真核基因转录激活的多位点协同调控

真核基因的转录激活具有协同性的特征,表现为多个转录调控位点的共同作用效果大于每个位点单独作用之和,受多个位点调控的基因转录呈S型曲线.多个激活蛋白之间的相互作用、激活蛋白与各DNA位点的协同结合以及激活蛋白与转录机器的协同作用,三种途径都对协同性转录激活行为产生影响.协同性转录激活的本质是多个结合在调控位点上的激活蛋白之间直接或间接的相互作用.多位点的协同转录调控机制有助于理解生物的多种调控过程和建立基因调控网络.     

利用转录因子工程重塑代谢网络实现细胞工厂高效生产

酿酒酵母已被广泛用作生产精细化学品的典型细胞工厂.但在生产过程中,各种环境胁迫以及异常的细胞代谢严重制约了生产成本降低和收益提高.解决此类瓶颈问题的一种有效方法是利用转录因子工程,通过重塑关键基因的转录水平来提高菌株的耐受性和生产效率.从运用转录因子工程提高耐受性、产量和基于人工转录因子设计在优化代谢通量、定量分析中的...     

Bookmarking by Non-pioneer Transcription Factors during Liver Development Establishes Competence for Future Gene Activation

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Expression of the p53 Gene and Activation of p53-Dependent Transcription in Melanoma Cell Lines

Malignant melanoma has poor prognosis because of its high metastatic potential and resistance to chemotherapy. A possible approach to more effective therapy is induction of p53-dependent apoptosis. This approach is promising, since the wild-type _p53 is expressed in most melanomas. An attempt was made to estimate the functional activity of p53 in several malignant melanoma cell lines. Most lines were characterized by a high protein level and nuclear localization of p53. All cell lines expressing the wild-type p53 showed stabilization of p53, its translocation into the nucleus, and activation of several target genes in response to DNA-damaging agents, suggesting that p53 was functionally active. A high-molecular-weight protein localized in the cytoplasm and mimicking a p53 epitope was found in several cell lines. It was shown that the DO-1 epitope is not derived from p53, ruling out cytoplasmic retention of p53 in melanoma cell lines. A mechanism of camptothecin-induced stabilization of p53 by decreasing the level of the HDM2 mRNA was described for melanoma cells but not for normal melanocytes, suggesting a differential effect of camptothecin on tumor-derived and primary cells.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 3, 2005, pp. 445–456.Original Russian Text Copyright © 2005 by Razorenova, Agapova, Chumakov.     

茶树CsCBF1基因克隆和转录活性分析

采用RACE技术克隆了一个受冷诱导的茶树CBF基因全长cDNA,命名为CsCBF1(GenBank登录号为EU563238)。CsCBF1cDNA全长序列为1 211bp,开放阅读框编码259个氨基酸。氨基酸序列分析表明,CsCBF1具有CBF家族典型的保守结构域,与其他植物的CBF具有较高的相似性;与拟南芥、辣椒和橡胶树编码的CBF相似性分别为56%、63%和56%。亚细胞定位结果表明,CsCBF1位于细胞核内。分别将10个CsCBF1缺失突变体与GAL4DNA结合域融合的结果显示,CsCBF1的羧基末端酸性结构域(第137位氨基酸至259位氨基酸)在酵母中具有转录激活活性。实时定量RT-PCR分析表明,CsCBF1基因受低温的快速诱导表达。     

Polo-Like Kinase 1 Depletion Induces DNA Damage in Early S Prior to Caspase Activation

