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Caetano-Anolles, Gustavo Caetano-Anolles, Gustavo Mittenthal, Jay Hudson, Matthew E. Vodkin, Lila O. Harish, Ajith 2011-01-21T22:51:31Z 2011-01-21T22:51:31Z 2013-01-22T11:00:15Z 2010-12 2011-01-21T22:51:31Z 2010-12 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. Item withdrawn by Alexis Thompson (athmpsn1@illinois.edu) on 2010-07-16T20:36:28Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 2 Harish_Ajith.docx: 28441934 bytes, checksum: 3d6029efe873010ecb264e3d0c5e4309 (MD5) HARISH_AJITH.pdf: 31780508 bytes, checksum: 02959ccc2e08dbd19cce2dc2ee3735c7 (MD5) Made available in DSpace on 2011-01-21T22:51:31Z (GMT). No. of bitstreams: 2 Harish_Ajith.pdf: 31818689 bytes, checksum: 7566ddb1a8f1be4059d2eef2f0243b7e (MD5) license.txt: 4060 bytes, checksum: 28acac30fa11c11a01fdc040c66a5567 (MD5) Item marked as restricted to the 'Administrator' Group (id=1) by William Ingram (wingram2@illinois.edu) on 2011-01-21T22:53:49Z Item is restricted until 2013-01-21T22:53:34Z Item reinstated by Sarah Shreeves (sshreeve@illinois.edu) on 2013-01-22T11:00:15Z Item was in collections: University of Illinois Dissertations and Theses (ID: 204) Dissertations and Theses - Biology (ID: 688) No. of bitstreams: 2 Harish_Ajith.pdf: 31818689 bytes, checksum: 7566ddb1a8f1be4059d2eef2f0243b7e (MD5) license.txt: 4060 bytes, checksum: 28acac30fa11c11a01fdc040c66a5567 (MD5) Item released from any restrictions by Sarah Shreeves (sshreeve@illinois.edu) on 2013-01-22T11:00:15Z http://hdl.handle.net/2142/18609 en Copyright 2010 Ajith Harish Ribosome RNA Translation RNP World Evolution of Ribosome Evolution of Translation The origin and evolution of the ribosome School of Integrative Biology 1383 Biology 0314 University of Illinois at Urbana-Champaign Dissertation Ph.D. PHD:Biology-PM Plant Bio -UIUC 10KS0317PHD