细菌的应激反应和生理代谢与耐药性及其控制策略

抗菌药在医疗和畜牧生产中的滥用导致了细菌抗药性的产生,这个公共卫生问题引起了人们越来越多的关注。除了基因突变和获得形成的抗药性 (Resistance) 外,细菌在自然环境中遇到的各种压力会引发其产生应激反应,这不仅可以保护细菌免受这些压力的影响,还会改变细菌对抗菌药的耐药性 (Tolerance)。耐药性的产生必然会影响细菌的生理代谢,但是细菌可以通过调节自身代谢恢复对药物的敏感性。文中综述了近年来细菌应激反应和生理代谢与细菌耐药性之间的相关研究,以期采取更加有效的措施来控制细菌抗药性的发生和蔓延。     

细菌群体感应及其调控应激反应的研究进展

细菌可利用群体感应系统进行种内及种间的交流,这种交流已经被证实对细菌存在多种调控功能。现有研究表明,细菌的群体感应系统也可以调控细菌的应激反应。本文中,笔者对细菌的群体感应及其对应激反应调控作用的相关研究现状进行了阐述,旨在为应对致病菌和乳酸菌的应激反应提供参考。     

复合菌系RSS-4腐解稻秆过程中的菌系动态变化

采用传统平扳分离培养方法和PCR—DGGE技术研究了水稻秸秆腐解复合菌系RSS-4在腐解稻秆过。程中菌种区系变化情况。结果表明：平板分离培养方法显示,在稻秆腐解过程中,微生物的数量呈现出先升后降的变化趋势,在整个腐解过程中细菌的数量占优势;DGGE图谱显示,至少有12种细菌和18种真菌的近缘种参与到稻秆的腐解过程。在其腐解过程中,不同腐解阶段真菌的组成呈现出多样性,数量变化差异也较大：细菌DGGE图谱中的条带1、9、10等以及真菌DGGE图谱中的条带8、9、13等为优势菌株,它们贯穿于稻秤腐解的整个过程;细菌中的条带12以及真菌中的条带4在腐解的前期起作用,而后迅速消失;细菌中的条带3、11等以及真菌中的条带3、10等在腐解的后期才出现而起作用;而细菌中的条带2以夏真菌中的条带1、5等仅出现在腐解的莱一时期。     

差异蛋白质组学技术在水生动物应激反应研究中的应用

差异蛋白质组学是蛋白质组学的主要研究内容之一,着重于研究特定因素引起的不同样品间蛋白质组的差异,揭示并验证蛋白质组在生理或病理过程中的变化,并从理论上推断造成这种变化的原因。近年来,差异蛋白质组学已逐步应用到水生动物的应激反应研究中。在周围环境发生变化,如非生物环境因子改变以及病原微生物感染时,水生动物会通过特异的应激反应削弱或者抵抗其危害,其与环境的相互作用机理可通过蛋白质的差异表达体现出来。本文就差异蛋白质组学技术在水生动物应激反应研究中的应用及进展进行了回顾和综述。     

藏灵菇微生物种群结构的分子特性研究*

用PCR-DGGE指纹技术,研究了藏灵菇中微生物多样性及藏灵菇发酵奶发酵过程微生物种群动力学。结果表明,藏灵菇中细菌的种群结构较酵母菌的复杂,不同来源的藏灵菇中细菌种群结构的相似性为78%~84%,酵母菌种群结构的相似性为80%~92%。发酵过程中细菌种群结构变化图谱中的条带B和条带E,以及酵母菌种群结构变化图谱中的条带N贯穿于整个发酵过程,是发酵过程的优势菌。序列分析表明,细菌种群结构的DGGE图谱中的绝大多数条带与乳酸菌相对应,其中最亮条带(条带E)的序列与乳酸乳球菌的相似性为100%。     

非编码RNAs在细菌代谢网络调控中的研究进展

非编码RNAs(non-coding RNAs,ncRNAs)是一类非常重要的调节子,此类调节子能够使细胞通过调节它们的生理特性而适应环境的改变。已有的研究表明ncRNAs在细菌的蔗糖代谢、细胞外膜应激反应、群体感应和细菌毒力等方面发挥了重要的调节作用,其调控模式已经成为细菌调控网络中的重要“分支”。本文综述了细菌ncRNAs近年来的研究进展,详细介绍了细菌ncRNAs的合成及调控机制,由于ncRNAs结构的独特性及调控网络的复杂性,因此ncRNAs的功能研究已经成为近几点的研究热点之一。     

