Protein methylation

Post-translation modification in Archaea: lessons from Haloferax volcanii and other haloarchaea

As an ever-growing number of genome sequences appear, it is becoming increasingly clear that factors other than genome sequence impart complexity to the proteome. Of the various sources of proteomic variability, post-translational modifications (PTMs) most greatly serve to expand the variety of proteins found in the cell. Likewise, modulating the rates at which different proteins are degraded also results in a constantly changing cellular protein profile. While both strategies for generating proteomic diversity are adopted by organisms across evolution, the responsible pathways and enzymes in Archaea are often less well described than are their eukaryotic and bacterial counterparts. Studies on halophilic archaea, in particular Haloferax volcanii, originally isolated from the Dead Sea, are helping to fill the void. In this review, recent developments concerning PTMs and protein degradation in the haloarchaea are discussed.

Methylation and in vivo expression of the surface-exposed Leptospira interrogans outer-membrane protein OmpL32

Recent studies have revealed that bacterial protein methylation is a widespread post-translational modification that is required for virulence in selected pathogenic bacteria. In particular, altered methylation of outer-membrane proteins has been shown to modulate the effectiveness of the host immune response. In this study, 2D gel electrophoresis combined with MALDI-TOF MS identified a Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 protein, corresponding to ORF LIC11848, which undergoes extensive and differential methylation of glutamic acid residues. Immunofluorescence microscopy implicated LIC11848 as a surface-exposed outer-membrane protein, prompting the designation OmpL32. Indirect immunofluorescence microscopy of golden Syrian hamster liver and kidney sections revealed expression of OmpL32 during colonization of these organs. Identification of methylated surface-exposed outer-membrane proteins, such as OmpL32, provides a foundation for delineating the role of this post-translational modification in leptospiral virulence.

Changes in the arginine methylation of organ proteins during the development of diabetes mellitus

AIM

In this study, we examined changes in asymmetric dimethylarginine (ADMA), dimethylarginine dimethylaminohydrolase (DDAH), nitric oxide synthesis (NOS), and the arginine methylation of organ proteins during the development of diabetes in mice.

METHODS

Db/db mice developed significant obesity and fasting hyperglycemia during diabetogenesis. During diabetogenesis, the expression of ADMA and nNOS was increased, while that of DDAH1 and protein-arginine methyltransferase 1 (PRMT1) was decreased. Additionally, arginine methylation in the liver and adipose tissue was altered during diabetogenesis.

RESULTS

Changes were evident at 75, 60, and 52 kDa in liver tissue and at 38 and 25 kDa in adipose tissue. Collectively, DDAH and ADMA are closely associated with the development of obesity and diabetes, and the arginine methylation levels of certain proteins were changed during diabetes development.

CONCLUSION

Protein arginine methylation plays a role in the pathogenesis of diabetes.

Symmetric dimethylarginine as a proinflammatory agent in chronic kidney disease

BACKGROUND & OBJECTIVES

Chronic kidney disease (CKD) is characterized by chronic inflammation, considered a nontraditional risk factor for cardiovascular disease, the major cause of death in CKD. Symmetric dimethylarginine (SDMA) was recently demonstrated to induce reactive oxygen species in monocytes. The present study further investigates the inflammatory character of SDMA compared with its structural counterpart asymmetric dimethylarginine (ADMA).

DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS

In vitro, the effect of SDMA on intracellular monocytic expression of IL-6 and TNF-α was studied followed by an evaluation of nuclear factor (NF)-κB activation. Additionally, an association of SDMA with inflammatory parameters in consecutive stages of CKD was evaluated in vivo.

RESULTS

Monocytes incubated with SDMA showed increased IL-6 and TNF-α expression and a rise in active NF-κB. N-acetylcysteine abrogated both these effects. No significant effects were observed with ADMA. In vivo, 142 patients (67 ± 12 years) at different stages of CKD showed an inverse association between serum SDMA and ADMA and renal function. Correlations between SDMA and IL-6, TNF-α, and albumin were more significant than for ADMA, while multiple regression analysis only retained TNF-α at a high significance for SDMA (P < 0.0001). In receiver operating characteristic analysis for inflammation, defined as an IL-6 level above 2.97 pg/ml (median), the discriminative power of SDMA (area under the curve [AUC]: 0.69 ± 0.05) directly followed that of C-reactive protein (AUC: 0.82 ± 0.04) and albumin (AUC: 0.72 ± 0.05; for all, P < 0.0001) and preceded that of ADMA (P = 0.002).

CONCLUSIONS

The present study shows that SDMA is involved in the inflammatory process of CKD, activating NF-κB and resulting in enhanced expression of IL-6 and TNF-α, which is corroborated by the clinical data pointing to an in vivo association of SDMA with inflammatory markers in CKD at different stages.

A transient kinetic analysis of PRMT1 catalysis

Post-translational modifications (PTMs) are important strategies used by eukaryotic organisms to modulate their phenotypes. One of the well-studied PTMs, arginine methylation, is catalyzed by protein arginine methyltransferases (PRMTs) with SAM as the methyl donor. The functions of PRMTs have been broadly studied in different biological processes and diseased states, but the molecular basis for arginine methylation is not well-defined. In this study, we report the transient-state kinetic analysis of PRMT1 catalysis. The fast association and dissociation rates suggest that PRMT1 catalysis of histone H4 methylation follows a rapid equilibrium sequential kinetic mechanism. The data give direct evidence that the chemistry of methyl transfer is the major rate-limiting step and that binding of the cofactor SAM or SAH affects the association and dissociation of H4 with PRMT1. Importantly, from the stopped-flow fluorescence measurements, we have identified a critical kinetic step suggesting a precatalytic conformational transition induced by substrate binding. These results provide new insights into the mechanism of arginine methylation and the rational design of PRMT inhibitors.

