide gel containing urea. The isolated Sm D1, Sm D3 or Sm B/B′ proteins were hydrolyzed to amino acids and the products were analyzed by high-resolution cation exchange chromatography. Sm D1, Sm D3, and Sm B/B′ isolated from nuclear fractions were all found to contain ω-N^G-monomethylarginine and symmetric ω-N^G,N^G′-dimethylarginine, modifications that have been previously described. In addition, Sm D1, Sm D3, and Sm B/B′ were also found to contain asymmetric ω-N^G,N^G-dimethylarginine in these nuclear fractions. Analysis of Sm B/B′ from cytosolic fractions and Sm B/B′ and Sm D1 from cytosolic 6S complexes showed only the presence of ω-N^G-monomethylarginine and symmetric ω-N^G,N^G′-dimethylarginine. These results indicate that Sm D1, Sm D3, and Sm B/B′ are asymmetrically dimethylated and that these modified proteins are located in the nucleus. In reactions in which Sm D1 or Sm D3 was methylated in vitro with a hemagglutinin-tagged PRMT5 purified from HeLa cells, we detected both symmetric ω-N^G,N^G′-dimethylarginine and asymmetric ω-N^G,N^G-dimethylarginine when reactions were done in a Tris/HCl buffer, but only detected symmetric ω-N^G,N^G′-dimethylarginine when a sodium phosphate buffer was used. These results suggest that the activity responsible for the formation of asymmetric dimethylated arginine residues in Sm proteins is either PRMT5 or a protein associated with it in the immunoprecipitated complex.     

NG-Methylarginines: Biosynthesis,biochemical function and metabolism

Summary N^G-Methylarginines (N^G-monomethylarginine, N^G, N^G-dimethylarginine and N^G, N^G-dimethylarginine) occur widely in nature in either proteinbound or in free states. They are posttranslationally synthesized by a group of enzymes called protein methylase I with S-adenosyl-L-methionine as the methyl donor. The enzymes are highly specific not only towards arginine residues but also towards the protein species. Since transmethylation reaction is energy-dependent in the form of S-adenosyl-L-methionine and is catalyzed a group of highly specific enzymes, it is quite logical to assume that the enzymatic methylation of protein-bound arginine residues play an important role in the regulation of the function and/or metabolism of the protein. When determined with histones asin vitro substrates, protein methylase I activity parallels closely the degree of cell proliferation, and the myelin basic protein (MBP)-specific protein methylase I activity decreases drastically in dysmyelinating mutant mouse brain during myelinating period, suggesting an important role played in the formation and/or maintenance of myelin. When the methylated proteins are degraded by intracellular proteolytic enzymes, free N^G-methylarginines are generated. Some of these free N^G-methylarginines, particularly N^G-monomethylarginine, are extensively metabolized by decarboxylation, hydrolysis, transfer of methylamidine and deimination reaction. Recent experiment demonstrates that some of the N^G-methylarginines may be involved in the neutralization of activity of nitric oxide (NO) which has attracted a great deal of attention as vascular smooth muscle relaxation factor.     

METHYLASES OF MYELIN BASIC PROTEIN AND HISTONE IN RAT BRAIN

—The two enzymes methylating myelin basic protein and histone were purified 170- and 250-fold respectively from the cell sap fraction of rat brain. These enzymes methylated only arginine residues of the two proteins. The enzyme activities were present in all organs tested. Testis has the highest, brain a moderate and liver the lowest activity. Most of the activities were present in the cell sap fraction in brain, liver and testis. Methylation of myelin basic protein and histone was examined in both the cell sap and solubilized nuclear fraction of rat brain during life span after birth. The myelin basic protein methylating activity in the cell sap fraction increased during myelination. Histone methylase from the nuclear fraction was highest at birth and dropped rapidly thereafter. The other activities remained unchanged. The natural occurrence of N^G-mono- and N^G,N^G-dimethylarginine residues in histones prepared from rabbit liver was demonstrated.     

Distribution of NG, NG-dimethylarginine in nuclear protein fractions

Nuclear proteins have been fractionated into five distinct classes according to their extractability from rat liver nuclei at different pH and salt concentrations. The fractions have been analyzed for their amino acid composition which shows the presence of N^G, N^G-dimethylarginine, in sizable amount, in non-histone nuclear proteins (NHNP). This modification is most prominent in proteins which are found associated with rapidly-labeled heterogeneous RNA (HnRNP proteins).     

Ng-Methylated Arginines in Broad Bean Seed

l-N^g-Methylarginine, l-N^g,N^g-dimethylarginine and ethanolamine were isolated from basic amino acids fraction of broad bean (Vicia faba L.) seed. The presence of N^g,N′^g-dimethylarginine was also suggested.     

