Activation of the glmS Ribozyme Confers Bacterial Growth Inhibition

The ever‐growing number of pathogenic bacteria resistant to treatment with antibiotics call for the development of novel compounds with as‐yet unexplored modes of action. Here, we demonstrate the in vivo antibacterial activity of carba‐α‐d ‐glucosamine (CGlcN). In this mode of action study, we provide evidence that CGlcN‐mediated growth inhibition is due to glmS ribozyme activation, and we demonstrate that CGlcN hijacks an endogenous activation pathway, hence utilizing a prodrug mechanism. This is the first report describing antibacterial activity mediated by activating the self‐cleaving properties of a ribozyme. Our results open the path towards a compound class with an entirely novel and distinct molecular mechanism.     

Heterodimerization of Group I Ribozymes Enabling Exon Recombination through Pairs of Cooperative trans‐Splicing Reactions

Group I (GI) self‐splicing ribozymes are attractive tools for biotechnology and synthetic biology. Several trans‐splicing and related reactions based on GI ribozymes have been developed for the purpose of recombining their target mRNA sequences. By combining trans‐splicing systems with rational modular engineering of GI ribozymes it was possible to achieve more complex editing of target RNA sequences. In this study we have developed a cooperative trans‐splicing system through rational modular engineering with use of dimeric GI ribozymes derived from the Tetrahymena group I intron ribozyme. The resulting pairs of ribozymes exhibited catalytic activity depending on their selective dimerization. Rational modular redesign as performed in this study would facilitate the development of sophisticated regulation of double or multiple trans‐splicing reactions in a cooperative manner.     

缺氧诱导因子-1α与Wnt/β-catenin信号通路在缺氧胃癌细胞中的相互作用

目的在缺氧环境下,探讨缺氧诱导因子-1α(Hypoxia-inducible factor-1α,HIF-1α)与Wnt/β-catenin信号通路在胃癌细胞SGC-7901中的相互作用。方法将质粒β-catenin-micRNA转染SGC-7091细胞,筛选稳定转染细胞株SGC-7901-β-catenin-micRNA。将SGC-7901细胞分为对照组、脂质体组和阴性对照组,对照组:常氧培养48 h;脂质体组:常氧培养24 h后,加入10μl脂质体,培养24 h;阴性对照组:常氧培养24 h后,转染阴性对照质粒,培养24 h;设稳定转染细胞株为干扰组,常氧培养48 h。采用倍增时间试验、平板克隆形成试验及流式细胞术检测各组细胞倍增时间、平板克隆集落数及细胞周期的变化。另取SGC-7901细胞,分为对照组、缺氧组、双重缺氧组;对照组:常氧培养48 h;缺氧组:常氧培养32 h,物理缺氧培养16 h;双重缺氧组:常氧培养24 h,化学缺氧培养8 h后,再同时物理缺氧培养16 h。同时取稳定转染细胞株,分为对照干扰组、缺氧干扰组和双重缺氧干扰组。对照干扰组:常氧培养48 h;缺氧干扰组:常氧培养32 h,物理缺氧培养16 h;双重缺氧干扰组:常氧培养24 h,化学缺氧培养8 h后,再同时物理缺氧培养16 h。采用RT-PCR和Western blot法检测各组细胞中HIF-1α、β-catenin的mRNA及蛋白的表达水平。结果与对照组、脂质体组、阴性对照组比较,干扰组倍增时间延长,平板克隆集落数减少,细胞阻滞在G1期比例增加,S期减少,差异均有统计学意义(P<0.05)。缺氧组与对照组、双重缺氧组与缺氧组、缺氧干扰组与对照干扰组及双重缺氧干扰组与缺氧干扰组相比,HIF-1α、β-catenin的mRNA及蛋白表达水平均升高,差异有统计学意义(P均<0.05)。缺氧干扰组与缺氧组及双重缺氧干扰组与双重缺氧组比较,β-catenin、HIF-1α的mRNA及蛋白表达水平均降低,差异有统计学意义(P均<0.05)。结论 HIF-1α激活可调控Wnt/β-catenin通路,但也受控于Wnt/β-catenin通路,二者之间相互影响,相互调节。     

