Interference with AI-2-mediated bacterial cell-cell communication

Bacteria communicate by means of chemical signal molecules called autoinducers. This process, called quorum sensing, allows bacteria to count the members in the community and to alter gene expression synchronously across the population. Quorum-sensing-controlled processes are often crucial for successful bacterial--host relationships--both symbiotic and pathogenic. Most quorum-sensing autoinducers promote intraspecies communication, but one autoinducer, called AI-2, is produced and detected by a wide variety of bacteria and is proposed to allow interspecies communication. Here we show that some species of bacteria can manipulate AI-2 signalling and interfere with other species' ability to assess and respond correctly to changes in cell population density. AI-2 signalling, and the interference with it, could have important ramifications for eukaryotes in the maintenance of normal microflora and in protection from pathogenic bacteria.     

The major Vibrio cholerae autoinducer and its role in virulence factor production

Vibrio cholerae, the causative agent of the human disease cholera, uses cell-to-cell communication to control pathogenicity and biofilm formation. This process, known as quorum sensing, relies on the secretion and detection of signalling molecules called autoinducers. At low cell density V. cholerae activates the expression of virulence factors and forms biofilms. At high cell density the accumulation of two quorum-sensing autoinducers represses these traits. These two autoinducers, cholerae autoinducer-1 (CAI-1) and autoinducer-2 (AI-2), function synergistically to control gene regulation, although CAI-1 is the stronger of the two signals. V. cholerae AI-2 is the furanosyl borate diester (2S,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran borate. Here we describe the purification of CAI-1 and identify the molecule as (S)-3-hydroxytridecan-4-one, a new type of bacterial autoinducer. We provide a synthetic route to both the R and S isomers of CAI-1 as well as simple homologues, and we evaluate their relative activities. Synthetic (S)-3-hydroxytridecan-4-one functions as effectively as natural CAI-1 in repressing production of the canonical virulence factor TCP (toxin co-regulated pilus). These findings suggest that CAI-1 could be used as a therapy to prevent cholera infection and, furthermore, that strategies to manipulate bacterial quorum sensing hold promise in the clinical arena.     

Quorum sensing in Gram-negative bacteria

Bacteria can communicate with each other by means of signal molecules to coordinate the behavior of the entire community,and the mechanism is referred to as quorum sensing (QS).Signal systems enable bacteria to sense the size of their densities by monitoring the concentration of the signal molecules.Among Gram-negative bacteria N-acyl-L-homoserine lactone (acyl-HSL)-dependent quorum sensing systems are particularly widespread.These systems are used to coordinate expression of phenotypes that are fundamental to the interaction of bacteria with each other and with their environment and particularly higher organisms,covering a variety of functions ranging from pathogenic to symbiotic interactions.The detailed knowledge of these bacterial communication systems has opened completely new perspectives for controlling undesired microbial activities.     

A taxa-area relationship for bacteria

A positive power-law relationship between the number of species in an area and the size of that area has been observed repeatedly in plant and animal communities. This species-area relationship, thought to be one of the few laws in ecology, is fundamental to our understanding of the distribution of global biodiversity. However, such a relationship has not been reported for bacteria, and little is known regarding the spatial distribution of bacteria, relative to what is known of plants and animals. Here we describe a taxa-area relationship for bacteria over a scale of centimetres to hundreds of metres in salt marsh sediments. We found that bacterial communities located close together were more similar in composition than communities located farther apart, and we used the decay of community similarity with distance to show that bacteria can exhibit a taxa-area relationship. This relationship was driven primarily by environmental heterogeneity rather than geographic distance or plant composition.     

