{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/86761"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/86761","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Archaeal Gene Identification","abstract":"Complete genome sequences from six archaeal lineages provide an unprecedented resource for studying molecular function and evolution in the domain Archaea. Phenotypic features that were previously considered to be characteristic of Archaea, such as antibiotic resistances and susceptibilities, were neither unique nor copious elements of the archaeal gene complement. In their stead were numerous proteins with no identified function and a significant literature describing biochemical reactions and phenotypes yet to be associated with genes. This thesis reports on several different projects, each addressing systems fundamental to Archaea. Purification of surface layer proteins from hyperthermophilic members of the Methanococcales, coupled with genomic analysis, shows that members of the Methanococcales and Thermococcales share a common cell wall structure, despite a 70°C range in optimal growth temperatures. Compilation of an archaeal genomic signature describes a set of proteins unique to Archaea. These 351 clusters of proteins from four euryarchaeal lineages represent some of the innovations that were introduced during the evolution of the archaeal lineage. Another section identifies an archaeal-type S-adenosylmethionine synthetase that is highly diverged from well-studied bacterial and eucaryal homologs. Studies of tRNA modification enzymes from M. jannaschii identify 7 enzymes, which use S-adenosylmethionine to methylate tRNAs in vitro . Inferred phylogenies of these enzymes imply that most were present in an ancestor of the archaeal/eucaryal lineage. Finally, genetic disruption of the N2 N2-dimethylguanosine-26 tRNA methyltransferase in M. maripaludis demonstrates the utility of combined genetic and biochemical approaches to characterizing archaeal tRNA methyltransferases.","abstract_html":"Complete genome sequences from six archaeal lineages provide an unprecedented resource for studying molecular function and evolution in the domain Archaea. Phenotypic features that were previously considered to be characteristic of Archaea, such as antibiotic resistances and susceptibilities, were neither unique nor copious elements of the archaeal gene complement. In their stead were numerous proteins with no identified function and a significant literature describing biochemical reactions and phenotypes yet to be associated with genes. This thesis reports on several different projects, each addressing systems fundamental to Archaea. Purification of surface layer proteins from hyperthermophilic members of the Methanococcales, coupled with genomic analysis, shows that members of the Methanococcales and Thermococcales share a common cell wall structure, despite a 70°C range in optimal growth temperatures. Compilation of an archaeal genomic signature describes a set of proteins unique to Archaea. These 351 clusters of proteins from four euryarchaeal lineages represent some of the innovations that were introduced during the evolution of the archaeal lineage. Another section identifies an archaeal-type S-adenosylmethionine synthetase that is highly diverged from well-studied bacterial and eucaryal homologs. Studies of tRNA modification enzymes from M. jannaschii identify 7 enzymes, which use S-adenosylmethionine to methylate tRNAs in vitro . Inferred phylogenies of these enzymes imply that most were present in an ancestor of the archaeal/eucaryal lineage. Finally, genetic disruption of the N2 N2-dimethylguanosine-26 tRNA methyltransferase in M. maripaludis demonstrates the utility of combined genetic and biochemical approaches to characterizing archaeal tRNA methyltransferases.","abstract_has_math":false,"creators":["Graham, David E."],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Microbiology","degree_department":null,"school":null,"contributors":["Olsen, Gary J."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2015,"date_issued":"2015-09-28T15:17:53Z","date_published":"2015-09-28T15:17:53Z","updated_at":"2026-07-22T22:26:27Z","subjects":["Biology, Genetics"],"languages":["eng"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["(MiAaPQ)AAI9990008"],"render_values":[{"text":"(MiAaPQ)AAI9990008","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/2142/86761","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Olsen, Gary J."]},{"key":"dc:creator","label":"Author","values":["Graham, David E."]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2015-09-28T15:17:53Z","10000-01-01","2000"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Microbiology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biology, Genetics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/86761","(MiAaPQ)AAI9990008"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Complete genome sequences from six archaeal lineages provide an unprecedented resource for studying molecular function and evolution in the domain Archaea. 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