Redefining Biology via Enzyme Engineering

A TV series from the 1970s, “The Six Million Dollar Man,” imagines a former astronaut with bionic implants and superhuman strength acting as a secret agent for the government. Such enhancement of human abilities with artificial components (all at a reasonable price tag) might resonate with some of today’s scientists who are working on a more modest goal of augmenting the properties of cells and biological systems. Their aim is to design new synthetic routes for compounds and even create completely new molecules that may not exist in nature by exploiting the versatility of the life’s systems.Image from istock/Greyfebruary.View Large Image | View Hi-Res Image | Download PowerPoint SlideTake the current work on silicon. Silicon is a ubiquitous element that sits next to carbon in the periodic table and shares some of its properties. The similarities in the ways silicon and carbon bond with other atoms have led to the idea that silicon might give rise to an alternative, silicon-based life with unique properties. Yet, silicon does not readily partake in biochemical couplings unless nudged to bind carbon via chemical synthesis. Organosilicon compounds that are thus created are highly valued for their ability to bind organic and inorganic substrates and are used as adhesives, sealants, and caulks. Their industrial synthesis is laborious, and thus the interest in bringing silicon into the fold of nature’s biochemistry persists. Now, advances in enzyme engineering have made it possible to incorporate silicon into organic compounds through bacterial biosynthetic pathways. Frances Arnold and her team (Kan et al., 2016xKan, S.B.J., Lewis, R.D., Chen, K., and Arnold, F.H. Science. 2016; 354: 1048–1051Crossref | PubMed | Scopus (43)See all ReferencesKan et al., 2016) have discovered that a cytochrome c protein from the thermophilic bacterium Rhodothermus marinus can, under the right conditions, catalyze the formation of a carbon-silicon bond to create short organosilicon compounds. The examination of the enzyme’s structure yields clues to the motifs driving this process, allowing the rapid directed evolution of an enzyme with high activity for making such products. Strikingly, this altered cytochrome c churns out silicon-containing compounds inside of bacteria, suggesting that relatively few tweaks are sufficient to bring silicon into the realm of in vivo synthesis, albeit under highly engineered conditions, and creating compounds that are not yet industrially relevant.Retooling an enzyme for a new production line may, however, require a more comprehensive overhaul of its properties. In a recent work from John Hartwig’s lab (Dydio et al., 2016xDydio, P., Key, H.M., Nazarenko, A., Rha, J.Y.-E., Seyedkazemi, V., Clark, D.S., and Hartwig, J.F. Science. 2016; 354: 102–106Crossref | PubMed | Scopus (28)See all References, Key et al., 2016xKey, H.M., Dydio, P., Clark, D.S., and Hartwig, J.F. Nature. 2016; 534: 534–537Crossref | PubMed | Scopus (52)See all References), myoglobins and cytochrome P450s, heme proteins that transport and react with oxygen, are fitted with iridium, a noble metal not found in biological molecules, to yield an artificial metalloenzyme with new capabilities, promoting reactions not catalyzed by native hemes or other metalloenzymes and with kinetics, productivity, and selectivity that are comparable with those of native enzymes. The widening of the biochemical space achieved with such manipulations is tantalizing, and the next frontier is making such artificial enzymes work inside of a cell, a challenging task, given the complex intracellular environment. Thomas Ward and colleagues (Jeschek et al., 2016xJeschek, M., Reuter, R., Heinisch, T., Trindler, C., Klehr, J., Panke, S., and Ward, T.R. Nature. 2016; 537: 661–665Crossref | PubMed | Scopus (32)See all ReferencesJeschek et al., 2016) tackle this problem by developing a process through which an artificial metathase can be assembled and put to work in the periplasm of a bacterium, bringing new, non-natural metabolic pathways inside cells.On a different spatial scale, other recent studies have endeavored to create large artificial structures within cells. Neil King, Wesley Sundquist, and colleagues (Votteler et al., 2016xVotteler, J., Ogohara, C., Yi, S., Hsia, Y., Nattermann, U., Belnap, D.M., King, N.P., and Sundquist, W.I. Nature. 2016; 540: 292–295Crossref | PubMed | Scopus (6)See all ReferencesVotteler et al., 2016) designed self-organizing protein nanocages nested inside of membrane vesicles. Such structures can be released from their host eukaryotic cells and taken up by other cells, allowing the transfer of encapsulated cargo and representing a prototype hybrid biological material that can be used to perform complex tasks, such as exchange of metabolites or information, in a controlled and tailored manner.These examples of repurposing natural solutions are still at their proof-of-principle stage; however, they support the idea that biochemical reactions and cellular functions can be augmented to bring new elements to life and create unexpected biological products.