Modulation of bacterial quorum sensing with synthetic ligands: systematic evaluation of N-acylated homoserine lactones in multiple species and new insights into their mechanisms of action

Bacteria use a language of low molecular weight ligands to assess their population densities in a process called quorum sensing. This chemical signaling process plays a pivotal role both in the pathogenesis of infectious disease and in beneficial symbioses. There is intense interest in the development of synthetic ligands that can intercept quorum-sensing signals and attenuate these divergent outcomes. Both broad-spectrum and species-selective modulators of quorum sensing hold significant value as small-molecule tools for fundamental studies of this complex cell-cell signaling process and for future biomedical and environmental applications. Here, we report the design and synthesis of focused collections of non-native N-acylated homoserine lactones and the systematic evaluation of these approximately 90 ligands across three Gram-negative bacterial species: the pathogens Agrobacterium tumefaciens and Pseudomonas aeruginosa; the model symbiont Vibrio fischeri. This study is the first to report and compare the activities of a set of ligands across multiple species and has revealed some of the most potent synthetic modulators of quorum sensing to date. Moreover, several of these ligands exhibit agonistic or antagonistic activity in all three species, while other ligands are only active in one or two species. Analysis of the screening data revealed that at least a subset of these ligands modulate quorum sensing via a partial agonism mechanism. We also demonstrate that selected ligands can either inhibit or promote the production of elastase B, a key virulence factor in wild-type P. aeruginosa, depending on their concentrations. Overall, this work provides broad insights into the molecular features required for small-molecule inhibition or activation of quorum sensing in Gram-negative bacteria. In addition, this study has supplied an expansive set of chemical tools for the further investigation of quorum-sensing pathways and responses.     

Proteome analysis and identification of symbiosis-related proteins from Medicago truncatula Gaertn. by two-dimensional electrophoresis and mass spectrometry

Time-course analysis of root protein profiles was studied by two-dimensional gel electrophoresis and silver staining in the model plant Medicago truncatula, inoculated either with the arbuscular mycorrhizal fungus Glomus mosseae or with the nitrogen fixing bacterium Sinorhizobium meliloti. Protein modifications in relation to the development of both symbioses included down- and upregulations, as well as newly induced polypeptides. Matrix assisted laser desorption/ionization-time of flight-mass spectrometry after trypsin digestion clearly identified one polypeptide induced in nodulated roots as a M. truncatula leghemoglobin. Internal sequencing with a quadrupole time-of-flight mass spectrometer and database searches confirmed the induction of proteins previously described in root symbioses, and revealed the implication of other proteins. In nodulated roots, one polypeptide was identified as an elongation factor Tu from S. meliloti, while another one could not be assigned a function. In mycorrhizal roots, analyzed proteins also included a protein of unknown function, as well as a glutathione-S-transferase, a fucosidase, a myosin-like protein, a serine hydroxymethyltransferase and a cytochrome-c-oxidase. These results emphasize the usefulness of proteome analysis in identifying molecular events occurring in plant root symbioses.     

Detection of bacterial quorum sensing <Emphasis Type="Italic">N</Emphasis>-acyl homoserine lactones in clinical samples

Bacteria communicate among themselves using certain chemical signaling molecules. These signaling molecules generally are N-acyl homoserine lactones (AHLs) in Gram-negative bacteria and oligopeptides in Gram-positive bacteria. In addition, both Gram-positive and Gram-negative bacteria produce a family of signaling molecules known as autoinducer-2 that they employ for their communications. Bacteria coordinate their behavior by releasing and responding to the chemical signaling molecules present in proportion to their population density. This phenomenon is known as quorum sensing. The role of bacteria in the pathogenesis of several diseases, including gastrointestinal (GI) disorders, is well established. Moreover, rather recently bacterial quorum sensing has been implicated in the onset of bacterial pathogenicity. Thus, we hypothesized that the signaling molecules involved in bacterial communication may serve as potential biomarkers for the diagnosis and management of several bacteria-related diseases. For that, we previously developed a method based on genetically engineered whole-cell sensing systems for the rapid, sensitive, cost-effective and quantitative detection of AHLs in biological samples, such as saliva and stool, from both healthy and diseased individuals with GI disorders. Although various analytical methods, based on physical-chemical techniques and bacterial whole-cell biosensors, have been developed for the detection of AHLs in the supernatants of bacterial cultures, only a few of them have been applied to AHL monitoring in real samples. In this paper, we report work performed in our laboratory and review that from others that describes the detection of AHLs in biological, clinical samples, and report some of our recent experimental results.     

