蛋白质翻译后修饰调控HIV-1潜伏感染

艾滋病是一种由人类免疫缺陷病毒 （HIV） 引起的获得性免疫缺陷综合征。HIV 可分为 HIV-1 型和 HIV-2 型。 HIV-1全球流行,造成严重的危害。尽管抗逆转录病毒联合疗法 （cART） 的应用可以延长患者寿命,但HIV-1感染目前仍然不能完全治愈。HIV-1感染治愈最主要的障碍就是病毒潜伏库的存在。HIV-1潜伏库可以被定义为一群携带具备复制潜力的 HIV-1前病毒的长寿命静息 CD4⁺ T 细胞。蛋白质翻译后修饰使得病毒蛋白和宿主细胞蛋白形成了更复杂的相互作用网络。 HIV-1潜伏库的形成与调控,也与病毒和宿主蛋白的翻译后修饰密切相关。因此,本文将从病毒蛋白和宿主蛋白翻译后修饰的角度阐述HIV-1潜伏的建立与调控的机制。这将有助于HIV-1治疗新靶点的探索和研发,并有利于实现HIV-1感染的功能性治愈目标。最后,本文还会综述有关以蛋白质翻译后修饰为靶点的HIV-1药物研究进展,为后续HIV-1治疗药物的研发提供思路和启发。     

Epigenetic control of B cell differentiation

Gene expression, differentiation and the specialized function of various cell types are controlled epigenetically by post-translational histone modifications. These modifications establish a "histone code" that is recognized by various regulatory proteins, thereby creating a stable pattern of gene expression. The focus of this review is to discuss how the chromatin modifications regulate immunoglobulin gene rearrangement and B cell differentiation.     

Tyrosine modifications in aging

Abstract Significance: The understanding of physiological and pathological processes involving protein oxidation, particularly under conditions of aging and oxidative stress, can be aided by proteomic identification of proteins that accumulate oxidative post-translational modifications only if these detected modifications are connected to functional consequences. The modification of tyrosine (Tyr) residues can elicit significant changes in protein structure and function, which, in some cases, may contribute to biological aging and age-related pathologies, such as atherosclerosis, neurodegeneration, and cataracts. Recent Advances: Studies characterizing proteins in which Tyr has been modified to 3-nitrotyrosine, 3,4-dihydroxyphenylalanine, 3,3'-dityrosine and other cross-links, or 3-chlorotyrosine are reviewed, with an emphasis on structural and functional consequences. Critical Issues: Distinguishing between inconsequential modifications and functionally significant ones requires careful biochemical and biophysical analysis of target proteins, as well as innovative methods for isolating the effects of the multiple modifications that often occur under oxidizing conditions. Future Directions: The labor-intensive task of isolating and characterizing individual modified proteins must continue, especially given the expanding list of known modifications. Emerging approaches, such as genetic and metabolic incorporation of unnatural amino acids, hold promise for additional focused studies of this kind. Antioxid. Redox Signal. 17, 1571-1579.     

Macromolecular deterioration as the ultimate constraint on human lifespan

A number of tissues and organs in the human body contain abundant proteins that are long-lived. This includes the heart, lung, brain, bone and connective tissues. It is proposed that the accumulation of modifications to such long-lived proteins over a period of decades alters the properties of the organs and tissues in which they reside. Such insidious processes may affect human health, fitness and ultimately may limit our lifespan. The human lens, which contains proteins that do not turnover, is used to illustrate the impact of these gradual deleterious modifications. On the basis of data derived from the lens, it is postulated that the intrinsic instability of certain amino acid residues, which leads to truncation, racemisation and deamidation, is primarily responsible for the age-related deterioration of such proteins. Since these post-translational modifications accumulate over a period of many years, they can only be studied using organisms that have lifespans measured in decades. One conclusion is that there may be important aspects of human aging that can be studied only using long-lived animals.     

