Evolution of the Proteasome

Evolution of the proteasome multigene family was examined across all domains of life using experimental and computational techniques. First, degenerate primers designed to universally amplify all alpha proteasomes were used in the polymerase chain reaction with genomic DNA to probe the diversity of the gene family in several species of euryarchaea, crenarchaea, and single-celled eukaryotes. The method was validated using Saccharomyces cerevisiae DNA, which encodes seven paralogs. Although several novel gene fragments were found, the method was insufficient to determine the precise number of paralogs in the eukaryotic genomes tested. Next, publicly available full genome sequences were mined to perform phylogenomic analyses of both the alpha and beta proteasome families. Results demonstrate an unusual, explosive gene family diversification in Eucarya at the time of its emergence as a coherent lineage. A taxonomically balanced sample of sequences clearly separates into fourteen orthologous groups; a degree of diversity that corresponds with the structural constraints imposed by the architecture of the proteasome particle. These results support the duplication, degeneration and complementation model of gene family expansion, which proposes that specialization of new gene family members would result from complementation of degenerated protein activity or restricted gene expression caused by random mutations to coding or regulatory elements of duplicated genes. The neutral theory is not supported by these results because unprocessed proteasome pseudogenes are not found. Finally, scoring tables calculated from numerical indices of amino acid properties were used to quantify the evolution of amino acid properties among aligned alpha proteasome sequences using step analyses. Significantly less change in side chain shape, volume, interactivity, hydrophobicity and charge was measured at solvent-inaccessible positions compared to solvent-accessible positions. Among amino acids involved in protein contact surfaces, only side chain shape and volume are conserved.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Molecular and Integrative Physiology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2015

Author dc:creator

• McNeil, Leslie Klis

Contributors dc:contributor

• Gary Olsen

• Biology, Microbiology

Language dc:language

eng

Identifier

(MiAaPQ)AAI3070385

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/87221