Analysis of the Innovation Trend in Cell-Free Synthetic Biology

Abstract

Cell-free synthetic biology is a maturing field that aims to assemble biomolecular reactions outside cells for compelling applications in drug discovery, metabolic engineering, biomanufacturing, diagnostics, and education. Cell-free systems have several key features. They circumvent mechanisms that have evolved to facilitate species survival, bypass limitations on molecular transport across the cell wall, enable high-yielding and rapid synthesis of proteins without creating recombinant cells, and provide high tolerance towards toxic substrates or products. Here, we analyze ~750 published patents and ~2000 peer-reviewed manuscripts in the field of cell-free systems. Three hallmarks emerged. First, we found that both patent filings and manuscript publications per year are significantly increasing (five-fold and 1.5-fold over the last decade, respectively). Second, we observed that the innovation landscape has changed. Patent applications were dominated by Japan in the early 2000s before shifting to China and the USA in recent years. Finally, we discovered an increasing prevalence of biotechnology companies using cell-free systems. Our analysis has broad implications on the future development of cell-free synthetic biology for commercial and industrial applications.

Streptomyces cell-free systems for natural product discovery and engineering

“…Rapid advances within the past two decades have demonstrated potential for cell-free systems to compete or replace traditional cell-based approaches. 23,24 Specically, cellfree systems allow the study of enzyme biosynthesis within a test tube, an approach that draws parallels to total synthesis from organic chemistry. In comparison, cell-free systems start from known substrates and proceed to completion through exhaustion of substrates or the accumulation of inhibitory products in batch reactions.…”

Exploration of the In Vitro Violacein Synthetic Pathway with Substrate Analogues

“…This issue can extend into cell-free biosynthesis if crude lysates are used without purification of enzymes away from endogenous substrates. However, these issues can be mitigated by using the purified enzyme(s) in a minimalist cell-free biosynthetic approach. ,,,,− …”

Enzyme assembly on nanoparticle scaffolds enhances cofactor recycling and improves coupled reaction kinetics

“…7 Cell-free synthetic biology looks to mitigate these specific issues by utilizing cellular extracts or designer reconstituted versions thereof to perform the required reactions. [8][9][10][11] Interest is also growing in 'minimalist' versions of a cell-free synthetic format where reactions only contain the minimal number of components required for a given multistep enzymatic pathway; these typically consist of just the necessary enzymes, cofactors, and substrates. 12,13 Potential liabilities associated with this latter approach center primarily on achiev-ing suitable mass transport and reaction efficiency along with maintaining long-term enzymatic stability.…”