The origin and evolution of the ribosome

THE ORIGIN AND EVOLUTION OF THE RIBOSOME Ajith Harish, Ph.D. Program in Physiological and Molecular Plant Biology University of Illinois at Urbana-Champaign, 2010 Prof. Gustavo Caetano-Anollés, Advisor The ribosome coordinates one of the most fundamental biological processes, protein biosynthesis. The evolutionary history of the ribosome has intrigued biologists and it’s understanding has been a major and elusive challenge. In this dissertation, the evolution of the ribosome is studied using a novel method that directly embeds structure and function of macromolecules into phylogenetic analyses. Macromolecular structure is more evolutionarily conserved than sequence due to constraints arising from the intricate structure-function relationship. Tracing the evolution of the structural elements of the ribosome, namely ribosomal RNA (rRNA) and ribosomal proteins (r-proteins) provided a deep and the most comprehensive insight possible yet into the origins and evolution of the ribosome. Using phylogenetic methods that reconstruct the evolutionary history of complex RNA and protein ensembles directly from their structure, we find the structures linked to ribosomal processivity that originated in the small subunit (SSU) evolved earlier than the catalytic centre in the large subunit (LSU). Molecular rRNA timelines and phylogenomic analysis of protein structure also show that ancient substructures of the rRNA subunits coevolved with ribosomal proteins at first independently, starting with interactions between the most ancient ribosomal proteins (S12 and S17) and the most ancient small subunit substructure (helix h44) and culminating with the evolutionary integration of the two subunits and most ribosomal proteins to form a modern functional proto-ribosome. These ancient rRNA structures have similarities to in vitro evolved RNA ligase and polymerase ribozymes. This indicates that structural elements and functional strategies of a primitive replication mechanism was recruited or co-opted for the process of protein biosynthesis. Functionally important and conserved regions of the ribosome are therefore relics of an ancient ribonucleoprotein world, supporting theories that translation was a functional takeover of a primitive replication apparatus.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2011

Author dc:creator

• Harish, Ajith

Contributors dc:contributor

• Caetano-Anolles, Gustavo
• Mittenthal, Jay
• Hudson, Matthew E.
• Vodkin, Lila O.

• Ribosome
• RNA
• Translation
• RNP World
• Evolution of Ribosome
• Evolution of Translation

Statement dc:rights

• Copyright 2010 Ajith Harish

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/18609

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/18609