Evolveing the transcriptional regulatory system - towards synthetic control of gene expression

随着合成微生物学的出现，遗传学面临着新的挑战。微生物、基因电路设计、合成途径和定制染色体都面临着一个主要的瓶颈-启动子活性和时间依赖于其自身的序列和背景。合成方法的本质是将DNA片段从其天然背景中移除。这对该片段上编码的基因具有广泛的影响。这些基因转录的变化可能导致相关调控或代谢网络的扭曲。因此，构建复杂的合成回路或途径目前尚不可行。在本项目中，我们将进一步阐明启动子序列和序列背景对启动子活性和时间的影响，以提供设计DNA的更好预测性，并进一步了解基因调控的支配规则。为了实现这一目标，我们将结合联合收割机遗传学和生物信息学的方法，并在基因组学中应用最先进的方法，转录组学和合成生物学。我们从三个层面研究了基因表达的位置效应。1）启动子序列及其直接背景对时间基因表达的影响。2）在不同生长阶段不同拷贝数的背景下，染色体基因定位对基因调控网络的影响。3)受干扰的调节系统的进化重建。所有这些水平将提高我们对基因调控的总体理解，并将为设计从单基因到完整染色体的人工构建体提供新的规则。此外，我们相信，在项目期间收集的数据对更广泛的科学界具有极大的兴趣。

With the advent of synthetic microbiology new challenges in Genetics arise. Minimal organisms, genetic circuit design, synthetic pathways and customized chromosomes all face a major bottleneck - the dependence of promoter activity and timing on its own sequence and context.The essence of synthetic approaches is the removal of a DNA segment from its native context. This has wide implications on the genes coded on this segment. Changes in the transcription of these genes may lead to a distortion of the linked regulatory or metabolic network.Therefore, the construction of complex synthetic circuits or pathways is currently not feasible.In this project we will further elucidate the impact of promoter sequence and the sequence context on promoter activity and timing to provide a better predictability of designed DNA and to further understand the governing rules of gene regulation.To accomplish this goal, we will combine Genetics and Bioinformatics approaches and apply state of the art approaches in Genomics, Transcriptomics and Synthetic Biology.We investigate positional effects on gene expression on three levels.1) The impact of promoter sequence and its direct context on temporal gene expression.2) The impact of chromosomal gene positioning on the gene regulatory network in the context of varying copy numbers during different growth stages. 3) The evolutionary reconstitution of a disturbed regulatory system. All levels will improve our general understanding of gene regulation and will provide new rules to design artificial constructs from single genes to full chromosomes.Furthermore, we are convinced that the data, gathered during the project, is of great interest for a broader scientific community.