RUI: Transcription Factor Discovery in the Extremophile Thermus Thermophilus

有了这个奖项，分子和细胞生物科学部的遗传机制集群：生物科学理事会正在资助来自州立大学肯尼索的Michael货车Dyke博士，以确定孤儿转录因子及其潜在的生物学作用。转录因子是大多数生物体中基因表达的主要调节因子，控制这些基因根据内在因素或外部线索而打开或关闭。目前，大多数转录因子的靶点尚不清楚。然而，使用一种新的选择方法，可以筛选数万亿的DNA序列，现在可以从假定的转录因子到理解其生物调节作用，在相对较短的顺序。该项目将探索嗜热栖热菌中潜在的转录因子，嗜热栖热菌是一种模式极端生物，其蛋白质广泛用于生物技术的许多方面。从该项目中获得的知识将适用于从农业综合企业到废物处理等一系列行业。此外，该项目还将在蛋白质-DNA相互作用的生物化学以及生物信息学和调节子开发方面培养本科生和研究生（MS）学生，从而为这些领域的未来科学家提供人才。 本研究计画的目的是为了更好的了解模式极端微生物T。嗜热菌HB 8。推定转录因子的结合特异性将通过限制性内切酶保护、选择和扩增的组合方法，随后进行大规模平行半导体测序和用于基序激发分析的多重期望最大化来确定。然后使用Find Individual Motif Occurrences将潜在结合位点定位到嗜热栖热菌HB 8基因组，并在体外（电泳迁移率变动试验）和体内（定量聚合酶链反应）进行功能验证。这项研究的信息将提供一个更好的了解调节子内的一个模型真细菌极端微生物，并将补充正在进行的研究，例如，结构生物学全细胞项目，该项目旨在了解生命的分子组成在原子水平。该项目开发的方法也应该普遍适用于表征孤儿转录因子和诱导其他生物体中的调节子。

With this award, the Genetic Mechanisms Cluster of the Division of Molecular and Cellular Biosciences: Biological Sciences Directorate is funding Dr. Michael Van Dyke from Kennesaw State University to identify orphan transcription factors and their potential biological roles. Transcription factors are the primary regulators of gene expression in most organisms, controlling those genes that are turned on or off in response to intrinsic factors or external cues. Presently, the targets of most transcription factors are not known. However, using a novel selection method that allows the screening of trillions of DNA sequences, it is now possible to go from putative transcription factor to understanding its biological regulatory roles in relatively short order. This project will explore potential transcription factors in Thermus thermophilus, a model extremophile organism whose proteins are widely used in many aspects of biotechnology. Knowledge derived from this project will be applicable to a host of industries, ranging from agribusiness to waste treatment. In addition, this project will train a mix of undergraduate and graduate (MS) students in the biochemistry of protein-DNA interactions as well as bioinformatics and regulon development, thereby providing future scientists in these fields. This research project will be undertaken to better understand transcriptional regulatory networks in the model extremophile T. thermophilus HB8. Binding specificity of putative transcription factors will be determined by the combinatorial approach Restriction Endonuclease Protection, Selection, and Amplification, followed by massively parallel semiconductor sequencing and Multiple Expectation Maximization for Motif Elicitation analysis. Potential binding sites will then be mapped to the Thermus thermophilus HB8 genome using Find Individual Motif Occurrences and functionally validated both in vitro (electrophoretic mobility shift assays) and in vivo (quantitative Polymerase Chain Reactions). Information from this study will provide a better understanding of regulons within a model eubacterial extremophile and will complement ongoing studies, for example, the Structural-Biological Whole Cell Project, which seeks to understand the molecular constituents of life at an atomic level. Methods developed by this project should also be generally applicable to characterizing orphan transcription factors and eliciting regulons in other organisms.