Rational strain design for value added products: a systems metabolic engineering and synthetic biology approach

Abstract

The grand challenge of metabolic engineering lies in the complexity and redundancy of cellular pathways and the evolutionary drive of a cell to maximize growth rather than a forced bioengineering objective. Engineering microorganisms to thus produce value added products from bulk chemicals as carbon source is now greatly accelerated by use of Synthetic Biology. The fast forwarding evolution has thus uncapped the limits of engineering biological systems. Rational strain design for production of value added products requires channeling of basic substrate molecules towards a desirable metabolic output to make products of interest. When complex pathways are introduced inside the cell, limitations including intermediate toxicity, low enzyme activity, metabolic burden (cofactor imbalance etc.) need to be overcome for high performance. Such bottlenecks can be addressed using pathway engineering that exploits the synergies of synthetic biology, metabolic engineering and systems biology. Successful metabolic engineering for platform cell factories to produce a wide range of fuels and chemicals necessitates identifying the sensitivity of product/process to nutrient precursors and cofactors by coupling of cellular objectives of growth and energy to desired bioengineering objectives. This thesis explores the application of these principles to develop scalable systems to make a drug molecule violacein and a biopolymer Polyhydroxyalkanoates (PHAs). Violacein is a bacterial bis-indole pigment of commercial interest having antibacterial, antitumoral, antiviral, trypanocidal and antiprotozoan properties. PHAs form a class of natural polyesters, commonly referred to as bioplastics, that many organisms accumulate as intracellular granules to store carbon and reducing equivalents in response to specific environmental conditions. This thesis discusses the rational strain design and development in the context of systems metabolic engineering and synthetic biology for violacein and polyhydroxybutyrate.