利用序列保守模体和局部构象信息预测转录因子结合位点

转录因子结合位点的计算预测是研究基因转录调控的重要环节,但常用的位置特异得分矩阵方法预测特异性偏低.通过深入分析结合位点的生物特征,提出了一种综合利用序列保守模体和局部构象信息的结合位点预测方法,以极大相关得分矩阵作为保守模体的描述模型,并根据二苷参数模型计算位点序列的局部构象,将两类信息得分组合为多维特征向量,在二次判别分析的框架下进行训练和滑动预测.预测过程中还引入了位置信息量以优化似然得分和过滤备选结果.针对大肠杆菌CRP和Fis结合位点数据的留一法测试结果表明,描述模型的改进和多种信息的融合能有效地改善预测方法的性能,大幅度提高特异性.     

Intrinsic RNA Binding by the Eukaryotic Initiation Factor 4F Depends on a Minimal RNA Length but Not on the m7G Cap

The eukaryotic initiation factor 4F (eIF4F) is thought to be the first factor to bind mRNA during 7-methylguanosine (m⁷G) cap-dependent translation initiation. The multipartite eIF4F contains the cap-binding protein eIF4E, and it is assumed that eIF4F binds mRNAs primarily at the 5′ m⁷G cap structure. We have analyzed equilibrium binding of rabbit eIF4F to a series of diverse RNAs and found no impact of the 5′-cap on the stability of eIF4F-RNA complexes. However, eIF4F preferentially and cooperatively binds to RNAs with a minimum length of ∼60 nucleotides in vitro. Furthermore, translation activity in rabbit reticulocyte lysate is strongly inhibited by RNAs exceeding this length, but not by shorter ones, consistent with the notion that eIF4F in its physiological environment preferentially binds longer RNAs, too. Collectively, our results indicate that intrinsic RNA binding by eIF4F depends on a minimal RNA length, rather than on cap recognition. The nonetheless essential m⁷G cap may either function at steps subsequent to eIF4F-RNA binding, or other factors facilitate preferential binding of eIF4F to the m⁷G cap.     

应用SELEX技术检测水稻RFL转录因子的DNA结合位点

FLORICAULA/LEAFY是植物特有的转录因子,其可以通过调控下游基因的表达对植物的发育起到调控作用。水稻(Oryza sativa)中的同源基因RFL(Rice FLORICAULA/LEAFY)能够调控多个发育过程,包括开花、叶间期以及枝梗和颖花分化。指数富集配体的系统进化(SELEX)技术已经被广泛应用于体外筛选转录因子的DNA结合位点。应用SELEX技术检测水稻RFL的DNA结合序列,经过7次PCR循环富集过程获得结合特异序列,通过测序和MEME分析,鉴定到RFL的DNA结合序列为(C/A)(C/T)NN(T/C/A)G(G/T)。实验结果为进一步阐明RFL分子功能奠定了基础。     

基于碱基关联二联体位置权重矩阵预测酵母转录因子结合位点

基于已知的酵母转录因子结合位点数据资料,构建转录因子结合位点碱基关联二联体位置权重矩阵,整合碱基关联二联体位置权重矩阵和碱基保守性参量M2i,提出一种新的预测转录因子结合位点的方法(PWMSA).利用self-consistency和cross-validation两种方法对此算法进行检验,均获得了较高的预测成功率,结果表明9种转录因子结合位点的总体预测成功率超过81%,明显高于单碱基位置权重矩阵,同时与已有预测转录因子结合位点的软件进行比较,核苷酸水平上的关联系数和结合位点水平上的关联系数分别达到0.42和0.52,优于现有预测方法.     

转录因子Ets-1与β1,3 N-乙酰氨基葡萄糖基转移酶基因启动子结合活性分析

β1,3-N-乙酰氨基葡萄糖转移酶-2,-8（β3GnT-2, β3GnT-8）共同参与多聚N-乙酰氨基乳糖(［Galβ1→4GlcNAcβ1→3］n)的合成,从而使得细胞表面的相应糖链结 构延长进而影响细胞的恶性转化.已有研究表明,在全反式维甲酸诱导人白血病细胞株 HL-60分化过程中β3GnT-2,-8的表达上调,但其分子机制不明.本文旨在探讨ATRA诱导 HL-60分化过程中,转录因子Ets-1对β3GnT-2,-8表达调控的分子机制.采用10-6 mol/L ATRA 诱导人白血病细胞株HL-60向粒系分化,RT-PCR检测到细胞中Ets-1的表达 明显增加;进一步采用染色质免疫沉淀（ChIP）结合电泳迁移率变动实验（EMSA）检测 证实,有活化的Ets-1结合至β3GnT-2/-8基因调控区. 以上结果表明,转录因子Ets-1对 人白血病细胞株HL-60分化过程中β3GnT-2,-8基因有表达调控作用.     

Effect of Methanol on the Nucleotide Binding to High-Affinity Sites on Chloroplast Coupling Factor 1

The effects of methanol on the nucleotide binding to isolatedchloroplast coupling factor 1 (CF₁) were investigated. IsolatedCF₁ has four kinds of nucleotide binding sites; a barely dissociableADP-binding site (site A), two slowly exchangeable high-affinitysites with different affinities for ADP (sites B and C) whichare not catalytic sites, and several low-affinity sites (Hisaboriand Sakurai 1984). Methanol at 20% (v/v) slightly acceleratedthe binding of ADP to CF₁ but did not influence the number ofbinding sites. Methanol at 10–24% (v/v) affected neitherthe total amounts of bound adenine nucleotides (2.5 mol/molCF₁) nor the incorporation of labeled ADP from the medium (1.5mol/mol CF₁ into the slowly exchangeable sites (sites A, B,C). These results indicate that no appreciable exchange of ADPoccurred at site A at 10–24% (v/v) methanol and excludethe possibility of direct participation of nucleotide bindingat this site in the regulation of ATPase. In 32% methanol, theamount of the labeled ADP bound increased, suggesting some exchangeat site A. Methanol at 20% (v/v) greatly increased the affinitiesof sites B and C for ADP, CDP, GDP, UDP and PP_i. Conformational change of CF₁ induced by the binding of nucleotidesto site(s) B (and C) increased the resistance of CF₁ to inactivationby methanol at high concentrations or by cold treatment. (Received August 16, 1984; Accepted January 23, 1985)     

