Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae

Some of the most productive metabolic engineering strategies involve genetic modifications that cause severe metabolic burden on the host cell. Growth-limiting genetic modifications can be more effective if they are ‘switched on’ after a population growth phase has been completed. To address this problem we have engineered dynamic regulation using a previously developed synthetic quorum sensing circuit in Saccharomyces cerevisiae. The circuit autonomously triggers gene expression at a high population density, and was linked with an RNA interference module to enable target gene silencing. As a demonstration the circuit was used to control flux through the shikimate pathway for the production of para-hydroxybenzoic acid (PHBA). Dynamic RNA repression allowed gene knock-downs which were identified by elementary flux mode analysis as highly productive but with low biomass formation to be implemented after a population growth phase, resulting in the highest published PHBA titer in yeast (1.1 mM).     

肉类腐败性假单胞菌群体感应信号分子的研究

【目的】研究两株假单胞菌的标准菌株荧光假单胞菌(Pseudomonas fluorescens)和铜绿假单胞菌(Pseudomonas aeruginosa)在纯培养条件下所释放的AHLs类信号分子种类、量和变化规律。【方法】利用乙酸乙酯等有机溶剂萃取菌种纯培养液的AHLs类信号分子, 检测手段利用HPLC-MS-MS。【结果】荧光假单胞菌释放信号分子的种类为: C4-HSL、C6-HSL、C8-HSL、3-oxo-C10-HSL、3-oxo-C12-HSL、3-oxo-C14-HSL。铜绿假单胞菌释放信号分子的种类为: C4-HSL、C6-HSL、C8-HSL、C10-SL、C12-HSL、C14-HSL、3-oxo-C8-HSL、3-oxo-C10-HSL、3-oxo-C12-HSL、3-oxo-C14-HSL。【结论】两株菌所释放各类信号分子的量均随时间变化, 当菌落数达到109?1010时信号分子的量达到峰值, 两株菌所释放各类信号分子含量差异较大。     

仿刺参“腐皮综合症”病灶处优势菌的分离鉴定及AHLs信号分子的检测

仿刺参"腐皮综合症"是一种由细菌引起的高传染性、高死亡率疾病.为了研究仿刺参"腐皮综合症"病灶处优势菌以及其是否存在N-酰基高丝氨酸内酯类化合物(AHLs)介导的群体感应系统,本文从患病仿刺参病灶处分离纯化出7株优势菌,生理生化指标测定和16S rDNA序列分析表明:菌株C6属Tenacibaculum属,菌株4属于腐败希瓦菌群(Shewanella putrefaciens group),菌株TB属于弧菌属(Vibrio),菌株BP2、BP3、BP4及BP6属于假交替单胞菌属(Pseudoalteromonas).采用AHLs的高效检测菌株根癌农杆菌(Agrobacterium tumefaciens KYC55)对优势菌的AHLs活性进行检测,其中菌株C6、4、TB、BP3及BP4存在以AHLs为信号分子的群体感应系统,菌株BP2与BP6则无AHLs活性;不同细菌AHLs活性不同,AHLs活性从高到低顺序为4＞TB＞BP4＞BP3＞C6.     

Rational design of ‘controller cells’ to manipulate protein and phenotype expression

Coordination between cell populations via prevailing metabolic cues has been noted as a promising approach to connect synthetic devices and drive phenotypic or product outcomes. However, there has been little progress in developing ‘controller cells’ to modulate metabolic cues and guide these systems. In this work, we developed ‘controller cells’ that manipulate the molecular connection between cells by modulating the bacterial signal molecule, autoinducer-2, that is secreted as a quorum sensing (QS) signal by many bacterial species. Specifically, we have engineered Escherichia coli to overexpress components responsible for autoinducer uptake (lsrACDB), phosphorylation (lsrK), and degradation (lsrFG), thereby attenuating cell–cell communication among populations. Further, we developed a simple mathematical model that recapitulates experimental data and characterizes the dynamic balance among the various uptake mechanisms. This study revealed two controller ‘knobs’ that serve to increase AI-2 uptake: overexpression of the AI-2 transporter, LsrACDB, which controls removal of extracellular AI-2, and overexpression of the AI-2 kinase, LsrK, which increases the net uptake rate by limiting secretion of AI-2 back into the extracellular environment. We find that the overexpression of lsrACDBFG results in an extraordinarily high AI-2 uptake rate that is capable of completely silencing QS-mediated gene expression among wild-type cells. We demonstrate utility by modulating naturally occurring processes of chemotaxis and biofilm formation. We envision that ‘controller cells’ that modulate bacterial behavior by manipulating molecular communication, will find use in a variety of applications, particularly those employing natural or synthetic bacterial consortia.     

A modular autoinduction device for control of gene expression in Bacillus subtilis

Intense synthesis of proteins and chemicals in engineered microbes impose metabolic burden, frequently leading to reduced growth and heterogeneous cell population. Thus, the correct balance between growth and production is important. Such balance can be engineered through dynamic control of pathways, but few broadly applicable tools are available to achieve this. We present an autonomous control of gene expression mediated by quorum sensing in Bacillus subtilis, able to self-monitor and induce expression without human supervision. Two variations of the induction module and seven of the response module were engineered generating a range of induction folds and strengths for gene expression control. Our strongest response promoter is 2.5 and 3.2 times stronger than the well-characterized promoters P_srfA and P_veg, respectively. We applied our strongest autoinduction device for the production of the vitamin B₂. This study presents a toolbox of autoinduction modules for B. subtilis that is modular and tunable.     

