Post-translational Modification Of Lysine Residues Research Articles

Post-translational modification of lysine residues in erythrocyte α-synuclein.

α-Synuclein is a protein linked to various synuclein-associated diseases ('synucleinopathies'), including Parkinson's disease, dementia with Lewy Bodies and multiple system atrophy, and is highly expressed in the central nervous system and in erythrocytes. Moreover, α-synuclein-containing erythrocyte-derived extracellular vesicles may be involved in the pathogenesis of synucleinopathies and their progression across the blood-brain barrier. Several post-translational modifications of α-synuclein have been reported in brain inclusions, including S129 phosphorylation, but fewer have been found in erythrocytes. In this study, we analysed the post-translational modifications of erythrocyte α-synuclein using liquid chromatography-mass spectrometry. We found that all lysine residues in the α-synuclein protein could be modified by acetylation, glycation, ubiquitination or SUMOylation but that phosphorylation, nitration and acylation were uncommon minor post-translational modifications in erythrocytes. Since the post-translational modification of lysine residues has been implicated in both membrane association and protein clearance, our findings provide new insight into how synucleinopathies may progress and suggest possible therapeutic strategies designed to target α-synuclein.

Incorporating hybrid models into lysine malonylation sites prediction on mammalian and plant proteins

Protein malonylation, a reversible post-translational modification of lysine residues, is associated with various biological functions, such as cellular regulation and pathogenesis. In proteomics, to improve our understanding of the mechanisms of malonylation at the molecular level,the identification of malonylation sites via an efficient methodology is essential. However, experimental identification of malonylated substrates via mass spectrometry is time-consuming, labor-intensive, and expensive. Although numerous methods have been developed to predict malonylation sites in mammalian proteins, the computational resource for identifying plant malonylation sites is very limited. In this study, a hybrid model incorporating multiple convolutional neural networks (CNNs) with physicochemical properties, evolutionary information,and sequenced-based features was developed for identifying protein malonylation sites in mammals. For plant malonylation, multiple CNNs and random forests were integrated into a secondary modeling phase using a support vector machine. The independent testing has demonstrated that the mammalian and plant malonylation models can yield the area under the receiver operating characteristic curves (AUC) at 0.943 and 0.772, respectively. The proposed scheme has been implemented as a web-based tool, Kmalo (https://fdblab.csie.ncu.edu.tw/kmalo/home.html), which can help facilitate the functional investigation of protein malonylation on mammals and plants.

SUMO2 regulates vascular endothelial function and oxidative stress in mice.

SUMOylation is a posttranslational modification of lysine residues. Modification of proteins by small ubiquitin-like modifiers (SUMO)1, -2, and -3 can achieve varied, and often unique, physiological and pathological effects. We looked for SUMO2-specific effects on vascular endothelial function. SUMO2 expression was upregulated in the aortic endothelium of hypercholesterolemic low-density lipoprotein receptor-deficient mice and was responsible for impairment of endothelium-dependent vasorelaxation in these mice. Moreover, overexpression of SUMO2 in aortas ex vivo, in cultured endothelial cells, and transgenically in the endothelium of mice increased vascular oxidative stress and impaired endothelium-dependent vasorelaxation. Conversely, inhibition of SUMO2 impaired physiological endothelium-dependent vasorelaxation in normocholesterolemic mice. These findings indicate that while endogenous SUMO2 is important in maintenance of normal endothelium-dependent vascular function, its upregulation impairs vascular homeostasis and contributes to hypercholesterolemia-induced endothelial dysfunction.NEW & NOTEWORTHY Sumoylation is known to impair vascular function; however, the role of specific SUMOs in the regulation of vascular function is not known. Using multiple complementary approaches, we show that hyper-SUMO2ylation impairs vascular endothelial function and increases vascular oxidative stress, whereas endogenous SUMO2 is essential for maintenance of normal physiological function of the vascular endothelium.