分子生态学方法对油藏细菌群落结构分析的比较

目前对油藏细菌群落结构分析方法繁多,为得到准确全面的群落分析结果,必须选取合适的方法。群落分析方法的优劣进行比较分析,选取从新疆陆梁油田注水井筛出的11株单菌,测定其16srDNA序列,制成包含7个菌属、9个菌种的混合菌液。应用基于PCR扩增的三种分子生态技术DGGE、T-RFLP、建立16SrDNA文库比较和分析了混合菌液细菌多样性。使用PCR-DGGE方法时发现,DGGE方法可灵敏地检测到序列1 bp的变化,能将不同菌株分开,但该方法经过切胶测序后的的目标序列较短,信息量不大且有时有一定误差,较适合用于定性对比;而用于菌群结构的分析时应结合其他方法。T-RFLP法可区分大部分菌属,但数据库不够完整,不能确定细菌群落组成;因此也不适合单独用在细菌群落检测中,可用作多个样品种群多样性的对比或结合其他方法对样品进行系统透彻解析。建立16srDNA克隆文库法成功鉴定到7个菌属8个菌种16SrDNA序列,更适用于油藏细菌群落结构的分析。     

Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase.

Bacterial cells sense their population density through a sophisticated cell-cell communication system and trigger expression of particular genes when the density reaches a threshold. This type of gene regulation, which controls diverse biological functions including virulence, is known as quorum sensing. Quorum-sensing signals, such as acyl-homoserine lactones (AHLs), are the essential components of the communication system. AHLs regulate virulence gene expression in a range of plant and animal (including human) bacterial pathogens. AHL-producing tobacco restored the pathogenicity of an AHL-negative mutant of Erwinia carotovora. Different bacterial species may produce different AHLs, which vary in the length and substitution of the acyl chain but contain the same homoserine lactone moiety. Here we show that the acyl-homoserine lactonase (AHL-lactonase), a new enzyme from Bacillus sp., inactivates AHL activity by hydrolysing the lactone bond of AHLs. Plants expressing AHL-lactonase quenched pathogen quorum-sensing signalling and showed significantly enhanced resistance to E. carotovora infection. Our results highlight a promising potential to use quorum-sensing signals as molecular targets for disease control, thereby broadening current approaches for prevention of bacterial infections.     

冀东油田微生物驱油技术室内研究

在对冀东油田高浅北和老爷庙区块油藏状况、原油物理性质、产出水化学性质和细菌群落组成分析的基础上,通过物理模拟驱油实验来研究这2个区块实施微生物驱油技术的潜力.利用最大或然数法、倾注平板法和滚管法对产出水中的细菌群落状况进行了分析.结果表明,产出水中细菌群落较为单一,硫酸盐还原菌为优势菌群,部分油井产出水中含有好氧腐生菌,说明这2个区块具备微生物生长繁殖的条件.室内物理模拟驱油实验表明,在一次水驱的基础上,经过7周期85 d培养驱替,高浅北和老爷庙区块模型的采收率分别提高15.6%和10.7%.综合微生物学、油藏条件以及物理模拟驱油实验的研究结果,在冀东油田高浅北和老爷庙区块实施微生物驱油技术是可行的.     

Protein delivery into eukaryotic cells by type III secretion machines

Bacteria that have sustained long-standing close associations with eukaryotic hosts have evolved specific adaptations to survive and replicate in this environment. Perhaps one of the most remarkable of those adaptations is the type III secretion system (T3SS)--a bacterial organelle that has specifically evolved to deliver bacterial proteins into eukaryotic cells. Although originally identified in a handful of pathogenic bacteria, T3SSs are encoded by a large number of bacterial species that are symbiotic or pathogenic for humans, other animals including insects or nematodes, and plants. The study of these systems is leading to unique insights into not only organelle assembly and protein secretion but also mechanisms of symbiosis and pathogenesis.     

细菌Hfq蛋白的结构、功能及作用机制

非编码小RNA(small RNA, sRNA)是细菌基因转录后调控的一个重要层次,也是近十年来原核生物研究领域的焦点之一。大多数sRNA的作用与Hfq蛋白密切相关,即Hfq可以促进sRNA与其靶标mRNA的互补配对,进而影响翻译的进行或者mRNA的稳定性。笔者对Hfq的结构、Hfq参与sRNA调节作用的机制、Hfq在多种细菌中的功能表型进行了综述。Hfq是一个保守的蛋白质,在很多细菌中广泛存在,并与真核生物中参与mRNA剪切与降解活动的Sm蛋白同源。在结构上,Hfq具有两个非等同的RNA结合面,可以结合并介导多个RNA分子的相互作用,其结构体现了和功能的高度统一性。目前,对Hfq的研究主要集中于革兰氏阴性细菌中,在革兰氏阳性细菌中,Hfq的功能尚不明晰; 此外,在许多重要的细菌中,Hfq影响功能表型的具体机制也不清楚。因此,今后有必要进一步精细研究Hfq的分子结构特征和功能特点,深入分析Hfq对细菌表型多样化的影响机制,探究Hfq影响靶标分子和功能表型的详尽机制。     

