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Applications of quantitative proteomics in environmental science and engineering

Zhe Du, University of Nebraska - Lincoln


Quantitative proteomics is a powerful tool to discover novel proteins, investigate protein-protein interactions, and identify metabolism pathways. So far its applications in environmental science and engineering have been limited. This dissertation was designed to explore the applications of quantitative proteomics in three different areas in environmental science and engineering: bacterial stress response, contaminant biodegradation, and soil carbon transformation. First, the molecular mechanisms that prepare starved cells for disinfection tolerance were investigated at the protein level. Starved Escherichia coli cells showed significantly higher disinfection tolerance than normal cells. Proteomic analyses suggested that starvation prepared cells for the oxidative stress that they might face during chlorine-based disinfection by affecting glutathione metabolism and synthesizing methylglyoxal. Second, the molecular mechanisms of microbial estrone (E1) degradation were elucidated using quantitative proteomics under various background nitrogen (nitrate or ammonia) and substrate (none, acetic acid, or humic acid) conditions. The E1 degradation kinetics was faster when ammonia was used as the nitrogen source and when a background carbon substrate was present. Proteomic analyses showed that the up-regulation of enzymes involved in the glutamate metabolism and tyrosine metabolism were responsible for the faster degradation kinetics. Finally, the structure and function of microbial communities in a subalpine forested watershed were characterized using Illumina sequencing of the 16S rRNA gene and quantitative metaproteomics, respectively. Microbial composition differed significantly among different landscape positions. Soil water content exhibited the highest correlation with the microbial community structure and soil enzymes activities. This work demonstrates the great potential of quantitative proteomics in environmental studies.

Subject Area

Civil engineering|Environmental engineering

Recommended Citation

Du, Zhe, "Applications of quantitative proteomics in environmental science and engineering" (2015). ETD collection for University of Nebraska-Lincoln. AAI3718078.