Novel family shuffling methods for the in vitro evolution of enzymes

It has recently been shown that shuffling of the amino acid sequences of fa mily enzymes allows the generation of improved enzymes. Family shuffling is generally achieved by a DNase I treatment and then by PCR. Shuffling of th e xylE and nahH genes, both encoding catechol 2,3-dioxygenases, was carried out by the published method. However, nahH-xylE hybrids were only formed a t a very low frequency (less than 1%). Therefore, we developed improved met hods for family shuffling by which DNA was cleaved by restriction enzymes i nstead of by DNase I. With the first improved method, five nahH fragments a nd five xylE fragments that had been generated by restriction enzyme digest ion were subjected to the PCR reactions in two steps, the first being witho ut a primer and the second with a set of primers. This method enabled nahH- xylE hybrid genes to be formed at a high frequency (almost 100%). With the second improved method, nahH and xylE were cleaved by several sets of restr iction enzymes, and these digests were then reassembled in two steps. The n ahH and xylE DNAs were each cleaved by two (or three) sets of restriction e nzymes, and one type of nahH digest and one type of xylE digest were mixed, thus making four (or nine) different mixtures of the nahH and xylE digests . These mixtures were used as templates to carry out PCR without a primer. After the first PCR reaction, all the mixtures were combined, and a second PCR reaction was carried out without a primer. Following these two PCR asse mbly steps, a third PCR reaction was carried out with two primers to amplif y the full-length nahH-xcylE hybrid genes. This second method also yielded nahH-xylE hybrids at a frequency of 100%. The degree of recombination of th e products with the second method was higher than that with the first metho d. These methods were used to isolate catechol 2,3-dioxygenases exhibiting relatively high stability at high temperature, one of them being respective ly 13- and 26-fold more thermostable than XylE and NahH at 50 degrees C. (C ) 1999 Elsevier Science B.V. All rights reserved.