NSF Award
0848815
In modern organisms, three main reactions enable the conversion of the information contained in genes into functional proteins through the rules of the genetic code. The first reaction (1) corresponds to the formation of aa-AMP from of an amino acid (aa) and an ATP molecule, and is a thermodynamic requirement for the second reaction (2), the attachment of the amino acid onto the 3 end of a cognate transfer RNA (tRNA). The third reaction (3) leads to the polymerization of tRNA-bound amino acids into proteins during the translation process (on the ribosome). Approximately twenty versions of the aminoacyl-tRNA synthetase are capable of successively catalyzing reactions 1 and 2. The early genetic system could not possibly have relied on any such coded proteins, and it is therefore thought that some RNA molecules were able to catalyze these reactions following the rules of a simplified genetic code. The goal of this project is to clarify the mechanisms of interaction among RNA structures, ATP and amino acids (as well as AMP-activated amino acids) by which these three main chemical reactions could be fulfilled without protein. Studies have already demonstrated that reaction 2 and an analog of reaction 1 can be catalyzed by certain RNAs. The product of reaction 1 (aa-AMP) is however quickly hydrolyzed in water, proving difficult to study. This instability requires the coupling of reactions 1 and 2 on a same molecule, and occurs precisely on the aminoacyl-tRNA synthetases. It is therefore expected that some yet unidentified RNAs have this same catalytic property. The resolution of this issue constitutes the basis of the present research project. Data from earlier experimental studies, suggest mechanisms by which this coupling can be achieved on very short RNAs (~25 bases) that form simple folding structures, such as small bulges. The critical parameters allowing these reactions will be studied both experimentally and computationally (with molecular dynamic simulations). The PIs will also use selection-amplification procedures (SELEX) to uncover these RNAs from pools of random molecules. Reaction 3 will also be investigated, in particular to establish whether the ribosome is indispensable for peptide bond formation, or if it is only necessary to establish a ratchet-like mechanism. This work will clarify the implications of the elementary properties of the amino acids and the nucleotides in water for the mechanisms responsible for the emergence of the genetic code. Since the polymerization of the amino acids through reactions 1-3 is a process out of equilibrium, new results in this field will help to clarify the connection between biological coding and the laws of non-equilibrium thermodynamics. This project will be beneficial to undergraduate students, introducing them to one of most fundamental issues of modern biophysics, the bridge between the work of Boltzmann (thermodynamics) and Turing (coding).