Protein phosphorylation is a key event of flagellar disassembly revealed by analysis of flagellar phosphoproteins during flagellar shortening in Chlamydomonas

Cilia are disassembled prior to cell division, which is proposed to regulate proper cell cycle progression. The signaling pathways that regulate cilia disassembly are not well-understood. Recent biochemical and genetic data demonstrate that protein phosphorylation plays important roles in cilia disassembly. Here, we analyzed the phosphoproteins in the membrane/matrix fraction of flagella undergoing shortening as well as flagella from steady state cells of Chlamydomonas. The phosphopeptides were enriched by a combination of IMAC and titanium dioxide chromatography with a strategy of sequential elution from IMAC (SIMAC) and analyzed by tandem mass spectrometry. A total of 224 phosphoproteins derived from 1296 spectral counts of phosphopeptides were identified. Among the identified phosphoproteins are flagellar motility proteins such as outer dynein arm, intraflagellar transport proteins as well as signaling molecules including protein kinases, phosphatases, G proteins, and ion channels. Eighty-nine of these phosphoproteins were only detected in shortening flagella, whereas 29 were solely in flagella of steady growing cells, indicating dramatic changes of protein phosphorylation during flagellar shortening. Our data indicates that protein phosphorylation is a key event in flagellar disassembly, and paves the way for further study of flagellar assembly and disassembly controlled by protein phosphorylation.

Histone H4 acetylation differentially modulates arginine methylation by an in Cis mechanism

Histone H4 undergoes extensive post-translational modifications (PTMs) at its N-terminal tail. Many of these PTMs profoundly affect the on and off status of gene transcription. The molecular mechanism by which histone PTMs modulate genetic and epigenetic processes is not fully understood. In particular, how a PTM mark affects the presence and level of other histone modification marks needs to be addressed and is essential for better understanding the molecular basis of histone code hypothesis. To dissect the interplaying relationship between different histone modification marks, we investigated how individual lysine acetylations and their different combinations at the H4 tail affect Arg-3 methylation in cis. Our data reveal that the effect of lysine acetylation on arginine methylation depends on the site of acetylation and the type of methylation. Although certain acetylations present a repressive impact on PRMT1-mediated methylation (type I methylation), lysine acetylation generally is correlated with enhanced methylation by PRMT5 (type II dimethylation). In particular, Lys-5 acetylation decreases the activity of PRMT1 but increases that of PRMT5. Furthermore, circular dichroism study and computer simulation demonstrate that hyperacetylation increases the content of ordered secondary structures at the H4 tail region. These findings provide new insights into the regulatory mechanism of Arg-3 methylation by H4 acetylation and unravel the complex intercommunications that exist between different the PTM marks in cis. The divergent activities of PRMT1 and PRMT5 with respect to different acetyl-H4 substrates suggest that type I and type II protein-arginine methyltransferases use distinct molecular determinants for substrate recognition and catalysis.

Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri

Background

The bacterial pathogen Edwardsiella ictaluri is a primary cause of mortality in channel catfish raised commercially in aquaculture farms. Additional treatment and diagnostic regimes are needed for this enteric pathogen, motivating the discovery and characterization of bacteriophages specific to E. ictaluri.

Results

The genomes of three Edwardsiella ictaluri-specific bacteriophages isolated from geographically distant aquaculture ponds, at different times, were sequenced and analyzed. The genomes for phages eiAU, eiDWF, and eiMSLS are 42.80 kbp, 42.12 kbp, and 42.69 kbp, respectively, and are greater than 95% identical to each other at the nucleotide level. Nucleotide differences were mostly observed in non-coding regions and in structural proteins, with significant variability in the sequences of putative tail fiber proteins. The genome organization of these phages exhibit a pattern shared by other Siphoviridae.

Conclusions

These E. ictaluri-specific phage genomes reveal considerable conservation of genomic architecture and sequence identity, even with considerable temporal and spatial divergence in their isolation. Their genomic homogeneity is similarly observed among E. ictaluri bacterial isolates. The genomic analysis of these phages supports the conclusion that these are virulent phages, lacking the capacity for lysogeny or expression of virulence genes. This study contributes to our knowledge of phage genomic diversity and facilitates studies on the diagnostic and therapeutic applications of these phages.

Histone modifications and cancer

It is now widely recognized that epigenetic events are important mechanisms underlying cancer development and progression. Epigenetic information in chromatin includes covalent modifications (such as acetylation, methylation, phosphorylation, and ubiquitination) of core nucleosomal proteins (histones). A recent progress in the field of histone modifications and chromatin research has tremendously enhanced our understanding of the mechanisms underlying the control of key physiological and pathological processes. Histone modifications and other epigenetic mechanisms appear to work together in establishing and maintaining gene activity states, thus regulating a wide range of cellular processes. Different histone modifications themselves act in a coordinated and orderly fashion to regulate cellular processes such as gene transcription, DNA replication, and DNA repair. Interest in histone modifications has further grown over the last decade with the discovery and characterization of a large number of histone-modifying molecules and protein complexes. Alterations in the function of histone-modifying complexes are believed to disrupt the pattern and levels of histone marks and consequently deregulate the control of chromatin-based processes, ultimately leading to oncogenic transformation and the development of cancer. Consistent with this notion, aberrant patterns of histone modifications have been associated with a large number of human malignancies. In this chapter, we discuss recent advances in our understanding of the mechanisms controlling the establishment and maintenance of histone marks and how disruptions of these chromatin-based mechanisms contribute to tumorigenesis. We also suggest how these advances may facilitate the development of novel strategies to prevent, diagnose, and treat human malignancies.

