细菌与噬菌体相互抵抗机制研究进展

噬菌体作为一种侵染细菌的病毒,能够特异性识别宿主细菌。近年来,抗生素的过度使用导致耐药细菌的出现,噬菌体有望成为对抗耐药细菌的新武器。在细菌与噬菌体长期共进化过程中,二者都演化出一系列抵御策略。本文从抑制噬菌体吸附、阻止噬菌体DNA进入、切割噬菌体基因组、流产感染以及群体感应对噬菌体的调控等方面,对细菌抵抗噬菌体的机制以及噬菌体应对细菌的策略进行了综述,同时还列举了细菌和噬菌体相互抵抗机制的检测方法,以期为噬菌体在细菌控制中的应用以及探究细菌抵抗噬菌体的机制提供理论依据。     

细菌的噬菌体感染抗性机制

噬菌体广泛存在于生态环境中。细菌在与噬菌体长期的共进化过程中,衍化出了多种针对噬茵体感染的抗性机制。我们从宿主菌的抑制吸附、阻止噬菌体DNA注入、切断噬菌体DNA和影响其功能及流产感染等方面,对宿主菌抵抗噬菌体感染的机制进行了综述。     

噬菌体编码的抑菌蛋白

噬菌体是细菌的天敌,它利用宿主的细胞机制完成自身的复制。在感染过程中噬菌体基因组进入细菌细胞后立即产生调节或重新定向宿主特定功能的蛋白质(即抑菌蛋白),以逃避多种细菌的防御机制或改变宿主的分子代谢机制。研究发现,这些噬菌体编码的抑菌蛋白可抑制细菌分裂,干扰细菌遗传物质的复制、转录及降解,影响CRISPR介导的细菌免疫以及代谢。明确噬菌体编码的抑菌蛋白如何影响这些宿主的防御或分子代谢机制可以优化目前基于噬菌体的抗菌策略,找出控制细菌感染的新途径,为抑菌药物的发现和设计打开新的大门。本文就近年来发现的噬菌体编码的抑菌蛋白及其抑菌机制的研究进展进行综述。     

噬菌体治疗中细菌对噬菌体的抗性

抗生素治疗尽管有几十年有效治疗的历史,但随着越来越多耐/抗药性细菌的出现,细菌对抗生素的抗药性已成为一个大问题。噬菌体治疗是使用噬菌体作为抗菌剂来感染细菌株系,它一直是人们倡导的一个很有前途的常规抗生素治疗的替代方案。然而,由于细菌与噬菌体的协同进化中,细菌可以通过多种机制获得对噬菌体的抗性。因此,人们对噬菌体治疗抱有期望的同时,也关注噬菌体治疗长时间的使用之后,是否会与抗生素使用之后结果相类似,导致抗性细菌病原菌感染的治疗困难。综述了细菌-噬菌体协同进化中细菌病原菌对有感染能力的噬菌体是否会产生抗性,及其在噬菌体治疗中影响的争论,并展望了噬菌体治疗的潜在前景。     

工业微生物的噬菌体感染与防治策略

以细菌为基础的生物技术在蓬勃发展的同时也不断受到噬菌体感染的威胁,噬菌体感染已成为微生物发酵过程中的一个顽疾,其实质是噬菌体与细菌之间复杂的共进化关系。在漫长的进化过程中,噬菌体已经形成了多种针对细菌抗性系统的逃逸机制。合理的工厂设计、菌株的轮换策略和传统的基因工程方法能在一定程度上降低噬菌体感染的风险,但仍然无法避免。基于CRISPR-Cas系统的防治策略仅需噬菌体的序列信息就可以理性设计噬菌体抗性菌株,且可以通过叠加效应不断增强菌种抗性,从而避免噬菌体的逃逸;群体感应信号分子则可以从整体水平上调节细菌的噬菌体抗性。这些新发现为噬菌体感染问题的解决带了新的希望,而噬菌体基因组编辑技术和合成生物学的快速发展则将进一步加深人们对噬菌体感染防治领域的认识。     

细菌CRISPR-Cas 系统功能及其与噬菌体相互作用

摘要:近来研究发现,细菌CRISPR-Cas 系统在宿主菌抵抗可移动基因元件(mobile genetic elements,MGEs)的过程中发挥重要作用。CRISPR-Cas还参与宿主菌群体行为和毒力基因调控、DNA修复和基因组进化过程。本文着重综述细菌CRISPR-Cas系统的结构、类型、作用机制及其适应性免疫之外的其他功能(如对内源性基因表达的调控、促进基因组进化、DNA修复等);概述噬菌体抵抗CRISPR-Cas系统的机制,并对噬菌体-宿主菌相互作用进行探讨和展望。     