布鲁氏菌对RAW264.7细胞内质网应激与细胞因子分泌的影响

【目的】布鲁氏菌与宿主相互作用的分子机制是目前的研究热点之一,布鲁氏菌通过形成来自于内质网的布氏小体而在巨噬细胞内生存和增殖,其机制目前尚不清楚,宿主细胞内质网应激反应对病原感染和炎症的调控密切相关。揭示内质网应激反应在布鲁氏菌感染巨噬细胞中的作用以及布鲁氏菌感染对巨噬细胞分泌免疫因子的影响。【方法】构建布鲁氏菌感染RAW264.7模型,在感染后不同时间收集细胞,通过实时荧光定量PCR检测细胞内质网应激反应标志分子GRP78和CHOP,以及TNF-α、IL-1β和IL-6在m RNA水平的变化;通过Western blot和ELISA分别检测其蛋白水平的变化。【结果】布鲁氏菌感染RAW264.7细胞的最佳感染复数MOI为100?1;证明在布鲁氏菌感染4-6 h,巨噬细胞可杀伤侵入的布鲁氏菌,之后存活的细菌可在细胞内增殖;感染后24 h出现细胞凋亡,48 h出现大量细胞坏死。布鲁氏菌感染可激活RAW264.7细胞的内质网应激反应,促进GRP78的表达,同时,抑制免疫因子的分泌。【结论】内质网应激反应参与了RAW264.7对布鲁氏菌感染的调节。     

藏灵菇微生物种群结构的分子特性研究

用PCR—DGGE指纹技术,研究了藏灵菇中微生物多样性及藏灵菇发酵奶发酵过程微生物种群动力学。结果表明,藏灵菇中细菌的种群结构较酵母菌的复杂,不同来源的藏灵菇中细菌种群结构的相似性为78％-84％,酵母菌种群结构的相似性为80％-92％。发酵过程中细菌种群结构变化图谱中的条带B和条带E,以及酵母菌种群结构变化图谱中的条带N贯穿于整个发酵过程,是发酵过程的优势菌。序列分析表明,细菌种群结构的DGGE图谱中的绝大多数条带与乳酸菌相对应,其中最亮条带（条带E）的序列与乳酸乳球菌的相似性为100％。     

细菌基因转录谱的DNA微点阵芯片分析

基于DNA微点阵芯片技术的细菌基因转录谱研究是基因功能分析的重要手段之一。本文阐述了细菌DNA芯片基因转录谱分析的基本问题,包括mRNA和双色荧光实验设计,详细介绍了目前细菌体内外DNA芯片基因转录谱的具体应用情况,并说明了体内外基因转录谱研究的优劣和互补。     

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。     

蛋白质组学在植物逆境胁迫研究中的进展

蛋白质组学是后基因组时代研究的热点领域之一,自从蛋白质组这个概念被提出以来,其研究一直受到广泛关注,其研究技术也有了极大地进步。植物时刻都面临各种非生物胁迫,包括干旱、冷、盐、金属等,在长期进化过程中,植物形成独特的机制来响应逆境,然而目前对于植物如何适应逆境的分子机制尚未完全阐明。因此蛋白质组学作为一种强有力的研究技术手段,将为研究植物响应胁迫的分子机制提供理论支撑。介绍了蛋白质组学的产生背景、研究技术手段及植物在各种胁迫条件下的蛋白质组学研究、植物亚细胞器的蛋白质组学研究状况,同时对植物蛋白质组学的发展前景进行了展望。     

Proteomic signatures in antibiotic research

Antibiotics disturb the physiological homeostasis of bacterial cells by interfering with essential cellular functions or structures. The bacterial proteome adjusts quickly in response to antibiotic challenge. This physiological response is specifically tailored to overcome the inflicted damage and, thus, closely linked to the antibiotic target and mechanism of action. In a way, the proteome mirrors the antibiotic insult. This connection can be exploited to guide the development of novel antibiotics. By using structurally different antibiotics, which cause the same physiological disturbance, proteomic signatures diagnostic of the mechanism of action can be defined. These proteomic signatures inform about mechanism-related differential protein expression as well as about protein modifications. This review recapitulates how antibiotic proteomic signatures are established and highlights areas of antibiotic research benefiting most from proteomic signatures. Antibacterial research programs designed to structurally advance existing antibiotic classes profit from rapid in vivo mechanism of action confirmation. What is more, a comprehensive reference compendium of antibiotic proteomic signatures allows rapid mechanism of action identification of those structurally novel compounds that inhibit known targets. Finally, novel proteomic response profiles indicate unprecedented mechanisms. Here, the proteome profile provides evidence on the nature of the antibiotic-caused physiological disturbance leading to testable hypotheses on the mechanism of action.     

Proteomic analyses of the response of cyanobacteria to different stress conditions

Cyanobacteria are significant contributors to global photosynthetic productivity, thus making it relevant to study how the different environmental stresses can alter their physiological activities. Here, we review the current research work on the response of cyanobacteria to different kinds of stress, mainly focusing on their response to metal stress as studied by using the modern proteomic tools. We also report a proteomic analysis of plastocyanin and cytochrome c₆ deletion mutants of the cyanobacterium Synechocystis sp. PCC 6803 grown under copper or iron deprivation, as compared to wild-type cells, so as to get a further understanding of the metal homeostasis in cyanobacteria and their response to changing environmental conditions.     

