A chemical proteomics approach for global analysis of lysine monomethylome profiling.

Methylation of lysine residues on histone proteins is known to play an important role in chromatin structure and function. However, non-histone protein substrates of this modification remain largely unknown. An effective approach for system-wide analysis of protein lysine methylation, particularly lysine monomethylation, is lacking. Here we describe a chemical proteomics approach for global screening for monomethyllysine substrates, involving chemical propionylation of monomethylated lysine, affinity enrichment of the modified monomethylated peptides, and HPLC/MS/MS analysis. Using this approach, we identified with high confidence 446 lysine monomethylation sites in 398 proteins, including three previously unknown histone monomethylation marks, representing the largest data set of protein lysine monomethylation described to date. Our data not only confirms previously discovered lysine methylation substrates in the nucleus and spliceosome, but also reveals new substrates associated with diverse biological processes. This method hence offers a powerful approach for dynamic study of protein lysine monomethylation under diverse cellular conditions and in human diseases.

Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation.

The protein substrates of sirtuin 5-regulated lysine malonylation (Kmal) remain unknown, hindering its functional analysis. In this study, we carried out proteomic screening, which identified 4042 Kmal sites on 1426 proteins in mouse liver and 4943 Kmal sites on 1822 proteins in human fibroblasts. Increased malonyl-CoA levels in malonyl-CoA decarboxylase (MCD)-deficient cells induces Kmal levels in substrate proteins. We identified 461 Kmal sites showing more than a 2-fold increase in response to MCD deficiency as well as 1452 Kmal sites detected only in MCD-/- fibroblast but not MCD+/+ cells, suggesting a pathogenic role of Kmal in MCD deficiency. Cells with increased lysine malonylation displayed impaired mitochondrial function and fatty acid oxidation, suggesting that lysine malonylation plays a role in pathophysiology of malonic aciduria. Our study establishes an association between Kmal and a genetic disease and offers a rich resource for elucidating the contribution of the Kmal pathway and malonyl-CoA to cellular physiology and human diseases.

Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli.

Lysine succinylation is a newly identified protein post-translational modification pathway present in both prokaryotic and eukaryotic cells. However, succinylation substrates and regulatory enzyme(s) remain largely unknown, hindering the biological study of this modification. Here we report the identification of 2,580 bacterial lysine succinylation sites in 670 proteins and 2,803 lysine acetylation (Kac) sites in 782 proteins, representing the first lysine succinylation dataset and the largest Kac dataset in wild-type E. coli. We quantified dynamic changes of the lysine succinylation and Kac substrates in response to high glucose. Our data showed that high-glucose conditions led to more lysine-succinylated proteins and enhanced the abundance of succinyllysine peptides more significantly than Kac peptides, suggesting that glucose has a more profound effect on succinylation than on acetylation. We further identified CobB, a known Sir2-like bacterial lysine deacetylase, as the first prokaryotic desuccinylation enzyme. The identification of bacterial CobB as a bifunctional enzyme with lysine desuccinylation and deacetylation activities suggests that the eukaryotic Kac-regulatory enzymes may have enzymatic activities on various lysine acylations with very different structures. In addition, it is highly likely that lysine succinylation could have unique and more profound regulatory roles in cellular metabolism relative to lysine acetylation under some physiological conditions.

SAHA regulates histone acetylation, Butyrylation, and protein expression in neuroblastoma.

Emerging evidence suggests that suberoylanilide hydroxamic acid (SAHA), a clinically approved HDAC inhibitor for cutaneous T-cell lymphoma, shows promising clinical benefits in neuroblastoma, the most common extra cranial solid neoplasm with limited choice of therapeutic intervention. However, the molecular mechanism under which the compound exerts its antitumor effect remains elusive. Here we report a quantitative proteomics study that determines changes of protein expression, histone lysine acetylation, and butyrylation in response to SAHA treatment. We detected and quantified 28 histone lysine acetylation and 18 histone lysine butyrylation marks, most of which are dramatically induced by SAHA. Importantly, we identified 11 histone Kbu sites as novel histone marks in human cells. Furthermore, quantitative proteomic analysis identified 5426 proteins, among which 510 proteins were up-regulated and 508 proteins were down-regulated (significant p value <0.05). The subsequent bioinformatics analysis identified distinct SAHA-response gene ontology (GO) categories and signaling pathways, including cellular metabolism and DNA-dependent pathways. Our study therefore reveals new histone epigenetic marks and offers key insights into the molecular mechanism by which SAHA regulates proteomic changes in neuroblastoma cells and identifies biomarker candidates for SAHA.

Analysis of PAEs in semen of infertile men.

OBJECTIVES: Phthalates are environmental chemicals with reproductive toxicity and estrogenic effects in animals. They are of increasing concern to human health. AIM: To determine whether phthalate levels in semen were associated with infertility. METHODS: Using semen samples from 107 infertile and 94 fertile men, the presence and quantity of five phthalate esters were measured using high-performance liquid chromatography (HPLC). Using data collected from questionnaires and clinical examinations, the correlation between phthalate exposure and semen quality was analyzed. RESULTS: The cumulative levels of the measured phthalate esters were significantly higher in the infertility group compared to the control group (P<0·05). Concentrations of the five phthalate esters in men varied by age with older men showing higher cumulative levels. CONCLUSIONS: The presence of phthalates may contribute to male infertility in our study population.

Serum fatty acid profiles using GC-MS and multivariate statistical analysis: potential biomarkers of Alzheimer's disease.

Previous studies showed the relationship between fatty acids and the risk of developing Alzheimer's disease (AD). However, they did not address potential differences in free fatty acid (FFA) profiles that could be used to distinguish between AD patients and healthy controls. In the present study we used gas chromatography-mass spectrometry (GC-MS) technology coupled with multivariate statistical analysis to study profiles of FFA in AD. The results indicated 2 saturated fatty acids (C14:0 and C16:0; p < 0.001 and p < 0.05, respectively), 3 unsaturated fatty acids (C18:1, C18:3, and C22:6; p < 0.05, p < 0.05, and p < 0.001, respectively), where mean levels in serum from AD patients were significantly lower than controls. Partial least squares discriminant analysis (PLS-DA) models with unit variance (UV) scaling and orthogonal signal correction (OSC) data preprocessing methods were employed to refine intergroup differences between FFA profiles. The results of the analysis have highlighted docosahexaenoic acid (DHA) as the FFA with the greatest potential as a biomarker of AD, and this study has demonstrated that FFA biomarkers have considerable potential in diagnosing and monitoring AD.