Roseobacticides: small molecule modulators of an algal-bacterial symbiosis

Marine bacteria and microalgae engage in dynamic symbioses mediated by small molecules. A recent study of Phaeobacter gallaeciensis, a member of the large roseobacter clade of α-proteobacteria, and Emiliania huxleyi, a prominent member of the microphytoplankton found in large algal blooms, revealed that an algal senescence signal produced by E. huxleyi elicits the production of novel algaecides, the roseobacticides, from the bacterial symbiont. In this report, the generality of these findings are examined by expanding the number of potential elicitors. This expansion led to the identification of nine new members of the roseobacticide family, rare bacterial troponoids, which provide insights into both their biological roles and their biosynthesis. The qualitative and quantitative changes in the levels of roseobacticides induced by the additional elicitors and the elicitors' varied efficiencies support the concept of host-targeted roseobacticide production. Structures of the new family members arise from variable substituents at the C3 and C7 positions of the roseobacticide core as the diversifying elements and suggest that the roseobacticides result from modifications and combinations of aromatic amino acids. Together these studies support a model in which algal senescence converts a mutualistic bacterial symbiont into an opportunistic parasite of its hosts.     

Differential analogue binding by two classes of c-di-GMP riboswitches

The ability of bacteria to adapt to a changing environment is essential for their survival. One mechanism bacteria have evolved to sense environmental cues and translate these signals into phenotypic changes uses the second messenger signaling molecule, cyclic diguanosine monophosphate (c-di-GMP). In addition to several classes of protein receptors, two classes of c-di-GMP-binding riboswitches (class I and class II) have been identified as downstream targets of the second messenger in this signaling pathway. The crystal structures of both riboswitch classes bound to c-di-GMP were previously reported. Here, we further investigate the mechanisms that RNA has evolved for recognition and binding of this second messenger. Using a series of c-di-GMP analogues, we probed the interactions made in the RNA-ligand complex for both classes of riboswitches to identify the most critical elements of c-di-GMP for binding. We found that the structural features of c-di-GMP required for binding differ between these two effectors and that the class II riboswitch is much less discriminatory in ligand binding than the class I riboswitch. These data suggest an explanation for the predicted preferential use of the class I motif over the class II motif in the c-di-GMP signaling pathway.     

Gel-based fluorescent proteomic tools for investigating cell redox signaling. A mini-review

The specific chemical reactivity of thiol groups makes protein cysteines susceptible to reactions with reactive oxygen species (ROS) and reactive nitrogen species (RNS) resulting in the formation of various reversible and irreversible oxidative post-translational modifications (oxPTMs). This review highlights a number of gel-based redox proteomic approaches to detect protein oxPTMs, with particular emphasis on S-nitrosylation, which we believe are currently one of the most accurate way to analyze changes in the redox status of proteins. The information collected in this review relates to the recent progress regarding methods for the enrichment and identification of redox-modified proteins, with an emphasis on fluorescent gel proteomics. Gel-based fluorescent proteomic strategies are low-cost and easy-to-use tools for investigating the thiol proteome and can provide substantial information on redox signaling.     

Low pH changes the profile of nodulation factors produced by Rhizobium tropici CIAT899

Rhizobium tropici CIAT899 has been cataloged as a nodulator of bean, a plant often growing in areas characterized by highly acidic soils. The purpose of this work was to explore the effects of acidity on the production of Nod factors by this strain and their impact on the establishment of effective symbioses. We report that acidity increases rhizobial Nod factors production, and we exhaustively study the nodulation factor structures produced under abiotic stress. Significant differences were observed between the structures produced at acid and neutral pH: 52 different molecules were produced at acid pH, 29 at neutral pH, and only 15 are common to bacteria grown at pH 7.0 or 4.5. The results indicate that R. tropici CIAT899 has successfully adapted to life in acidic soils and is a good inoculant for the bean under these conditions.     