The immune response to citrullinated antigens in autoimmune diseases

Post-translational modifications of proteins occur very frequently. One of these modifications, citrullination, is the result of arginine deimination operated by an enzyme, peptidylarginine deiminase (PAD), whose activity is under strict genetic control. Serum antibodies reactive with citrullinated proteins/peptides are a very sensitive and specific marker for rheumatoid arthritis. Genes encoding for PAD enzymes have been investigated in RA: the PADI4 gene confers susceptibility to RA in Japanese patients, but not in Caucasians.     

Post-translational protein modifications in antigen recognition and autoimmunity

It is estimated that 50-90% of the proteins in the human body are post-translationally modified. In the proper context, these modifications are necessary for the biological functions of a vast array of proteins and the effector functions of the cells in which they reside. However, it is now clear that some post-translational modifications can create new self antigens (Ags) or even mask Ags normally recognized by the immune system. In either case, they profoundly affect the recognition of Ag by bone marrow-derived cells, as well as their effector functions. How do post-translational protein modifications affect the processing of foreign and self Ags and what is their role in the origin of autoimmune responses?     

Detection of kynurenine modifications in proteins using a monoclonal antibody

N-formylkynurenine and kynurenine are oxidation products of tryptophan formed from the reaction catalyzed by indoleamine 2,3-dioxygenase. These kynurenines react with proteins to produce chemical modifications in the lens. We developed a novel monoclonal antibody that detects a kynurenine modification in proteins. The antibody recognized proteins (human lens proteins, RNase A and BSA) that were modified by either kynurenine or N-formylkynurenine. The antibody also reacted strongly with N-formylkynurenine-modified N(alpha)-acetyl histidine and weakly with N-formylkynurenine-modified N(alpha)-acetyl lysine, N(alpha)-acetyl cysteine and N(alpha)-acetyl arginine. The antibody recognized kynurenine and N-formylkynurenine but not other tryptophan oxidation products. We isolated and purified a major antigen from the reaction mixture of N(alpha)-acetyl histidine and N-formylkynurenine and identified the product as N-acetyl-1-[3-(2-aminophenyl)-1-carboxy-3-oxopropyl]-histidine. We then used our purified antibody to detect kynurenine modifications in kynurenine-treated human lens epithelial cells and human lens. We found epithelial immunoreactivity in a lens from an aged donor but not in one from a very young donor. This would suggest that the antibody detects age-related changes in lens proteins altered by kynurenines. We believe that our antibody could be used to establish the importance of kynurenine modifications in diseases where tryptophan oxidation is enhanced.     

Post-translational modifications of TRF1 and TRF2 and their roles in telomere maintenance

Telomeres, heterochromatic structures, found at the ends of linear eukaryotic chromosomes, function to protect natural chromosome ends from nucleolytic attack. Human telomeric DNA is bound by a telomere-specific six-subunit protein complex, termed shelterin/telosome. The shelterin subunits TRF1 and TRF2 bind in a sequence-specific manner to double-stranded telomeric DNA, providing a vital platform for recruitment of additional shelterin proteins as well as non-shelterin factors crucial for the maintenance of telomere length and structure. Both TRF1 and TRF2 are engaged in multiple roles at telomeres including telomere protection, telomere replication, sister telomere resolution and telomere length maintenance. Regulation of TRF1 and TRF2 in these various processes is controlled by post-translational modifications, at times in a cell-cycle-dependent manner, affecting key functions such as DNA binding, dimerization, localization, degradation and interactions with other proteins. Here we review the post-translational modifications of TRF1 and TRF2 and discuss the mechanisms by which these modifications contribute to the function of these two proteins.     

