Escherichia coli proteomics and bioinformatics
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A lot of things happen to proteins when Escherichia coli cells enter stationary phase, such as protein amount, post-translational modifications, conformation changes, and component of protein complex. Proteomics, which study the whole component of proteins, can be used to study the products of the genome and the physiology of Escherichia coli cells at different conditions. By comparing proteome from different growth phases, such as exponential and stationary phase, a lot of proteins with changes can be identified at the same time, which provides a pilot for further studies of mechanism. Current global proteomic studies have identified about 27% of the annotated proteins of E. coli, most of which are predicted to be abundance proteins. Subproteomics, the study of specific subsets of the proteome, can be used to study specific functional classes of proteins and low abundance proteins. In this dissertation, using non-denatured anion exchange column with 2D SDS-PAGE and tandem mass spectrometry, difference of E. coli cells between exponential and stationary phase were studied for whole soluble proteome. Also, using heparin column and mass spectrometry with tandem mass spectrometry, heparin-binding proteins were identified and analyzed for exponential growth and stationary phases. To manage and display the data generated by proteomics, a web-based database has been constructed for experiments in E. coli proteomics (EEP), which includes NonDeLC, Heparome, AIX/2D PAGE and other proteomic studies.
Niu, Lili (2007). Escherichia coli proteomics and bioinformatics. Doctoral dissertation, Texas A&M University. Available electronically from