高效液相色谱和质谱法对产酸克雷伯氏菌SG-11生物合成吲哚-3-乙酸代谢途径的研究

产酸克雷伯氏菌 (Klebsiellaoxytoca)SG 1 1是从水稻根面分离的植物根际促生细菌 ,具有生物固氮能力。利用HPLC和GC MS对该菌的代谢产物进行了定性定量分析 ,结果表明该菌能产生较高浓度的吲哚 3 乙酸(IAA) ;对其代谢途径的研究结果证明 ,该菌以吲哚 3 丙酮酸代谢途径合成IAA。     

Recent progress in small molecule fluorescent probes for nitroreductase

This review aims to provide a summary of the progress in fluorescent probes for nitroreductase (NTR) in recent years and displays the main fluorescent mechanisms that have been applied to design probes.     

高效液相色谱和质谱法对产酸克雷伯氏菌SG-11生物合成吲哚-3-乙酸代谢途径的研究

 产酸克雷伯氏菌 (Klebsiellaoxytoca)SG 1 1是从水稻根面分离的植物根际促生细菌 ,具有生物固氮能力。利用HPLC和GC MS对该菌的代谢产物进行了定性定量分析 ,结果表明该菌能产生较高浓度的吲哚 3 乙酸(IAA) ;对其代谢途径的研究结果证明 ,该菌以吲哚 3 丙酮酸代谢途径合成IAA。     

Establishing Communication Between Artificial Cells

Communication between artificial cells is essential for the realization of complex dynamical behaviors at the multi-cell level. It is also an important prerequisite for modular systems design, because it determines how spatially separated functional modules can coordinate their actions. Among others, molecular communication is required for artificial cell signaling, synchronization of cellular behaviors, computation, group-level decision-making processes and pattern formation in artificial tissues. In this review, an overview of various recent approaches to create communicating artificial cellular systems is provided. In this context, important physicochemical boundary conditions that have to be considered for the design of the communicating cells are also described, and a survey of the most striking emergent behaviors that may be achieved in such systems is given.     

Chemical signaling among bacteria and its inhibition

Generations of chemists and biologists have conducted research on natural products and other metabolites produced by bacteria and other microorganisms. This has led to an explosion in knowledge concerning the mechanism by which such natural products are made, ultimately allowing custom redesign of many of these molecules for increased potency and selectivity as therapeutic drugs. Along the way, scientists have begun to appreciate that the bacterial world is teeming with life on a scale hardly conceivable, with constant communication within the bacterial world and with outside neighbors, such as plants and mammals. Only in recent years have some of the signaling molecules that comprise these elaborate forms of communication been characterized in any sort of chemical detail, which has in turn peaked interest in the intricate biology of this micro-world and its interactions with the macro-world.     

Signal amplification by allosteric catalysis

In this article we unify a series of recent studies on bio- and chemosensors under a single signaling strategy: signal amplification by allosteric catalysis (SAAC). The SAAC strategy mimics biological signal transduction processes, where molecular recognition between an external signal and a protein receptor is allosterically transduced into catalytically amplified chemical information (usually second messengers). Several recent biosensing and chemosensing studies apply this nature-inspired strategy by using engineered allosteric enzymes, ribozymes, or regulatable organic catalysts. The factors pertinent to achieving high sensitivity and specificity in SAAC strategies are analyzed. The authors believe that these early studies from a variety of research groups have opened up a new venue for the development of sensing technologies where molecular recognition and catalysis can be coupled for practical purposes.     

用于检测生物体系中线粒体活性氧的荧光探针

In addition to being the energy powerhouse of the cell, mitochondria are an important source of reactive oxygen species (ROS) during the process of molecular oxygen metabolism. Mitochondrial ROS are closely associated with normal physiological functions as well as human diseases, and participate in cell signaling, nucleic acid and protein damage, and oxidative stress induction. However, the complicated interplay between mitochondrial ROS and the cellular pathological state has not been fully elucidated. It is expected that research on the mitochondrial ROS undertaking in the molecular pathogenesis of human diseases would benefit from development of efficient tools for the detection of these ROS. In recent years, an increasing number of fluorescent probes for mitochondrial ROS with high sensitivity and selectivity have been developed. Here, we present a review of the recent advances in small molecular fluorescent probes for selective detection of ROS inside the mitochondria. In this review, the design, synthesis, characteristics, and applications of the published fluorescent probes for mitochondrial ROS are discussed in detail.     