Biofilm and Quorum sensing mediated pathogenicity in Pseudomonas aeruginosa

The emergence of multidrug resistance has become an alarming and lifethreatening phenomenon for humans. Various mechanisms are involved in the development of resistance in bacteria towards antimicrobial compounds and immune system. Bacterial biofilm is a complicated, selfdefensive, rigid structure of bacteria crowded together to develop a selfrecessive nature, which enhances the ability to cause infections much easier in the living host. P. aeruginosa biofilm formation is supported by extracellular polymeric substances (EPS) such as exopolysaccharides, extracellular DNA (eDNA), proteins and biomolecules. Published evidences suggest that biofilm formation can also be the result of several other mechanisms such as cell signaling or communication. Bacterial biofilm is also regulated by strong intercellular communication known as Quorum Sensing (QS). It is a cellular communication mechanism involving autoinducers and regulators. In P. aeruginosa, Acyl Homoserine Lactone, the prime signaling molecule, controls approximately 300 genes responsible for various cellular functions, including its pathogenesis. The surrounding environment and metabolism have a specific effect on the biofilm and QS, thus, understanding the involvement of QS in the biofilm developing mechanism is still complicated and complex to understand. Therefore, this review will include basic knowledge of the biofilmforming mechanism and other regulatory factors involved in causing infections and diseases in the host organisms.     

A Constitutively Activating Mutation Alters the Dynamics and Energetics of a Key Conformational Change in a Ligand-free G Protein-coupled Receptor

G protein-coupled receptors (GPCRs) undergo dynamic transitions between active and inactive conformations. Usually, these conversions are triggered when the receptor detects an external signal, but some so-called constitutively activating mutations, or CAMs, induce a GPCR to bind and activate G proteins in the absence of external stimulation, in ways still not fully understood. Here, we investigated how a CAM alters the structure of a GPCR and the dynamics involved as the receptor transitions between different conformations. Our approach used site-directed fluorescence labeling (SDFL) spectroscopy to compare opsin, the ligand-free form of the GPCR rhodopsin, with opsin containing the CAM M257Y, focusing specifically on key movements that occur in the sixth transmembrane helix (TM6) during GPCR activation. The site-directed fluorescence labeling data indicate opsin is constrained to an inactive conformation both in detergent micelles and lipid membranes, but when it contains the M257Y CAM, opsin is more dynamic and can interact with a G protein mimetic. Further study of these receptors using tryptophan-induced quenching (TrIQ) methods indicates that in detergent, the CAM significantly increases the population of receptors in the active state, but not in lipids. Subsequent Arrhenius analysis of the TrIQ data suggests that, both in detergent and lipids, the CAM lowers the energy barrier for TM6 movement, a key transition required for conversion between the inactive and active conformations. Together, these data suggest that the lowered energy barrier is a primary effect of the CAM on the receptor dynamics and energetics.     

1H, 13C and 15N backbone assignments for the ligand binding domain of the Pseudomonas aeruginosa virulence regulator LasR

LasR regulates toxin production in Pseudomonas aeruginosa and its inhibition can attenuate the virulence of this opportunistic human pathogen. To aid studies of interactions with inhibitors, we report the NMR backbone assignments for the dimeric LasR ligand-binding domain.     

人血清白蛋白与金属离子作用的荧光光谱研究

通过金属离子对人血清白蛋白内源荧光的猝灭,探讨了金属离子Cu²⁺,Mn²⁺,Ni²⁺,Co²⁺,Cr³⁺等与人血清白蛋白的结合;基于Förster无辐射能量转移机理,得出了人血清白蛋白第一类Cu²⁺结合部位与214位色氨酸残基间的距离。     

Quorum sensing modulators exhibit cytotoxicity in Hodgkin’s lymphoma cells and interfere with NF-κB signaling

In recent years it has become evident that bacteria can modulate signaling pathways in host cells through the secretion of small signaling molecules. We have evaluated the cytotoxic effects and NF-κB inhibitory activities of a panel of quorum sensing molecules and their reactive analogs on Hodgkin's lymphoma cells (L428). We found that several molecules inhibited NF-κB signaling in a dose dependent manner. Three inhibitors (ITC-12, ITC-Cl and Br-Furanone) showed 50% NF-κB inhibition at concentrations less than 10 µM (4.1 µM, 12.8 µM and 9.9 µM, respectively). Furthermore, all three molecules displayed cytotoxic effects against L428 cells with IC50 values of 12.4 µM, 18.3 µM and 3.1 µM respectively after 48 h incubation. They also showed inhibition of A549 adenocarcinoma cell migration at low concentrations 5.6 µM, 2.6 µM and 7.9 µM respectively. Further analysis showed that these molecules significantly decrease the degree of expression of proteins of NF-κB subunits p50, p65 and RelB both in cytosolic and nuclear fractions. This confirms that these compounds have the potential to modulate the NF-κB pathway by suppressing their subunits and thus exhibit cytotoxicity and inactivation of NF-κB signaling in Hodgkin's lymphoma cells.