shRNA沉默P115基因对胃癌细胞增殖相关蛋白表达的影响及机制

目的探讨高尔基体囊泡转运蛋白(colgi-vesicular transport protein,P115)基因沉默对胃癌细胞株BGC-823中增殖相关因子细胞周期素D1(cyclinD1)、微小染色体维持缺陷蛋白2(mini chromosome maintenance protein 2,Mcm2)和增殖细胞核抗原(proliferating Cell Nuclear Antigen,PCNA)表达的影响及其可能的机制。方法采用脂质体介导法将重组表达质粒P115-shRNA2(P115-shRNA2组)和阴性对照质粒shNC(阴性对照组)转染至高表达P115的胃癌细胞株BGC-823中,并设未转染组,经G418筛选出稳定转染细胞,实时定量PCR(Real-time PCR)法检测细胞中P115、巨噬细胞移动抑制因子(macrophage migration inhibitory factor,MIF)、cyclinD1、Mcm2和PCNA基因mRNA的转录水平;Western blot法检测细胞中P115、MIF、pERK1/2、cyclinD1、Mcm2和PCNA蛋白表达水平;免疫共沉淀法检测BGC-823细胞中P115与MIF间的相互作用;ELISA法检测细胞上清液中MIF的分泌水平。结果与未转染组和阴性对照组相比,P115-shRNA2组细胞中P115、MIF、cyclinD1、Mcm2和PCNA的mRNA和蛋白表达水平均明显降低,ERK1/2的磷酸化水平明显下调,BGC-823细胞培养上清中MIF的含量明显降低;P115蛋白可在抗MIF的免疫沉淀物中检出,P115和MIF在BGC-823细胞中存在特异性的相互作用。结论 P115基因沉默下调胃癌细胞中cyclinD1、Mcm2和PCNA的表达,其分子机制可能与P115通过调控MIF的表达和分泌,进而启动下游的ERK1/2信号通路有关。P115可作为研究胃癌细胞增殖分子机制的新靶点。     

Structural Study of the Partially Disordered Full‐Length δ Subunit of RNA Polymerase from Bacillus subtilis

The partially disordered δ subunit of RNA polymerase was studied by various NMR techniques. The structure of the well‐folded N‐terminal domain was determined based on inter‐proton distances in NOESY spectra. The obtained structural model was compared to the previously determined structure of a truncated construct (lacking the C‐terminal domain). Only marginal differences were identified, thus indicating that the first structural model was not significantly compromised by the absence of the C‐terminal domain. Various ¹⁵N relaxation experiments were employed to describe the flexibility of both domains. The relaxation data revealed that the C‐terminal domain is more flexible, but its flexibility is not uniform. By using paramagnetic labels, transient contacts of the C‐terminal tail with the N‐terminal domain and with itself were identified. A propensity of the C‐terminal domain to form β‐type structures was obtained by chemical shift analysis. Comparison with the paramagnetic relaxation enhancement indicated a well‐balanced interplay of repulsive and attractive electrostatic interactions governing the conformational behavior of the C‐terminal domain. The results showed that the δ subunit consists of a well‐ordered N‐terminal domain and a flexible C‐terminal domain that exhibits a complex hierarchy of partial ordering.     

PLCε基因shRNA重组腺病毒表达质粒的构建及鉴定

目的构建携带绿色荧光蛋白(GFP)标签的表达PLCε基因shRNA的重组腺病毒质粒Ad-U6-PLCε,为应用基因沉默技术研究膀胱癌的基因治疗奠定基础。方法将干扰质粒pGenesil-PLCε及阴性对照质粒pGenesil-NP的表达启动子U6及shRNA序列克隆至带有增强型绿色荧光蛋白(EGFP)报告基因的穿梭质粒pAdTrack,经酶切及测序鉴定正确后,将重组穿梭质粒经PmeI线性化,转化感受态AdEasier。重组pAdEasy-U6-PLCε质粒经PacI线性化后,转染HEK-293细胞,包装重组腺病毒Ad-U6-PLCε,经大量扩增后测定病毒滴度,RT-PCR及Western blot检测T24细胞内PLCε的表达情况。结果酶切及测序鉴定证实pAdTrack-U6-PLCε及重组pAdEasy-U6-PLCε质粒构建正确,并成功转染至HEK-293细胞,重组腺病毒Ad-U6-PLCε滴度达1.5×1012,经重组腺病毒感染的T24细胞内PLCεmRNA及蛋白表达均明显降低(P<0.05)。结论已成功构建针对PLCε基因的shRNA重组腺病毒载体Ad-U6-PLCε,为应用基因沉默技术研究PLCε对膀胱癌发生发展的作用奠定了基础。     

Nanopore-Based Analysis of Chemically Modified DNA and Nucleic Acid Drug Targets

Nucleic acids are central figures in many of life’s key molecular processes, e.g., enzymatic activity, epigenetics/gene regulation, viral replication, aging, cancer, and other diseases. Over the past two decades, nanopores have emerged as a new tool for studying the properties of nucleic acids at the single-molecule level. In this review, we summarize the use of nanopores as sensors of nucleic acid structure, particularly for studying chemically modified and damaged DNA, and for probing the interactions of small-molecule drugs with nucleic acid targets.