title: Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli.
abstract: To elucidate the physiological adaptation of Escherichia coli due to cra gene knockout, a total of 3,911 gene expressions were investigated by DNA microarray for continuous culture. About 50 genes were differentially regulated for the cra mutant. TCA cycle and glyoxylate shunt were down-regulated, while pentose phosphate (PP) pathway and Entner Doudoroff (ED) pathway were up-regulated in the cra mutant. The glucose uptake rate and the acetate production rate were increased with less acetate consumption for the cra mutant. To identify the genes controlled by Cra protein, the Cra recognition weight matrix from foot-printing data was developed and used to scan the whole genome. Several new Cra-binding sites were found, and some of the result was consistent with the DNA microarray data. The ED pathway was active in the cra mutant; we constructed cra.edd double genes knockout mutant to block this pathway, where the acetate overflowed due to the down-regulation of aceA,B and icd gene expressions. Then we further constructed cra.edd.iclR triple genes knockout mutant to direct the carbon flow through the glyoxylate pathway. The cra.edd.iclR mutant showed the least acetate production, resulting in the highest cell yield together with the activation of the glycolysis pathway, but the glucose consumption rate could not be improved.
authors.affiliation: Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4, Kawazu, Iizuka, Fukuoka 820-8502, Japan.
authors.forename: Dayanidhi
authors.initials: D
authors.lastname: Sarkar
authors.forename: Khandaker Al Zaid
authors.initials: KA
authors.lastname: Siddiquee
authors.forename: Marcos J
authors.initials: MJ
authors.lastname: Araúzo-Bravo
authors.forename: Takahiro
authors.initials: T
authors.lastname: Oba
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Shimizu
mesh_terms: D019342:Acetic Acid / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D018533:Biomass; D002952:Citric Acid Cycle; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D017353:Gene Deletion; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005947:Glucose / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D010427:Pentose Phosphate Pathway; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D056968:Lac Repressors
chemical_list: D019342:Acetic Acid; D001426:Bacterial Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D005947:Glucose; D012097:Repressor Proteins; C067479:IclR protein, E coli; C068837:FruR protein, Bacteria; D056968:Lac Repressors