Occurrence,horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts

VDE is a homing endonuclease gene originally discovered as an intervening element in VMA1s of Saccharomyces cerevisiae. There have been two independent subfamilies of VDE, one from S. cerevisiae strain X2180-1A and the other from Saccharomyces sp. DH1-1A in the host VMA1 gene, and they share the identity of 96.3%. In order to search the occurrence, intra/interspecies transfer and molecular degeneration of VDE, complete sequences of VMA1 in 10 strains of S. cerevisiae, eight species of saccharomycete yeasts, Candida glabrata and Kluyveromyces lactis were determined. We found that six of 10 S. cerevisiae strains contain VDEs 99.7-100% identical to that of the strain X2180-1A, one has no VDE, whereas the other three harbour VDEs 100% identical to that of the strain DH1-1A. S. carlsbergensis has two VMA1s, one being 99.8% identical to that of the strain X2180-1A with VDE 100% identical to that of the strain DH1-1A and the other containing the same VMA1 in S. pastorianus with no VDE. This and other evidence indicates that intra/interspecies transmissions of VDEs have occurred among saccharomycete yeasts. Phylogenetic analyses of VMA1 and VDE suggest that the S. cerevisiae VDEs had branched earlier than other VDEs from an ancestral VDE and had invaded into the host loci as relatively late events. The two VDEs seemed to degenerate in individual host loci, retaining their splicing capacity intact. The degeneration of the endonuclease domains was distinct and, if compared, its apparent rate was much faster than that of the protein-splicing domains.     

Synthesis and In Vitro Evaluation of C-7 and C-8 Luteolin Derivatives as Influenza Endonuclease Inhibitors

The part of the influenza polymerase PA subunit featuring endonuclease activity is a target for anti-influenza therapies, including the FDA-approved drug Xofluza. A general feature of endonuclease inhibitors is their ability to chelate Mg²⁺ or Mn²⁺ ions located in the enzyme’s catalytic site. Previously, we screened a panel of flavonoids for PA inhibition and found luteolin and its C-glucoside orientin to be potent inhibitors. Through structural analysis, we identified the presence of a 3′,4′-dihydroxyphenyl moiety as a crucial feature for sub-micromolar inhibitory activity. Here, we report results from a subsequent investigation exploring structural changes at the C-7 and C-8 positions of luteolin. Experimental IC₅₀ values were determined by AlphaScreen technology. The most potent inhibitors were C-8 derivatives with inhibitory potencies comparable to that of luteolin. Bio-isosteric replacement of the C-7 hydroxyl moiety of luteolin led to a series of compounds with one-order-of-magnitude-lower inhibitory potencies. Using X-ray crystallography, we solved structures of the wild-type PA-N-terminal domain and its I38T mutant in complex with orientin at 1.9 Å and 2.2 Å resolution, respectively.     

Generation of Rho Zero Cells: Visualization and Quantification of the mtDNA Depletion Process

Human mitochondrial DNA (mtDNA) is located in discrete DNA-protein complexes, so called nucleoids. These structures can be easily visualized in living cells by utilizing the fluorescent stain PicoGreen^®. In contrary, cells devoid of endogenous mitochondrial genomes (ρ⁰ cells) display no mitochondrial staining in the cytoplasm. A modified restriction enzyme can be targeted to mitochondria to cleave the mtDNA molecules in more than two fragments, thereby activating endogenous nucleases. By applying this novel enzymatic approach to generate mtDNA-depleted cells the destruction of mitochondrial nucleoids in cultured cells could be detected in a time course. It is clear from these experiments that mtDNA-depleted cells can be seen as early as 48 h post-transfection using the depletion system. To prove that mtDNA is degraded during this process, mtDNA of transfected cells was quantified by real-time PCR. A significant decline could be observed 24 h post-transfection. Combination of both results showed that mtDNA of transfected cells is completely degraded and, therefore, ρ⁰ cells were generated within 48 h. Thus, the application of a mitochondrially-targeted restriction endonuclease proves to be a first and fast, but essential step towards a therapy for mtDNA disorders.     