Proteomic profile of the saliva and plasma protein layer adsorbed on Ti–Zr alloy: the effect of sandblasted and acid-etched surface treatment

Abstract

Titanium–zirconium (Ti–Zr) alloy has been widely used as a biomaterial for implant devices, and it is commonly treated by sandblasting followed by acid etching (SLA) to improve biological responses. Although protein adsorption is the first biological response, the effect of this SLA treatment on the proteomic profile of proteins adsorbed from saliva and blood plasma has not been tested. In this study, the proteomic profile was evaluated by liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS). Streptococcus sanguinis was used to test whether the protein layer affects bacterial adhesion. SLA treatment affected the proteomic profile, showing exclusive proteins adsorbed from saliva (14) and plasma (3). However, both groups exhibited close patterns of intensity for common proteins, molecular functions and biological processes mediated by proteins. Interestingly, Ti–Zr_SLA showed higher bacterial adhesion (～1.9 fold over) for the surface coated with plasma proteins. Therefore, SLA treatment of Ti–Zr alloy changed the proteomic profile, which may affect bacterial adhesion.     

Proteomics techniques for the development of flood tolerant crops

Proteomics is a useful analytical approach for investigating crop responses to stress. Recent remarkable advances in proteomic techniques allow for the identification of a wider range of proteins than was previously possible. The application of proteomic techniques to clarify the molecular mechanisms underlying crop responses to flooding stress may facilitate the development of flood tolerant crops. Flooding is an environmental stress found worldwide and may increase in frequency due to changes in global climate. Waterlogging resulting from flooding causes significant reductions in the growth and yield of several crops. Transient flooding displaces gases in soil pores and often causes hypoxia in plants grown on land with poor drainage. Changes in protein expression and post-translational modification of proteins occur as plants activate their defense system in response to flooding stress. In this review, we discuss the contributions that proteomic studies have made toward increasing our understanding of the well-organized cellular response to flooding in soybean and other crops. The biological relevance of the proteins identified using proteomic techniques in regard to crop stress tolerance will be discussed as well.     

植物质膜蛋白质组的逆境应答研究进展

质膜作为原生质体与外界环境的屏障, 除了维持正常的细胞内稳态和营养状况, 还参与感知和应答各种环境胁迫。近年来, 植物质膜蛋白质组学研究为深入分析植物应答不同生物和非生物胁迫的分子机制提供了重要信息, 已经报道了模式植物拟南芥(Arabidopsis thaliana)和水稻(Oryza sativa)等10种植物质膜应对生物胁迫(白叶枯病菌(Xanthomonas oryzae pv. oryzae)感染)与非生物胁迫(冷、盐、水淹、渗透、高pH值、Fe缺乏及过量、氮素、脱落酸、壳聚糖和壳寡糖)过程的蛋白质丰度模式变化。通过整合分析植物质膜响应逆境的蛋白质组学研究结果, 揭示了质膜在植物应答逆境胁迫过程中的重要作用。植物通过调节转运蛋白、通道蛋白及膜泡运输相关蛋白的丰度变化促进细胞内外的信号传递、物质交换与运输; 同时利用膜相关的G蛋白、Ca²⁺信号、磷酸肌醇信号途径及BR信号途径等多种信号通路, 通过蛋白质可逆磷酸化作用感知和传递胁迫信号, 调节植物抵御胁迫。研究结果为从蛋白质水平认识质膜逆境应答分子调控机制提供了新线索。     

Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii

In this work, we performed for the first time a proteomic approach to the processes induced by long-term potassium starvation in the halotolerant yeast Debaryomyces hansenii. The proteomic profile under this ionic stress conditions shows that important changes in gene expression take place as an adaptive response. We found a significant protein expression repression as well as metabolic changes such as the inhibition of the upper part of the glycolysis, the amino acid synthesis, and the Krebs cycle. On the other hand, genes related to stress responses, protein degradation, and sterols synthesis were upregulated in response to potassium deprivation. The findings in this study provide important information about how this particular yeast copes with ionic stress at molecular levels, which might further enrich the global understanding of salt tolerance processes in eukaryal systems and moreover highlighting the importance of the 'omics' approaches as a complement to the classical physiological studies.     

Quantitative proteomic analyses of crop seedlings subjected to stress conditions; a commentary

Quantitative proteomics is one of the analytical approaches used to clarify crop responses to stress conditions. Recent remarkable advances in proteomics technologies allow for the identification of a wider range of proteins than was previously possible. Current proteomic methods fall into roughly two categories: gel-based quantification methods, including conventional two-dimensional gel electrophoresis and two-dimensional fluorescence difference gel electrophoresis, and MS-based quantification methods consists of label-based and label-free protein quantification approaches. Although MS-based quantification methods have become mainstream in recent years, gel-based quantification methods are still useful for proteomic analyses. Previous studies examining crop responses to stress conditions reveal that each method has both advantages and disadvantages in regard to protein quantification in comparative proteomic analyses. Furthermore, one proteomics approach cannot be fully substituted by another technique. In this review, we discuss and highlight the basis and applications of quantitative proteomic analysis approaches in crop seedlings in response to flooding and osmotic stress as two environmental stresses.