LEANPROT aims to develop an iterative systems biology-based strain engineering platform based on a novel approach of proteome optimization in iterative cycles of modeling and biological experiments which carries a substantial potential for addressing the aforementioned challenges in bioprocess development. That potential arises from the fact that cells express proteins unnecessary for growth under well-controlled optimal conditions, typically realized in biotechnological processes (e.g. flagellar, heat or acid stress proteins). This leads to non-efficient use of protein synthesis capacity (translation machinery) and energy for bioprocesses. Thus removing the expression burden of unnecessary proteins i.e. creation of lean-proteome strains, could enable to specifically manipulate the allocation of ribosomes for higher synthesis of proteins leading to increased target molecule production. One could theoretically greatly increase the key metrics of bioprocess performance (titer, yield, productivity) by deleting as few as ca 10 unnecessary genes with the highest translational burden in E. coli (in total 7% of proteome) and substituting the freed 7% of the total proteome with target molecule-related proteins. In LEANPROT we will demonstrate the potential of this concept as proof-of-principle by creating superior E. coli strains of recombinant protein production through reducing the expression of unnecessary proteins. LEANPROT will yield E. coli strains with superior performance of recombinant protein production - theoretically at least 50% higher productivity and titer - as a result of proteome optimization. Since targeted optimization of the layer of protein synthesis capacity should be applicable to a broad range of organisms, from bacteria to yeasts to higher eukaryotes, LEANPROT has potentially a big impact in the advancement of cell design overall.