Identification and characterization of the packaging proteins of core 40S hnRNP particles

The proteins involved in protein-RNA and protein-protein interactions to form the core structure of nuclear 40S hnRNP particles in HeLa cells have been identified and characterized. Through complete analysis of nuclear extracts on sucrose density gradients and controlled salt dissociation of particle proteins, six lower molecular weight polypeptides are identified as the protein constituents of the 40S ribonucleoprotein complex which appears in the electron microscope as 210 A spherical particles. 40S hnRNP particles isolated from Chinese hamster lung fibroblasts show a strikingly similar protein composition to the human cells. The proteins are specifically associated with rapidly labeled nonribosomal nuclear RNA. Particle proteins from HeLa cells migrate in polyacrylamide gels as three groups of closely spaced doublets (groups A, B and C) and are present in a simple fixed stoichiometry. The group C proteins (C₁ and C₂ of 42,000 and 44,000 daltons) interact directly with RNA to form a smaller high salt-resistant RNP complex. The group A proteins (A₁ and A₂ of 32,000 and 34,000 daltons) are major nuclear proteins and constitute 60% total particle protein mass. These two proteins are basic with isoelectric points near 9.2 and 8.4, respectively, and are characterized by an unusual amino acid composition, including high glycine (25%) and the unusual modified basic residue identified as N^G,N^G-dimethylarginine. The major particle proteins (A₁ and A₂) interact electrostatically with nucleic acids and apparently function structurally in the packaging and stabilization of hnRNA in a manner analogous to the histones in chromatin υ bodies. The similarity in protein composition of core RNP particles from different cell types (especially in the basic proteins, A₁, A₂ and B₁) is consistent with a conserved particle structure and function in eucaryotes.     

Post-synthetic modifications of nuclear proteins. High mobility group proteins are methylated.

Calf thymus high mobility group proteins 1 and 2 (HMG-1 and HMG-2) were purified to homogeneity from a 0.35 M NaCl extract of chromatin by selective precipitation with trichloroacetic acid followed by ion exchange chromatography on CM-Sephadex. Amino acid analysis of an acid hydrolyzate of HMG-1 and HMG-2 proteins revealed the presence of a ninhydrin-positive peak identified as N^G,N^G-dimethylarginine. Radioactive tracer experiments confirmed the presence of methylated arginine in HMG proteins.     

Phospholipid vesicle aggregation induced by human myelin basic protein

Human myelin basic protein isolated from the brains of individuals who died with multiple sclerosis was more potent in inducing the aggregation of egg phosphatidylcholine vesicles than was the basic protein isolated from the brains of normal individuals. The portion of myelin basic protein which bound to egg phosphatidylcholine vesicles was separated from the free protein by sucrose density gradient centrifugation. Similar amounts of basic protein from normal or from multiple sclerosis brains are bound to the lipid and no consistent differences in the N^G, N^G dimethyl-arginine content of the protein fractions have been found.     

PRMT5 (Janus kinase-binding protein 1) catalyzes the formation of symmetric dimethylarginine residues in proteins.

We have identified a new mammalian protein arginine N-methyltransferase, PRMT5, formerly designated Janus kinase-binding protein 1, that can catalyze the formation of omega-N(G)-monomethylarginine and symmetric omega-N(G),N(G')-dimethylarginine in a variety of proteins. A hemagglutinin peptide-tagged PRMT5 complex purified from human HeLa cells catalyzes the S-adenosyl-l-[methyl-(3)H]methionine-dependent in vitro methylation of myelin basic protein. When the radiolabeled myelin basic protein was acid-hydrolyzed to free amino acids, and the products were separated by high-resolution cation exchange chromatography, we were able to detect two tritiated species. One species co-migrated with a omega-N(G)-monomethylarginine standard, and the other co-chromatographed with a symmetric omega-N(G),N(G')-dimethylarginine standard. Upon base treatment, this second species formed methylamine, a breakdown product characteristic of symmetric omega-N(G),N(G')-dimethylarginine. Further analysis of these two species by thin layer chromatography confirmed their identification as omega-N(G)-monomethylarginine and symmetric omega-N(G),N(G')-dimethylarginine. The hemagglutinin-PRMT5 complex was also able to monomethylate and symmetrically dimethylate bovine histone H2A and a glutathione S-transferase-fibrillarin (amino acids 1-148) fusion protein (glutathione S-transferase-GAR). A mutation introduced into the S-adenosyl-l-methionine-binding motif I of a myc-tagged PRMT5 construct in COS-1 cells led to a near complete loss of observed enzymatic activity. PRMT5 is the first example of a catalytic chain for a type II protein arginine N-methyltransferase that can result in the formation of symmetric dimethylarginine residues as observed previously in myelin basic protein, Sm small nuclear ribonucleoproteins, and other polypeptides.     

Biological significance of methylated derivatives of lysine and arginine.

It has been shown by biological trials that L-lysine and L-arginine are essential for the undisturbed growth of living organisms. These amino acids show different reactivity in the molecular processes of the cell which explains their antagonistic function. As a result of enzymatic methylation the N-? as well as N^G-methylated derivatives of lysine and arginine are produced. The biological function of the methylated basic amino acids is almost unknown. Some N-?-methylated lysines, but first of all N-?-trimethyl lysine /TML/ exhibits a proliferation promoting effect on several normal and neoplastic cell systems. N^G-methylated arginines proved to have a proliferation inhibiting effect. Thus, methylation of basic amino acids may have a special significance in the regulation of cell proliferation.     

