Fungi and oomycete promoters and systems analyses of mycorrhizae gene interactions

Bioinformatic, computational, and molecular approaches were utilized to elucidate insights about the various constituents of plant-microbe interactions. Computational and systems approaches enabled the development of de novo gene regulatory network (GRNs) specific plant genes and their regulation while associated with an arbuscular mycorrhiza. This network was created using previously published microarray data obtained from a model plant system grown under basal or high phosphorus levels.;Gene regulatory networks were developed through a novel discrete dynamical system (DDS) and verified computationally and biologically. For each of the GRNs developed, only two possible parents influencing a node showed computational viability and exhibited the least amount of biological noise. This GRN showed that genes could be functionally-grouped into clusters associated with pathogenicity, stress, defense, ripening, maturation and senescence. Another GRN was developed for regulated genes when the plant was grown in higher phosphate levels. These genes were clustered with defense, stress and maturation. For both GRNs, putative functions of previously unannotated genes were determined based on the biological function with which they clustered.;This dissertation also investigated the effects of alternative carbon sources on the two glyoxylate cycle promoters derived from the beneficial fungi---the arbuscular mycorrhizae Glomus intraradices and the ectomycorrhizae Laccaria bicolor. Vector constructs containing these promoters were transformed into Laccaria and assayed for promoter activity through eGFP levels. Box-and-whisker plots showed that even with Laccaria hyphae containing the positive control, wide variations were observed between and among transformants. Various mechanisms acting singly or synergistically were hypothesized to cause such variations.;A novel statistics-based approach was used to determine putative promoters that were active during all life stages of the pathogenic oomycete, Phytophthora capsici. Promoters for two ribosomal proteins and actin were cloned from the pathogenic fungi P. capsici and assayed for promoter activity and strength. These promoters were able to drive GUS expression in different Phytophthora species and a plant system. The promoters had stronger activity within the transformed Phytophthora zoospores than the CaMV 35S CaMV promoter. However, the CaMV 35S promoter activity was significantly greater in planta than the Phytophthora promoters. Bioinformatic analyses of promoter motifs elucidated specific candidate motifs that explain the difference in promoter activity in oomycetes and in plants.