Talk on Friday 01:00-01:15pm submitted by Saurja DasGupta
Emergence of ribonuclease activity in ribozymes through intersection of neutral networks
Saurja DasGupta (The University of Chicago), Joseph A. Piccirilli (The University of Chicago)
Ribozymes present the most primitive catalytic systems in Biology, and are thought to have played a central role in jumpstarting life. A major class of ribozymes, referred to as small endonucleolytic ribozymes catalyze site-specific RNA cleavage. While the structural and mechanistic features of these RNAs have been studied extensively, we have little understanding about their evolutionary histories. It is generally thought that enzymes acquire novel functions through adaptive walks along paths virtually neutral to mutational perturbations. This involves gradual acquisition of new functions while conserving its existing ones till the emergence of an ‘optimally evolved’ catalyst through bifunctional intermediates. We explored mutational landscapes in the sequence spaces of two functional RNAs – the VS and hairpin endonucleolytic ribozymes, by rational design, in-silico structure prediction and in-vitro functional assays. We discovered ‘neutral networks’ or mutational paths in the fitness landscapes containing sequences that retained cleavage activity for both ribozymes, and identified a sequence space where neutral networks for both ribozymes intersect. Sequences that fall in this region could potentially adopt secondary structures corresponding to both VS and hairpin folds and are catalytically active toward both VS and hairpin substrates. Catalytic promiscuity in primitive RNA might have driven exploration of sequence space and eventually certain sequences through mutations could’ve acquired a new function on encountering a novel functional space. Intersection of neutral networks therefore provide an evolutionary mechanism for the acquisition of new function in catalytic RNA. Subsequently, the gene for intersection sequences could duplicate and diverge by adaptive evolution to more optimal activities exemplified by wild-type VS and hairpin ribozymes, relieving constraints of dual and therefore decreased activities. This work paves a way for further investigations into the neutral networks of other related ribozymes and might provide insights into their evolutionary origins, enriching our understanding of RNA evolution in general, and in the context of primitive life prevalent in the RNA World.
1. The RNA World, 3rd Edition. Edited by Gesteland, ,R. F., Cech, T. R. and Atkins, J. F. 2006.
2. Lilley, D. M. J. The Origins of RNA Catalysis. TiBS, 28 (9), 2003.
3. Wagner, A. Robustness, evolvability and neutrality. FEBS Lett, 579, 2003.
4. Schultes, E. A. & Bartel, D. P. One sequence, two ribozymes: Implications for the emergence of New Ribozyme folds. Science, 289, 2000.
Keywords: Ribozymes, Evolution, Neutral Networks