Biotin synthase exhibits burst kinetics and multiple turnovers in the absence of inhibition by products and product-related biomolecules

Biotin synthase (BS) is a member of the "SAM radical" superfamily of enzymes, which catalyze reactions in which the reversible or irreversible oxidation of various substrates is coupled to the reduction of the S-adenosyl-l-methionine (AdoMet) sulfonium to generate methionine and 5'-deoxyadenosine (dAH). Prior studies have demonstrated that these products are modest inhibitors of BS and other members of this enzyme family. In addition, the in vivo catalytic activity of Escherichia coli BS requires expression of 5'-methylthioadenosine/S-adenosyl-l-homocysteine nucleosidase, which hydrolyzes 5'-methylthioadenosine (MTA), S-adenosyl-l-homocysteine (AdoHcy), and dAH. In the present work, we confirm that dAH is a modest inhibitor of BS (K(i) = 20 μM) and show that cooperative binding of dAH with excess methionine results in a 3-fold enhancement of this inhibition. However, with regard to the other substrates of MTA/AdoHcy nucleosidase, we demonstrate that AdoHcy is a potent inhibitor of BS (K(i) ≤ 650 nM) while MTA is not an inhibitor. Inhibition by both dAH and AdoHcy likely accounts for the in vivo requirement for MTA/AdoHcy nucleosidase and may help to explain some of the experimental disparities between various laboratories studying BS. In addition, we examine possible inhibition by other AdoMet-related biomolecules present as common contaminants in commercial AdoMet preparations and/or generated during an assay, as well as by sinefungin, a natural product that is a known inhibitor of several AdoMet-dependent enzymes. Finally, we examine the catalytic activity of BS with highly purified AdoMet in the presence of MTAN to relieve product inhibition and present evidence suggesting that the enzyme is half-site active and capable of undergoing multiple turnovers in vitro.

Deficiency in a glutamine-specific methyltransferase for release factor causes mouse embryonic lethality

Biological methylation is a fundamental enzymatic reaction for a variety of substrates in multiple cellular processes. Mammalian N6amt1 was thought to be a homologue of bacterial N(6)-adenine DNA methyltransferases, but its substrate specificity and physiological importance remain elusive. Here, we demonstrate that N6amt1 functions as a protein methyltransferase for the translation termination factor eRF1 in mammalian cells both in vitro and in vivo. Mass spectrometry analysis indicated that about 70% of the endogenous eRF1 is methylated at the glutamine residue of the conserved GGQ motif. To address the physiological significance of eRF1 methylation, we disrupted the N6amt1 gene in the mouse. Loss of N6amt1 led to early embryonic lethality. The postimplantation development of mutant embryos was impaired, resulting in degeneration around embryonic day 6.5. This is in contrast to what occurs in Escherichia coli and Saccharomyces cerevisiae, which can survive without the N6amt1 homologues. Thus, N6amt1 is the first glutamine-specific protein methyltransferase characterized in vivo in mammals and methylation of eRF1 by N6amt1 might be essential for the viability of early embryos.

Stabilization of proteins for storage

Following isolation and purification, it is often necessary to store proteins and peptides for extended periods of time before performing detailed biophysical, enzymatic, and structural proteomics. Therefore, it is essential that the pure target protein maintain its original biological (or functional) behavior over an extended period of storage which may range from weeks to years. Protein pharmaceuticals must remain viable following extensive shipping and storage, and they must remain devoid of all possible inactivation processes. The shelf life of a protein depends on both the intrinsic nature of the protein and the storage conditions. Proteins (especially enzymes) must be stored at an appropriate temperature and pH range and frequently in the presence of concentrated (approximately 1 M) glycerol, sucrose, or a similar substance, for the proteins to retain activity and prevent aggregation. This article discusses the major causes of protein inactivation and describes a range of measures that can be adopted to maintain the stability and solubility of proteins.

Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate

Aspartates in proteins are isomerized non-enzymatically to isoaspartate via succinimide in vitro and in vivo. In order to elucidate the mechanism of isoaspartate formation within the Asp45-Glu46 sequence of Ustilago sphaerogena ribonuclease U2 based on three-dimensional structure, crystal structures of ribonuclease U2 complexed with adenosine 3'-monophosphate have been solved at 0.96 and 0.99 A resolution. The crystal structures revealed that the C(gamma) atom of Asp45 is located just beside the main-chain N atom of Glu46 and that the conformation which is suitable for succinimide formation is stabilized by a hydrogen-bond network mediated by water molecules 190, 219 and 220. These water molecules are suggested to promote the formation of isoaspartate via succinimide: in the succinimide-formation reaction water 219 receives a proton from the N atom of Glu46 as a general base and waters 190 and 220 stabilize the tetrahedral intermediate, and in the succinimide-hydrolysis reaction water 219 provides a proton for the N atom of Glu46 as a general acid. The purine-base recognition scheme of ribonuclease U2 is also discussed.

MS/MS/MS reveals false positive identification of histone serine methylation

Methylation of lysine and arginine residues is known to play a key role in regulating histone structure and function. However, methylation of other amino acid residues in histones has not been previously described. Using exhaustive nano-HPLC/MS/MS and blind protein sequence database searches, we tentatively assigned methylation to serine 28 of histone H3 from calf thymus. The assignment was in agreement with our stringent manual verification rules, coelution in HPLC/MS/MS with its corresponding synthetic peptide, the dynamic nature of such methylation in distinct cell lines, and isotopic labeling. However, careful inspection of the MS/MS and MS/MS/MS spectra of a series of synthetic peptides confirmed that methylation actually occurs on K27 rather than on S28. The misassignment was caused by the fact that the (y(9) + 14) of the putative S28-methylated peptide and (b(9) + 18) ions of the K27 methylated peptide share the same m/z value (m/z 801). This MS/MS peak was used as the major evidence to assign methylation to S28 (consecutive y(8) and (y(9) + 14) ions). MS/MS/MS analysis revealed the false positive nature of serine methylation: the ambiguous ion at m/z 801 is indeed (b(9) + 18), an ion resulting from an in vitro reaction in the gas phase during collisionally activated dissociation (CAD). When lysine (K27) was acetylated, the degree of such in vitro reactions was greatly reduced, and such reactions were completely eliminated when the C-terminus was blocked by carboxylic group derivatization. Moreover, such side-chain assisted C-terminal rearrangement was found to be charge dependent. In aggregate, these results suggest that extra caution should be taken in interpretation of post-translational modification (PTM) data and that MS/MS as well as MS/MS/MS of synthetic peptides are needed for verifying the identity of peptides bearing a novel PTM.

