大肠杆菌yigP基因转录调控序列的鉴定

【目的】调查yigP基因启动子的活性,并对该转录调控序列进行分析。【方法】以lacZ为报告基因,克隆启动子片段至启动子探针质粒中,通过检测β-半乳糖苷酶活性判断启动子活性,并通过克隆一系列逐步缩短的启动子片段来确定启动子所在区域。利用定点突变技术,对启动子的重要序列进行定点突变,调查其对启动子活性的影响。【结果】确定了yigP基因启动子的区域,鉴定了启动子的-10区和-35区,并发现了启动子上游存在一个负调控序列,对该序列进行了初步的研究显示其中部分序列是这种负调控作用的核心序列。【结论】对yigP基因的转录调控序列进行了鉴定,丰富了我们对基因转录调控的认识。     

Growth phase-dependent changes in the expression of global regulatory genes and associated metabolic pathways in Escherichia coli

Metabolic regulation in Escherichia coli was studied in terms of the changes in the expression of the global regulatory genes rpoD, rpoS, soxRS, cra, fadR, iclR and arcA at three different growth phases, in batch culture. The expression of rpoS and several rpoS-dependent metabolic pathway genes, such as tktB, talA, fumC, acnA, sucA, acs and sodC, were increased (∼1.5 to 2-fold) as the cells entered the late phase of growth. The changes in the expression of other global regulators and their effects on different metabolic pathway genes were less significant, as compared to rpoS, during the later phases of growth.     

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli

The genome‐scale model (GEM) of metabolism in the bacterium Escherichia coli K‐12 has been in development for over a decade and is now in wide use. GEM‐enabled studies of E. coli have been primarily focused on six applications: (1) metabolic engineering, (2) model‐driven discovery, (3) prediction of cellular phenotypes, (4) analysis of biological network properties, (5) studies of evolutionary processes, and (6) models of interspecies interactions. In this review, we provide an overview of these applications along with a critical assessment of their successes and limitations, and a perspective on likely future developments in the field. Taken together, the studies performed over the past decade have established a genome‐scale mechanistic understanding of genotype–phenotype relationships in E. coli metabolism that forms the basis for similar efforts for other microbial species. Future challenges include the expansion of GEMs by integrating additional cellular processes beyond metabolism, the identification of key constraints based on emerging data types, and the development of computational methods able to handle such large‐scale network models with sufficient accuracy.     

小鼠内耳发育核心转录因子的保守性及调控网络的比较分析

在脊椎动物内耳发育中, Six1、Six4、Pax2、Pax8、Foxi1、Dlx5、Gbx2、Irx2/3、Msx1等基因作为核心调控基因参与听基板的诱导过程。文章通过生物信息学方法, 对小鼠内耳发育的核心转录因子进行保守性分析并研究其相互调控关系, 得到小鼠内耳发育过程中核心转录因子的基因调控网络。与文献中已知的小鼠内耳发育基因调控关系相比, Pax2、Pax8、Foxi1、Dlx5基因在内耳发育中仍然起主要调控者的角色, Six1则处于被多个转录因子调节的地位, Gbx2、Irx2/3、Msx1在调控网络中也起到重要作用。对出现的差异进行了合理的分析, 同时结合构建的调控网络预测了可能存在的Msx1对Six1、Gbx2的调控作用。序列预测结果也发现了一些新的调控关系, 所涉及的转录因子包括Sox5、Lhx2、Rax、Otx1、Otx2、Pitx1、Pitx2、Nkx2-5、Irx4、Irx6、Dlx2、Hmx1/2/3、Pou4f3、Pax4、Tlx2。文章为深入了解内耳发育调控机制提供了基础信息。     

拟南芥在盐胁迫环境下SOS转录调控网络的构建及分析

研究拟南芥在高浓度盐处理环境下的基因调控网络, 有助于了解其在盐胁迫环境下保持正常生长的防御机制。针对目前广泛研究的SOS (Salt Overly Sensitive)耐盐机制, 文章整合公共数据库中盐胁迫相关的拟南芥基因组表达谱芯片, 通过反向工程方法构建了拟南芥在盐胁迫状态下的SOS转录调控网络。所获得的调控网络包含70个盐胁迫相关且高度互作的互作基因, 其中27个转录因子为主要调控节点。进而根据SOS核心基因的表达特性, 所得调控网络内的不同表达模式得到了鉴别。     

An in silico compartmentalized metabolic model of Brassica napus enables the systemic study of regulatory aspects of plant central metabolism

Biochemical network reconstructions represent valuable tools for the computational metabolic modeling of organisms that present a great biotechnological interest. An in silico multi-compartmental model of the central metabolism of the plant Brassica napus (Rapeseed) was constructed, aiming to investigate the metabolic properties of the Brassicaceae family. This family comprises many plants with major importance for the energy and nutrition sector, including the model plant Arabidopsis thaliana. The model utilized as objective function to be subsequently optimized, the biomass production of rapeseed developing embryos, which are characterized by a very high, oil content, up to 60% of biomass weight. In order to study global network properties of seed metabolism, various methods were employed, like Flux Balance Analysis, Principal Component Analysis of the flux space and reaction deletion studies, which simulate the effect of gene knock-out experiments. The model successfully simulated seed growth during the stage of oil accumulation and provided insight, regarding certain aspects of network plasticity, with the emphasis given in lipid biosynthesis regulation.     

转录因子调控植物萜类化合物生物合成研究进展

萜类化合物是植物次生代谢物中结构和数量最多的一类化合物, 它们在植物体内以及植物与环境和其它生命体的相互作用中发挥重要作用。转录因子通过调控代谢通路中基因的转录起始来调节次生代谢物质的产量。目前, 研究发现参与萜类合成的转录因子家族主要有6个, 包括AP2/ERF、bHLH、MYB、NAC、WRKY和bZIP。该文主要对其家族的结构特点、调控模式以及研究进展进行综述, 以期进一步丰富萜烯合成的网络调控, 为植物萜类相关的分子育种、优质栽培和病虫害生物防治等提供新的思路与方法。     

人与小鼠核糖体蛋白基因内含子中的转录调控位点分析

前期对酵母和果蝇核糖体蛋白(Ribosomal protein, RP)基因内含子序列中的寡核苷酸分析表明, 内含子中含有潜在的转录因子结合位点。为进一步发掘核糖体蛋白基因内含子参与转录调控的证据, 文章首先基于频率分析方法抽提出人和小鼠核糖体蛋白基因第一内含子中高频(Over-represented)出现的寡核苷酸片段 (亦称模体, Motif), 这些寡核苷酸中超过85%与已知的转录因子结合位点吻合, 是潜在的转录调控元件。对抽提出的寡核苷酸进行碱基组成分析, 发现95%以上的寡核苷酸富含碱基C和G, 而较少富含A和T。从寡核苷酸在内含子中的分布情况看, 它们相对靠近第一内含子的5′端, 即距离基因转录起始位点和上游区域较近。推测这些特征可能与基因转录调控有关。     

精子发生过程中基因表达转录水平的调控

哺乳动物精子发生于睾丸的生精小管, 是一个高度复杂的细胞分裂和分化过程, 涉及到错综复杂的基因表达调控过程, 包括转录和转录后水平的调控, 其中任何一个环节出错都可能导致雄性不育。因此, 揭示精子发生过程中的分子调控机理, 对发现新的男性避孕方法及治疗不育症有重要意义。文章重点综述了近年有关雄激素及其受体、雌激素及其受体、转录因子和染色质相关因子在精子发生转录水平调控的研究进展。