Alteration of global protein SUMOylation in neurons and astrocytes in response to Alzheimer's disease-associated insults

SUMOylation, a post-translational modification of lysine residues by small ubiquitin-like modifier (SUMO) proteins, has been implicated in the pathogenesis of neurodegenerative disorders including Alzheimer's disease (AD), and in neuron- and astrocyte-specific physiological functions. Global SUMOylation is increased in the AD mouse brain in the pre-plaque-forming stage but returns to wild-type levels in the plaque-bearing stage. To clarify the reason for the transient change in SUMOylation, we analyzed the alteration of global SUMOylation induced by AD-associated cytotoxic stimuli in neurons and astrocytes individually. In neurons, amyloid β42 oligomers induced some but not significant increase in levels of SUMO1-modified proteins. Both hydrogen peroxide and glutamate significantly reduced SUMO1-modified protein levels. These changes were more prominent in neurons than in astrocytes. The opposite effect of Aβ and oxidative/excitotoxic stimuli on SUMO1 modification may cause the pathological stage-associated change in the level of SUMO-modified proteins in the AD mouse brain.

Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity.

Ubiquitination is initiated by transfer of ubiquitin (Ub) from a ubiquitin-activating enzyme (E1) to a ubiquitin-conjugating enzyme (E2), producing a covalently linked intermediate (E2-Ub) 1 . Ubiquitin ligases (E3s) of the 'really interesting new gene' (RING) class recruit E2-Ub via their RING domain and then mediate direct transfer of ubiquitin to substrates 2 . By contrast, 'homologous to E6-AP carboxy terminus' (HECT) E3 ligases undergo a catalytic cysteine-dependent transthiolation reaction with E2-Ub, forming a covalent E3-Ub intermediate3,4. Additionally, RING-between-RING (RBR) E3 ligases have a canonical RING domain that is linked to an ancillary domain. This ancillary domain contains a catalytic cysteine that enables a hybrid RING-HECT mechanism 5 . Ubiquitination is typically considered a post-translational modification of lysine residues, as there are no known human E3 ligases with non-lysine activity. Here we perform activity-based protein profiling of HECT or RBR-like E3 ligases and identify the neuron-associated E3 ligase MYCBP2 (also known as PHR1) as the apparent single member of a class of RING-linked E3 ligase with esterification activity and intrinsic selectivity for threonine over serine. MYCBP2 contains two essential catalytic cysteine residues that relay ubiquitin to its substrate via thioester intermediates. Crystallographic characterization of this class of E3 ligase, which we designate RING-Cys-relay (RCR), provides insights into its mechanism and threonine selectivity. These findings implicate non-lysine ubiquitination in cellular regulation ofhigher eukaryotes and suggest that E3 enzymes have an unappreciated mechanistic diversity.

Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH).

Post-translational modification of lysine residues by NƐ-acylation is an important regulator of protein function. Many large-scale protein acylation studies have assessed relative changes of lysine acylation sites after antibody enrichment using mass spectrometry-based proteomics. Although relative acylation fold-changes are important, this does not reveal site occupancy, or stoichiometry, of individual modification sites, which is critical to understand functional consequences. Recently, methods for determining lysine acetylation stoichiometry have been proposed based on ratiometric analysis of endogenous levels to those introduced after quantitative per-acetylation of proteins using stable isotope-labeled acetic anhydride. However, in our hands, we find that these methods can overestimate acetylation stoichiometries because of signal interferences when endogenous levels of acylation are very low, which is especially problematic when using MS1 scans for quantification. In this study, we sought to improve the accuracy of determining acylation stoichiometry using data-independent acquisition (DIA). Specifically, we use SWATH acquisition to comprehensively collect both precursor and fragment ion intensity data. The use of fragment ions for stoichiometry quantification not only reduces interferences but also allows for determination of site-level stoichiometry from peptides with multiple lysine residues. We also demonstrate the novel extension of this method to measurements of succinylation stoichiometry using deuterium-labeled succinic anhydride. Proof of principle SWATH acquisition studies were first performed using bovine serum albumin for both acetylation and succinylation occupancy measurements, followed by the analysis of more complex samples of E. coli cell lysates. Although overall site occupancy was low (<1%), some proteins contained lysines with relatively high acetylation occupancy. Graphical ᅟ Electronic supplementary materialThe online version of this article (doi:10.1007/s13361-016-1476-z) contains supplementary material, which is available to authorized users.

Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins.

Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, over the past decade or so, it has been discovered that posttranslational modification of lysine residues plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases themselves are now known to be ubiquitinated. In the case of human polymerase η, ubiquitination at four lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases η, ι, κ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo.

Abstract 2942: Acetylation of intracellular protein induces apoptotic cell death in Aspirin-treated human breast cancer cells.