PLA非织造材料可生物降解环境中菌群结构分析及调控

为建立非织造材料可生物降解性能的快速检测方法,选择土壤这一自然降解环境介质进行生物降解试验,通过对富集土壤中的混合菌群液配制成生物快速降解环境,运用平板计数和PCR-DGGE技术对该环境中降解前后的细菌菌群结构变化进行分析。结果表明,所富集的土壤细菌混合菌群不仅在传代转接过程,还是在整个生物降解试验周期中,优势菌的数量和种类始终保持相对稳定,确保生物降解的持续性。同时根据对非织造材料生物降解过程中的无机碳含量检测分析,验证了在整个降解周期中细菌菌群发生生物降解的有效性,并通过调节不同浓度的降解试验菌液,可以调控生物降解的速度,从而实现不同的生物降解效果。     

Sulphide mining by the superextensile foot of symbiotic thyasirid bivalves

In a symbiotic association between an invertebrate host and chemoautotrophic bacteria, each partner has different metabolic requirements, and the host typically supplies the bacteria with necessary reduced chemicals (sulphide or methane). Some combination of anatomical, physiological and behavioural adaptations in the host often facilitates uptake and transport of reduced chemicals to the symbionts. We have studied five species of bivalve molluscs of the family Thyasiridae (that is, thyasirids) three of which harbour chemoautotrophic bacteria. Here we show that the symbiotic bivalves extend their feet to form elongated and ramifying burrows in the sediment, most probably to gain access to reduced sulphur. Closely related bivalves (including some thyasirid species) without bacterial symbionts show no comparable foot extension behaviour. The length and number of burrows formed by chemosymbiotic thyasirids are related to the concentration of hydrogen sulphide in the sediment. The burrows are formed by the foot of each bivalve, which can extend up to 30 times the length of the shell, and may be the most extreme case of animal structure elongation documented to date.     

A receptor kinase gene of the LysM type is involved in legume perception of rhizobial signals

Plants belonging to the legume family develop nitrogen-fixing root nodules in symbiosis with bacteria commonly known as rhizobia. The legume host encodes all of the functions necessary to build the specialized symbiotic organ, the nodule, but the process is elicited by the bacteria. Molecular communication initiates the interaction, and signals, usually flavones, secreted by the legume root induce the bacteria to produce a lipochitin-oligosaccharide signal molecule (Nod-factor), which in turn triggers the plant organogenic process. An important determinant of bacterial host specificity is the structure of the Nod-factor, suggesting that a plant receptor is involved in signal perception and signal transduction initiating the plant developmental response. Here we describe the cloning of a putative Nod-factor receptor kinase gene (NFR5) from Lotus japonicus. NFR5 is essential for Nod-factor perception and encodes an unusual transmembrane serine/threonine receptor-like kinase required for the earliest detectable plant responses to bacteria and Nod-factor. The extracellular domain of the putative receptor has three modules with similarity to LysM domains known from peptidoglycan-binding proteins and chitinases. Together with an atypical kinase domain structure this characterizes an unusual receptor-like kinase.     

Bacterial disease resistance in Arabidopsis through flagellin perception

Plants and animals recognize microbial invaders by detecting pathogen-associated molecular patterns (PAMPs) such as flagellin. However, the importance of flagellin perception for disease resistance has, until now, not been demonstrated. Here we show that treatment of plants with flg22, a peptide representing the elicitor-active epitope of flagellin, induces the expression of numerous defence-related genes and triggers resistance to pathogenic bacteria in wild-type plants, but not in plants carrying mutations in the flagellin receptor gene FLS2. This induced resistance seems to be independent of salicylic acid, jasmonic acid and ethylene signalling. Wild-type and fls2 mutants both display enhanced resistance when treated with crude bacterial extracts, even devoid of elicitor-active flagellin, indicating the existence of functional perception systems for PAMPs other than flagellin. Although fls2 mutant plants are as susceptible as the wild type when bacteria are infiltrated into leaves, they are more susceptible to the pathogen Pseudomonas syringae pv. tomato DC3000 when it is sprayed on the leaf surface. Thus, flagellin perception restricts bacterial invasion, probably at an early step, and contributes to the plant's disease resistance.     