Free amino acids in some sponges

Most invertebrates, particularly those of marine origin, have relatively high concentrations of free amino acids which are considered an important constituent of their osmoregulatory mechanisms [1]. Very little information is available on the free amino acid distribution in Porifera [2,3]. Common amino acids in some sponges were recognised by paper chromatography by Inskip and Cassidy [4] and Ackermann et al. [5,6] included a few sponges in their survey of the occurence of nitrogen compounds in marine invertebrates. More recently Bergquist and Hartman [7] surveyed semiquantitatively the distribution of free amino acids in several sponges. In the present paper we report on the amino acid composition of 12 species of sponges belonging to the class Demospongiae as a part of a study on the metabolites of Porifera [8]. Fresh sponges were extracted with aqueous ethanol. The organic solvent was removed and the aqueous solution, after removal of the ether soluble compounds, was separated into cationic, anionic and neutral fractions by ion-exchange chromatography. The cation fraction was analysed for amino acids using an automatic amino acid analyser. The results, which are presented in Table 1, show that all species of sponges examined have a similar composition in common amino acids. Glycine almost always appears as the dominant protein amino acid, followed by high concentrations of alanine and glutamic acid, whereas relatively lower concentrations of basic amino acids are present. In Axinella cannabina, Chondrosia reniformis, Chondrilla nucula, Cliona viridis and Hymeniacidon sanguinea, glycine represents more than 77% of the total amino acids. The high percentage of free glycine (90.4%) in Chondrosia reniformis is noteworthy. The anionic and the neutral fractions were examined for sulfur-containing amino acids using PC. Taurine (Table 2) was detected in all the Porifera examined; this is in agreement with previous observations [5–7]. N-Methyltaurine was identified in some of the species examined, whereas neither N,N-dimethyltaurine nor N,N,N-trimethyltaurine were found.     

Inhibitory effect of arginine-derivatives from ginseng extract and basic amino acids on protein-arginine N-methyltransferase

Summary Protein-arginine N-methyltransferase (protein methylase I) catalyzes methylation of arginyl residues on substrate protein posttranslationally utilizing S-adenosyl-L-methionine as the methyl donor and yields N^G-methylarginine residues. Arginyl-fructose and arginyl-fructosyl-glucose from Korean red ginseng were found to inhibit protein methylase I activity in vitro. This inhibitory activity was shown to be due to arginyl moiety in the molecules, rather than that of carbohydrates. Several basic amino acids as well as polyamines were also found to inhibit protein methylase I activity. Interestingly, the intensity of the inhibitory activity was correlated with the number of amino-group in polyamines, thus, in the order of spermine > spermidine > putrescine > agmatine-sulfate, with IC₅₀ at approximately 15 mM, 25 mM, 35 mM, and 50 mM, respectively. On the other hand, neutral amino acids or NaCI did not inhibit the enzyme activity. Lineweaver-Burk plot analysis of the protein methylase I activity in the presence of arginine and spermidine indicated that the inhibition was competitive in nature in respect to protein substrate, with the Ki values of 24.8 mM and 11.5 mM, respectively.Polyamines Abbreviations AdoMet S-adenosyl-L-methionine - PM I protein methylase I - Arg-Fru arginyl-fructose - Arg-Fru-Glu arginyl-fructosyl-glucose - PMSF phenylmethylsulfonyl fluoride - MBP myelin basic protein - hnRNP heterogeneous ribonuclear particle - TCA trichloroacetic acid - EDTA ethylenediamine tetraacetic acid     

Preparative-scale isolation of isotopically labeled amino acids

Over 10 g of individual ²H, ¹⁵N-labeled amino acids was resolved and recovered on a laboratory-scale ion-exchange system from a crude bacterial protein hydrolyzate derived from 20 g of lyophilized cells. The 17 amino acids (cystine was not isolated) were recovered containing less than 1.0% of other contaminating amino acids except for proline (4.0%). The aromatic and basic amino acids were isolated on a dual-column carrier displacement system (390-ml resin bed volume) while most of the neutral and acidic amino acids were separated on a pyrazolium chloride elution system (560-ml resin bed volume). The two remaining overlapping pairs were resolved on small carrier displacement columns. In addition, the overlapping fractions from adjacent peaks of the pyrazolium chloride elution system represent only 3.5% (0.37 g) of the total sample.     

N(omega)-arginine dimethylation modulates the interaction between a Gly/Arg-rich peptide from human nucleolin and nucleic acids

We studied the interaction between a synthetic peptide (sequence Ac-GXGGFGGXGGFXGGXGG-NH₂, where X = arginine, N^ω,N^ω-dimethylarginine, DMA, or lysine) corresponding to residues 676–692 of human nucleolin and several DNA and RNA substrates using double filter binding, melting curve analysis and circular dichroism spectroscopy. We found that despite the reduced capability of DMA in forming hydrogen bonds, N^ω,N^ω-dimethylation does not affect the strength of the binding to nucleic acids nor does it have any effect on stabilization of a double-stranded DNA substrate. However, circular dichroism studies show that unmethylated peptide can perturb the helical structure, especially in RNA, to a much larger extent than the DMA peptide.