Adenoviral-mediated overexpression of DDAH improves vascular tone regulation

Dimethylarginine dimethylaminohydrolase (DDAH) degrades asymmetric dimethylarginine (ADMA), an endogenously produced nitric oxide (NO) synthase inhibitor. In mammals, two isoforms of DDAH, DDAH1 and DDAH2, are expressed in the cardiovascular system, suggesting that ADMA concentrations are actively regulated in blood vessels, raising the possibility that cardiovascular metabolism of ADMA constitutes a novel mechanism for the regulation of NO production. The purpose of this study was to determine the role of DDAH-catalyzed asymmetric methylarginine metabolism in the regulation of vascular function. We developed adenoviral vectors for the expression of human DDAH1 and 2. Overexpression of DDAH1 or 2 in human umbilical vein endothelial cells (HUVEC) increases DDAH activity, reduces ADMA concentrations and increases NO production. Similarly, overexpression of DDAH1 or 2 in DDAH1+/ — mice carotid vessels increases NO production and attenuates the response to phenylephrine (PE), enhances acetylcholine (ACh) relaxation and attenuates the effect of exogenously applied ADMA. Finally, overexpression of either DDAH1 or 2 completely reversed the vascular dysfunction seen in DDAH1+/— mice. These data indicate that basal concentrations of ADMA in blood vessels are sufficient to regulate NO production, that increases in the level of either DDAH1 or 2, improves vascular function and that overexpression of either DDAH1 or 2 is sufficient to compensate for life-long exposure to elevated ADMA. Thus, therapeutic manipulation of DDAH expression or activity may represent a novel approach to improve vascular dysfunction in various cardiovascular diseases.

The emerging role of symmetric dimethylarginine in vascular disease

Asymmetric dimethylarginine (ADMA), an endogenous methylated form of the amino acid L-arginine, inhibits the activity of the enzyme endothelial nitric oxide synthase (eNOS), with consequent reduced synthesis of nitric oxide (NO). An increased synthesis and/or a reduced catabolism of ADMA might contribute to the onset and progression of atherosclerosis and thrombosis. The detrimental effects of ADMA on endothelial function, cardiovascular homeostasis, and cardiovascular outcomes have been extensively investigated. However, little attention has been paid to another methylated form of L-arginine, symmetric dimethylarginine (SDMA), as a potential modulator of vascular homeostasis and vascular disease. The first part of this chapter discusses the synthesis, transport, and metabolism of ADMA and SDMA and summarizes the evidence linking ADMA with vascular disease and adverse cardiovascular outcomes. The second part describes the results of recent studies highlighting the important role of SDMA in modulating vascular homeostasis and vascular damage. Suggestions for future research directions on SDMA are also discussed.

Identification of a flavin mononucleotide module residue critical for activity of inducible nitrite oxide synthase

Inducible NO synthase (iNOS) contains an amino-terminal oxygenase domain, a carboxy-terminal reductase domain, and an intervening calmodulin-binding domain. For the synthesis of NO, iNOS is active as a homodimer formed by oxygenase domains, while the reductase domain is required to transfer electrons from NADPH. In this study, we identify glutamate 658 in the FMN domain of human iNOS to be a critical residue for iNOS activity and we explore the underlying mechanism for such role. Mutation of glutamate to aspartate almost abolished iNOS activity and reduced dimer formation. Substitution of this residue with noncharged alanine and glutamine, or positively charged lysine did not affect dimer formation and maintained around 60% of iNOS activity. These results suggest that the negative charge specific to glutamate plays an important role in iNOS activity.

Asymmetric dimethylarginine association with antioxidants intake in healthy young adults: a role as an indicator of metabolic syndrome features

The purpose of this study was to evaluate the potential associations between serum asymmetric dimethylarginine (ADMA) and several anthropometric, biochemical, and lifestyle features in healthy young adults, emphasizing on the putative effects of the antioxidant intake on ADMA concentrations. Anthropometric and blood pressure measurements as well as lifestyle features and antioxidant intake were analyzed in 93 healthy young adults aged 18 to 34 years. Fasting blood samples were collected for the measurement of glucose, total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, triacylglycerols, and ADMA concentrations, as well as erythrocyte glutathione peroxidase activity. Nail samples were collected for the analysis of selenium and zinc concentrations. Values of body mass index (P = .004), waist circumference (P = .008), waist-to-height ratio (P = .046), systolic blood pressure (P < .001), serum glucose (P < .001), and nail selenium (P = .004) and zinc (P = .018) were significantly different between subjects with serum ADMA higher and lower than the median (cutoff, 458 nmol/L). Furthermore, ADMA showed a positive association with several adiposity markers such as body weight (P < .001), body mass index (P < .001), waist circumference (P = .006), waist-to-height ratio (P = .020), body fat mass (P = .001), systolic blood pressure (P = .001), and serum glucose (P < .001), whereas erythrocyte glutathione peroxidase activity (P = .021) and nail selenium (P = .040) and zinc values (P = .013) were statistically significant negative predictors of ADMA concentrations. In conclusion, ADMA seems to be related with selenium and zinc status and several anthropometric and biochemical measurements linked to metabolic syndrome in apparently healthy young adults. These findings support a role for antioxidant/trace element intake in the modulation of ADMA, whose assessment may be a marker of metabolic syndrome manifestations.

Altered asymmetric dimethyl arginine metabolism in allergically inflamed mouse lungs

Asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide synthase (NOS), causes uncoupling of NOS leading to generation of reactive nitrogen species, such as peroxynitrite. The lung generates a significant amount of ADMA, potentially contributing to plasma ADMA levels that have been related to endothelial dysfunction. ADMA infusion causes increased collagen deposition in lungs, suggesting that it could influence the development of chronic lung diseases such as fibrosis, chronic obstructive pulmonary disease, and asthma. To explore the link between endogenous ADMA and asthma, we determined the levels of ADMA, enzymes implicated in its metabolism, and peroxynitrite in murine models of allergic airway inflammation (AAI) resembling asthma. ADMA levels and nitrosative stress were found to be positively correlated in cytosol and mitochondria during AAI. This was associated with increased expression of protein-arginine methyltransferase-2, an ADMA-synthesizing enzyme, and reduced expression of dimethylarginine dimethylaminohydrolase-2, an ADMA-degrading enzyme, in bronchial epithelia. Increased nitrotyrosine similarly localized to the bronchial epithelium, as well as in infiltrated inflammatory cells. Administration of L-arginine, which was expected to compete with ADMA and reverse the uncoupling/inhibition of NOS, restored normal ADMA metabolism, along with the expected reduction of nitrosative stress in lung. Because dimethylarginine dimethylaminohydrolase-2 function is known to be negatively related to oxidative stress, this may represent a feed-forward loop effect. We conclude that a delicate balance between ADMA-metabolizing enzymes is disturbed in bronchial epithelium during AAI, potentially causing increased nitrosative stress in a self-propagating cycle. This represents a potential therapeutic target in asthma.