Recent Progress in Two-Dimensional Antimicrobial Nanomaterials

Nowadays, microorganisms, including bacteria and viruses, are regarded as new environmental pollutants and pose serious threats to public health. Yet, traditional disinfection approaches for bacteria and viruses are generally ineffective. Furthermore, they exhibit the disadvantages of high-energy consumption, environmental pollution, high cost, and toxic byproduct generation. In this respect, nanomaterials display promising antimicrobial capabilities due to their unique properties and provide solutions to the abovementioned issues. Herein, recent progress in the development of 2D nanomaterials displaying antimicrobial capabilities is highlighted. The structures, morphologies, and performances of essential metal, graphene, and nitride-based 2D antibacterial nanomaterials are summarized in detail. In addition, possible antimicrobial mechanisms and the relationship between structure and antimicrobial efficiency are elaborated.     

Recent Advances on Electrochemical Sensors Based on Electroactive Bacterial Systems for Toxicant Monitoring: A Minireview

In recent years, there have been advancements in the development of bacterial electrochemical sensors for toxicity monitoring, especially through utilization of electroactive bacteria. Accordingly, this mini review summarizes the recent advances in the design of bacterial-based electrochemical sensors with a specific discussion of main methodologies used for preparation of bioelectrodes based on electroactive bacteria. Additionally, current trends in the design of efficient and high performing bacterial electrochemical sensors for toxicity monitoring are presented. An overview of the most relevant findings and challenges of this technology for practical are provided and might serve as a general outlook for planning further research.     

食源性致病菌快速检测方法研究进展

食源性致病菌污染是导致食品安全问题的重要因素,食源性致病菌的检测已成为近年来研究的热点。以免疫分析、分子生物学、生物传感器、代谢组学、核酸适配体等技术为基础的快速检测方法发展迅速,已成为检测食源性致病菌的主要方法。该文结合近年来各种快速检测方法的相关研究进展,介绍了以上述技术为基础的快速检测食源性致病菌的方法,并讨论了现有方法存在的问题和未来的发展方向,以期为食源性致病菌的防控和保障消费者身心健康提供借鉴。     

非金属掺杂改性TiO_2光催化剂的机理

为了扩展TiO2光催化剂对可见光的利用,以非金属元素对其进行掺杂和改性是近年来很活跃的研究内容,文献报道主要有氮、碳、硫、氟等非金属元素的改性结果。各种不同的改性方法如高温气氛还原、脉冲激光沉积、离子溅射、机械化学、溶液湿法等都可以得到非金属元素改性。本文重点探讨了氮改性TiO2光催化剂的结果,氮改性TiO2的方法和改性机理,讨论了氮改性TiO2的结构及其对可见光的利用机理等,对碳、硫、氟等元素掺杂改性也作了简要介绍。     

Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations

Deoxyribonucleic acid (DNA) is composed of five major elements carbon, hydrogen, nitrogen, oxygen, and phosphorus. The substitution of any of these elements in DNA would be anticipated to have major biological implications. However, recent studies have suggested that the substitution of arsenic into DNA (As-DNA) in bacteria may be possible. To help evaluate this possibility, ab initio quantum mechanical calculations are used to show that arsenodiester and phosphodiester linkages have similar geometric and conformational properties. Based on these results, it is suggested that the As-DNA will have similar conformational properties to phosphorus-based DNA, including the maintenance of base stacking.     

Der menschlichen Duftchemie auf der Spur

Human body odours are based on an intricate interplay between skin bacteria and specific secretions of glands in the axillary region. In recent years the structure of the odorant volatiles and of amino‐acid conjugates acting as their secreted precursors were elucidated. Specific enzymes in skin bacteria cleaving the amino‐acid conjugates and thus releasing the odours were cloned, offering new targets to develop specific deodorant active molecules. At the same time, questions on the evolutionary significance of human body odours may be asked based on a number of population studies.