Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach.
Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach.
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大肠杆菌的环境条件和转录调控：一种生理综合方法。
DOI：
10.1002/bit.10846
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发表时间：
2003
期刊：
影响因子：
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通讯作者：
Collado-Vides,Julio
中科院分区：
文献类型：
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作者：
Martinez-Antonio,Agustino;Salgado,Heladia;Gama-Castro,Socorro;Gutierrez-Rios,RosaMaria;Jimenez-Jacinto,Veronica;Collado-Vides,Julio
细菌发展出许多用于感知、响应和适应不同环境条件的装置。从基因组的角度理解细菌的转录机制是如何调节的，作为对不断变化的条件的反应，是生物学家面临的一项重大挑战。了解哪些基因在特定条件下打开或关闭对于我们理解细胞行为至关重要。在这项研究中，我们描述了如何从文献中收集与基因表达和相关生长条件相关的信息（即使对相关调控机制知之甚少）并将其纳入RegulonDB（一个关于大肠杆菌转录调控和操纵子组织的数据库）中。大肠杆菌。生长条件、信号转导和转录调控之间的联系以简单的格式在数据库中建模，突出显示生物相关信息。据我们所知，没有其他数据库明确阐明环境条件对基因转录的影响。我们讨论这些知识如何构成一个基准，该基准将影响未来旨在整合细胞调节反应的研究；例如，微阵列分析、预测生物技术过程中的培养行为以及调控网络动态的理解。这些综合知识将有助于实现对大肠杆菌行为进行建模的未来目标。大肠杆菌是整个细胞。 RegulonDB 数据库可以通过以下 URL 访问：http://www.cifn.unam.mx/Computational_Biology/regulondb/。 © 2003 Wiley 期刊公司。
Bacteria develop a number of devices for sensing, responding, and adapting to different environmental conditions. Understanding within a genomic perspective how the transcriptional machinery of bacteria is modulated, as a response for changing conditions, is a major challenge for biologists. Knowledge of which genes are turned on or turned off under specific conditions is essential for our understanding of cell behavior. In this study we describe how the information pertaining to gene expression and associated growth conditions (even with very little knowledge of the associated regulatory mechanisms) is gathered from the literature and incorporated into RegulonDB, a database on transcriptional regulation and operon organization inE. coli. The link between growth conditions, signal transduction, and transcriptional regulation is modeled in the database in a simple format that highlights biological relevant information. As far as we know, there is no other database that explicitly clarifies the effect of environmental conditions on gene transcription. We discuss how this knowledge constitutes a benchmark that will impact future research aimed at integration of regulatory responses in the cell; for instance, analysis of microarrays, predicting culture behavior in biotechnological processes, and comprehension of dynamics of regulatory networks. This integrated knowledge will contribute to the future goal of modeling the behavior ofE. colias an entire cell. The RegulonDB database can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/. © 2003 Wiley Periodicals, Inc.