Synthetic and systems biology for microbial production of commodity chemicals

Abstract

The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli

“…Although natural metabolic pathways have evolved intricate regulation to prevent the buildup of toxic metabolites, heterologous pathways, which frequently consist of non-native reactions from different organisms, typically lack such sophistication (Chubukov et al, 2016). Without regulation, imbalances in assembled pathways frequently lead to metabolite accumulation and toxicity (Jones et al, 2015).…”

Portable, On-Demand Biomolecular Manufacturing

“…This approach has helped create whole-cell biosensors (Kobayashi et al, 2004), genetically modified probiotics (Danino et al, 2015), and a growing capability for cell-based biomolecular manufacturing. Rooted in genetically engineered production cell lines, biosynthesis is increasingly a mainstay for industrial drug production (Fossati et al, 2014), protein therapeutics (Dimitrov, 2012), fuels (Torella et al, 2015), and other commodities (Chubukov et al, 2016). However, the reliance on living cellular hosts to operate the genetic programs that underpin biosynthesis is accompanied by biosafety regulations, practical hurdles, and specialized skills that limit their operation to laboratory settings.…”

Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

“…Various technical platforms for assembling a library of DNA segments into synthetic pathways or circuits, which in turn inserted into the host genome while manipulating existing genes in the host, have recently been developed. Synthetic biology and metabolic engineering techniques have been widely used in Escherichia coli, S. cerevisiae, and Zymomonas mobilis to enhance ethanol production (Chubukov et al, 2016). So investigation and findings in synthetic biology hold extreme importance and need to accelerate the new design and optimization of pathways.…”