CAREER: Epigenetics of Synthetic Biology

University Of Illinois At Chicago, Chicago IL

Investigators

Abstract

Constructing or reprogramming cells by editing their DNA sequence is central to synthetic biology. The creation of tools that drive this process have applications in not only understanding the fundamental mechanisms that govern molecular processes, but also in the development of a sustainable bioeconomy. This proposal seeks to elucidate how epigenetics improves product yields to enhance natural product discovery in microbes. The mechanisms of epigenetic control will be examined in Gram-negative and Gram-positive bacteria to engineer a programmable system. This research will form the basis of a new synthetic biology course at the University of Illinois at Chicago and will provide research opportunities for students at various levels, including high school. A key goal of the educational activities is to make synthetic biology accessible to students. Epigenetic DNA methylation is involved in bacterial host defense as mediated by Restriction-Modification systems, and in the control of DNA replication and gene expression. Synthetic biologists have recently started to explore epigenetics and Restriction-Modification systems to engineer memory in biological systems. Unfortunately, understanding of this mechanism is hindered by numerous challenges, including the low production yield of heterologous gene expression. An industrial Burkholderia strain, which produces 580-times the normal levels of the peptide capistruin, will be employed as a heterologous test host. Preliminary studies have demonstrated that this overproduction is most likely mediated by epigenetic factors that impact plasmid copy number and gene transcription. This research seeks to identify the underlying basis for this regulation, by perturbation of enzymes within the Restriction-Modification system. Methylome and transcriptome datasets will be generated separately and then integrated to determine methylation patterns. In addition, the role of epigenetic factors in controlling product yields will be further explored in both Gram-positive and Gram-negative bacteria model organisms. The project is expected to provide critical understanding of the basis for stochastic variation in product yields and thereby to contribute to construction of improved synthetic biology tools in diverse model organisms. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.