Post-translational myristoylation: Fat matters in cellular life and death

Myristoylation corresponds to the irreversible covalent linkage of the 14-carbon saturated fatty acid, myristic acid, to the N-terminal glycine of many eukaryotic and viral proteins. It is catalyzed by N-myristoyltransferase. Typically, the myristate moiety participates in protein subcellular localization by facilitating protein-membrane interactions as well as protein-protein interactions. Myristoylated proteins are crucial components of a wide variety of functions, which include many signalling pathways, oncogenesis or viral replication. Initially, myristoylation was described as a co-translational reaction that occurs after the removal of the initiator methionine residue. However, it is now well established that myristoylation can also occur post-translationally in apoptotic cells. Indeed, during apoptosis hundreds of proteins are cleaved by caspases and in many cases this cleavage exposes an N-terminal glycine within a cryptic myristoylation consensus sequence, which can be myristoylated. The principal objective of this review is to provide an overview on the implication of myristoylation in health and disease with a special emphasis on post-translational myristoylation. In addition, new advancements in the detection and identification of myristoylated proteins are also briefly reviewed.     

Rational design and synthesis of potent aminoglycoside antibiotics against resistant bacterial strains

Based on the structural information of biomacromolecule-aminoglycoside complexes, a series of kanamycin B analogues were rationally designed and synthesized. A convenient approach to the construction of kanamycin derivatives, in which the C4′-position on ring I of neamine moiety was modified, was developed. Most synthetic analogues exhibited good to excellent antibiotic activity against some typical drug-resistant bacteria. The disclosed results suggested that the C4′-position of aminoglycosides such as kanamycin may be an ideal site for modification to gain new modifying enzyme-resistant aminoglycoside antibiotics.     

Advances in fungal proteomics

Proteomics, the global analysis of proteins, will contribute greatly to our understanding of gene function in the post-genomic era. This review summarizes recent developments in fungal proteomics and also generalizes protocols for sample preparation from plant pathogenic fungi. Challenges and future perspectives of proteomics are discussed as well.     

Protein Arginylation in Rat Brain Cytosol: A Proteomic Analysis

Arginine can be post-translationally incorporated from arginyl-tRNA into the N-terminus of soluble acceptor proteins in a reaction catalyzed by arginyl-tRNA protein transferase. In the present study, several soluble rat brain proteins that accepted arginine were identified after arginine incorporation by two dimensional electrophoresis and mass spectrometry. They were identified as: contrapsin-like protease inhibitor-3, α-1-antitrypsin, apolipoprotein E, hemopexin, calreticulin and apolipoprotein A-I. All of these proteins shared a signal sequence for the translocation of proteins across endoplasmic reticulum membranes. After losing the signal peptide, these proteins expose amino acids described as compatible for post-translational arginylation. Although the enzymatic system involved in arginylation is confined mainly in cytosol and nucleus, all the substrates described herein enter to the exocytic pathway co-translationally. Therefore, we postulate that the substrates for arginylation could reach the cytosol by retro-translocation and be then arginylated.     

Protein myristoylation in protein-lipid and protein-protein interactions

Various proteins in signal transduction pathways are myristoylated. Although this modification is often essential for the proper functioning of the modified protein, the mechanism by which the modification exerts its effects is still largely unknown. Here we discuss the roles played by protein myristoylation, in both protein-lipid and protein-protein interactions. Myristoylation is involved in the membrane interactions of various proteins, such as MARCKS and endothelial NO synthase. The intermediate hydrophobic nature of the modification plays an important role in the reversible membrane anchoring of these proteins. The anchoring is strengthened by a basic amphiphilic domain that works as a switch for the reversible binding. Protein myristoylation is also involved in protein-protein interactions, which are regulated by the interplay between protein phosphorylation, calmodulin binding, and membrane phospholipids.     

Identification of Novel Protein Targets of Dimethyl Fumarate Modification in Neurons and Astrocytes Reveals Actions Independent of Nrf2 Stabilization

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Highlights

• •Dimethyl fumarate covalently modifies cysteine residues in neurons and astrocytes.
• •Cofilin-1, tubulin and collapsin response mediator protein 2 (CRMP2) are targets.
• •DMF-modified cofilin-1 reduces actin-severing ability, preserving filamentous actin.

     

A chemical field guide to histone nonenzymatic modifications

Histone nonenzymatic covalent modifications (NECMs) have recently emerged as an understudied class of posttranslational modifications that regulate chromatin structure and function. These NECMs alter the surface topology of histone proteins, their interactions with DNA and chromatin regulators, as well as compete for modification sites with enzymatic posttranslational modifications. NECM formation depends on the chemical compatibility between a reactive molecule and its target site, in addition to their relative stoichiometries. Here we survey the chemical reactions and conditions that govern the addition of NECMs onto histones as a manual to guide the identification of new physiologically relevant chemical adducts. Characterizing NECMs on chromatin is critical to attain a comprehensive understanding of this new chapter of the so-called “histone code”.     

