细菌体内的蛋白质降解

摘要:为了适应多变的外界环境,细菌利用蛋白降解来清除体内不需要的蛋白质。AAA+蛋白酶降解机制在细菌蛋白质质量控制系统中发挥重要作用,而在放线菌中发现的蛋白酶体揭示了原核生物体内一个崭新的蛋白质降解机制。蛋白酶只识别携带降解决定子的底物,确保了蛋白质降解的特异性,除此之外细菌还通过一些其他方式调控蛋白质的降解与否。随着真核生物体内泛素依赖的蛋白酶体降解途径的发现,蛋白质降解过程参与调控机体生理活动的功能也逐渐为人所知。研究发现,蛋白质降解参与调控细菌的生长、分化,并与细菌的应激反应以及毒力等相关。本文将对细菌中存在的AAA + 蛋白质降解机制,包括其结构、对底物的降解过程及其生理功能等进行阐述。     

表观遗传和蛋白质翻译后修饰在细菌耐药中的作用

日益严重的细菌耐药性有可能使人类重回前抗生素时代。细菌的耐药机理多样,深入研究细菌的耐药性形成机理有助于开发控制耐药细菌感染的新措施。表观遗传和蛋白质翻译后修饰在细胞代谢、信号转导、蛋白质降解、调控DNA复制、应激反应等方面都具有重要作用。近年来研究表明表观遗传和蛋白质翻译后修饰在细菌耐药中也扮演着重要的角色。本文总结了DNA甲基化、调控型RNAs等表观遗传因素和磷酸化、琥珀酰基化等蛋白质翻译后修饰因素在细菌耐药性中的调控作用,以期为抗生素靶标选择和抗生素开发设计提供新思路。     

泛素介导的蛋白质降解系统——从基础研究到临床应用

20世纪60～80年代,大多数生物科研人员都致力于核酸和遗传信息传递的研究。蛋白质降解被认为是非特异的过程,因此没有人感兴趣。泛素修饰的发现使蛋白质降解领域发生革命性的变化,人们逐渐认识到蛋白质降解是一个特异的受严格调控的过程。细胞内蛋白质降解事件的发生会调节许多生命过程,如细胞增殖、分化、衰老和死亡。细胞内蛋白质降解调控异常也会引发多种疾病,包括癌症和神经退行性疾病。人们对细胞内蛋白质降解的研究已经取得一定成果,但是还有很多问题没有解决,全面解读该过程还需要更多的努力和探索。     

细菌对细胞因子网络的干扰

在细菌感染中,细菌可通过多种方式参与宿主细胞因子网络的调控,对其调控方式和机制的探讨,有助于了解细菌的致病机制,对细菌性感染防治有重要意义。     

基于翻译调控的细菌耐药研究进展

由于抗生素的大量使用,细菌耐药问题凸显,直接威胁人类生命健康和世界经济发展。过去对于细菌耐药的遗传和分子机制研究较为透彻,而对应的调控机制研究相对较少。翻译调控作为生命体最重要的调控方式之一,在细菌耐药研究领域的重要性尚未被学术界充分重视。本文介绍了影响翻译过程的抗生素的主要作用机制,重点从核糖体的修饰和突变、tRNA总量的动态调控、tRNA氨酰化、tRNA甲基化、核糖体保护蛋白和翻译因子这几个方面概述了基于翻译调控的细菌耐药研究进展,为研究者们提供了一个基于翻译调控角度研究细菌耐药的新视角,同时也为开发靶向细菌翻译调控的新型抗生素提供一些新思路。     

细菌蛋白质磷酸化修饰研究进展

细菌蛋白质磷酸化修饰是调控细菌基因表达的一种重要方式,在细菌诸多生命活动中发挥非常关键的作用。本文系统概括了近年来细菌蛋白质磷酸化修饰的种类、双组分调控系统中磷酸化修饰调控信号传导、酪氨酸残基磷酸化修饰以及丝/苏氨酸残基磷酸化修饰等,同时对不同种类细菌蛋白质磷酸化修饰的功能进行综述,这些研究将对人类了解细菌蛋白质翻译后修饰的磷酸化调控及其与控制细菌感染的关系提供参考价值。     

