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Project Progress

In the effort to understand the evolutionary origins of functional biological macromolecules we have evolved, for the first time, a new enzyme having a catalytic activity that has not been observed in nature. The ability to evolve novel enzymatic activities from relatively small libraries of randomized sequences suggests that the evolution of functional proteins may not have been a difficult or slow stage in the early evolution of life.

In the DNA-binding domain of the human retinoid-X-receptor (hRXRα) we replaced the two recognition loops with segments of random amino acids. We then applied an mRNA-display technique to select protein sequences capable of catalyzing the template-directed ligation of two RNA oligonucleotides. Enzymatic activity was subsequently optimized in additional rounds of selection following mutagenesis and recombination. Proteins from the final round were screened for activity, and the best one was chosen for further analysis. It was shown that the chemistry of the ligation reaction is the same as that catalyzed by protein polymerases, and the rate enhancement conferred by the evolved enzyme is at least a million fold.

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Also, we continued to explore the evolution of the previously evolved ATP-binding protein. Using a combination of biochemical, biophysical and computational studies, we have been able to explain how the sequence and structure of this protein affect its stability, strength and selectivity of binding ATP, and its evolutionary potential towards performing new functions.

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Our experimental results support the assumption that emergence of functional proteins from random amino acid sequences was a probable event during evolution. This assumption forms the basis for our computational studies on the origin of metabolic networks. Using a model chemistry that takes into account realistic thermodynamic and kinetic constraints, we have shown a possibility of self-organization of simple metabolism into pathways and cycles that persist in the population (i.e. are “collectively inherited”) even though they are not inherited at the level of individual protocells. Our results support a view that the formation of protocellular metabolism was largely deterministic, strongly constrained by laws of chemistry, even though it might have been driven by non-genomic, highly stochastic processes.