Project description:Escherichia coli strains are widely used in academic research and biotechnology. New technologies for quantifying strain-specific differences and their underlying contributing factors promise greater understanding of how these differences significantly impact physiology, synthetic biology, metabolic engineering, and process design. Here, we quantified strain-specific differences in seven widely used strains of E. coli (BL21, C, Crooks, DH5a, K-12 MG1655, K-12 W3110, and W) using genomics, phenomics, transcriptomics, and genome-scale modeling. Metabolic physiology and gene expression varied widely with downstream implications for productivity, product yield, and titer. These differences could be linked to differential regulatory structure. Analyzing high-flux reactions and expression of encoding genes resulted in a correlated and quantitative link between these sets, with strain-specific caveats. Integrated modeling revealed that certain strains are better suited to produce given compounds or express desired constructs considering native expression states of pathways that enable high-production phenotypes. This study yields a framework for quantitatively comparing strains in a species with implications for strain selection.
Project description:au07-07_salmonella - infection with Salmonella or Pseudomonas or E. coli. Identification of genes involved in early Arabidopsis response to pathogenic and non-pathogenic bacteria. Arabidopsis thaliana Col-0 seedlings were infected for 2 hours with a) Salmonella typhimurium strain 14028s, b) Pseudomonas syringae DC3000 or c) Escherichia coli DH5A Keywords: treated vs untreated comparison Overall design: 6 dye-swap - CATMA arrays
Project description:au07-07_salmonella - infection with Salmonella or Pseudomonas or E. coli. Identification of genes involved in early Arabidopsis response to pathogenic and non-pathogenic bacteria. Arabidopsis thaliana Col-0 seedlings were infected for 2 hours with a) Salmonella typhimurium strain 14028s, b) Pseudomonas syringae DC3000 or c) Escherichia coli DH5A Keywords: treated vs untreated comparison 6 dye-swap - CATMA arrays
Project description:Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects.