Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation

PLoS One. 2009 Oct 19;4(10):e7466. doi: 10.1371/journal.pone.0007466.


The phosphoenolpyruvate: carbohydrate transferase system (PTS) transports glucose in Escherichia coli. Previous work demonstrated that strains lacking PTS, such as PB11, grow slow on glucose. PB11 has a reduced expression of glycolytic, and upregulates poxB and acs genes as compared to the parental strain JM101, when growing on glucose. The products of the latter genes are involved in the production of AcetylCoA. Inactivation of rpoS that codes for the RNA polymerase sigma(38) subunit, reduces further (50%) growth of PB11, indicating that sigma(38) plays a central role in the expression of central metabolism genes in slowly growing cells. In fact, transcription levels of glycolytic genes is reduced in strain PB11rpoS(-) as compared to PB11. In this report we studied the role of sigma(70) and sigma(38) in the expression of the complete glycolytic pathway and poxB and acs genes in certain PTS(-) strains and their rpoS(-) derivatives. We determined the transcription start sites (TSSs) and the corresponding promoters, in strains JM101, PB11, its derivative PB12 that recovered its growth capacity, and in their rpoS(-) derivatives, by 5'RACE and pyrosequencing. In all these genes the presence of sequences resembling sigma(38) recognition sites allowed the proposition that they could be transcribed by both sigma factors, from overlapping putative promoters that initiate transcription at the same site. Fourteen new TSSs were identified in seventeen genes. Besides, more than 30 putative promoters were proposed and we confirmed ten previously reported. In vitro transcription experiments support the functionality of putative dual promoters. Alternatives that could also explain lower transcription levels of the rpoS(-) derivatives are discussed. We propose that the presence if real, of both sigma(70) and sigma(38) dependent promoters in all glycolytic genes and operons could allow a differential transcription of these central metabolism genes by both sigma subunits as an adaptation response to carbon limitation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Outer Membrane Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Carbon / chemistry
  • Carbon / metabolism*
  • Codon
  • DNA-Directed RNA Polymerases / metabolism*
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / metabolism
  • Gene Expression Regulation, Bacterial*
  • Glycolysis
  • Models, Biological
  • Models, Genetic
  • Operon
  • Phosphoenolpyruvate / metabolism
  • Sigma Factor / metabolism*
  • Transcription, Genetic*


  • Bacterial Outer Membrane Proteins
  • Bacterial Proteins
  • Codon
  • Escherichia coli Proteins
  • Sigma Factor
  • sigma factor KatF protein, Bacteria
  • Phosphoenolpyruvate
  • Carbon
  • RNA polymerase sigma 70
  • DNA-Directed RNA Polymerases