Structure and functions of keratin proteins in simple, stratified, keratinized and cornified epithelia

Historically, the term ‘keratin’ stood for all of the proteins extracted from skin modifications, such as horns, claws and hooves. Subsequently, it was realized that this keratin is actually a mixture of keratins, keratin filament‐associated proteins and other proteins, such as enzymes. Keratins were then defined as certain filament‐forming proteins with specific physicochemical properties and extracted from the cornified layer of the epidermis, whereas those filament‐forming proteins that were extracted from the living layers of the epidermis were grouped as ‘prekeratins’ or ‘cytokeratins’. Currently, the term ‘keratin’ covers all intermediate filament‐forming proteins with specific physicochemical properties and produced in any vertebrate epithelia. Similarly, the nomenclature of epithelia as cornified, keratinized or non‐keratinized is based historically on the notion that only the epidermis of skin modifications such as horns, claws and hooves is cornified, that the non‐modified epidermis is a keratinized stratified epithelium, and that all other stratified and non‐stratified epithelia are non‐keratinized epithelia. At this point in time, the concepts of keratins and of keratinized or cornified epithelia need clarification and revision concerning the structure and function of keratin and keratin filaments in various epithelia of different species, as well as of keratin genes and their modifications, in view of recent research, such as the sequencing of keratin proteins and their genes, cell culture, transfection of epithelial cells, immunohistochemistry and immunoblotting. Recently, new functions of keratins and keratin filaments in cell signaling and intracellular vesicle transport have been discovered. It is currently understood that all stratified epithelia are keratinized and that some of these keratinized stratified epithelia cornify by forming a Stratum corneum. The processes of keratinization and cornification in skin modifications are different especially with respect to the keratins that are produced. Future research in keratins will provide a better understanding of the processes of keratinization and cornification of stratified epithelia, including those of skin modifications, of the adaptability of epithelia in general, of skin diseases, and of the changes in structure and function of epithelia in the course of evolution. This review focuses on keratins and keratin filaments in mammalian tissue but keratins in the tissues of some other vertebrates are also considered.     

Systemic redox regulation of cellular information processing

Receptor-mediated signaling leads to transient changes in redox state, resulting in reversible oxidation of protein cysteine thiols. Numerous signaling proteins have been identified as being redox sensitive; however, to date, most investigations have focused on the ramifications of isolated protein modifications on cellular phenotypes. We propose that reversible thiol oxidation of proteins in a signaling network and their systemic interactions introduce features in the dynamics and control of cellular responses that are unique compared with isolated oxidative protein modifications. Simulations of dynamic redox regulation in different cellular contexts reveal feasible regulatory features for future experimental investigation. We suggest that location within a network, compartmentalization, and the degree of connectivity between redox proteins can dramatically modulate cellular information processing.     

Global methods to monitor the thiol-disulfide state of proteins in vivo

Cysteines play an important role in protein biochemistry. The unique chemical property and high reactivity of the free thiol group makes reduced cysteine a versatile component of catalytic centers and metal binding sites in many cytosolic proteins and oxidized cystine a stabilizing component in many secreted proteins. Moreover, cysteines readily react with reactive oxygen and nitrogen species to form reversible oxidative thiol modifications. As a result, these reversible thiol modifications have found a use as regulatory nano-switches in an increasing number of redox sensitive proteins. These redox-regulated proteins are able to adjust their activity quickly in response to changes in their redox environment. Over the past few years, a number of techniques have been developed that give insight into the global thiol-disulfide state of proteins in the cell. They have been successfully used to find substrates of thiol-disulfide oxidoreductases and to discover novel redoxregulated proteins. This review will provide an overview of the current techniques, focus on approaches to quantitatively describe the extent of thiol modification in vivo, and summarize their applications.     

Tissue transglutaminase: apoptosis versus autoimmunity

Autoimmune diseases are characterized by multiple autoantibodies and/or autoreactive T cells that recognize a large number of antigens. Many of these antigens undergo extensive post-translational modifications during apoptosis and act as substrates for the proapoptotic cystein proteases. Here, Mauro Piacentini and Vittorio Colizzi discuss the effects on autoimmunity produced by post-translational modifications of proteins catalysed by the proapoptotic enzyme tissue transglutaminase.     

