Artificial evolution of enzymes

Scientific pulications - Artificial evolution of enzymes

Eijsink, V.G.H., GÅseidnes, S., Borchert, T.V., Van Den Burg, B.

"Directed evolution of enzyme stability"

Biomolecular Engineering, 22 (1-3), pp. 21-30. (2005) 

Modern enzyme development relies to an increasing extent on strategies based on diversity generation followed by screening for variants with optimised properties. In principle, these directed evolution strategies might be used for optimising any enzyme property, which can be screened for in an economically feasible way, even if the molecular basis of that property is not known. Stability is an interesting property of enzymes because (1) it is of great industrial importance, (2) it is relatively easy to screen for, and (3) the molecular basis of stability relates closely to contemporary issues in protein science such as the protein folding problem and protein folding diseases. Thus, engineering enzyme stability is of both commercial and scientific interest. Here, we review how directed evolution has contributed to the development of stable enzymes and to new insight into the principles of protein stability. Several recent examples are described. These examples show that directed evolution is an effective strategy to obtain stable enzymes, especially when used in combination with rational or semi-rational engineering strategies. With respect to the principles of protein stability, some important lessons to learn from recent efforts in directed evolution are (1) that there are many structural ways to stabilize a protein, which are not always easy to rationalize, (2) that proteins may very well be stabilized by optimizing their surfaces, and (3) that high thermal stability may be obtained without forfeiture of catalytic performance at low temperatures. © 2005 Elsevier B.V. All rights reserved.

J.R Cherry; A.L. Fidantsef.

"Directed evolution of industrial enzymes: An update."

Curr Opin Biotechnol., 14(4), 438-43 (2003)

The use of enzymes in industrial processes can often eliminate the use of high temperatures, organic solvents and extremes of pH, while at the same time offering increased reaction specificity, product purity and reduced environmental impact. The growing use of industrial enzymes is dependent on constant innovation to improve performance and reduce cost. This innovation is driven by a rapidly increasing database of natural enzyme diversity, recombinant DNA and fermentation technologies that allow this diversity to be produced at low cost, and protein modification tools that enable enzymes to be tuned to fit into the industrial marketplace.

J.E. Ness; S. Kim; A. Gottman; R. Pak; A. Krebber; T.V. Borchert; S. Govindarajan; E.C. Miundorff; J. Minshull.

"Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently".

Nature Biotechnology, 20, 1251-1255 (2002)

We describe synthetic shuffling, an evolutionary protein engineering technology in which every amino acid from a set of parents is allowed to recombine independently of every other amino acid. With the use of degenerate oligonucleotides, synthetic shuffling provides a direct route from database sequence information to functional libraries. Physical starting genes are unnecessary, and additional design criteria such as optimal codon usage or known beneficial mutations can also be incorporated. We performed synthetic shuffling of 15 subtilisin genes and obtained active and highly chimeric enzymes with desirable combinations of properties that we did not obtain by other directed-evolution methods.

S. Danielsen; M. Eklund: H-J. Deussen; T. GrSslund; P-Å. Nygren;T. V. Borchert.

"In vitro selection of enzymatically active lipase variants from phage libraries using a mechanism-based inhibitor".

Gene, 272, 267-274 (2001)

The 'detergent lipase' Lipolasel((R)), from Thermomyces lanuginosa was subjected to a combinatorial protein engineering/phage display approach with the aim of identifying new enzyme variants with improved characteristics in the presence of detergents. First it was demonstrated that wild-type Lipolase((R)) could be produced in Escherichia coli retaining full activity and be displayed as an active enzyme fused to coat protein 3 on E. coli phage M13. A phagemid library designed to result in approximately two to three mutations per lipase gene was then constructed. Nine amino acids located in two regions close to the active site were targeted for randomization. Selections using a mechanism-based biotinylated inhibitor showed that phages displaying Lipolase((R)) could be specifically enriched from a population of control phages. Selections on a library phage stock in the presence of inhibitor and a commercial powder detergent resulted in a step-wise increase in the proportion of active clones. Analysis of 84 active clones revealed that they all expressed lipase activity, but with lower activities than that of a wild-type Lipolase((R))- producing clone. In six of the seven most active clones a wild-type serine at position 83 had been replaced by threonine, a substitution known to alter the substrate chain length preference of Lipolase((R)) variants. Furthermore, the selection had enriched enzyme variants with a high degree of conservatism in one of the variegated regions, suggesting that this region is important for enzymatic activity and that the designed selection procedure was relevant. The selected variants contained primarily basic amino acid residues within the other variegated region. Taken together, the described results show that selection protocols based on enzymatic activity can be designed for this enzyme class which should be of importance for future protein engineering attempts.