The prominent role of the liver in the elimination of asymmetric dimethylarginine (ADMA) and the consequences of impaired hepatic function

Asymmetric dimethylarginine (ADMA) is an endogenous inhibitor of nitric oxide synthase (NOS), the enzyme which converts the amino acid arginine into nitric oxide (NO). ADMA has been identified as an important risk factor for cardiovascular diseases. Besides the role of ADMA in cardiovascular diseases, it also seems to be an important determinant in the development of critical illness, (multiple) organ failure, and the hepatorenal syndrome. ADMA is eliminated from the body by urinary excretion, but it is mainly metabolized by the dimethylarginine dimethylaminohydrolase (DDAH) enzymes that convert ADMA into citrulline and dimethylamine. DDAH is highly expressed in the liver, which makes the liver a key organ in the regulation of the plasma ADMA concentration. The prominent role of the liver in the elimination of ADMA and the consequences of impaired hepatic function on ADMA levels will be discussed in this article.

A feedback regulatory loop between methyltransferase PRMT1 and orphan receptor TR3

PRMT1, an arginine methyltransferase, plays an important role in numerous cellular processes. In this study, we demonstrate a feedback regulatory loop between PRMT1 and the orphan receptor TR3. Unlike another orphan receptor HNF4, TR3 is not methylated by PRMT1 although they physically interact with each other. By delaying the TR3 protein degradation, PRMT1 binding leads to the elevation of TR3 cellular protein level, thereby enhances the DNA binding and transactivation activity of TR3 in a non-methyltransferase manner. Another coactivator SRC-2 acts synergistically with PRMT1 to regulate TR3 functions. In turn, TR3 binding to the catalytic domain of PRMT1 causes an inhibition of the PRMT1 methyltransferase activity. This repression results in the functional changes in some of PRMT1 substrates, including STAT3 and Sam68. The negative regulation of PRMT1 by TR3 was further confirmed in both TR3-knockdown cells and TR3-knockout mice with the use of an agonist for TR3. Taken together, our study not only identifies a regulatory role of PRMT1, independent on methyltransferase activity, in TR3 transactivation, but also characterizes a novel function of TR3 in the repression of PRMT1 methyltransferase activity.

Nebivolol treatment reduces serum levels of asymmetric dimethylarginine and improves endothelial dysfunction in essential hypertensive patients

BACKGROUND

This study was conducted to evaluate (i) the effect of nebivolol, a selective beta1-adrenergic receptor antagonist, on plasma concentration of asymmetric dimethylarginine (ADMA) and on flow-mediated dilation (FMD) in essential hypertensive patients; (ii) the effect of serum derived from the treated hypertensive patients on ADMA and on dimethylarginine dimethylaminohydrolase 2 (DDAH2), the enzyme that selectively degrades ADMA, in human umbilical vein endothelial cells (HUVECs).

METHODS

Forty healthy subjects and 40 matched essential hypertensive patients treated with atenolol and nebivolol according to a double-blind, randomized design participated in the study. Evaluation of brachial artery (BA) reactivity was performed by a longitudinal B-mode scan of the right BA. ADMA and L-arginine were measured by high-performance liquid chromatography. DDAH2 expression and endothelial nitric oxide synthase activity (eNOS) were also evaluated in HUVECs.

RESULTS

ADMA levels were significantly decreased and FMD increased only in patients receiving nebivolol (P < 0.01). Furthermore, in nebivolol group, we found a significant correlation between changes in ADMA levels and changes in FMD (P < 0.01). Sera derived from patients treated with nebivolol but not with atenolol decreased ADMA and increased DDAH2 expression and eNOS activity (P < 0.001) in HUVECs.

CONCLUSIONS

The results of this study demonstrate that the improvement of endothelial dysfunction induced by nebivolol in hypertensive patients may be related to its effect on circulating ADMA levels. Although the mechanism by which nebivolol reduces circulating ADMA in hypertensive patients remains unclear, our ex vivo results suggest that the upregulation of DDAH2 expression may have a role.

Specificity of protein lysine methyltransferases and methods for detection of lysine methylation of non-histone proteins

Post translational modification of histone proteins including lysine methylation is an important epigenetic mark, essential for gene regulation and development. Recently, several examples of lysine methylation of non-histone proteins have been discovered suggesting that this is a common post-translational modification for regulation of protein activity. Here, we review assays for the detection of protein methylation based on mass spectrometry, radiolabel and immunological approaches using protein and peptide substrates including application of SPOT peptide arrays. Candidates for new methylation targets of protein methyltransferases can be predicted using the specificity of the enzyme and protein interaction data.

A spectral clustering approach to MS/MS identification of post-translational modifications

Unidentified tandem mass spectra typically represent 50-90% of the spectra acquired in proteomics studies. This manuscript describes a novel algorithm, "Bonanza", for clustering spectra without knowledge of peptide or protein identifications. Further analysis leverages existing peptide identifications to infer related, likely valid identifications. Significantly more spectra can be identified with this approach, including spectra with unexpected potential modifications or amino-acid substitutions.

