Holistic approach to the bacterial genetic regulation system

细菌遗传调控系统的探索对于系统和合成生物学的进步以及在生物技术和生物医学中建立有效的基于知识的方法至关重要。采用高通量技术的强有力的国际研究揭示了问题的真正复杂性，迫切需要一种适当的方法来整合遗传调控系统的不同结构和组织特征。归根结底，主要的要求是了解遗传系统中信息流的控制。我们开发了一种新的整体方法，将DNA序列组织，DNA拓扑结构，基因顺序，基因功能以及染色体大结构域中调节因子与其靶标之间相互作用的动力学整合在一起。利用这种方法，我们最近首次提供了一个机制的见解，了解完整的细菌染色体的组织如何编码整合DNA复制和全局基因表达的时空程序。我们的工作阐明了为什么基因的表达时间与其在细菌染色体上的位置有关，并提供了一个观点，即类核是一个高度有组织的动态实体，在快速生长和停止期间优化了氧气和营养可用性与时空基因表达的协调。预测在细菌生长周期中，转录重组是由DNA超螺旋密度从染色体复制起点到终点的时空梯度驱动的。这种梯度是由丰富的核相关蛋白（nap）的组成变化调节的，nap将DNA超圈限制在可变染色体区域，从而协调重组染色体形状和转录。观察到的细菌染色体转录的区域效应表明，调控基因的战略性定位可能为控制细菌基因的表达和适应提供新的有力手段。本项目的工作旨在为在涉及细菌基因调控的基础和应用方面的一系列相关领域实施基于知识的方法提供关键的新工具。

Exploration of the bacterial genetic regulation system is central for the advancement of both systems and synthetic biology and for establishing efficient knowledge-based approaches in biotechnology and biomedicine. Vigorous international research employing high-throughput technologies revealed the true complexity of the problem and a critical need for an appropriate methodological approach integrating different structural and organisational features of the genetic regulation system. At the bottom line, the major requirement is to understand the control of information flow in the genetic system. We have developed a new holistic methodology integrating the DNA sequence organization, DNA topology, gene order, gene function and the dynamics of interactions between the regulators and their targets in chromosomal macrodomains. Using this methodology we recently provided a first mechanistic insight into how the organization of a complete bacterial chromosome encodes a spatiotemporal program integrating DNA replication and global gene expression. Our work illuminated why the timing of the expression of a gene is linked to its position on the bacterial chromosome and provided a view of the nucleoid as a highly organized dynamic entity optimized for coordinating oxygen and nutrient availability with spatiotemporal gene expression during rapid growth and its cessation. The prediction is that during the bacterial growth cycle reorganization of transcription is driven by a spatiotemporal gradient of DNA superhelical density from the origin to terminus of chromosomal replication. This gradient is modulated by compositional changes of the abundant nucleoid-associated proteins (NAPs), which constrain DNA supercoils in variable chromosomal regions thus coordinately reorganizing the chromosomal shape and transcription. The observed regional effects on transcription in the bacterial chromosome suggest that strategic positioning of regulatory genes may provide new powerful means for controlling bacterial gene expression and adaptation. The work intended in this project aims to provide such novel tools crucial for implementing knowledge-based approaches in a range of related fields concerned with both fundamental and applied aspects of the bacterial gene regulation.