烟草TTG2蛋白质对NPRI介导的抗病防卫反应与ARF8影响的生长发育进行交叉调控的机制

NPR1蛋白是水杨酸信号和系统获得性抗性的转录调节因子,它的功能受蛋白质降解酶体CUL3．E3的控制。植物的发育主要受生长素信号通路的控制,生长素反应因（ARF）参与生长素信号转导转录调控。植物转录因于NPR1和ARF8分别在蛋白质降解酶体CUL3-E3与CUL1-E3控制下,调控抗病防卫与生长发育。烟草TTG2促进ARF8从细胞质向细胞核转运及其转录调控作用,因此促进生长发育;相反,TTG2把NPR1扣留在细胞质,阻止它对防卫反应基因的转录调控作用,从而抑制抗病性。TTG2与NPR1或ARF8并不直接互作,说明存在协助因子。     

细菌细胞壁生长调控机制研究进展

在细菌生长过程中,细胞壁起到维持细胞形状和完整性,抵抗内部膨胀压的作用。细胞壁的合成、分裂、再生、循环再利用等与细菌自身生长繁殖和应对环境压力息息相关。目前,细胞壁生长机理,细菌如何调控细胞壁生长及如何与其他细胞过程相协调的机制尚未研究清楚。细胞壁调控机制的解析对了解细菌细胞壁功能、确定药物的作用方式和发展新一代的治疗方法至关重要。对细菌调控细胞壁生长机制的国外研究进展进行了概述,重点阐述了支架蛋白、转录因子、非编码小RNA及蛋白相互作用调控细胞壁的合成、细胞分裂、压力响应的机制,总结了细胞壁调控机制在抗菌药物研发中的应用,并对未来的研究方向进行了展望。     

具有真细菌和真核生物融合特征的古生菌转录系统

古生菌是一类区别于真细菌和真核生物的第三域生命形式 ,转录是生物体遗传信息传递系统中的一个中心环节。近年来研究结果表明 ,古生菌的转录系统具有真细菌和真核生物的融合特征 :古生菌的基本转录装置包括RNA聚合酶、基本转录因子、启动子元件等与真核生物相似 ;而古生菌的转录调控机制却更加类似于真细菌 ,在古生菌中发现并鉴定了许多类似于真细菌的转录调控蛋白。另外古生菌还具有某些独特的转录调控方式     

细菌蛋白酶体及蛋白酶体抑制剂研究进展

蛋白酶体在真核生物、古菌和部分细菌(主要是放线菌)的胞内蛋白质降解中起着至关重要的作用。虽然三域生物蛋白酶体的结构相似,但细菌蛋白酶体在组装、调节、生理功能等方面与真核生物和古菌都截然不同。研究细菌蛋白酶体不仅有助于认识其起源和进化历程,也将为发掘蛋白酶体抑制剂(proteasome inhibitor, PI)这类具有广阔药用前景的化合物提供指导。本文综述了细菌蛋白酶体的结构、功能和进化假说,并概括了细菌蛋白酶体抑制剂的最新研究进展,期望为相关研究提供参考。     

Proteolysis in the Escherichia coli heat shock response: a player at many levels

Proteolysis is a fundamental process used by all forms of life to maintain homeostasis, as well as to remodel the proteome following environmental changes. Here, we explore recent advances in understanding the role of proteolysis during the heat shock response of Escherichia coli. Proteolysis both regulates and contributes directly to and the heat shock response at multiple different levels, from adjusting the levels of the master heat shock response regulator (σ(32)), to eliminating damaged cellular proteins, to altering the activity of chaperones that refold heat-denatured proteins. Recent results illustrate the complexity of the heat shock response and the pervasive role that proteolysis plays in both the cellular response to heat shock and the subsequent limiting of the response, as cells return to a more 'normal' physiological state.     