Abstract Acetylation is one of the dynamic post-translational modification of lysine residues on protein determining the structure, function and intracellular localization that plays an important role in the signal transduction pathways related to diverse cell functions - proliferation, cell death, and differentiation as well as transcriptional regulation. Recently, it has been reported that acetylating agents including chemical histone deacetylase inhibitors and plant polyphenols lead to the increased acetylation of histone and non-histone proteins, which induces to rapid cancer cell death. In this present study, we are focused on molecular mechanism of cell death in two Aspirin-treated human breast cancer cells, MCF-7 and MDA-MB-231. Trichostatin A (TSA) treatment was combined for maintaining acetylation of intracellular proteins at 0.1 μM concentration, which was not caused cell death itself. It was observed that Aspirin/TSA treatment caused the significant inhibition of cell growth in a dose- and time-dependent manner in both MDA-MB-231 and MCF-7 cells. The induced cell death in MDA-MB-231 by Aspirin/TSA treatment was associated with several specific features of apoptosis, which were proved by biochemical assays containing DNA fragmentation, Annexin V staining and cell cycle analysis. On the other hand, the exposure of MCF-7 to Aspirin/TSA caused necrotic rather than apoptotic mechanism judged by DNA fragmentation assay. These results suggest that different cell death pathway in two breast cancer cell lines is implicated in acetylated protein mediated signals. Previous reports suggest sporadic tumor cell necrosis is associated with extracellular release of cellular protein such as the high mobility group box 1 and may activate innate immune system. Interestingly, we confirmed secretory protein in cell-culture supernatant by immunoprecipitation using anti-acetyllysin antibody. Secretion of the acetylated protein was elevated dose- and time- dependent manner after Asprin treatment. Although extracellular role of the secretory protein in response to acetylation has not been clearly identified yet, this acetylated protein may be involved in initiation of apoptotic cell death signals and/or activating innate immune response. Taken together, theses results indicated that acetylated protein plays an essential role in anti-tumorigenesis in response to acetylating agent such as Aspirin. Citation Format: Yu Ran Lee, Byeong Hwa Jeon, Sunga Choi. Acetylation of intracellular protein induces apoptotic cell death in Aspirin-treated human breast cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2942. doi:10.1158/1538-7445.AM2013-2942 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Gains of ubiquitylation sites in highly conserved proteins in the human lineage

BackgroundPost-translational modification of lysine residues of specific proteins by ubiquitin modulates the degradation, localization, and activity of these target proteins. Here, we identified gains of ubiquitylation sites in highly conserved regions of human proteins that occurred during human evolution.ResultsWe analyzed human ubiquitylation site data and multiple alignments of orthologous mammalian proteins including those from humans, primates, other placental mammals, opossum, and platypus. In our analysis, we identified 281 ubiquitylation sites in 252 proteins that first appeared along the human lineage during primate evolution: one protein had four novel sites; four proteins had three sites each; 18 proteins had two sites each; and the remaining 229 proteins had one site each. PML, which is involved in neurodevelopment and neurodegeneration, acquired three sites, two of which have been reported to be involved in the degradation of PML. Thirteen human proteins, including ERCC2 (also known as XPD) and NBR1, gained human-specific ubiquitylated lysines after the human-chimpanzee divergence. ERCC2 has a Lys/Gln polymorphism, the derived (major) allele of which confers enhanced DNA repair capacity and reduced cancer risk compared with the ancestral (minor) allele. NBR1 and eight other proteins that are involved in the human autophagy protein interaction network gained a novel ubiquitylation site.ConclusionsThe gain of novel ubiquitylation sites could be involved in the evolution of protein degradation and other regulatory networks. Although gains of ubiquitylation sites do not necessarily equate to adaptive evolution, they are useful candidates for molecular functional analyses to identify novel advantageous genetic modifications and innovative phenotypes acquired during human evolution.

A method to distinguish between lysine acetylation and lysine methylation from protein sequences

Lysine acetylation and methylation are two major post-translational modifications of lysine residues. They play vital roles in both biological and pathological processes. Specific lysine residues in H3 histone protein tails appear to be targeted for either acetylation or methylation. Hence it is very challenging to distinguish between acetylated and methylated lysine residues using computational methods. This work presents a method that incorporates protein sequence information, secondary structure and amino acid properties to differentiate acetyl-lysine from methyl-lysine. We apply an encoding scheme based on grouped weight and position weight amino acid composition to extract sequence information and physicochemical properties around lysine sites. The proposed method achieves an accuracy of 93.3% using a jackknife test. Feature analysis demonstrates that the prediction model with multiple features can take full advantage of the supplementary information from different features to improve classification performance and prediction robustness. Analysis of the characteristics of lysine residues which can be either methylated or acetylated shows that they are more similar to methyl-lysine than to acetyl-lysine.

