Evolving enzymes in the lab
This week's paper is another example of how nonrandom selection from among random variants can solve problems so difficult that we are unable to "design" a solution. As in an earlier post, the selection process was automated, not requiring the human judgement used in breeding crops or dogs.
"Selection and evolution of enzymes from a partially randomized non-catalytic scaffold" was written by Burckhard Seelig and Jack Szostak, both of Boston, and published in Nature (448:828). Their goal was to evolve an enzyme to link two RNA bases together in a particular way, a reaction not found in nature.
Enzymes are biological catalysts, which speed the rates of chemical reactions. Most natural enzymes (that we know of) are made from protein, but a few are made from RNA, possible relics from a hypothesized "RNA world" where RNA acted both as enzymes and as genetic material. Enzymes made of DNA have never been seen in nature, but laboratory conditions have been designed that allow them to evolve from random DNA sequences (Science 286:2441).
Designing an environment where protein-based enzymes could evolve, without using living cells, was actually trickier than earlier evolutionary systems for RNA- and DNA-based enzymes. The authors used a huge library of 1000 billion random DNA variants. All the DNA sequences had two loops, but the contents of the loops varied randomly.
Transcribing all of the DNA variants into messenger RNA and translating the messenger RNAs into proteins is a routine operation; the trick was to leave each protein variant linked to its particular mRNA. Then they stuck one of the substrates of the desired reaction to the RNA-protein combination and turned them loose over a surface with lots of the other substrate bound to it. If the protein could catalyze a reaction to link the two substrates together, the whole complex got tied to the surface and used in the next generation. All the nonfunctional variants got washed away.
The DNA sequences that survived 8 generations of this selective "sieve" were randomly mutated and subject to additional cycles of selection. The whole process took a few days. Evolution can be fast, if the conditions are right. The final product accelerated the reaction over a million times. The authors suggest that this approach could be used to evolve other enzymes that link substrates together. A modified method, saving the enzyme complexes that wash away, could be used to select
enzymes that break chemical bonds rather than make them.
Other recent papers on evolution in major journals: