Exploiting bacterial growth laws to characterize indirect mechanisms for generating phenotypic heterogeneity from isogenic populations

从雅各布和莫诺时代起，贯穿微生物学和细菌生理学的一个主导主题是，DNA中编码的信息可以通过简单元素的多尺度组合与生物体的生理状态联系起来：操纵子内的基因、网络内的操纵子和细胞内的网络。这种自下而上理解(以及最近的合成)遗传网络的方法类似于电路设计的工程原理-一个富有成效的类比导致了重大的概念进步，特别是在新兴的系统生物学领域。但这种类比的局限性当然是，电路不会生长和分裂。 人们越来越认识到，必须在生长有机体的背景下理解遗传网络；导致细胞快速增殖的核心代谢过程对辅助任务中涉及的基因表达施加了限制。最近，我发现了一些经验关系(称为“增长定律”)，可以从数量上理解增长速度和基因表达之间的相互依赖关系。在目前的提案中，我研究了这些生长规律的后果，特别是作为一种在共享相同DNA的文化中产生不同亚种群的机制。 通过在大肠杆菌中建立一个简单的人工诱导蛋白表达系统，我建议确定生长介导的反馈效应在多大程度上负责建立观察到的表型异质性。研究结果对蛋白质表达系统的工业优化、在细菌中合成昂贵的治疗药物以及治疗毒力细菌感染具有直接意义。在更广泛的背景下，这项研究强调了对细菌中基因表达调控的整体观点的重要性，在细菌中，细胞生长和蛋白质合成密切相关，并通过间接反馈对一类新的基因调控提供了洞察。

From the time of Jacob and Monod, a dominant theme running through microbiology and bacterial physiology is the idea that the information encoded in DNA can be connected to the physiological state of the organism through a multi-scale assembly of simple elements: the gene within an operon, the operon within a network and the network within the cell. This bottom-up approach to the understanding (and, more recently, the synthesis) of genetic networks is analogous to the engineering principles of electrical circuit design - a fruitful analogy that has lead to significant conceptual advances particularly in the burgeoning field of systems biology. But the limitation of this analogy is, of course, that electrical circuits do not grow and divide. There is an increasing appreciation that genetic networks must be understood within the context of the growing organism; that core metabolic processes leading to rapid cell proliferation impose constraints on gene expression involved in auxiliary tasks. Recently, I have uncovered empirical relationships (called 'growth laws') that allow the interdependence between growth-rate and gene expression to be understood quantitatively. In the present proposal, I examine the consequences of these growth laws, specifically as a mechanism for generating distinct sub-populations in a culture that shares identical DNA. With focus on a simple synthetic inducible protein-expression system in Escherichia coli, I propose to determine the extent to which growth-mediated feedback effects are responsible for establishing observed phenotypic heterogeneity. The results of the investigation have immediate implications for the industrial optimization of protein expression systems to synthesize expensive therapeutics in bacteria, and for the treatment of virulent bacterial infections. In a broader context, the study highlights the importance of a holistic view of the regulation of gene expression in bacteria, where cell growth and protein synthesis are intimately interconnected, and provides insight into a new class of gene regulation through indirect feedback.