Polo-like kinase 1 (Plk1) plays several roles in mitosis, and it has been suggested to have a role in tumorigenesis. We have previously reported that Plk1 depletion results in cell death in cancer cells, whereas normal cells survive similar depletion. However, Plk1 depletion together with p53 depletion induces cell death in normal cells as well. This communication presents evidence on the sequence of events that leads to cell death in cancer cells. DNA damage is detected at the first S phase following Plk1 depletion and is more severe in Plk1-depleted p53-null cancer cells. As a consequence of Plk1 depletion using lentivirus-based small interfering RNA techniques, prereplicative complex (pre-RC) formation is disrupted at the G₁/S transition, and DNA synthesis is reduced during S phase of the first cycle after depletion. The levels of geminin, an inhibitor of DNA pre-RC, and Emi1, an inhibitor of anaphase-promoting complex/cyclosome, are elevated in Plk1-depleted cells. The rate of cell cycling is slower in Plk1-depleted cells than in control cells when synchronized by serum starvation. Plk1 depletion results in disrupted DNA pre-RC formation, reduced DNA synthesis, and DNA damage before cells display severe mitotic catastrophe or apoptosis. Our data suggest that Plk1 is required for cell cycle progression not only in mitosis but also for DNA synthesis, maintenance of DNA integrity, and prevention of cell death.Progression of the cell cycle is tightly regulated in eukaryotic cells by coordinated control of phosphorylation and proteolytic events. Duplication of genetic information for the next cell generation requires the precise coordination of numerous proteins (2). To ensure the accurate division of duplicated DNA, cells require condensed chromosomes, a mitotic spindle, and correct attachment of duplicated chromosomes to the spindle. Errors in DNA replication and mitosis may lead to cell death through apoptosis or result in mutations that lead to cancer (3). Polo-like kinase 1 (Plk1) is essential for several steps in mitosis and is highly expressed in proliferating cells. Expression of Plk1 increases in S phase and peaks during M phase (8). In addition, at the G₂/M boundary, Plk1 is activated by phosphorylation and promotes mitotic entry. Its primary role in mammalian cells appears to be control of mitotic progression, particularly in the metaphase/anaphase transition, and mitotic exit (37). At the G₂/M transition, Plx1, a counterpart of Plk1 in Xenopus, activates cyclin B1/Cdk1 by phosphorylation of Cdc25C (14) or of cyclin B1 (29). During mitotic entry, Plk1 is required for recruitment of the γ-tubulin ring complex (7). Phosphorylation of Emi1 by Plk1 leads to its destruction, release of Cdc20, and activation of the anaphase-promoting complex/cyclosome (APC/C) (10, 22, 26). Active APC/C mediates the degradation of proteins such as cyclin A, cyclin B1, securin, and geminin to promote exit from mitosis (6, 26). The multiple roles of Plk1 from the entry to and exit from mitosis indicate its importance as a regulator of these events.Recently, several reports suggest that Plk1 may play a role in other phases of the cell cycle. Plk1 interacts with prereplicative complex (pre-RC) proteins, such as Mcm2 and Orc2, in yeast two-hybrid studies (32), and coimmunoprecipitates with Mcm2 to Mcm7 and Orc2 (32, 35). Orc2, Mcm4, Mcm6, and Mcm7 proteins colocalize in the centrosome with Plk1 (25, 32). In addition, ectopic expression of Plk1-S137D arrests HeLa cells at the G₁/S boundary (12). Moreover, microinjection of in vitro-transcribed sense mRNA of Plk1 into serum-starved NIH 3T3 cells induced thymidine incorporation, whereas microinjection of antisense mRNA into growing NIH 3T3 cells that were stimulated with serum blocked thymidine incorporation (9). This observation suggests that Plk1 is required for DNA synthesis and that overexpression of Plk1 appears to be sufficient for induction of DNA synthesis. These data raise the possibility that Plk1 might have a required function in DNA replication.Depletion of Plk1 activity by microinjection of neutralizing anti-Plk1 antibody impairs centrosome maturation in HeLa cells (15). When Plk1 function is blocked by dominant-negative Plk1, several human tumor cells undergo mitotic catastrophe independent of Cdc25C (1). In Plk1-deficient human cancer cells, centrosomes do not separate to form bipolar spindles. The cells undergo prometaphase arrest and cell death caused by mitotic catastrophe (18, 33, 38). These effects are more severe in p53-deficient cancer cells. Cells codepleted for p53 and Plk1 undergo cell death as a consequence of mitotic defects (17). However, it is unclear how Plk1 depletion induces cell death or what the sequence of events is prior to cell death.Here, we provide evidence that Plk1 depletion induces DNA damage at G₁/S before cell death responses, such as caspase activation, are initiated.     

负调节基因nsdA在链霉菌中同源性及激活沉默抗生素合成基因簇的研究

nsdA基因是在天蓝色链霉菌中发现的抗生素合成负调控基因。以nsdA基因片段为探针,通过Southern杂交发现nsdA存在于多种链霉菌中。根据天蓝色链霉菌和阿维链霉菌的nsdA序列设计PCR引物,扩增多种链霉菌中nsdA基因并测序。发现在不同链霉菌中nsdA基因的相似性高达77%~100%。其中变铅青链霉菌与天蓝色链霉菌A3(2)的nsdA序列100%一致。变铅青链霉菌通常不合成放线紫红素,中断nsdA获得的突变菌株WQ2能够合成放线紫红素;在WQ2中重新引入野生型nsdA,又失去产抗生素能力。表明nsdA的中断可以激活变铅青链霉菌中沉默的放线紫红素生物合成基因簇的表达;nsdA的广泛存在及其序列高度保守则提示可以尝试用于这些菌种的抗生素高产育种。     

GO-PCA: An Unsupervised Method to Explore Gene Expression Data Using Prior Knowledge

Method

Genome-wide expression profiling is a widely used approach for characterizing heterogeneous populations of cells, tissues, biopsies, or other biological specimen. The exploratory analysis of such data typically relies on generic unsupervised methods, e.g. principal component analysis (PCA) or hierarchical clustering. However, generic methods fail to exploit prior knowledge about the molecular functions of genes. Here, I introduce GO-PCA, an unsupervised method that combines PCA with nonparametric GO enrichment analysis, in order to systematically search for sets of genes that are both strongly correlated and closely functionally related. These gene sets are then used to automatically generate expression signatures with functional labels, which collectively aim to provide a readily interpretable representation of biologically relevant similarities and differences. The robustness of the results obtained can be assessed by bootstrapping.

Results

I first applied GO-PCA to datasets containing diverse hematopoietic cell types from human and mouse, respectively. In both cases, GO-PCA generated a small number of signatures that represented the majority of lineages present, and whose labels reflected their respective biological characteristics. I then applied GO-PCA to human glioblastoma (GBM) data, and recovered signatures associated with four out of five previously defined GBM subtypes. My results demonstrate that GO-PCA is a powerful and versatile exploratory method that reduces an expression matrix containing thousands of genes to a much smaller set of interpretable signatures. In this way, GO-PCA aims to facilitate hypothesis generation, design of further analyses, and functional comparisons across datasets.