Directed evolution of enzymes for biocatalysis and the life sciences

Engineering the specificity and properties of enzymes and proteins within rapid time frames has become feasible with the advent of directed evolution. In the absence of detailed structural and mechanistic information, new functions can be engineered by introducing and recombining mutations, followed by subsequent testing of each variant for the desired new function. A range of methods are available for mutagenesis, and these can be used to introduce mutations at single sites, targeted regions within a gene or randomly throughout the entire gene. In addition, a number of different methods are available to allow recombination of point mutations or blocks of sequence space with little or no homology. Currently, enzyme engineers are still learning which combinations of selection methods and techniques for mutagenesis and DNA recombination are most efficient. Moreover, deciding where to introduce mutations or where to allow recombination is actively being investigated by combining experimental and computational methods. These techniques are already being successfully used for the creation of novel proteins for biocatalysis and the life sciences.Received 8 June 2004; received after revision 22 July 2004; accepted 2 August 2004     

Stage-structured cycles promote genetic diversity in a predator-prey system of Daphnia and algae

Competition theory predicts that population fluctuations can promote genetic diversity when combined with density-dependent selection. However, this stabilizing mechanism has rarely been tested, and was recently rejected as an explanation for maintaining diversity in natural populations of the freshwater herbivore Daphnia pulex. The primary limitation of competition theory is its failure to account for the alternative types of population cycles that are caused by size- or stage-dependent population vital rates--even though such structure both explains the fluctuating dynamics of many species and may alter the outcome of competition. Here we provide the first experimental test of whether alternative types of cycles affect natural selection in predator-prey systems. Using competing Daphnia genotypes, we show that internally generated, stage-structured cycles substantially reduce the magnitude of selection (thereby contributing to the maintenance of genetic diversity), whereas externally forced cycles show rapid competitive exclusion. The change in selection is ecologically significant, spanning the observed range in natural populations. We argue that structured cycles reduce selection through a combination of stalled juvenile development and stage-specific mortality. This potentially general fitness-equalizing mechanism may reduce the need for strong stabilizing mechanisms to explain the maintenance of genetic diversity in natural systems.     

The structure of an oligo(dA).oligo(dT) tract and its biological implications

Poly(dA).poly(dT) has unusual properties in that it cannot associate into nucleosomes and short, phased runs of it cause DNA bending. The crystal structure of a B-type DNA dodecamer containing a homopolymeric run of six A.T base pairs shows that this region possesses special structural features, including a system of bifurcated hydrogen bonds, which explains some of the properties of this simple homopolymer.     

Complex inheritance of familial hypercholanemia with associated mutations in TJP2 and BAAT

Familial hypercholanemia (FHC) is characterized by elevated serum bile acid concentrations, itching, and fat malabsorption. We show here that FHC in Amish individuals is associated with mutations in tight junction protein 2 (encoded by TJP2, also known as ZO-2) and bile acid Coenzyme A: amino acid N-acyltransferase (encoded by BAAT). The mutation of TJP2, which occurs in the first PDZ domain, reduces domain stability and ligand binding in vitro. We noted a morphological change in hepatic tight junctions. The mutation of BAAT, a bile acid-conjugating enzyme, abrogates enzyme activity; serum of individuals homozygous with respect to this mutation contains only unconjugated bile acids. Mutations in both TJP2 and BAAT may disrupt bile acid transport and circulation. Inheritance seems to be oligogenic, with genotype at BAAT modifying penetrance in individuals homozygous with respect to the mutation in TJP2.     

Rapid evolution drives ecological dynamics in a predator-prey system

Ecological and evolutionary dynamics can occur on similar timescales. However, theoretical predictions of how rapid evolution can affect ecological dynamics are inconclusive and often depend on untested model assumptions. Here we report that rapid prey evolution in response to oscillating predator density affects predator-prey (rotifer-algal) cycles in laboratory microcosms. Our experiments tested explicit predictions from a model for our system that allows prey evolution. We verified the predicted existence of an evolutionary tradeoff between algal competitive ability and defence against consumption, and examined its effects on cycle dynamics by manipulating the evolutionary potential of the prey population. Single-clone algal cultures (lacking genetic variability) produced short cycle periods and typical quarter-period phase lags between prey and predator densities, whereas multi-clonal (genetically variable) algal cultures produced long cycles with prey and predator densities nearly out of phase, exactly as predicted. These results confirm that prey evolution can substantially alter predator-prey dynamics, and therefore that attempts to understand population oscillations in nature cannot neglect potential effects from ongoing rapid evolution.