Current status of age altered enzymes: alternative mechanisms.

The occurrence of inactive enzyme molecules in a variety of tissues and animal species has been shown to be of a general nature. The levels of inactive enzyme molecules found in old animals were produced by amino acid analogs in young animals. These levels have been shown to be initially detrimental but subsequently the young system shows recovery by efficiently disposing of the analog-modified proteins. In old animals this disposal is considerably less efficient. Evidence is presented which suggests that post-translational modifications of proteins are the main cause of enzyme inactivation in old animals. Amino acid substitutions and modifications involving charge differences apparently do not contribute significantly to this phenomenon.     

Modeling formalin fixation and histological processing with ribonuclease A: effects of ethanol dehydration on reversal of formaldehyde cross-links

Understanding the chemistry of protein modification by formaldehyde fixation and subsequent tissue processing is central to developing improved methods for antigen retrieval in immunohistochemistry and for recovering proteins from formalin-fixed, paraffin-embedded (FFPE) tissues for proteomic analysis. Our initial studies of single proteins, such as bovine pancreatic ribonuclease A (RNase A), in 10% buffered formalin solution revealed that upon removal of excess formaldehyde, monomeric RNase A exhibiting normal immunoreactivity could be recovered by heating at 60 degrees C for 30 min at pH 4. We next studied tissue surrogates, which are gelatin-like plugs of fixed proteins that have sufficient physical integrity to be processed using normal tissue histology. Following histological processing, proteins could be extracted from the tissue surrogates by combining heat, detergent, and a protein denaturant. However, gel electrophoresis revealed that the surrogate extracts contained a mixture of monomeric and multimeric proteins. This suggested that during the subsequent steps of tissue processing protein-formaldehyde adducts undergo further modifications that are not observed in aqueous proteins. As a first step toward understanding these additional modifications we have performed a comparative evaluation of RNase A following fixation in buffered formaldehyde alone and after subsequent dehydration in 100% ethanol by combining gel electrophoresis, chemical modification, and circular dichroism spectroscopic studies. Our results reveal that ethanol-induced rearrangement of the conformation of fixed RNase A leads to protein aggregation through the formation of large geometrically compatible hydrophobic beta-sheets that are likely stabilized by formaldehyde cross-links, hydrogen bonds, and van der Waals interactions. It requires substantial energy to reverse the formaldehyde cross-links within these sheets and regenerate protein monomers free of formaldehyde modifications. Accordingly, the ethanol-dehydration step in tissue histology may be important in confounding the successful recovery of proteins from FFPE tissues for immunohistochemical and proteomic analysis.     

Some principles emerging from the study of short- and long-term memory

Recent studies indicate that in invertebrates short-term memory for various forms of learning involves covalent modifications of pre-existing proteins. By contrast, long-term memory utilizes genes and proteins not required for short-term memory.     

Involvement of the nucleolus in replication of human viruses

Viruses are intracellular pathogens that have to usurp some of the cellular machineries to provide an optimal environment for their own replication. An increasing number of reports reveal that many viruses induce modifications of nuclear substructures including nucleoli, whether they replicate or not in the nucleus of infected cells. Indeed, during infection of cells with various types of human viruses, nucleoli undergo important morphological modifications. A large number of viral components traffic to and from the nucleolus where they interact with different cellular and/or viral factors, numerous host nucleolar proteins are redistributed in other cell compartments or are modified and some cellular proteins are delocalised in the nucleolus of infected cells. Well‐documented studies have established that several of these nucleolar modifications play a role in some steps of the viral cycle, and also in fundamental cellular pathways. The nucleolus itself is the place where several essential steps of the viral cycle take place. In other cases, viruses divert host nucleolar proteins from their known functions in order to exert new unexpected role(s). Copyright © 2009 John Wiley & Sons, Ltd.