Homocysteine inhibits arterial endothelial cell growth through transcriptional downregulation of fibroblast growth factor-2 involving G protein and DNA methylation

Homocysteine (Hcy) contributes to atherogenesis and angiostasis by altering the phenotype of arterial endothelial cells (ECs). The present study was aimed at elucidating potential mechanisms by which Hcy can slow EC proliferation and induce EC apoptosis, thereby disrupting endothelial integrity. Given the strong mitogenic and antiapoptotic properties of fibroblast growth factor (FGF)2, we examined whether Hcy can modulate its expression. In cultured human coronary and bovine aortic ECs, Hcy exerted time- and concentration-dependent (0 to 500 micromol/L) reduction of the mRNA and protein levels of FGF2, whereas vascular endothelial growth factor expression was not affected until Hcy reached a proapoptotic 500 micromol/L. By testing a panel of signal transduction inhibitors, we found that the Hcy-induced downregulation of FGF2 was specifically attenuated by pertussis toxin, an inhibitor of Gi protein signaling. Hcy induced cell cycle arrest at the G(1)/S transition and increased TUNEL-positive apoptotic cells in a graded manner. These effects were effectively counteracted by exogenous FGF2. Reporter gene assays showed that Hcy downregulated FGF2 by transcriptional repression of the gene promoter encompassed in a CpG dinucleotide-rich island. This region was heavily methylated at the cytosine residues by Hcy despite decreased methylation potential (S-adenosylmethionine to S-adenosylhomocysteine ratio). Normal levels of FGF2 transcription were restored to ECs simultaneously exposed to Hcy and 5-aza-deoxycytidine. We conclude that homocysteine disrupts the growth and survival of ECs through a G protein-mediated pathway associated with altered promoter DNA methylation and the transcriptional repression of FGF2.

Complications in the assignment of 14 and 28 Da mass shift detected by mass spectrometry as in vivo methylation from endogenous proteins

Identification of protein methylation sites typically starts with database searching of MS/MS spectra of proteolytic digest of the target protein by allowing addition of 14 and 28 Da in the selected amino acid residues that can be methylated. Despite the progress in our understanding of lysine and arginine methylation, substrates and functions of protein methylation at other amino acid residues remain unknown. Here we report the analysis of protein methylation for p53, SMC3, iNOS, and MeCP2. We found that a large number of peptides can be modified on the lysine, arginine, histidine, and glutamic acid residues with a mass increase of 14 or 28 Da, consistent with methylation. Surprisingly, a majority of which did not demonstrate a corresponding mass shift when cells were cultured with isotope-labeled methionine, a precursor for the synthesis of S-adenosyl-l-methionine (SAM), which is the most commonly used methyl donor for protein methylation. These results suggest the possibility of either exogenous protein methylation during sample handling and processing for mass spectrometry or the existence of SAM-independent pathways for protein methylation. Our study found a high occurrence of protein methylation from SDS-PAGE isolated endogenous proteins and identified complications for assigning such modifications as in vivo methylation. This study provides a cautionary note for solely relying on mass shift for mass spectrometric identification of protein methylation and highlights the importance of in vivo isotope labeling as a necessary validation method.

Identification and validation of eukaryotic aspartate and glutamate methylation in proteins

Methylation of lysine and arginine is known to be critical in cellular processes. However, methylation of other amino acidic residues has been largely overlooked. Here, we report a systematic screening for methylation of side chains of aspartate and glutamate (D/E-methylation), involving exhaustive nano-HPLC/MS/MS, a protein sequence database search, and manual verification. The putative D/E-methylated peptides were confirmed by MS/MS of synthetic peptides. Our analysis identified several D/E-methylation substrate proteins and their modification sites in human and yeast cells. To our knowledge, this is the first report conclusively identifying in vivo D/E-methylation substrates and their modification sites in eukaryotic cells, demonstrating that D/E-methylations are abundant protein modifications. The substrate proteins identified here provide a stepping stone for future biochemical characterization of protein methylation pathways.

Health-associated reference values for arginine, asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA) measured with high-performance liquid chromatography

OBJECTIVE

Asymmetric dimethylarginine (ADMA) is an endogenous inhibitor of nitric oxide production. It has been implicated in various pathological processes, especially processes involving the cardiovascular system. Plasma concentration of ADMA (p-ADMA) has been measured in several studies with different techniques, and a wide range of normal values has been published. With use of high performance liquid chromatography (HPLC) with fluorescence detection, we have established health-associated reference values for p-ADMA, p-arginine, p-SDMA and the p-arginine/p-ADMA and p-arginine/p-SDMA ratios.

MATERIAL AND METHODS

Blood samples were taken from 238 blood donors (112 F and 126 M). HPLC was used to analyse arginine, ADMA and SDMA. Reference values are presented as 2.5 and 97.5 percentiles estimated by the bootstrap method.

RESULTS

The reference interval for p-ADMA is 0.40-0.77 micromol/L for the whole population, 0.41-0.79 micromol/L for men, 0.38-0.73 micromol/L for women 45 years or less, and 0.41-0.84 micromol/L for women >45 years.

CONCLUSIONS

Age affects p-ADMA in healthy women, but not in men.

Methylation of proteins involved in translation

Methylation is one of the most common protein modifications. Many different prokaryotic and eukaryotic proteins are methylated, including proteins involved in translation, including ribosomal proteins (RPs) and translation factors (TFs). Positions of the methylated residues in six Escherichia coli RPs and two Saccharomyces cerevisiae RPs have been determined. At least two RPs, L3 and L12, are methylated in both organisms. Both prokaryotic and eukaryotic elongation TFs (EF1A) are methylated at lysine residues, while both release factors are methylated at glutamine residues. The enzymes catalysing methylation reactions, protein methyltransferases (MTases), generally use S-adenosylmethionine as the methyl donor to add one to three methyl groups that, in case of arginine, can be asymetrically positioned. The biological significance of RP and TF methylation is poorly understood, and deletions of the MTase genes usually do not cause major phenotypes. Apparently methylation modulates intra- or intermolecular interactions of the target proteins or affects their affinity for RNA, and, thus, influences various cell processes, including transcriptional regulation, RNA processing, ribosome assembly, translation accuracy, protein nuclear trafficking and metabolism, and cellular signalling. Differential methylation of specific RPs and TFs in a number of organisms at different physiological states indicates that this modification may play a regulatory role.

Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression

It is more evident now than ever that nucleosomes can transmit epigenetic information from one cell generation to the next. It has been demonstrated during the past decade that the posttranslational modifications of histone proteins within the chromosome impact chromatin structure, gene transcription, and epigenetic information. Multiple modifications decorate each histone tail within the nucleosome, including some amino acids that can be modified in several different ways. Covalent modifications of histone tails known thus far include acetylation, phosphorylation, sumoylation, ubiquitination, and methylation. A large body of experimental evidence compiled during the past several years has demonstrated the impact of histone acetylation on transcriptional control. Although histone modification by methylation and ubiquitination was discovered long ago, it was only recently that functional roles for these modifications in transcriptional regulation began to surface. Highlighted in this review are the recent biochemical, molecular, cellular, and physiological functions of histone methylation and ubiquitination involved in the regulation of gene expression as determined by a combination of enzymological, structural, and genetic methodologies.

Protein methylation is required to maintain optimal HIV-1 infectivity

Background:

Protein methylation is recognized as a major protein modification pathway regulating diverse cellular events such as protein trafficking, transcription, and signal transduction. More recently, protein arginine methyltransferase activity has been shown to regulate HIV-1 transcription via Tat. In this study, adenosine periodate (AdOx) was used to globally inhibit protein methyltransferase activity so that the effect of protein methylation on HIV-1 infectivity could be assessed.

Results:

Two cell culture models were used: HIV-1-infected CEM T-cells and HEK293T cells transfected with a proviral DNA plasmid. In both models, AdOx treatment of cells increased the levels of virion in culture supernatant. However, these viruses had increased levels of unprocessed or partially processed Gag-Pol, significantly increased diameter, and displayed reduced infectivity in a MAGI X4 assay. AdOx reduced infectivity equally in both dividing and non-dividing cells. However, infectivity was further reduced if Vpr was deleted suggesting virion proteins, other than Vpr, were affected by protein methylation. Endogenous reverse transcription was not inhibited in AdOx-treated HIV-1, and infectivity could be restored by pseudotyping HIV with VSV-G envelope protein. These experiments suggest that AdOx affects an early event between receptor binding and uncoating, but not reverse transcription.

Conclusion:

Overall, we have shown for the first time that protein methylation contributes towards maximal virus infectivity. Furthermore, our results also indicate that protein methylation regulates HIV-1 infectivity in a complex manner most likely involving the methylation of multiple viral or cellular proteins and/or multiple steps of replication.

Asymmetric dimethylarginine is an independent risk factor for coronary heart disease: results from the multicenter Coronary Artery Risk Determination investigating the Influence of ADMA Concentration (CARDIAC) study

BACKGROUND

Asymmetric dimethylarginine (ADMA) plasma levels have been shown to be elevated in diseases related to endothelial dysfunction such as hypertension, hyperlipidemia, diabetes mellitus, and others. It has been shown that ADMA predicts cardiovascular mortality in patients who have coronary heart disease (CHD). However, the question whether ADMA is an independent risk factor for CHD still remains unresolved.

METHODS

The CARDIAC study is a multicenter case-control study, designed to detect differences in ADMA plasma levels between patients with CHD and controls from the general population. We included in our analysis 131 cases and 131 controls, matched for age, sex, and body mass index.

RESULTS

We found that cases had higher ADMA plasma levels than controls (0.70 micromol/L [0.59-0.87 micromol/L] vs 0.60 micromol/L [0.54-0.69 micromol/L], P < .001). To evaluate the predictive power of ADMA regarding CHD, we calculated 2 multivariate logistic regression models including laboratory parameters and traditional risk factors. The odds ratio for ADMA in the multivariate model including the laboratory characteristics was 2.59 (1.61-4.17; P < .001); the odds ratio for the multivariate model including other risk factors was 6.04 (2.56-14.25; P < .001) for the third tertile (>0.72 micromol/L) versus the first (<0.58 micromol/L).

CONCLUSIONS

We conclude from the results of our study that ADMA is an independent risk factor for CHD.

Endogenous production of nitric oxide synthase inhibitors

Numerous reports have indicated that the plasma concentration of endogenously produced inhibitors of nitric oxide synthase are elevated in human disease states. In this review we discuss recent advances in our understanding of the enzymes responsible for the synthesis of these inhibitors.

DDAH gene and cardiovascular risk

The crucial role of nitric oxide (NO) for normal endothelial function is well known. In many conditions associated with increased risk of cardiovascular diseases such as hypercholesterolemia, hypertension, abdominal obesity, diabetes and smoking, NO biosynthesis is dysregulated, leading to endothelial dysfunction. The growing evidence from animal and human studies indicates that endogenous inhibitors of endothelial NO synthase such as asymmetric dimethylarginine (ADMA) and NG-monomethyl-L-arginine (L-NMMA) are associated with the endothelial dysfunction and potentially regulate NO synthase. The major route of elimination of ADMA is metabolism by the enzymes dimethylarginine dimethylaminohydrolase-1 and -2 (DDAH). In our recent study 16 men with either low or high plasma ADMA concentrations were screened to identify DDAH polymorphisms that could potentially be associated with increased susceptibility to cardiovascular diseases. In that study a novel functional mutation of DDAH-1 was identified; the mutation carriers had a significantly elevated risk for cardiovascular disease and a tendency to develop hypertension. These results confirmed the clinical role of DDAH enzymes in ADMA metabolism. Furthermore, it is possible that more common variants of DDAH genes contribute more widely to increased cardiovascular risk.

Analysis of methylarginine metabolism in the cardiovascular system identifies the lung as a major source of ADMA

Protein arginine methylation is catalyzed by a family of enzymes called protein arginine methyltransferases (PRMTs). Three forms of methylarginine have been identified in eukaryotes: monomethylarginine (l-NMMA), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA), all characterized by methylation of one or both guanidine nitrogen atoms of arginine. l-NMMA and ADMA, but not SDMA, are competitive inhibitors of all nitric oxide synthase isoforms. SDMA is eliminated almost entirely by renal excretion, whereas l-NMMA and ADMA are further metabolized by dimethylarginine dimethylaminohydrolase (DDAH). To explore the interplay between methylarginine synthesis and degradation in vivo, we determined PRMT expression and DDAH activity in mouse lung, heart, liver, and kidney homogenates. In addition, we employed HPLC-based quantification of protein-incorporated and free methylarginine, combined with immunoblotting for the assessment of tissue-specific patterns of arginine methylation. The salient findings of the present investigation can be summarized as follows: 1) pulmonary expression of type I PRMTs was correlated with enhanced protein arginine methylation; 2) pulmonary ADMA degradation was undertaken by DDAH1; 3) bronchoalveolar lavage fluid and serum exhibited almost identical ADMA/SDMA ratios, and 4) kidney and liver provide complementary routes for clearance and metabolic conversion of circulating ADMA. Together, these observations suggest that methylarginine metabolism by the pulmonary system significantly contributes to circulating ADMA and SDMA levels.

