title: Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture.
abstract: Combined transcriptome and proteome analysis was carried out to understand metabolic and physiological changes of Escherichia coli during the high cell density cultivation (HCDC). The expression of genes of TCA cycle enzymes, NADH dehydrogenase and ATPase, was up-regulated during the exponential fed-batch period and was down-regulated afterward. However, expression of most of the genes involved in glycolysis and pentose phosphate pathway was up-regulated at the stationary phase. The expression of most of amino acid biosynthesis genes was down-regulated as cell density increased, which seems to be the major reason for the reduced specific productivity of recombinant proteins during HCDC. The expression of chaperone genes increased with cell density, suggesting that the high cell density condition itself can be stressful to the cells. Severe competition for oxygen at high cell density seemed to make cells use cytochrome bd, which is less efficient but has a high oxygen affinity than cytochrome bo(3). Population cell density itself strongly affected the expression of porin protein genes, especially ompF, and hence the permeability of the outer membrane. Expression of phosphate starvation genes was most strongly up-regulated toward the end of cultivation. It was also found that sigma(E) (rpoE) plays a more important role than sigma(S) (rpoS) at the stationary phase of HCDC. These findings should be invaluable in designing metabolic engineering and fermentation strategies for the production of recombinant proteins and metabolites by HCDC of E. coli.
authors.affiliation: Department of Chemical and Biomolecular Engineering, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea.
authors.forename: Sung Ho
authors.initials: SH
authors.lastname: Yoon
authors.forename: Mee-Jung
authors.initials: MJ
authors.lastname: Han
authors.forename: Sang Yup
authors.initials: SY
authors.lastname: Lee
authors.forename: Ki Jun
authors.initials: KJ
authors.lastname: Jeong
authors.forename: Jong-Shin
authors.initials: JS
authors.lastname: Yoo
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019149:Bioreactors / Q000382:microbiology; D002452:Cell Count; D018929:Cell Culture Techniques / Q000295:instrumentation / Q000379:methods*; D002478:Cells, Cultured; D003470:Culture Media; D004269:DNA, Bacterial / Q000145:classification; D004734:Energy Metabolism / Q000235:genetics / Q000502:physiology; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism* / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics / Q000502:physiology*; D015971:Gene Expression Regulation, Enzymologic / Q000235:genetics / Q000502:physiology; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D011506:Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D020543:Proteome / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D040901:Proteomics / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D014158:Transcription, Genetic
chemical_list: D003470:Culture Media; D004269:DNA, Bacterial; D011506:Proteins; D020543:Proteome