Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
Ribosomal Paleontology and Resurrection: Molecular Fossils from before Coded Protein
The origins and early development of the translation machinery remain imprinted in the extant ribosome (1-3), in sequences, folding, and function. To mine the information contained within the ribosome, we are developing new methods of molecular paleontology. We are developing experimental and computational tools to understand and recapitulate fundamental steps in the origin and evolution of the ribosome, and to estimate the relative ages of ribosomal components. We are biochemically resurrecting working models of ancestral ribosomes. We are developing timelines for critical steps in the evolutionary history of the ribosome. The results of these studies will help provide keys to understanding the origin of proteins and RNA, and the origin of life. We use structure- and sequence-based comparisons of the Large Subunits (LSUs) of Haloarcula marismortui and Thermus thermophilus. These are the highest resolution ribosome structures available, and represent the two primary branches of the evolutionary tree. Using an onion analogy, we have sectioned the superimposed bacterial and archaeal LSUs into concentric shells, using the sites of peptidyl transfer as the centers (4). This spherical approximation allows shell-by-shell dissections and comparisons that clearly capture significant information along the evolutionary timeline. The results support the notion that ever-older molecular fossils are revealed as one bores toward the center of the LSU onion. The conformations and interactions of both RNA and proteins change over time. The frequency with which macromolecules assume regular secondary structural elements, such as A-form helices containing Watson-Crick base pairs (RNA) and α-helices and β-sheets (protein), increases with time. The conformations of the oldest ribosomal protein components suggest they are molecular fossils of the non-coded peptide ancestors of ribosomal proteins. We hypothesize that abbreviated lengths and mixed sequences in the ancestral state proscribed secondary structure, which is indeed nearly absent near the centers of the LSU onions.
Loren Dean Williams
NASA Astrobiology Institute and the Center for Ribosomal Origins and Evolution at the Georgia Institute of Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400