Enhancement of murine T cell I-J expression by limited proteolysis

I-J-encoded structures on peripheral T cells and thymocytes appear normally to be blocked or shielded by material that is susceptible to proteolysis. Limited proteolysis with trypsin, papain, pronase, or chymotrypsin increased the number of peripheral T cells and thymocytes lysed by anti-I-Jk serum and complement. Proteolysis did not induce I-Jk expression on B cells or on negative strain T cells. Increased lysis was enzyme concentration and time dependent and was not due to increased susceptibility of protease-treated cells to lysis by antibody plus complement; proteolysis rendered T cells and thymocytes less susceptible to lysis by anti-H-2Kk, anti-H-2Dd, and anti-Lyt-2 antibodies. Absorption experiments showed that I-Jk determinant density was increased in the protease-treated T cell population. The I-Jk determinants detected are proteins or glycoproteins; extended proteolysis removed these molecules from the T cell surface. Treatment of T cells or thymocytes with activated macrophage culture supernatant containing proteolytic activity produced a small but reproducible increase in I-Jk expression. Proteolysis of lymphocyte membranes, possibly mediated by macrophages, may have a role in cellular differentiation and immune activation.     

Proteolytic enhancement of gelation of ascites tumor cell extracts. Relationship to actin binding protein

Proteolysis of cytoplasmic extracts of sarcoma 180 and MAT-C1 adenocarcinoma ascites cells enhances the rate of gelation. Only high molecular weight polypeptides, including actin binding protein and myosin, are cleaved during the process; actin is not cleaved. In MAT-B1 adenocarcinoma extracts the gelation rate was not enhanced by proteolysis and actin binding protein was not readily cleaved. Electrophoretic comparisons of trypsin-treated and untreated extracts of MAT-B1 and MAT-C1 cells show that actin binding protein is the only readily discernible polypeptide which is cleaved in the C1 cells but not in the B1 cells. These results suggest that actin binding protein may act as an inhibitor of gelation.     

The ClpB homolog Hsp78 is required for the efficient degradation of proteins in the mitochondrial matrix

Molecular chaperones perform vital functions in mitochondrial protein import and folding. In yeast mitochondria, two members of the Clp/Hsp100 chaperone family, Hsp78 and Mcx1, have been identified as homologs of the bacterial proteins ClpB and ClpX, respectively. In this report we employed a novel quantitative assay system to assess the role of Hsp78 and Mcx1 in protein degradation within the matrix. Mitochondria were preloaded with large amounts of two purified recombinant reporter proteins exhibiting different folding stabilities. Proteolysis of the imported substrate proteins depended on the mitochondrial level of ATP and was mediated by the matrix protease Pim1/LON. Degradation rates were found to be independent of the folding stability of the reporter proteins. Mitochondria from hsp78Delta cells exhibited a significant defect in the degradation efficiency of both substrates even at low temperature whereas mcx1Delta mitochondria showed wild-type activity. The proteolysis defect in hsp78Delta mitochondria was independent from the aggregation behavior of the substrate proteins. We conclude that Hsp78 is a genuine component of the mitochondrial proteolysis system required for the efficient degradation of substrate proteins in the matrix.     

Resolving individual steps in the operation of ATP-dependent proteolytic molecular machines: from conformational changes to substrate translocation and processivity

Clp, Lon, and FtsH proteases are proteolytic molecular machines that use the free energy of ATP hydrolysis to unfold protein substrates and processively present them to protease active sites. Here we review recent biochemical and structural studies relevant to the mechanism of ATP-dependent processive proteolysis. Despite the significant structural differences among the Clp, Lon, and FtsH proteases, these enzymes share important mechanistic features. In these systems, mechanistic studies have provided evidence for ATP binding and hydrolysis-driven conformational changes that drive translocation of substrates, which has significant implications for the processive mechanism of proteolysis. These studies indicate that the nucleotide (ATP, ADP, or nonhydrolyzable ATP analogues) occupancy of the ATPase binding sites can influence the binding mode and/or binding affinity for protein substrates. A general mechanism is proposed in which the communication between ATPase active sites and protein substrate binding regions coordinates a processive cycle of substrate binding, translocation, proteolysis, and product release.     