The myristoylation site of meiotic lamin C2 promotes local nuclear membrane growth and the formation of intranuclear membranes in somatic cultured cells

Lamin C2 is a splice product of the mammalian lamin A gene and expressed in primary spermatocytes where it is distributed in the form of discontinuous plaques at the nuclear envelope. We have previously shown that the aminoterminal hexapetide GNAEGR of lamin C2 following the start methionine is essential for its association with the nuclear envelope and that the aminoterminal glycine of the hexapeptide is myristoylated. Here we have analyzed the ultrastructural changes induced in COS-7 and Xenopus A6 cells by overexpressing rat lamin C2 or a human lamin C mutant possessing the lamin C2-specific hexapeptide at its aminoterminus. Both lamins were targeted to the nuclear envelope of mammalian and amphibian cells and induced the formation of intranuclear membranes, whereas wild-type human lamin C and a lamin C2 mutant, that both lack this lipid moiety, did not. Our data indicate that the myristoyl group of lamin C2 has besides its demonstrated role in nuclear envelope association additional functions during spermatogenesis. Our present study complements previously published results where we have shown that the CxxM motif of lamins promotes nuclear membrane growth (Prüfert et al., 2004. J. Cell Sci. 117, 6105-6116).     

Machine learning for target discovery in drug development

The discovery of macromolecular targets for bioactive agents is currently a bottleneck for the informed design of chemical probes and drug leads. Typically, activity profiling against genetically manipulated cell lines or chemical proteomics is pursued to shed light on their biology and deconvolute drug–target networks. By taking advantage of the ever-growing wealth of publicly available bioactivity data, learning algorithms now provide an attractive means to generate statistically motivated research hypotheses and thereby prioritize biochemical screens. Here, we highlight recent successes in machine intelligence for target identification and discuss challenges and opportunities for drug discovery.     

Single-step purification of myristoylated and nonmyristoylated recoverin and substrate dependence of myristoylation level

Recoverin is cotranslationally modified by the covalent linkage of a myristoyl group to its N terminus. It is a member of a family of Ca(2+)-myristoyl switch proteins. Recombinant myristoylated revoverin is currently produced by the cotransformation of bacteria with recoverin and an enzyme that allows N-myristoylation and by supplementing the culture medium with myristic acid. A large variation in the myristoylation level of recoverin and in the amount of myristic acid supplied to the culture medium can be found in the literature. Moreover, although it is known to strongly affect bacterial growth, the amount of ethanol used to solubilize myristic acid is only scarcely mentioned. To improve our understanding of the parameters responsible for recombinant recoverin myristoylation, the effects of myristic acid and ethanol on recoverin myristoylation and expression levels have been systematically studied. In addition, a single-step purification procedure to produce purified myristoylated and nonmyristoylated recombinant recoverin has also been devised. Finally, sodium myristate has been used as an efficient alternative substrate to achieve high myristoylation and expression levels of recoverin. Given that a large number of proteins are myristoylated, these procedures could be applied to several other proteins in addition to recoverin.     

Protein acylation and localization in T cell signaling (Review)

Many proteins with pivotal roles in T cell activation are modified by fatty acylation. Examples of these include transmembrane proteins such as the co-receptors CD4 and CD8, the adaptors LAT and Cbp/PAG, the pre-TCR as well as proteins synthesized on free cytosolic ribosomes, such as the Src-related tyrosine kinases Lck and Fyn. The two main types of fatty acylations in eukaryotic cells are N-myristoylation and S-acylation, the latter being more commonly referred to as palmitoylation. N-Myristoylation occurs exclusively on proteins synthesized on soluble ribosomes and provides substrates with an affinity for membranes. Palmitoylation modifies a wide range of substrates that includes both cytosolic and transmembrane proteins, its functions are diverse and in many cases not yet understood. Like myristoylation, palmitoylation promotes membrane-binding of cytosolic proteins, but it has also been implicated in protein targeting, trafficking, stability and activity. In addition, many palmitoylated proteins are insoluble in cold non-ionic detergent, and have therefore been proposed to localize to lipid rafts. The organization of receptors and signaling proteins into microdomains such as lipid rafts provides an attractive model for the initiation and propagation of T cell signaling, although many aspects of this are still poorly understood. This review will discuss the current evidence for the involvement of acylations in the localizations and functions of T cell signaling proteins.     

新型蛋白质修饰剂的合成及修饰牛血红蛋白的初步研究

以L-谷氨酸和己二酸为原料合成了一种新型的四官能团蛋白质修饰剂,并用核磁共振和红外光谱对其结构进行了表征。然后以其为修饰剂,对牛血红蛋白的化学修饰进行了初步的研究,并通过高效液相色谱、聚丙烯酰胺凝胶电泳和血氧分析仪对交联牛血红蛋白的分子量和携氧性能进行了表征。结果表明,该修饰剂可以使牛血红蛋白同时在分子内和分子间发生化学交联,并较好地保持携氧能力（P50:21.7mmHg,Hill系数:2.01）,因此在众多用于开发人工血液代用品的化学修饰剂中该修饰剂具有良好的应用前景。     

Characterizing disease-associated changes in post-translational modifications by mass spectrometry

Introduction: Exploring post-translational modifications (PTMs) with the use of mass spectrometry (PTMomics) is a rapidly developing area, with methods for discovery/quantification being developed and advanced on a regular basis. PTMs are highly important for the regulation of protein function, interaction and activity, both in physiological and disease states. Changes in PTMs can either cause, or be the result of a disease, making them central for biomarker studies and studies of disease pathogenesis. Recently, it became possible to study multiple PTMs simultaneously from low amount of sample material, thereby increasing coverage of the PTMome obtainable from a single sample. Thus, quantitative PTMomics holds great potential to discover biomarkers from tissue and body fluids as well as elucidating disease mechanisms through characterization of signaling pathways.

