Getting Momentum: From Biocatalysis to Advanced Synthetic Biology

• Published in: Trends in biochemical sciences (Amsterdam. Regular ed.) Vol. 43; no. 3; pp. 180 - 198
• Main Authors: Badenhorst, Christoffel P.S., Bornscheuer, Uwe T.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.03.2018
• Subjects: biocatalysis; broad mutational scanning; deep mutational scanning; high-throughput screening; metabolic engineering; protein engineering; broad mutational scanning; protein engineering; metabolic engineering; deep mutational scanning; biocatalysis; high-throughput screening
• ISSN: 0968-0004; 1362-4326
• DOI: 10.1016/j.tibs.2018.01.003

Applied biocatalysis is driven by environmental and economic incentives for using enzymes in the synthesis of various pharmaceutical and industrially important chemicals. Protein engineering is used to tailor the properties of enzymes to catalyze desired chemical transformations, and some engineered enzymes now outperform the best chemocatalytic alternatives by orders of magnitude. Unfortunately, custom engineering of a robust biocatalyst is still a time-consuming process, but an understanding of how enzyme function depends on amino acid sequence will speed up the process. This review demonstrates how recent advances in ultrahigh-throughput screening, mutational scanning, DNA synthesis, metagenomics, and machine learning will soon make it possible to model, predict, and manipulate the relationship between protein sequence and function, accelerating the tailor design of novel biocatalysts. Protein engineering makes use of the unique macromolecular nature of enzymes to catalyze reactions for which efficient synthetic chemical catalysts have not been created. Enzymes can be engineered to catalyze unnatural reactions such as carbene and nitrene transfers, even forming carbon–silicon and carbon–boron bonds that are not observed in biology. Synthetic biochemistry and metabolic engineering allow economical multistep syntheses of complex molecules in one-pot processes or within engineered microorganisms, without the need for purification of intermediates. Deep mutational scanning, based on ultrahigh-throughput screening and next-generation sequencing, can address our fundamental lack of understanding of sequence–function relationships. Broad mutational scanning, based on the synthesis of hundreds or thousands of orthologous protein sequences, enables sequence space to be explored on an unprecedented scale. DNA synthesis, which offers precise, noncombinatorial control over DNA sequence composition, will likely become the standard method for mutant enzyme library creation in the near future.