Acetylation Versus Ubiquitination

Posttranslational modification of lysine residues is an important regulatory mechanism controlling protein activity and stability. Giandomenico et al. report that the activity of transcription factors of the sterol regulatory element binding protein (SREBP) family is increased by acetylation of a residue that can also be the target for ubiquitin conjugation, which promotes proteasome-mediated degradation. The histone acetylase and transcriptional cofactors p300 and CBP interacted with SREBP1 and 2 and acetylated these proteins in vitro and in vivo. The major residue acetylated, based on mutational analysis of SREBP1, was K 333 in the DNA binding domain; however, acetylation did not inhibit DNA binding. Mutation of K 333 decreased both acetylation and ubiquitination of SREBP1. In vitro, acetylation decreased ubiquitination of SREBP1, suggesting that this lysine may be the target for both types of posttranslational modifications. Coexpression of p300 with SREBP1 yielded increased levels of SREBP1, and expression of a K333Q mutant showed increased cholesterol synthesis activity compared to expression of wild-type SREBP in transfected cells. Thus, acetylation and ubiquitination may be competing reactions controlling the stability and activity of transcription factors, such as SREBPs. V. Giandomenico, M. Simonsson, E. Grönroos, J. Ericsson, Coactivator-dependent acetylation stabilizes members of the SREBP family of transcription factors. Mol. Cell. Biol. 23 , 2587-2599 (2003). [Abstract] [Full Text]

In vivo carbamylation and acetylation of water-soluble human lens alphaB-crystallin lysine 92.

Several post-translational modifications of lysine residues of lens proteins have been implicated in cataractogenesis. In the present study, the molecular weight of an alpha-crystallin isolated from the water-soluble portion of a cataractous human eye lens indicated that it was a modified alphaB-crystallin. Further analysis by mass spectrometry of tryptic digests of this modified protein showed that Lys 92 was modified and that the sample was structurally heterogeneous. Lys 92 was acetylated in one population and carbamylated in another. Although carbamylation of lens crystallins has been predicted, this is the first documentation of in vivo carbamylation of a specific site. These results are also the first documentation of in vivo lysine acetylation of alphaB-crystallin. Both modifications alter the net charge on alphaB-crystallin, a feature that may have significance to cataractogenesis.

Collagen Biosynthesis in Systemic Scleroderma: Regulation of Posttranslational Modifications and Synthesis of Procollagen in Cultured Fibroblasts

Activities of prolyl hydroxylase (PH), lysyl hydroxylase (LH), and the collagen glycosyltransferases and the extent of the posttranslational modification of lysine residues in newly synthesized collagen were studied in fibroblast cultures obtained from 9 scleroderma patients. The rate of procollagen synthesis had increased more than 3-fold in 3 scleroderma fibroblast lines, but had not changed to the same extent in the others, even though these did not differ from the "high-producers" histologically, clinically, or immunohistologically. The activities of PH and LH correlated significantly with the rate of procollagen synthesis in the same cell lines (p less than 0.001), but the glycosyltransferase activities were not elevated in the scleroderma fibroblasts. Further studies nevertheless indicated that the extent of the posttranslational modification of lysine residues had not significantly changed in the procollagen synthesized by any of the scleroderma fibroblasts investigated.

Aging, and crosslinking in mammalian collagen

The amount and type of borohydride-reducible crosslinks in collagen have been examined as a function of animal age. In a variety of bovine, canine and human tissues the level of redicible crosslinks decreases with time and the ratios of individual compounds change. There is both tissue and species specificity in the extent of these changes. A decrease in the level of reducible crosslinks correlates with the cessation of growth. Loss of reducible crosslinks does not imply a small total number of crosslinks since physical changes with age imply the opposite. We conclude that reducible crosslinks are converted to a stable nonreducible state and the persistence of low levels of reducible crosslinks may be indicative of a low level of turnover in the tissue. Changes in ratios of reducible crosslinks are of doubtful functioal significance and may simply reflect variation in post-translational modification of lysine residues.