Beyond the outer limits of nature by directed evolution

Abstract

For more than thirty years, biotechnology has borne witness to the power of directed evolution in designing molecules of industrial relevance. While scientists all over the world discuss the future of molecular evolution, dozens of laboratory-designed products are being released with improved characteristics in terms of turnover rates, substrate scope, catalytic promiscuity or stability. In this review we aim to present the most recent advances in this fascinating research field that are allowing us to surpass the limits of nature and apply newly gained attributes to a range of applications, from gene therapy to novel green processes. The use of directed evolution in non-natural environments, the generation of catalytic promiscuity for non-natural reactions, the insertion of unnatural amino acids into proteins or the creation of unnatural DNA, is described comprehensively, together with the potential applications in bioremediation, biomedicine and in the generation of new bionanomaterials. These successful case studies show us that the limits of directed evolution will be defined by our own imagination, and in some cases, stretching beyond that.

Directed evolution of polypropylene and polystyrene binding peptides

“…An additional attractive application is the functionalization of sophisticated 3D structures. Many enzymes in laundry, bakery, or production of chemicals have been reengineered in order to match applications conditions (Korfer, Pitzler, Vojcic, Martinez, & Schwaneberg, ; Molina‐Espeja et al, ; Sheldon & Pereira, ); since 2010 yearly ∼500 successful directed evolutions campaigns reported (Cheng et al, ).…”

“…Directed PBP evolution offers novel and exciting opportunities to tailor binding peptides for surface bio-functionalization. Polymer binding anchor peptides (PBPs) have an excellent potential to become Many enzymes in laundry, bakery, or production of chemicals have been reengineered in order to match applications conditions (Korfer, Pitzler, Vojcic, Martinez, & Schwaneberg, 2016;Molina-Espeja et al, 2016;Sheldon & Pereira, 2017); since 2010 yearly ∼500 successful directed evolutions campaigns reported (Cheng et al, 2015).…”

Biocatalysis and Biotransformations

“…With the discovery of the mechanisms by which proteins fold and the development of protein engineering and computational tools, the engineering and re-design of natural enzymes or even the design of enzymes from scratch became possible [9][10][11]. Whatever the capacity to identify or engineer new and better performing enzymes, it is increasingly recognized that biocatalysts are delicate materials that need to be stabilized to survive a range of challenging conditions typically used in industrial processes and any conversion in general.…”

Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis

“…In order to improve cellulases, several strategies ranging from rational and computational design to de novo enzyme design and directed evolution have been implemented, aimed at obtaining biocatalysts with improved performance 5,8,9 . Despite these advances, the limitations of engineered cellulases under the highly demanding industrial conditions (in terms of pH, temperatures, the presence of nonconventional media, and more) are still a barrier that must be overcome.…”