噬菌体：微小却不简单

噬菌体是专一感染细菌等微生物的病毒,是地球上多样性最高和最丰富的生物体,是生物学研究中重要的模式生物,同时是抗生素耐药菌的天然抗菌剂。噬菌体研究的相关成果极大地推动了生物学各个领域的发展。     

噬菌体吸附及受体结合蛋白 (RBP) 的研究进展与应用

噬菌体通过受体结合蛋白(Receptor binding protein,RBP)结合到细菌表面,其过程需要复杂的原子结构的参与和构象改变。针对噬菌体侵染,细菌发展了多种抗性机制,同时,噬菌体也进化出多种逃逸宿主抗性的机制。对噬菌体与细菌间"吸附-抗吸附-逃逸过程"的探索有助于我们理解噬菌体与细菌共进化的过程,对科学发展噬菌体治疗技术以及噬菌体的生物应用技术具有重要意义。本文概述了噬菌体吸附相关蛋白及吸附发生过程、基于RBP改变的噬菌体逃逸机制和RBP相关的生物技术研究进展。     

噬菌体与细菌相互作用的分子机制研究进展

噬菌体与细菌是自然界中存在最广泛的两类微生物,两者在群体水平、个体水平以及分子水平上均存在复杂的相互作用关系。细菌能够影响溶原性噬菌体的溶原-裂解决策,而被噬菌体感染的细菌基因表达谱也会受到噬菌体影响,使宿主菌的代谢、应激、抵抗力、毒性等多种性状发生改变。现从细菌和噬菌体两者的角度,分别综述细菌抵抗噬菌体感染以及噬菌体对具有抗性的细菌进行再感染的机制。     

噬菌体治疗细菌性感染及其限制因素

近年来,细菌耐药性已成为抗感染领域面临的严峻问题,临床对一些细菌性感染疾病束手无策。噬菌体疗法是一种通过噬菌体裂解细菌来治疗病原菌感染的治疗手段。噬菌体在抗菌领域表现出显著的优越性,成为目前治疗细菌性感染的研究热点。本文对近年来噬菌体治疗动物和人类病原菌感染、限制其临床应用的因素及解决措施进行综述。     

Bacteriophage and bacteriophage resistance in lactic acid bacteria

Abstract: The study of bacteriophage-host interactions has been instrumental in the development of genetic systems in many genera, and laid many of the foundations of modern molecular genetics. Research into bacteriophage and bacteriophage resistance in the lactic acid bacteria has moved into a new and exciting dimension in recent years. Mechanisms such as adsorption inhibition, restriction and modification, and abortive infection which have been detected and described phenotypically over the past decade are now being subjected to molecular analysis, and this has led to a better understanding of the nature and variety of resistance systems employed by lactic acid bacteria to combat phage attack. In addition, analysis of different bacteriophage has increased our knowledge of these ubiquitous particles to the point where it is possible to construct novel phage resistances based on the phage genome itself. This review outlines the recent progress in the molecular analysis of bacteriophage, bacteriophage resistance and counter resistance, and the construction of novel resistance mechanisms.     

A promiscuous antitoxin of bacteriophage T4 ensures successful viral replication

Bacteria are constantly threatened by predation from bacteriophage parasites and, in response, have evolved an array of resistance mechanisms. These resistance mechanisms then place greater selection pressure on the infecting bacteriophages, which develop counter-strategies in a perpetual 'arms race' between virus and host. Toxin-antitoxin (TA) loci are widespread in bacteria and can confer multiple benefits, including resistance to bacteriophages. The study by Otsuka and Yonesaki, published in this issue of Molecular Microbiology, describes a new plasmid-encoded TA system, lsoAB, which confers resistance to a dmd(-) mutant of bacteriophage T4 through the activity of the LsoA toxin. Infections with wild-type T4, however, are unaffected as the Dmd protein acts as an alternative antitoxin to LsoA, thus preventing its anti-bacteriophage activity. Dmd has also been shown to negate the activity of a related toxin, RnlA. This is a striking result indicating that Dmd can act as a promiscuous antitoxin, binding and inhibiting multiple toxin partners, when antitoxin activity is generally considered to be limited to a single cognate toxin. This study is an exciting addition to both the bacteriophage resistance and TA fields, and suggests a greater role for TA system-based resistance and counter-resistance in the world's oldest predator-prey relationship.     

Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage

A major goal of community ecology is to link biological processes at lower scales with community patterns. Microbial communities are especially powerful model systems for making these links. In this article, we review recent studies of laboratory communities of bacteria and bacteriophage (viruses that infect bacteria). We focus on the ecology and evolution of bacteriophage-resistance as a case study demonstrating the relationship between specific genes, individual interactions, population dynamics, community structure, and evolutionary change. In laboratory communities of bacteria and bacteriophage, bacteria rapidly evolve resistance to bacteriophage infection. Different resistance mutations produce distinct resistance phenotypes, differing, for example, in whether resistance is partial or complete, in the magnitude of the physiological cost associated with resistance, and in whether the mutation can be countered by a host-range mutation in the bacteriophage. These differences determine whether a mutant can invade, the effect its invasion has on the population dynamics of sensitive bacteria and phage, and the resulting structure of the community. All of these effects, in turn, govern the community's response to environmental change and its subsequent evolution.     

基因工程技术在建立噬菌体抗性机制研究中的应用

在自然发生的噬菌体抗性机制的基础上,应用基因工程技术可以建立广泛的噬菌体抗性机制,为有效解决噬菌体感染问题提供了新的策略。噬菌体编码的抗性、反义RNA技术、自杀陷阱及限制/修饰系统的应用是近年来发展起来的几种抗噬菌体策略,着重对其作用机制、研究进展及其意义作一介绍。同时指出应用基因工程技术构建的噬菌体抗性菌株应用于食品发酵工业中所存在的问题,并对其应用前景作了展望。     

Bacteriophage resistance inLactococcus

Lactic acid bacteria are industrial microorganisms used in many food fermentations.Lactococcus species are susceptible to bacteriophage infections that may result in slowed or failed fermentations. A substantial amount of research has focused on characterizing natural mechanisms by which bacterial cells defend themselves against phage. Numerous natural phage defense mechanisms have been identified and studied, and recent efforts have improved phage resistance by using molecular techniques. The study of how phages overcome these resistance mechanisms is also an important objective. New strategies to minimize the presence, virulence, and evolution of phage are being developed and are likely to be applied industrially.     

Abundance of Antibiotic Resistance Genes in Bacteriophage following Soil Fertilization with Dairy Manure or Municipal Biosolids,and Evidence for Potential Transduction

Animal manures and municipal biosolids recycled onto crop production land carry antibiotic-resistant bacteria that can influence the antibiotic resistome of agricultural soils, but little is known about the contribution of bacteriophage to the dissemination of antibiotic resistance genes (ARGs) in this context. In this work, we quantified a set of ARGs in the bacterial and bacteriophage fractions of agricultural soil by quantitative PCR. All tested ARGs were present in both the bacterial and phage fractions. We demonstrate that fertilization of soil with dairy manure or human biosolids increases ARG abundance in the bacterial fraction but not the bacteriophage fraction and further show that pretreatment of dairy manure can impact ARG abundance in the bacterial fraction. Finally, we show that purified bacteriophage can confer increased antibiotic resistance to soil bacteria when combined with selective pressure. The results indicate that soilborne bacteriophage represents a substantial reservoir of antibiotic resistance and that bacteriophage could play a significant role in the horizontal transfer of resistance genes in the context of an agricultural soil microbiome. Overall, our work reinforces the advisability of composting or digesting fecal material prior to field application and suggests that application of some antibiotics at subclinical concentrations can promote bacteriophage-mediated horizontal transfer of ARGs in agricultural soil microbiomes.     

提高噬菌体裂解酶抗菌活性的研究进展

随着细菌耐药性问题的日益严重,人们开始寻求新型抗菌制剂。噬菌体裂解酶是一种由ds DNA噬菌体编码的水解酶,能高效特异性地裂解细菌细胞壁且不易使细菌产生耐药性。由于天然裂解酶具有宿主谱窄,不能裂解革兰阴性菌等缺点,研究者对裂解酶进行了大量的设计改造。本研究主要对提高噬菌体裂解酶抗菌活性的研究进展进行综述。     

Bacteriophage lytic enzymes: novel anti-infectives

Bacteriophage lytic enzymes, or lysins, are highly evolved molecules produced by bacterial viruses (bacteriophage) to digest the bacterial cell wall for bacteriophage progeny release. Small quantities of purified recombinant lysin added to gram-positive bacteria causes immediate lysis resulting in log-fold death of the target bacterium. Lysins have now been used successfully in animal models to control pathogenic antibiotic resistant bacteria found on mucosal surfaces and in blood. The advantages over antibiotics are their specificity for the pathogen without disturbing the normal flora, the low chance of bacterial resistance to lysins and their ability to kill colonizing pathogens on mucosal surfaces, capabilities that were previously unavailable. Thus, lysins could be an effective anti-infective in an age of mounting antibiotic resistance.