Browsing by Subject "Secondary metabolism"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Genomic analysis of regulatory mechanisms involved in secondary metabolite production.
    (2010-09) Castro-Melchor, Marlene
    Many secondary metabolites have beneficial uses for humans. In addition to their use as antibacterial and antifungal agents, secondary metabolites have been used as immunosuppressants, anti-tumor agents, and antiparasitics. Most of the secondary metabolites known today are produced by filamentous fungi or by members of the Streptomyces genus. Production of secondary metabolites by microorganisms involves a complex, dynamic system, with interconnected elements acting at different levels. Diverse tools were used in this work to explore regulation of secondary metabolite production, mostly in Streptomyces. The tools have a common characteristic: they either generate large amounts of data, or require large amounts of data. Regulation of secondary metabolite production in Streptomyces coelicolor was analyzed at the genome level, by using network modules inferred from a large transcriptome dataset. The upstream sequence of the elements in the network modules was searched for the presence of consensus sequences, and these results combined with information on known interactions, binding sites, and functional relatedness. The combination of this information resulted in a set of twenty networks that have a high likelihood of representing true interactions and represent a starting point for further experimental studies. The characteristics of high productivity were analyzed by comparing the genomes of two strains of the clavulanic acid producer Streptomyces clavuligerus. One of the strains is a high producer of clavulanic acid. Next generation sequence data was used to perform a genome-wide screening to identify all the differences between the two genomes. In addition to mutations in genes involved in β-lactam antibiotic production or their upstream region, structural differences were detected between the two strains. Next generation sequencing technologies were also used to assemble a draft genome for the curdlan producer Agrobacterium sp. ATCC 31749. Curdlan production mimics that of secondary metabolites, it is triggered under starvation conditions. These varied approaches exemplify some of the paths that can lead to a better understanding of secondary metabolism and its regulation.
  • Thumbnail Image
    Item
    Influence of plant diversity and perennial plant identity on Fusarium communities in soil
    (2013-09) LeBlanc, Nicholas
    Fusarium communities in soil are highly diverse and may play key functional roles in native and agricultural ecosystems. Despite the diversity and functional relevance of soil Fusarium communities, very little is known about what determines their diversity, structure, and function. This work tested the effects of perennial plant identity and plant community diversity on Fusarium communities in soil. Soil was collected from the rhizosphere of native perennial legumes and grasses growing in monoculture and polyculture at the Cedar Creek, Long Term Ecological Research site in Minnesota, USA. To characterize Fusarium communities, soil DNAs were used to create and pyrosequence amplicon libraries from a single copy protein-coding locus (RPB2). For functional characterization, individual isolates of Fusarium were cultured from the same soil. A portion of the RPB2 locus was sequenced for phylogenetic characterization of each isolate. Isolates were also tested for carbon use as measured by growth on 95 carbon substrates using Biolog phenotype arrays, and for the capacity to produce multiple secondary metabolites as measured using a PCR assay developed from genomic resources. Fusarium communities were influenced by plant diversity and perennial plant identity. Fusarium community structure was differentiated between monoculture and polyculture plant communities and by plant species in monoculture. Drivers of the richness within Fusarium communities were lineage specific; one lineage showed a positive response to soil edaphic characteristics and another a negative response. Cultured Fusarium isolates from the same soil showed isolates from rhizosphere soil of the legume L. capitata used more carbon substrates than isolates from the grass A. gerardii. Phylogenetic characterization showed that isolates within a given phylogenetic clade displayed more similar carbon use profiles than isolates between different clades, highlighting functional consequences of changes in the communities of the these fungi in response to plants. Screening for genes underlying the production of secondary metabolites in the Fusarium isolates showed the genetic potential to produce the plant hormones indoleacetic acid or gibberellic acid was correlated with reduced fungal growth.