Man versus Machine versus Ribozyme

Primer The steam drill was on the right hand side, John Henry was on the left, Says before I let this steam drill beat me down, I'll hammer myself to death " —The Ballad of John Henry (American, traditional) O rganisms and molecules achieve evolutionary success via many possible paths, what evolutionary biologists sometimes call the " tempo and mode " of evolution [1]. In contrast, engineered machines do not typically adapt to new functions during their normal operation. This seemingly inherent difference between the vicissitudes of living things and the exactitudes of mechanisms has frequently fascinated writers. One famous folktale of the Americas, the legend of John Henry, pits the evolved strength of a railroad worker, a " steel-driving man, " against the inhuman strength of a steam-powered rail driver. In a recent issue of PLoS Biology, a similar competition improbably played out again, with an RNA enzyme as the backdrop. Experimentalists can carry out a wide range of in vitro evolution experiments that " force " the selection of molecules with particular phenotypes. One of the greatest successes of in vitro evolution to date was the evolution of ribozyme ligases from a random sequence population by David Bartel and Jack Szostak [2]. These authors asked a pool that spanned 220 random sequence positions to ligate an oligonucleotide to itself (Figure 1A). Those ribozymes that could do so would gain access to a covalently linked primer-binding site, and thus to replication via reverse transcription and PCR amplifi cation. After multiple cycles of selection and amplifi cation, a number of ligases indeed emerged from the population, having outperformed their nonligase (and nonreplicable) competitors. One of the ligases was both extremely complex and extremely fast, for a ribozyme (k cat of 100 min –1 , upon optimization) [3]. While evolution had obviously occurred, it was very different from biological evolution: the original population was exceedingly complex (containing upwards of 10 15 different variants) and was progressively winnowed through a selection process in which enzymatic function and sequence amplifi cation were separated from one another in both time and space. The so-called Bartel ligase was further evolved for catalytic effi ciency by Martin Wright and Jerry Joyce [4]. These authors made a very clever adaptation to the original ligase in which a functional promoter was formed only upon ligation of the oligonucleotide substrate to the ribozyme (Figure 1B). This adaptation allowed enzymatic …