title: Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium.
abstract: BACKGROUND
  Efficient production of SA in Escherichia coli has been achieved by modifying key genes of the central carbon metabolism and SA pathway, resulting in overproducing strains grown in batch- or fed-batch-fermentor cultures using a complex broth including glucose and YE. In this study, we performed a GTA to identify those genes significantly upregulated in an engineered E. coli strain, PB12.SA22, in mid EXP (5 h), early STA (STA1, 9 h), and late STA (STA2, 44 h) phases, grown in complex fermentation broth in batch-fermentor cultures.
  
  
  RESULTS
  Growth of E. coli PB12.SA22 in complex fermentation broth for SA production resulted in an EXP growth during the first 9 h of cultivation depending of supernatant available aromatic amino acids provided by YE because, when tryptophan was totally consumed, cells entered into a second, low-growth phase (even in the presence of glucose) until 26 h of cultivation. At this point, glucose was completely consumed but SA production continued until the end of the fermentation (50 h) achieving the highest accumulation (7.63 g/L of SA). GTA between EXP/STA1, EXP/STA2 and STA1/STA2 comparisons showed no significant differences in the regulation of genes encoding enzymes of central carbon metabolism as in SA pathway, but those genes encoding enzymes involved in sugar, amino acid, nucleotide/nucleoside, iron and sulfur transport; amino acid catabolism and biosynthesis; nucleotide/nucleoside salvage; acid stress response and modification of IM and OM were upregulated between comparisons.
  
  
  CONCLUSIONS
  GTA during SA production in batch-fermentor cultures of strain PB12.SA22 grown in complex fermentation broth during the EXP, STA1 and STA2 phases was studied. Significantly, upregulated genes during the EXP and STA1 phases were associated with transport, amino acid catabolism, biosynthesis, and nucleotide/nucleoside salvage. In STA2, upregulation of genes encoding transporters and enzymes involved in the synthesis and catabolism of Arg suggests that this amino acid could have a key role in the fuelling of carbon toward SA synthesis, whereas upregulation of genes involved in pH stress response, such as membrane modifications, suggests a possible response to environmental conditions imposed on the cell at the end of the fermentation.
authors.forename: Larisa
authors.initials: L
authors.lastname: Cortés-Tolalpa
authors.forename: Rosa María
authors.initials: RM
authors.lastname: Gutiérrez-Ríos
authors.forename: Luz María
authors.initials: LM
authors.lastname: Martínez
authors.forename: Ramón
authors.initials: R
authors.lastname: de Anda
authors.forename: Guillermo
authors.initials: G
authors.lastname: Gosset
authors.forename: Francisco
authors.initials: F
authors.lastname: Bolívar
authors.affiliation: Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av, Universidad 2001, Col, Chamilpa, Cuernavaca, Morelos 62210, México. adelfo@ibt.unam.mx.
authors.forename: Adelfo
authors.initials: A
authors.lastname: Escalante
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D061249:Batch Cell Culture Techniques; D003470:Culture Media / Q000737:chemistry; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D005818:Genetic Engineering; D010728:Phosphoenolpyruvate / Q000737:chemistry*; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000378:metabolism*; D012765:Shikimic Acid / Q000378:metabolism*; D015854:Up-Regulation
chemical_list: D000596:Amino Acids; D003470:Culture Media; D029968:Escherichia coli Proteins; D012765:Shikimic Acid; D010728:Phosphoenolpyruvate; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System