Quantitation of the Effect of ErbB2 on Epidermal Growth Factor Receptor Binding and Dimerization

The epidermal growth factor (EGF) receptor is a member of the ErbB family of receptors that also includes ErbB2, ErbB3, and ErbB4. These receptors form homo- and heterodimers in response to ligand with ErbB2 being the preferred dimerization partner. Here we use (125)I-EGF binding to quantitate the interaction of the EGF receptor with ErbB2. We show that the EGFR/ErbB2 heterodimer binds EGF with a 7-fold higher affinity than the EGFR homodimer. Because it cannot bind a second ligand, the EGFR/ErbB2 heterodimer is not subject to ligand-induced dissociation caused by the negatively cooperative binding of EGF to the second site on the EGFR homodimer. This increases the stability of the heterodimer relative to the homodimer and is associated with enhanced and prolonged EGF receptor autophosphorylation. These effects are independent of the kinase activity of ErbB2 but require back-to-back dimerization of the EGF receptor with ErbB2. Back-to-back dimerization is also required for phosphorylation of ErbB2. These findings provide a molecular explanation for the apparent preference of the EGF receptor for dimerizing with ErbB2 and suggest that the phosphorylation of ErbB2 occurs largely in the context of the EGFR/ErbB2 heterodimer, rather than through lateral phosphorylation of isolated ErbB2 subunits.     

Effect of DNA Local Conformation on the Affinity and Binding Specificity of bis-Netropsins to DNA

The interaction of short nucleotide duplexes with bis-netropsins, in which netropsin fragments are linked tail-to-tail via cis-diammineplatinum group (Nt–Pt(NH ₃ )–Nt) or aliphatic pentamethylene chain (Nt–(CH ₂ ) ₅ –Nt), has been studied. Both bis-netropsins have been shown to bind to DNA oligomer 5"-CCTATATCC-3" (I) as a hairpin with parallel orientation of netropsin fragments in 1:1 stoichiometry. Monodentate binding has been detected upon binding of bis-netropsins to other duplexes of sequences 5"-CCXCC-3" [where X = TTATT (II), TTAT (III), TTTTT (IV), and AATTT (V)] along with the binding of bis-netropsins as a hairpin. The formation of dimeric antiparallel motif between the halves of two bound bis-netropsin molecules has been observed in the complexes of Nt–(CH ₂ ) ₅ –Nt with DNA oligomers IV and V. The ratio of binding constant of bis-netropsin as a hairpin ( ₂) to monodentate binding constant ( ₁) has been shown to correlate with the width and/or conformational lability of DNA in the binding site. The share of bis-netropsin bound as a hairpin decreases in the order: TATAT > TTATT > TTAAT > TTTTT > AATTT, whereas the contribution of monodentate binding rises. The minimal strong binding site for Nt–Pt(NH ₃ )–Nt and Nt–(CH ₂ ) ₅ –Nt binding as a hairpin has been found to be DNA duplex 5"-CGTATACG-3".     

三七转录因子PnWRKY1对三七皂苷生物合成的影响

该研究以野生型三七为材料,采用同源克隆的方法,获得三七转录因子PnWRKY1基因,运用农杆菌转化法构建转基因细胞系,通过测定转基因细胞系中的总皂苷含量以及重要单体皂苷的含量,并采用qRT-PCR分析皂苷合成途径中相关基因的表达情况,为三七皂苷生物合成高效调控策略的建立提供理论依据。结果显示:(1)转录因子PnWRKY1长度为810bp,编码269个氨基酸。(2)成功构建PnWRKY1过表达载体pCAMBIA2300sPnWRKY1,经农杆菌转化获得了6株具有卡那霉素抗性的转基因细胞系(T_1~T_6),对卡那霉素基因nptⅡ进行PCR检测表明,所有细胞系均有与预期大小一致的450bp特异性条带,说明成功获得了6株PnWRKY1过表达转基因细胞系。(3)6株转基因细胞系中的PnWRKY1表达水平均极显著高于野生型细胞系,其中表达量最高的T_3细胞系比野生型增加了5.36倍。(4)过表达PnWRKY1基因细胞系的总皂苷生物合成均得到显著提高,其中T_1~T_6中总皂苷含量分别为野生型细胞系的2.46、1.98、2.67、1.74、2.54和1.98倍;6株过表达PnWRKY1细胞系中的4种单体皂苷R1、Rg1、Re、Rb1的含量与野生型细胞系相比均有不同程度的提高,且T_3细胞系中的单体皂苷Re含量最高(37.81mg/g)。(5)与野生型细胞系(WT)相比,过表达PnWRKY1细胞系中三七皂苷合成途径中的关键酶基因PnDS、PnSS和PnSE的最高表达水平分别增加3.1、4.0和4.5倍。研究表明,转录因子PnWRKY1在三七细胞中的过表达可能参与调节皂苷生物合成部分重要酶基因的表达,且PnWRKY1可能通过调控三七皂苷生物合成途径中关键酶基因的表达间接影响三七皂苷的合成。