published_or_final_version / abstract / Botany / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Chemistry / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Biological Sciences / Master / Master of Philosophy

published_or_final_version / Pathology / Doctoral / Doctor of Philosophy

Aflatoxins, toxic secondary metabolites produced by some Aspergillus species, are a universal agricultural economic problem and a critical health issue. Despite decades of control efforts, aflatoxin contamination is responsible for a global loss of millions of tons of crops each year. We show that host-induced gene silencing is an effective method for eliminating this toxin in transgenic maize. We transformed maize plants with a kernel-specific RNA interference (RNAi) gene cassette targeting the aflC gene, which encodes an enzyme in the Aspergillus aflatoxin biosynthetic pathway. After pathogen infection, aflatoxin could not be detected in kernels from these RNAi transgenic maize plants, while toxin loads reached thousands of parts per billion in nontransgenic control kernels. A comparison of transcripts in developing aflatoxin-free transgenic kernels with those from nontransgenic kernels showed no significant differences between these two groups. These results demonstrate that small interfering RNA molecules can be used to silence aflatoxin biosynthesis in maize, providing an attractive and precise engineering strategy that could also be extended to other crops to improve food security.

ABSTRACT Cassava is currently the second most important source of carbohydrates on the African continent. In the last two decades, cassava crops have been severely affected by outbreaks of cassava mosaic disease (CMD). South African cassava mosaic virus (SACMV) has been associated with CMD outbreaks in the Mpumalanga province. Advances in post-transcriptional gene silencing (PTGS) technology have provided promising new strategies for the engineering of virus resistance in plants. Inverted repeat (IR) constructs are currently the most potent inducers of PTGS, however, these constructs are inherently unstable. The purpose of this study was to develop IR constructs with an improved stability for the efficient induction of PTGS in plants. Two mismatched inverted repeat constructs, one targeting the SACMV BC1 open reading frame, the other targeting the Maize streak virus (MSV) AC1 open reading frame, were successfully created. Sodium bisulfite was used to deaminate cytosine residues on the sense arm of the constructs. The resulting number of GT mismatches was seemingly sufficient to stabilize the linear conformation of the IR constructs, as they were efficiently propagated by E.coli DH5!, and subsequently behaved like linear DNA molecules. Furthermore, it was found that the number of mismatches on the BC1 construct (17.5%) was ideal, as the subsequent stability of the predicted RNA hairpin was not affected. Due to the higher number of mismatches on the AC1 construct (23.5%), it was found that the loop region of the RNA hairpin was marginally destabilized. Despite this, long stretches of stable dsRNA were still produced from the AC1 IR construct, and is likely to induce PTGS. Interestingly, it was observed that the mismatched IR constructs, although still replicated in E.coli, were marginally destabilized in Agrobacterium. Therefore, it was deduced that the stability of a mismatched IR construct may be influenced by the particular intracellular environment of an organism. Due to the recalcitrance of cassava to transformation, a model plant system, Nicotiana benthamiana, was used to screen constructs for toxicity, stability, and efficiency of PTGS induction. Agrobacteriummediated transformation and regeneration of N. benthamiana was optimized, and 86% transformation efficiency was achieved when using leaf disk explants. It was found that the addition of an ethylene scrubber, potassium permanganate, substantially increased the rate of regeneration by reducing the frequency of hyperhydritic plants. Transgene iv integration was confirmed by PCR amplification of the hptII gene in the T-DNA region. Transgene expression was confirmed by screening for GUS and GFP reporter genes. No toxic responses to the transgene have been observed thus far. Studies are currently underway to confirm the stability of the mismatched IR constructs in N. benthamiana. PAGE Northern blotting is being done, as the detection of siRNAs derived from the transgene will confirm that constructs are functional. In addition, infectivity assays are underway to determine the efficacy of BC1 knockdown by a stably integrated construct. Due to the enhanced stability of mismatched IR constructs, they may be an appealing alternative to currently available intron-spliced, or exact matched hairpin systems.

Eukaryotic nuclear DNA is folded with histone and non-histone proteins into chromatin, a nucleoprotein structure regulated by histone post-translational modifications and substitution with histone variants. Chromatin mediates processes such as DNA damage repair, cell differentiation, gene silencing, and centromere specification. Mistaken inheritance of chromatin-mediated gene silencing, for instance, can cause both aberrant development and cancer. Gene silencing at pericentromeres and centromeres, which can be attained through obstruction of transcription as well as through recruitment of specific RNA-degrading proteins, is essential for centromere specification. However, the molecular mechanisms of these processes are not yet thoroughly understood, and therefore they will be the focus of this thesis. A structure termed heterochromatin, for which the essential hallmark is histone H3 lysine 9 methylation (H3K9me), preferentially assembles at repetitive DNA such as pericentric regions, playing roles in transcriptional silencing, recombination suppression, and chromosome segregation. The RNA interference (RNAi) machinery is required for heterochromatin assembly over DNA repeats in diverse organisms by targeting histone-modifying activities. Surprisingly, RNA splicing factors are also required for this process. A widely-held model derived from studies in fission yeast is that splicing factors provide a platform for siRNA generation independently of their splicing activity. Here, we discovered the requirement of four non-essential splicing factors for pericentric heterochromatin assembly, allowing us to more clearly address the role of splicing in heterochromatin assembly. Sequencing total cellular RNA from the strongest of these mutants, cwf14Δ, showed intron retention in mRNAs of several RNAi factors, which correspond to strong reduction in levels of a central RNAi protein, Argonaute. Moreover, introducing cDNA versions of RNAi factors significantly restores pericentric heterochromatin in splicing mutants. We also found that mutation of splicing factors affects telomeric heterochromatin, and replacement of mis-spliced factor tpz1+ with its cDNA partially rescued heterochromatin defects at telomeres in splicing mutants. Thus proper splicing of RNAi and shelterin factors contributes to heterochromatin assembly at pericentric regions and telomeres. In addition to post-translational modifications, chromatin silencing can be regulated by histone variants such as H2A.Z. The incorporation of H2A.Z into chromatin regulates chromatin structure and gene expression. The Swr1 chromatin remodeling complex deposits H2A.Z in budding yeast and mammals. Here we characterize a novel component of the fission yeast Swr1 complex, Msc1, which is a Jumonji domain protein frequently associated with histone demethylation. We found that Msc1 is required for Swr1-mediated incorporation of H2A.Z into chromatin at gene promoters. We demonstrated that H2A.Z is required for the expression of CENP-C, which in turn regulates centromere silencing and chromosome segregation. Together, these results show that chromatin silencing at pericentromeres and centromeres is mediated by splicing factors and H2A.Z, respectively, to promote proper regulation of other chromatin factors, thus ensuring faithful chromosome segregation.

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

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

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