Effect of rpoS gene knockout on the metabolism of Escherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzyme activities and intracellular metabolite concentrations

Mahbuba Rahman, Mohammad Rubayet Hasan, Takahiro Oba, Kazuyuki Shimizu

Research output: Contribution to journalArticle

63 Citations (Scopus)

Abstract

The RNA polymerase sigma factor, encoded by rpoS gene, controls the expression of a large number of genes in Escherichia coli under stress conditions. The present study investigated the growth characteristics and metabolic pathways of rpoS gene knockout mutant of E. coli growing in LB media under aerobic condition. The analyses were made based on gene expressions obtained by DNA microarray and RT-PCR, enzyme activities and intracellular metabolite concentrations at the exponential and early stationary phases of growth. Although the glucose utilization pattern of the mutant was similar to the parent strain, the mutant failed to utilize acetate throughout the cultivation period. Microarray data indicated that the expression levels of several important genes of acetate metabolism such as acs, aceAB, cysDEK, fadR, etc. were significantly altered in the absence of rpoS gene. Interestingly, there was an increased activity of TCA cycle during the exponential growth phase, which was gradually diminished at the onset of stationary phase. Moreover, rpoS mutation had profound effect on the expression of several other genes of E. coli metabolic pathways that were not described earlier. The changes in the gene expressions, enzyme activities and intracellular metabolite concentrations of the rpoS mutant are discussed in details with reference to the major metabolic pathways of E. coli.

Original languageEnglish
Pages (from-to)585-595
Number of pages11
JournalBiotechnology and Bioengineering
Volume94
Issue number3
DOIs
Publication statusPublished - 20 Jun 2006
Externally publishedYes

Fingerprint

Gene Knockout Techniques
Enzyme activity
Metabolites
Metabolism
Gene expression
Escherichia coli
Genes
Metabolic Networks and Pathways
Gene Expression
Enzymes
Growth
Acetates
Microarrays
Activity Cycles
Sigma Factor
DNA-Directed RNA Polymerases
Oligonucleotide Array Sequence Analysis
RNA
Glucose
Polymerase Chain Reaction

Keywords

  • Acetate
  • DNA microarray
  • Escherichia coli
  • Metabolic pathways
  • rpoS
  • TCA cycle

ASJC Scopus subject areas

  • Biotechnology
  • Microbiology

Cite this

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AU - Shimizu, Kazuyuki

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AB - The RNA polymerase sigma factor, encoded by rpoS gene, controls the expression of a large number of genes in Escherichia coli under stress conditions. The present study investigated the growth characteristics and metabolic pathways of rpoS gene knockout mutant of E. coli growing in LB media under aerobic condition. The analyses were made based on gene expressions obtained by DNA microarray and RT-PCR, enzyme activities and intracellular metabolite concentrations at the exponential and early stationary phases of growth. Although the glucose utilization pattern of the mutant was similar to the parent strain, the mutant failed to utilize acetate throughout the cultivation period. Microarray data indicated that the expression levels of several important genes of acetate metabolism such as acs, aceAB, cysDEK, fadR, etc. were significantly altered in the absence of rpoS gene. Interestingly, there was an increased activity of TCA cycle during the exponential growth phase, which was gradually diminished at the onset of stationary phase. Moreover, rpoS mutation had profound effect on the expression of several other genes of E. coli metabolic pathways that were not described earlier. The changes in the gene expressions, enzyme activities and intracellular metabolite concentrations of the rpoS mutant are discussed in details with reference to the major metabolic pathways of E. coli.

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