The 80 S cytoplasmic ribosome is the largest of three populations of ribosomes responsible for protein synthesis in plants. It is comprised of two RNA/protein subunits of unequal size: the small (40 S) subunit selects messages to be translated and performs proofreading, while the large (60 S) subunit has peptidyl transferase acitivity, adding new amino acids to the growing polypeptide. In the model flowering plant <i>Arabidopsis thaliana</i> (hereafter <i>Arabidopsis</i>), four ribosomal RNAs and 81 ribosomal proteins (r-proteins) assemble to form the 80S ribosome. Although the <i>Arabidopsis</i> ribosome contains only a single copy of each of the 81 r-proteins (with the exception of small number of acidic phophoproteins), all r-proteins are encoded from multi-gene families containing two or more expressed members. Herein, I investigated r-protein paralogy in Arabidopsis via specific examination of a two member gene family, RPL23a. By analyzing patterns of reporter gene expression driven by full-length and truncated regulatory regions, I was able to identify a core promoter that is largely conserved between paralogs. Regulation was found to be complex, involving transcriptional, post-transcriptional and translational components. The effects of knocking-out a single RPL23a paralog (RPL23aB) were determined. Results indicated that this paralog is broadly dispensable, and Arabidopsis does not compensate for its loss at the transcriptional level. Subcellular localization was investigated by tagging RPL23aA/B with fluorescent proteins, demonstrating that RPL23aA is targeted to nucleolus more efficiently than RPL23aB, possibly due to a stronger nucleolar localization signal. RNA-interference was used to individually silence RPL23a paralogs to characterize functional overlap. Results showed that RPL23aA, and not RPL23aB, is required for normal development. Mutants with reduced levels of RPL23aA develop a pointed first leaf phenotype that I postulate may be due to disruption of miRNA-mediated degradation of specific auxin response genes. Lastly, the 26 S proteasome was inhibited to determine the importance of protein turnover in regulating RPL23a levels. Findings suggest that proteasome-mediated degradation of RPL23a is essential for preventing accumulation of unincorporated r-proteins. Overall, results indicate that the Arabidopsis RPL23a paralogs have diverged from each other: RPL23aA has become the predominant paralog, while RPL23aB functions in an anciliary capacity and/or is undergoing neofunctionalization.

The 80 S cytoplasmic ribosome is the largest of three populations of ribosomes responsible for protein synthesis in plants. It is comprised of two RNA/protein subunits of unequal size: the small (40 S) subunit selects messages to be translated and performs proofreading, while the large (60 S) subunit has peptidyl transferase acitivity, adding new amino acids to the growing polypeptide. In the model flowering plant <i>Arabidopsis thaliana</i> (hereafter <i>Arabidopsis</i>), four ribosomal RNAs and 81 ribosomal proteins (r-proteins) assemble to form the 80S ribosome. Although the <i>Arabidopsis</i> ribosome contains only a single copy of each of the 81 r-proteins (with the exception of small number of acidic phophoproteins), all r-proteins are encoded from multi-gene families containing two or more expressed members. Herein, I investigated r-protein paralogy in Arabidopsis via specific examination of a two member gene family, RPL23a. By analyzing patterns of reporter gene expression driven by full-length and truncated regulatory regions, I was able to identify a core promoter that is largely conserved between paralogs. Regulation was found to be complex, involving transcriptional, post-transcriptional and translational components. The effects of knocking-out a single RPL23a paralog (RPL23aB) were determined. Results indicated that this paralog is broadly dispensable, and Arabidopsis does not compensate for its loss at the transcriptional level. Subcellular localization was investigated by tagging RPL23aA/B with fluorescent proteins, demonstrating that RPL23aA is targeted to nucleolus more efficiently than RPL23aB, possibly due to a stronger nucleolar localization signal. RNA-interference was used to individually silence RPL23a paralogs to characterize functional overlap. Results showed that RPL23aA, and not RPL23aB, is required for normal development. Mutants with reduced levels of RPL23aA develop a pointed first leaf phenotype that I postulate may be due to disruption of miRNA-mediated degradation of specific auxin response genes. Lastly, the 26 S proteasome was inhibited to determine the importance of protein turnover in regulating RPL23a levels. Findings suggest that proteasome-mediated degradation of RPL23a is essential for preventing accumulation of unincorporated r-proteins. Overall, results indicate that the Arabidopsis RPL23a paralogs have diverged from each other: RPL23aA has become the predominant paralog, while RPL23aB functions in an anciliary capacity and/or is undergoing neofunctionalization.

No description available.

"October, 2003" / Bibliography: leaves 130-141. / xvii, 150, [10] leaves : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This study describes the silencing of tobacco transgenes carrying TLCV promoters following TLCV infection. / Thesis (Ph.D.)--University of Adelaide, School of Agriculture and Wine. 2003

Thesis (Ph. D.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

My research mainly focused on the functional redundancy and expression divergence of gene duplicates to address currently unsolved problems. Herein, we employed a method based on GO terms to measure functional overlap between paralogs. We established that functional similarity between duplicate genes is the key determinant of their backup capacity. Later, we also investigated expression divergence. Recent studies suggest that only a small proportion of expression variation can be explained by transcriptional variation between paralogs. Here, the contribution from diverged TF-regulations was re-examined and differential promoter chromatin status was also found as an important contributor to expression divergence. To better understand the role of gene duplication in great detail, a case study was performed on the yeast chaperone system, which includes many gene duplicates. Taken together, this study sheds light on the roles of redundancy and divergence in long-term retention of gene duplicates.

My research mainly focused on the functional redundancy and expression divergence of gene duplicates to address currently unsolved problems. Herein, we employed a method based on GO terms to measure functional overlap between paralogs. We established that functional similarity between duplicate genes is the key determinant of their backup capacity. Later, we also investigated expression divergence. Recent studies suggest that only a small proportion of expression variation can be explained by transcriptional variation between paralogs. Here, the contribution from diverged TF-regulations was re-examined and differential promoter chromatin status was also found as an important contributor to expression divergence. To better understand the role of gene duplication in great detail, a case study was performed on the yeast chaperone system, which includes many gene duplicates. Taken together, this study sheds light on the roles of redundancy and divergence in long-term retention of gene duplicates.

Thesis (M.S. in biochemistry)--Washington State University, December 2009. / Title from PDF title page (viewed on Jan. 4, 2010). "School of Molecular Biosciences." Includes bibliographical references (p. 18-20).

Thesis (Ph. D.)--University of Texas at Arlington, 2008.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (p. 107-111).