Gene transfer to plants by diverse species of bacteria

Agrobacterium is widely considered to be the only bacterial genus capable of transferring genes to plants. When suitably modified, Agrobacterium has become the most effective vector for gene transfer in plant biotechnology. However, the complexity of the patent landscape has created both real and perceived obstacles to the effective use of this technology for agricultural improvements by many public and private organizations worldwide. Here we show that several species of bacteria outside the Agrobacterium genus can be modified to mediate gene transfer to a number of diverse plants. These plant-associated symbiotic bacteria were made competent for gene transfer by acquisition of both a disarmed Ti plasmid and a suitable binary vector. This alternative to Agrobacterium-mediated technology for crop improvement, in addition to affording a versatile 'open source' platform for plant biotechnology, may lead to new uses of natural bacteria-plant interactions to achieve plant transformation.     

A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria

Bacteria have developed mechanisms to communicate and compete with one another in diverse environments. A new form of intercellular communication, contact-dependent growth inhibition (CDI), was discovered recently in Escherichia coli. CDI is mediated by the CdiB/CdiA two-partner secretion (TPS) system. CdiB facilitates secretion of the CdiA 'exoprotein' onto the cell surface. An additional small immunity protein (CdiI) protects CDI(+) cells from autoinhibition. The mechanisms by which CDI blocks cell growth and by which CdiI counteracts this growth arrest are unknown. Moreover, the existence of CDI activity in other bacteria has not been explored. Here we show that the CDI growth inhibitory activity resides within the carboxy-terminal region of CdiA (CdiA-CT), and that CdiI binds and inactivates cognate CdiA-CT, but not heterologous CdiA-CT. Bioinformatic and experimental analyses show that multiple bacterial species encode functional CDI systems with high sequence variability in the CdiA-CT and CdiI coding regions. CdiA-CT heterogeneity implies that a range of toxic activities are used during CDI. Indeed, CdiA-CTs from uropathogenic E.?coli and the plant pathogen Dickeya dadantii have different nuclease activities, each providing a distinct mechanism of growth inhibition. Finally, we show that bacteria lacking the CdiA-CT and CdiI coding regions are unable to compete with isogenic wild-type CDI(+) cells both in laboratory media and on a eukaryotic host. Taken together, these results suggest that CDI systems constitute an intricate immunity network with an important function in bacterial competition.     

Protective role of phospholipid oxidation products in endotoxin-induced tissue damage

Lipopolysaccharide (LPS), an outer-membrane component of Gram-negative bacteria, interacts with LPS-binding protein and CD14, which present LPS to toll-like receptor 4 (refs 1, 2), which activates inflammatory gene expression through nuclear factor kappa B (NF kappa B) and mitogen-activated protein-kinase signalling. Antibacterial defence involves activation of neutrophils that generate reactive oxygen species capable of killing bacteria; therefore host lipid peroxidation occurs, initiated by enzymes such as NADPH oxidase and myeloperoxidase. Oxidized phospholipids are pro-inflammatory agonists promoting chronic inflammation in atherosclerosis; however, recent data suggest that they can inhibit expression of inflammatory adhesion molecules. Here we show that oxidized phospholipids inhibit LPS-induced but not tumour-necrosis factor-alpha-induced or interleukin-1 beta-induced NF kappa B-mediated upregulation of inflammatory genes, by blocking the interaction of LPS with LPS-binding protein and CD14. Moreover, in LPS-injected mice, oxidized phospholipids inhibited inflammation and protected mice from lethal endotoxin shock. Thus, in severe Gram-negative bacterial infection, endogenously formed oxidized phospholipids may function as a negative feedback to blunt innate immune responses. Furthermore, identified chemical structures capable of inhibiting the effects of endotoxins such as LPS could be used for the development of new drugs for treatment of sepsis.     

