TheEscherichia coliProteome: Past, Present, and Future Prospects

Abstract

SUMMARY 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.

Two-dimensional gel electrophoresis in bacterial proteomics

“…In the field of bacterial proteomics, 2D-DIGE has become a standard comparative proteomic approach for the study of gene regulation, stress responses, virulence mechanisms as well as environmental adaptation in both Gram-negative and Gram-positive species (Gade et al, 2005;Al Dahouk et al, 2008;Alteri et al, 2009;Franco et al, 2009). Investigators have previously compared directly the use of 2D-DIGE and colorimetric protein stains to quantify changes in protein expression patterns in E. coli cells treated with benzoic acid (Yan et al, 2002;Han and Lee, 2006). Analogous results were obtained, revealing that both techniques may be reliably used for protein expression profiling.…”

“…The use of proteomics, especially 2-DE, is of central importance to such efforts, as it can be used to take 'snapshots' of a large proportion of the entire protein complements of the cell. As transcriptomic (mRNA) information is not always capable of giving a true reflection of the adaptation of microbes towards their changing environment, proteomics is an invaluable tool for directly identifying the functions or connectivities of specific gene products (Han and Lee, 2006;Hecker et al, 2008;Bumann, 2010).…”

“…2-DE has been the method of choice for research in the field of stress response/environmental adaptation, due to its capability of quantifying differential protein expression in a global manner (Renzone et al, 2005;Hecker et al, 2008). Extensive comparative proteomic analyses have been performed in E. coli and several other bacterial species, successfully revealing several novel regulatory networks (Han and Lee, 2006). The ability of a bacterium to detect and appropriately respond to various stresses/environmental stimuli is of paramount significance to its survival abilities within different hosts or natural reservoirs.…”

A novel organic-inorganic hybrid monolith for trypsin immobilization

“…Freshly extracted E. coli cells (8 µg) [14] in a protein mixture were digested using the organic-inorganic hybrid IMER (10 cm length). It is well known that E. coli is a convincing model for investigation of IMER.…”

Effects of high-pressure carbon dioxide on proteins and DNA in Escherichia coli

“…To our knowledge, no study has carried out a proteomic analysis of E. coli proteins subjected to HPCD stress. Therefore, as 2-DE coupled with MS is a powerful technique for analysing complex protein mixtures (Han & Lee, 2006), a proteomic 2-DE method coupled with liquid chromatography-electrospray ionization MS-MS (LC-ESI-MS-MS) was applied to elucidate the mechanism of microbial response to HPCD in this study.…”