Graphene Oxide‐Assisted and DNA‐Modulated SERS of AuCu Alloy for the Fabrication of Apurinic/Apyrimidinic Endonuclease 1 Biosensor

Fabrication of high‐performance surface‐enhanced Raman scattering (SERS) biosensors relies on the coordination of SERS substrates and sensing strategies. Herein, a SERS active AuCu alloy with a starfish‐like structure is prepared using a surfactant‐free method. By covering the anisotropic AuCu alloy with graphene oxide (GO), enhanced SERS activity is obtained owing to graphene‐enhanced Raman scattering and assembly of Raman reporters. Besides, stability of SERS is promoted based on the protection of GO to the AuCu alloy. Meanwhile, it is found that SERS activity of AuCu/GO can be regulated by DNA. The regulation is sequence and length dual‐dependent, and short polyT reveals the strongest ability of enhancing the SERS activity. Relying on this phenomenon, a SERS biosensor is designed to quantify apurinic/apyrimidinic endonuclease 1 (APE1). Because of the APE1‐induced cycling amplification, the biosensor is able to detect APE1 sensitively and selectively. In addition, APE1 in human serum is analyzed by the SERS biosensor and enzyme‐linked immunosorbent assay (ELISA). The data from the SERS method are superior to that from ELISA, indicating great potential of this biosensor in clinical applications.     

限制性内切酶NcoI的高效重组表达、硒代与结晶条件初步筛选

来源于珊瑚诺卡氏菌Nocardia corallina的限制性内切酶NcoI是基因工程中常用的工具酶之一。然而目前NcoI蛋白质三维结构尚未被解析,对其基因改造缺乏理论指导。为了解析NcoI的三维结构,采用大肠杆菌表达系统,高效重组表达和纯化,获得了纯度>95%的NcoI野生型和Se-NcoI硒代蛋白。质谱分析表明,重组Se-NcoI蛋白中所有硫原子成功被硒原子取代。酶切实验表明,硒代蛋白与野生型具有相似的限制酶活性。采用坐滴法筛选重组NcoI蛋白结晶条件,已在3种条件下获得针状晶体,1种条件下获得颗粒状晶体。X射线衍射初步分析晶体分辨率在0.8 nm左右,为下一步解析NcoI三维结构提供了基础。     

Interplay of population genetics and dynamics in the genetic control of mosquitoes

Some proposed genetics-based vector control methods aim to suppress or eliminate a mosquito population in a similar manner to the sterile insect technique. One approach under development in Anopheles mosquitoes uses homing endonuclease genes (HEGs)—selfish genetic elements (inherited at greater than Mendelian rate) that can spread rapidly through a population even if they reduce fitness. HEGs have potential to drive introduced traits through a population without large-scale sustained releases. The population genetics of HEG-based systems has been established using discrete-time mathematical models. However, several ecologically important aspects remain unexplored. We formulate a new continuous-time (overlapping generations) combined population dynamic and genetic model and apply it to a HEG that targets and knocks out a gene that is important for survival. We explore the effects of density dependence ranging from undercompensating to overcompensating larval competition, occurring before or after HEG fitness effects, and consider differences in competitive effect between genotypes (wild-type, heterozygotes and HEG homozygotes). We show that population outcomes—elimination, suppression or loss of the HEG—depend crucially on the interaction between these ecological aspects and genetics, and explain how the HEG fitness properties, the homing rate (drive) and the insect''s life-history parameters influence those outcomes.     

Unraveling and Overcoming Platinum Drug-Resistant Cancer Tumors with DNA Nanostructures

All chemotherapeutic treatments worldwide (>50%) use platinum-based compounds. Despite their clinical success, an increasing number of platinum drug-resistant tumors are reported, limiting the therapeutic application of these compounds. While various kinds of strategies are pursued to circumvent resistances, there remains a lack of understanding of how cancer cells develop platinum drug resistances. Within this study, the involvement of the DNA repair enzyme apurinic/apyrimidinic endonuclease 1 (APE1) in the occurrence of platinum drug resistance is directly visualized in living cells by a DNA tetrahedron-based molecular probe. Capitalizing on this biochemical insight, the suppression of the expression of APE1 in cancer cells is realized using a DNA tetrahedron-based RNA interference technique, presenting a novel strategy to overcome platinum drug resistance. This study presents the first example of Pt(IV) complex loaded tumor aptamer-modified DNA tetrahedrons with an APE1 specific small interfering RNA (siRNA) strand for suppression of APE1 expression and therapeutic treatment of patient-derived platinum drug-resistant lung cancer tumors.     

基于DNA和限制性核酸内切酶的基本逻辑门设计

由于DNA分子具有特异性、高并行性、微小性等天然特性,在信息处理过程中展现出了强大的并行计算能力和数据存储能力。该文研究将具有特异性识别功能的限制性核酸内切酶引入DNA链置换反应中,作为DNA电路的输入,通过控制立足点的生成和移除设计了是门、非门和与门3种基本逻辑门。采用Visual DSD对逻辑模型进行模拟仿真,并通过凝胶电泳实验验证设计。与以往的分子逻辑门比较,该设计反应迅速,操作简便,具有良好的扩展性,为大规模电路的设计提供了可能性。