Arginine methylation regulates DNA polymerase beta

Alterations in DNA repair lead to genomic instability and higher risk of cancer. DNA base excision repair (BER) corrects damaged bases, apurinic sites, and single-strand DNA breaks. Here, a regulatory mechanism for DNA polymerase beta (Pol beta) is described. Pol beta was found to form a complex with the protein arginine methyltransferase 6 (PRMT6) and was specifically methylated in vitro and in vivo. Methylation of Pol beta by PRMT6 strongly stimulated DNA polymerase activity by enhancing DNA binding and processivity, while single nucleotide insertion and dRP-lyase activity were not affected. Two residues, R83 and R152, were identified in Pol beta as the sites of methylation by PRMT6. Genetic complementation of Pol beta knockout cells with R83/152K mutant revealed the importance of these residues for the cellular resistance to DNA alkylating agent. Based on our findings, we propose that PRMT6 plays a role as a regulator of BER.

Quantitative assessment of arginine methylation in free versus protein-incorporated amino acids in vitro and in vivo using protein hydrolysis and high-performance liquid chromatography

Arginine methylation constitutes a posttranslational modification dependent on the action of protein arginine methyltransferases (PRMTs). Using S-adenosylmethionine as a methyl donor, PRMTs catalyze the formation of monomethylarginine (L-NMMA), asymmetric dimethylarginine (ADMA), or symmetric dimethyl arginine (SDMA). Protein arginine methylation is involved in the regulation of signal transduction, RNA export, and cell proliferation, but a quantitative view of arginine methylation of the cell and tissue proteome remains to be performed. In this study, we developed a high-performance liquid chromatography (HPLC)-based method to accurately quantify methylated arginines in free and protein-incorporated amino acid pools of cell and tissue extracts, using protein precipitation and hydrolysis, HPLC separation, and fluorescence detection for the simultaneous quantification of L-arginine (L-Arg), L-NMMA, ADMA, and SDMA. This method permits accurate assessment of the degree of protein arginine methylation in complex biological samples. Using this method, we determined dynamic changes in protein methylation in vitro in cells subjected to proteasome inhibition. We furthermore demonstrate differential methylation patterns in heart and kidney lysates in vivo. Thus, the described method will greatly facilitate our understanding of the role of arginine methylation in physiology and pathophysiology and of the effects of pharmacological interventions on arginine methylation in select cell culture models.

Homocysteine metabolism, hyperhomocysteinaemia and vascular disease: an overview

Hyperhomocysteinaemia has been regarded as a new modifiable risk factor for atherosclerosis and vascular disease. Homocysteine is a branch-point intermediate of methionine metabolism, which can be further metabolised via two alternative pathways: degraded irreversibly through the transsulphuration pathway or remethylated to methionine by the remethylation pathway. Both pathways are B-vitamin-dependent. Plasma homocysteine concentrations are determined by nongenetic and genetic factors. The metabolism of homocysteine, the role of B vitamins and the contribution of nongenetic and genetic determinants of homocysteine concentrations are reviewed. The mechanisms whereby homocysteine causes endothelial damage and vascular disease are not fully understood. Recently, a link has been postulated between homocysteine, or its intermediates, and an alterated DNA methylation pattern. The involvement of epigenetic mechanisms in the context of homocysteine and atherosclerosis, due to inhibition of transmethylation reactions, is briefly overviewed.

The DDAH-ADMA-NOS Pathway

An increasing number of reports in the literature indicate that endogenously produced inhibitors of nitric oxide synthase (NOS),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.

Asymptomatic Helicobacter pylori infection increases asymmetric dimethylarginine levels in healthy subjects

BACKGROUND

Chronic infections have been demonstrated to be early factors of atherosclerosis and cardiovascular diseases, and their relevance increases when they are caused by agents with extremely broad spectrum of disease outcome such as Helicobacter pylori. The consequent endothelial impairment leads to a reduced bioavailability of nitric oxide. Increasing evidences have pointed out that the endogenous inhibitor of nitric oxide synthase, asymmetric dimethylarginine, defined as a risk factor for cardiovascular disease, may increase in infections and plays an important role impairing the vascular functions of the endothelium. Starting from these findings, we aim to investigate whether H. pylori may affect asymmetric dimethylarginine levels.

MATERIALS AND METHODS

The study was carried out on a group of 186 subjects (age 46.2 +/- 14.9 years). We evaluated asymmetric dimethylarginine, symmetric dimethylarginine, L-arginine, presence of H. pylori by 13C-urea breath test, and the main parameters of glyco and lipo metabolic balance.

RESULTS

Increased levels of asymmetric dimethylarginine were found in H. pylori-positive subjects with respect to H. pylori-negative subjects (0.46 x/ / 1.13 versus 0.42 x/ / 1.23 mol/l, p < .001, respectively). No differences were detected in L-arginine levels between the two groups. Multiple regression analysis performed in H. pylori-positive subjects and H. pylori-negative subjects showed profound differences in the variables related to asymmetric dimethylarginine (R2 = 66.9%, p < .01 versus 34.3%, p < .01, respectively) and symmetric dimethylarginine (R2 = 39.2%, p < .01 versus 20.6%, p = .09, respectively) levels.

CONCLUSIONS

Our data clearly demonstrate that H. pylori infection increases asymmetric dimethylarginine levels. Moreover, this infection causes a profound metabolic modification that alters the role of the known determinants of asymmetric dimethylarginine levels. We conclude that H. pylori infection must be taken into account as a cause of increased asymmetric dimethylarginine levels and that the eradication of H. pylori may therefore lead to a decrease in asymmetric dimethylarginine levels, which is a further reason for the reduction of the risk for cardiovascular disease in this large portion of population.