ClpP hydrolyzes a protein substrate processively in the absence of the ClpA ATPase: mechanistic studies of ATP-independent proteolysis

ATP-dependent proteases are processive, meaning that they degrade full-length proteins into small peptide products without releasing large intermediates along the reaction pathway. In the case of the bacterial ATP-dependent protease ClpAP, ATP hydrolysis by the ClpA component has been proposed to be required for processive proteolysis of full-length protein substrates. We present here data showing that in the absence of the ATPase subunit ClpA, the protease subunit ClpP can degrade full-length protein substrates processively, albeit at a greatly reduced rate. Moreover, the size distribution of peptide products from a ClpP-catalyzed digest is remarkably similar to the size distribution of products from a ClpAP-catalyzed digest. The ClpAP- and ClpP-generated peptide product size distributions are fitted well by a sum of multiple underlying Gaussian peaks with means at integral multiples of approximately 900 Da (7-8 amino acids). Our results are consistent with a mechanism in which ClpP controls product sizes by alternating between translocation in steps of 7-8 (+/-2-3) amino acid residues and proteolysis. On the structural and molecular level, the step size may be controlled by the spacing between the ClpP active sites, and processivity may be achieved by coupling peptide bond hydrolysis to the binding and release of substrate and products in the protease chamber.     

The Polo-like kinase Cdc5p and the WD-repeat protein Cdc20p/fizzy are regulators and substrates of the anaphase promoting complex in Saccharomyces cerevisiae.

Proteolysis mediated by the anaphase promoting complex (APC) has a crucial role in regulating the passage of cells through anaphase. Destruction of the anaphase inhibitor Pds1p is necessary for separation of sister chromatids, whereas destruction of the mitotic cyclin Clb2p is important for disassembly of the mitotic spindle, cytokinesis and re-replication of the genome. Pds1p proteolysis precedes that of Clb2p by at least 15 min, which helps to ensure that cells never re-replicate their genome before they have separated sister chromatids at the previous mitosis. What triggers Pds1p proteolysis and why does it not also trigger that of Clb2p? Apart from sharing a dependence on the APC, these two proteolytic events differ in their dependence on other cofactors. Pds1p proteolysis depends on a WD-repeat protein called Cdc20p, whereas Clb2p proteolysis depends on another, related WD protein called Hct1/Cdh1p. On the other hand, destruction of Clb2p, but not that of Pds1p, depends on the Polo-like kinase, Cdc5p. Cdc20p is essential for separation of sister chromatids, whereas Cdc5p is not. We show that both Cdc5p and Cdc20p are unstable proteins whose proteolysis is regulated by the APC. Both proteins accumulate during late G2/M phase and disappear at a late stage of anaphase. Accumulation of Cdc20p contributes to activation of Pds1p proteolysis in metaphase, whereas accumulation of Cdc5p facilitates the activation of Clb2p proteolysis.     

Proteolysis of N-ethylmaleimide-modified aldolase loaded into erythrocyte ghosts: prevention by inhibitors of calpain.

1. When rabbit muscle aldolase labelled with tritium and inactivated by N-ethylmaleimide (NEM) was loaded into erythrocyte ghosts, significant proteolysis of the loaded protein occurred. The major product of this proteolysis, separated by electrophoresis under dissociating conditions, was found to be approx. 2 kDa smaller than the parent protein. 2. Proteolysis was detectable during erythrocyte ghost loading at 0 degrees C, reaching a plateau after approx. 12 min. Subsequent incubation at 37 degrees C to allow resealing of the ghosts resulted in additional proteolysis, and up to 20% of the loaded protein was converted to the smaller 38 kDa derivative. 3. EDTA, EGTA, leupeptin and chymostatin, each inhibitors of calcium-activated neutral proteinases (calpains), were the most effective inhibitors of the proteolysis of NEM-inactivated aldolase in ghosts. Other proteinase inhibitors were ineffective, while phenylmethanesulphonyl fluoride was only partially effective. 4. Inhibition of the proteolysis by EGTA was prevented by CaCl2, supporting the involvement of erythrocyte calpain. 5. Pretreatment of ghosts with EGTA prior to loading of NEM-modified aldolase followed by microinjection of the protein into HeLa cells did not result in a different rate of its overall breakdown to acid-soluble products. EGTA is suggested as a useful agent for the erythrocyte ghost-mediated microinjection of calpain-sensitive proteins.