Dynamic gene expression profiling of Escherichia coli in carbon source transition from glucose to acetate

Min-Kyu Oh, Mee Jeong Cha, Sun Gu Lee, Lars Rohlin, James C. Liao

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

DNA microarray was used to study the transcription profiling of Escherichia coli adapting to acetate as a sole carbon source. Bacteria grown in glucose minimal media were used as a reference. The dynamic expression levels of 3,497 genes were monitored at seven time points during this adaptation. Among the central metabolic genes, the glycolytic and glucose phosphotransferase genes were repressed as the bacteria entered stationary phase, whereas the glyoxylate pathway, TCA cycle, and gluconeogenic genes were induced. Distinct induction or repression patterns were recognized among different pathway genes. For example, the repression of glycolytic genes and the induction of gluconeogenic ones started immediately after glucose was depleted. On the other hand, the regulation of the pentose phosphate pathway genes and glyoxylate genes gradually responded to the glucose depletion or was more related to growth in acetate. When the whole genome was considered, many of the CRP, FadR, and Cra regulons were immediately responsive to the glucose depletion, whereas the σs, Lrp, and IHF regulons were gradually responsive to the glucose depletion. The expression profiling also provided differential regulations between isoenzymes; for example, malic enzymes A (sfcA) and B (maeB). The expression profiles of three genes were confirmed with RT-PCR.

Original languageEnglish
Pages (from-to)543-549
Number of pages7
JournalJournal of Microbiology and Biotechnology
Volume16
Issue number4
Publication statusPublished - 2006 Apr 1

Fingerprint

Gene Expression Profiling
Gene expression
Escherichia coli
Glucose
Acetates
Carbon
Genes
Regulon
Bacteria
Pentose Phosphate Pathway
Isoenzymes
Pentoses
Oligonucleotide Array Sequence Analysis
Transcriptome
Transcription
Microarrays
Phosphotransferases
Genome
Phosphates
DNA

Keywords

  • Acetate
  • Carbon source
  • DNA microarray
  • Escherichia coli
  • Gene expression profiling
  • Glucose

ASJC Scopus subject areas

  • Biotechnology
  • Applied Microbiology and Biotechnology
  • Microbiology
  • Bioengineering

Cite this

Dynamic gene expression profiling of Escherichia coli in carbon source transition from glucose to acetate. / Oh, Min-Kyu; Cha, Mee Jeong; Lee, Sun Gu; Rohlin, Lars; Liao, James C.

In: Journal of Microbiology and Biotechnology, Vol. 16, No. 4, 01.04.2006, p. 543-549.

Research output: Contribution to journalArticle

Oh, Min-Kyu ; Cha, Mee Jeong ; Lee, Sun Gu ; Rohlin, Lars ; Liao, James C. / Dynamic gene expression profiling of Escherichia coli in carbon source transition from glucose to acetate. In: Journal of Microbiology and Biotechnology. 2006 ; Vol. 16, No. 4. pp. 543-549.
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