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Open Access Publications from the University of California

Scholarly Works (2 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2009)
In this thesis I describe the results of experiments aimed at characterizing different aspects of the immune system in plants, through the investigation of the Arabidopsis thaliana and Pseudomonas syringae interaction. First, we explored the ability of different microbe associated molecular patterns, MAMPS to induce certain defense marker genes. Additionally we explored specific single bacterial avirulence effectors for their ability to suppress MAMP induced defense signaling in R-gene-deficient plants (Chapter 1). Flagellin (flg22), cellulase, and salicylic acid induced the chosen marker genes in different ways, but plants seemed to respond to a lesser extent to the E.coli compound Kdo₂-lipid A, which induces defense in mammalian cells. The Pseudomonas effectors avrRpm1, avrRpt2, avrRps4, avrB, and avrPphB did not clearly suppress any of the marker-gene inductions. Moreover, some induction of markers was observed, suggesting recognition of the effectors by unknown (R-) proteins. We also explored the effects that light and temperature have on the hypersensitive response (HR) during the resistance (R) -gene defense response induced by expression of a single bacterial effector (Chapter 2). As expected deprivation of light delayed the HR. Surprisingly, and in contrast to other studies, HR was functional at high temperatures, and instead HR was delayed at low temperature (17⁰C). Since the function of many proteins in immune signaling is unknown, as well as potential protein-protein interactions, we explored the interactome of the protein NDR1. We identified 286 potential NDR1 interacting proteins with potential roles in plant immunity. Currently, candidate proteins are being tested for their role in defense.
    Cover page: Exploring plant immune signaling through the Arabidopsis and Pseudomonas syringae interaction
    • Thesis
    • Peer Reviewed
    UC San Diego Electronic Theses and Dissertations (2014)

    In this dissertation I explore trinucleotide repeat instability as well as the characterization of the ataxin-7 protein through the interrogation of its yeast ortholog Sgf73. Upon expansion of its CAG tract, ataxin-7 is known to cause the neurodegenerative disease, spinocerebellar ataxia type 7 (SCA7). Using microarray expression analysis, we sought to identify the genetic basis of regional instability differences between two different brain tissues, the striatum and the cerebellum. These tissues are known to have high and low levels of trinuclotide expansion, respectively. We identified eight candidate genes involved in DNA replication and repair enriched in cerebellum, and validated five - Pcna, Rpa1, Msh6, Fen1, and Lig1. Expression levels of these candidates are significantly higher in the cerebellum than in the striatum, but were not dependent on disease status in a line of transgenic Huntington disease mice. In Chapters 2 and 3, we studied the function of the ataxin-7 yeast ortholog, Sgf73, a member of the deubiquitinase module (DUBm) in the SAGA transcriptional co-activator complex. It is known that the yeast sgf73Δ mutant has an extended replicative life span (RLS). We tested the role of different SAGA complex members in RLS and found that other DUBm mutants have increased RLS, but not to the degree seen in sgf73Δ. Deleting other non-DUBm SAGA components did not extend RLS. Additionally we found that the sgf73Δ RLS extension is dependent on the presence of the histone deacetylase, Sir2, which physically interacts with Sgf73. Lastly, we performed ChIP-Seq to determine the DNA binding locations of Sgf73. We identified 389 genomic regions bound by Sgf73, with an enrichment in the region 5' to ribosomal protein encoding genes. Additionally, 31 of the 389 identified Sgf73 genomic targets had previously been described to be involved in RLS. Using these data and transcriptome data from SAGA-related mutants, we were able to pinpoint several high-confidence Sgf73 targets for further studies on the mechanism of RLS in yeast as well as expanded ataxin-7 mediated neurodegeneration in humans.

    • 1 supplemental file
    Cover page: Exploring mechanisms of trinucleotide expansion and studying the normal function of the ataxin-7 yeast ortholog Sgf73
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