<p>As part of development of a human
pathogen suppressing in plantae model system within <i>Spinacia oleracea</i>, a
known pathogen transmitting produce plants, the secretome of the <i>Stemphylium</i>
strain PNW2016-02, an endophytic fungal isolate of spinach plants, was studied.
This strain was previously isolated in Purdue University Northwest laboratories
in the Biological Sciences Department. As the secondary metabolite secretions
of PNW2016-02 were shown to have antibiotic properties against a broad range of
bacteria, we sought to improve our understanding of these properties and other
characteristics of PNW2016-02 by sequencing and annotating the genome of this
strain. Chemical compound characterization was achieved using HPLC-MS, which
provided the ability to identify and quantify chemical compounds contained
within the PNW2016-02 secretome. Through multi-gene phylogenetic analysis and
comparative genomics, we found that PNW2016-02 clusters with a clade
representing <i>Stemphylium vesicarium</i>; however, genome annotation also
uncovered several genes unique to PNW2016-02. To assist in more fully
understanding the secondary metabolites PNW2016-02, a semi-automated
bioinformatic pipeline was developed in the R statistical environment in order
to reconstruct and characterize the metabolic pathways, especially those
pertinent to antibiotic production. Analysis using the bioinformatic pipeline
revealed the presence of a number of antimicrobial metabolites, such as
flavonoids, and suggests these compounds are produced and transformed in
pathways, such as the phenylpropanoid synthesis pathway. These findings also
suggest an important vital role of the shikimate pathway for antimicrobial
metabolite production within PNW2016-02. Overall, the findings presented here
have implications for understanding the antimicrobial strategies employed by <i>Stemphylium</i>
PNW2016-02 and its potential for use in the above-mentioned model system.</p>
| Identifer | oai:union.ndltd.org:purdue.edu/oai:figshare.com:article/17213564 |
| Date | 20 December 2021 |
| Creators | Nathaniel Thomas Tobey (11845817) |
| Source Sets | Purdue University |
| Detected Language | English |
| Type | Text, Thesis |
| Rights | CC BY 4.0 |
| Relation | https://figshare.com/articles/thesis/A_MULTIPHASIC_PHYLOGENETIC_AND_GENOMIC_CHARACTERIZATION_OF_THE_FUNGAL_ENDOPHYTE_STEMPHYLIUM_STRAIN_PNW2016-02_AND_A_SEMI-AUTOMATED_BIOINFORMATIC_APPROACH_TO_INVESTIGATING_THE_STRAIN_SECRETOME/17213564 |
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