title: Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli.
abstract: Separation and relative quantitation of complex protein mixtures remain two of the most challenging aspects of proteomics. Here an advanced technique called fluorescence difference 2-D gel electrophoresis technology (2D-DIGE) has been applied to a model system study of the Escherichia coli proteome after benzoic acid treatment. The molecular weight and charge matched cyanine dyes enable pre-electrophoretic labelling of control and treated samples which are then mixed and run in the same gel. Pooled control and treated samples labelled with Cy trade mark 3 were used as an internal standard for both Cy5 labelled control and treated E. coli samples. Together with DeCyder trade mark imaging analysis software, more accurate quantitative analysis than conventional two-dimensional polyacrylamide gel electrophoresis was achieved. Using matrix-assisted laser desorption/ionization-time of flight and quadrupole-time of flight mass spectrometry a total of 179 differentially expressed protein spots were identified. These included enzymes, stress related and substrate (e.g. amino acids, maltose, ribose and TRP repressor) binding proteins. Of the spots analysed, 77% contained only one protein species per spot, hence the change in protein expression measured was solely attributed to the identified protein. Many membrane proteins and protein isoforms were identified indicating both adequate solubilization of E. coli samples and potential post-translational modification. The results indicate that the regulatory mechanisms following benzoic acid treatment of E. coli are far more complicated than hitherto expected.
authors.affiliation: Amersham Biosciences, Little Chalfont, UK. jun.yan@uk.amershambiosciences.com
authors.forename: Jun X
authors.initials: JX
authors.lastname: Yan
authors.forename: Angelica T
authors.initials: AT
authors.lastname: Devenish
authors.forename: Robin
authors.initials: R
authors.lastname: Wait
authors.forename: Tim
authors.initials: T
authors.lastname: Stone
authors.forename: Steve
authors.initials: S
authors.lastname: Lewis
authors.forename: Sue
authors.initials: S
authors.lastname: Fowler
mesh_terms: D019817:Benzoic Acid / Q000737:chemistry; D002232:Carbocyanines / Q000737:chemistry; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D004926:Escherichia coli / Q000737:chemistry* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000032:analysis*; D015964:Gene Expression Regulation, Bacterial; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D020543:Proteome / Q000032:analysis*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D002232:Carbocyanines; D029968:Escherichia coli Proteins; D020543:Proteome; D019817:Benzoic Acid