THESIS
2018
xv, 83, that is, xvii, 84 pages : illustrations (some color) ; 30 cm
Abstract
Escherichia coli isolates (collectively termed UNISED) repeatedly harvested from marine
sediment are identified as distinctly environmental-specific, showing the ability to survive
outside the gastrointestinal tracts of warm-blooded animals. This discovery leads to the
hypothesis that UNISED E. coli may gain certain functions that allow them to persist in the
external environment and challenges the use of E. coli as a fecal indicative bacteria (FIB) for
water pollution detection.
LC-MS-based shotgun proteomics was performed on E. coli monocultures, and co-cultures of
two or more UNISED isolates in nutritional-limited (M9) media and in the presence of
mitomycin C (DNA damaging compound) to explore stress responses. Label-free
quantification is performed to overlay differentially...[
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Escherichia coli isolates (collectively termed UNISED) repeatedly harvested from marine
sediment are identified as distinctly environmental-specific, showing the ability to survive
outside the gastrointestinal tracts of warm-blooded animals. This discovery leads to the
hypothesis that UNISED E. coli may gain certain functions that allow them to persist in the
external environment and challenges the use of E. coli as a fecal indicative bacteria (FIB) for
water pollution detection.
LC-MS-based shotgun proteomics was performed on E. coli monocultures, and co-cultures of
two or more UNISED isolates in nutritional-limited (M9) media and in the presence of
mitomycin C (DNA damaging compound) to explore stress responses. Label-free
quantification is performed to overlay differentially changed proteins with known protein-protein
interaction networks to provide insights of bacterial interactions and survival as
shown in our results. Hypothetical and unannotated proteins discovered to be differentially
expressed between strains and between mono-culture and co-culture conditions might be
future targets for follow-up studies in environmental E. coli and in bacterial communities’
research.
Using the protein database from UniProt E. coli K12 (a commonly used lab strain), around
900 – 1000 proteins were identified on average at a false discovery rate of 0.01 by the search
engine Comet, indicating a large degree of sequence overlaps among the strains. Notably,
using our custom-generated protein sequence databases from the whole genome sequences of
the strains, we could identify around 100-200 more unique proteins, compared to the highly
curated K12 database. This result implied that there exist substantial number of strain-specific
protein sequences not found in the K12 genome, and these proteins are expressed
under the conditions examined. By comparing the observed proteomes of different strains
quantitatively, hundreds of proteins, some clustered in known pathways, were identified to be
differentially expressed in UNISED strains compared to K12, offering biological insights
regarding the physiology and ecology of these E. coli strains.
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