Areas covered: Recent mass spectrometry-based methods for assessment of the PTMome, with focus on the most studied PTMs, are highlighted. Furthermore, both data dependent and data independent acquisition methods are evaluated. Finally, current challenges in the field are discussed.

Expert commentary: PTMomics holds great potential for clinical and biomedical research, especially with the generation of spectral libraries of peptides and PTMs from individual patients (permanent PTM maps) for use in personalized medicine.     

Protein glutathionylation in health and disease

Background

It is now recognized that protein cysteines exist not only as free thiols or intramolecular disulfides, that help maintain the 3D structure of proteins, but can also undergo different types of oxidation, one of which is glutathionylation, or the formation of mixed disulfides with glutathione (GSH).

Scope of the review

We will discuss how proteins can undergo glutathionylation and how this can affect the protein characteristics/function. Glutathionylation is reversible and de-glutathionylation can be catalysed by protein thiol–disulfide oxidoreductases. Genetic modification of the expression of these enzymes, particularly glutaredoxin, using overexpression, knockout mice or siRNA, is becoming an important tool to study the role of protein glutathionylation. While in the past this post-translational modification was mainly known in the context of oxidative stress, measurement of glutathionylated proteins in patients is pointing out a potential importance if this modification in pathogenesis and could identify new biomarkers. We also wanted to point out the main findings in the role of glutathionylation in diseases and drug action.

Major conclusions

We identify two major open problems in the field, namely the complexity of the mechanisms responsible for glutathionylation and de-glutathionylation, as well as what makes a protein susceptible to glutathionylation.

General significance

This review underlines the peculiarities of this post-translational modification and their biological role. This article is part of a Special Issue entitled Cellular functions of glutathione.     

Robust in-gel fluorescence detection of mucin-type O-linked glycosylation

Mucin-type O-linked glycosylation is a common post translational modification of cell-surface and secretory pathway proteins and is implicated in vital biological processes as well as human disease. We report here the use of the metabolic chemical reporter GalNAz along with Cu(I)-catalyzed [3+2] azide-alkyne cycloaddition conditions for the robust, in-gel fluorescent visualization of mucin-type O-linked glycoproteins.     

Post-translational modifications of ATP synthase in the heart: biology and function

The ATP synthase complex is a critical enzyme in the energetic pathways of cells because it is the enzyme complex that produces the majority of cellular ATP. It has been shown to be involved in several cardiac phenotypes including heart failure and preconditioning, a cellular protective mechanism. Understanding the regulation of this enzyme is important in understanding the mechanisms behind these important phenomena. Recently there have been several post-translational modifications (PTM) reported for various subunits of this enzyme complex, opening up the possibility of differential regulation by these PTMs. Here we discuss the known PTMs in the heart and other mammalian tissues and their implication to function and regulation of the ATP synthase.     

泛醌结合蛋白（QPs）羧基的化学修饰与重组活性

研究了羧基修饰剂ＤＣＣＤ对泛醌结合蛋白ＱＰｓ重组活力的影响;用０．１％ＴｒｉｔｏｎＸ－１００增溶ＱＰｓ后,用２５０ｍｏｌ／ｍｏｌＱＰｓ的ＤＣＣＤ于室温处理５ｍｉｎ,处理后的ＱＰｓ丧失约５０％与琥珀酸脱氢酶的重组活力。先将ＱＰｓ与琥珀酸脱氢酶重组再用ＤＣＣＤ处理没有发现重组的琥珀酸泛醌还原酶活性的降低。此结果说明ＱＰｓ中存在重组活性必需的羧基。     

motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs

With an exponential growth in applications identifying protein post‐translational modifications via mass spectrometry, discovery and presentation of motifs surrounding those modification sites have become increasingly desirable. Despite a few tools being designed, there is still a scarcity of effective and polyfunctional software for such analysis and illustrations. In this study, a versatile and user‐friendly web tool is developed, motifeR, for extracting and visualizing statistically significant motifs from large datasets. Particularly, several functions are also integrated for processing multi‐modification sites enrichment. Public datasets are applied to test their usability, indicating that some concurrent modification sites may form motifs and that peptides with low location probability may be not identified randomly and can be included to support motif discovery. In addition, for human phosphoproteomics datasets, the characterization of differential kinase signaling networks can be estimated and modeled by combining kinase‐substrate relations based on the NetworKIN database as an optional feature for users. The motifeR toolkit can be conveniently operated by any scientific community or individuals, even those without any bioinformatics background and is freely available at https://www.omicsolution.org/wukong/motifeR .