青岛海域固氮细菌的系统发育多样性研究

采用严格人工无氮海水培养基富集、分离培养方法及用3对固氮基因(nifH)引物进行PCR检测,从青岛近海沉积物和海水中分离到16株异养型可培养海洋固氮细菌,经16S rDNA全序列测定分析了它们的系统发育多样性。结果显示,16株菌分布于Alphaproteobacteria、Gammaproteobacteria、Flavobacteria的3个纲中,分别代表着6个属、10个种,其中有50%归于Pseudoalteromonas属;海底沉积物中固氮菌的多样性要远高于海水,并在其中发现2个潜在新种。研究表明,青岛近海海域的固氮菌具有一定程度的多样性,它们大部分在系统发育关系上与分离自韩国、南极洲、新喀里多尼岛等海水的标准菌高度同源,但也存在少量潜在新物种。结果可为其他不同海域异养固氮菌的多样性及其生态功能研究提供有益参考。     

仁扇舟蛾幼虫肠道可培养细菌群落结构分析

【目的】了解仁扇舟蛾(Clostera restitura)肠道共生细菌的主要类群及其群落结构特征,明确仁扇舟蛾幼虫前、中和后肠可培养细菌的种类及群落结构组成,为进一步研究特异功能细菌的生理生化特征和功能提供基础。【方法】选取仁扇舟蛾5龄幼虫进行肠道解剖,分离前、中和后肠不同肠段,研磨稀释10^-1~10^-6,分别涂布于NA和LB固体培养基上,每个处理重复3次,28 ℃培养72 h。后对前、中和后肠可培养细菌进行分离纯化培养,提取细菌基因组DNA,利用 16S rDNA 基因序列分析和PCR扩增技术,获得细菌基因组序列,后与NCBI GenBank数据库进行Blast同源性比对,参考序列相似度98%以上近缘序列的物种信息,结合菌落形态特征和生理生化特性鉴定细菌种类,利用MEGA 7.0软件,采用邻接法(Neighbor-Joining)构建系统进化树。【结果】从仁扇舟蛾5龄幼虫的前、中和后肠中共分离获得22株可培养细菌,分属于变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)和放线菌门(Actinobacteria),共13个属,22个种。其中:假单胞菌属(Pseudomonas)4株,罗尔斯通菌属(Ralstonia)3株,芽孢杆菌属(Bacillus)3株,嗜麦芽寡养单胞菌属(Stenotrophomonas)2株,气球菌属(Aerococcus)2株,其余微小杆菌属(Exiguobacterium)、微球菌属(Micrococcus)、短小杆菌属(Curtobacterium)、伯克氏菌属(Burkholderia)、类芽孢杆菌属(Paenibacillus)、节杆菌属(Arthrobacter)、短状杆菌属(Brachybacterium)和两面神菌属(Janibacter)各1株。细菌的种类存在差异,前、中和后肠不同肠段的细菌种类分别为5、10和7种。3个肠段共有的细菌种类是皮氏罗尔斯菌(Ralstonia pickettii)和斯氏假单胞菌(Pseudomonas stutzeri)。【结论】仁扇舟蛾5龄幼虫肠道的可培养细菌种类较为丰富,其中以变形菌门和厚壁菌门为优势菌群。不同肠段中可培养细菌的多样性和群落结构存在差异,其中以中肠可培养细菌种类较为丰富。此次从仁扇舟蛾肠道中分离到与单宁降解相关的细菌,分析表明仁扇舟蛾肠道菌群与宿主的取食习性有关,肠道细菌可能在克服植物次生代谢物质的化学防御上发挥作用。     

Synthetic biology: engineering Escherichia coli to see light

We have designed a bacterial system that is switched between different states by red light. The system consists of a synthetic sensor kinase that allows a lawn of bacteria to function as a biological film, such that the projection of a pattern of light on to the bacteria produces a high-definition (about 100 megapixels per square inch), two-dimensional chemical image. This spatial control of bacterial gene expression could be used to 'print' complex biological materials, for example, and to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps.