Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis

Nucleic Acids Res. 2001 Feb 1;29(3):683-92. doi: 10.1093/nar/29.3.683.

Abstract

We used 2D protein gel electrophoresis and DNA microarray technologies to systematically analyze genes under glucose repression in B:acillus subtilis. In particular, we focused on genes expressed after the shift from glycolytic to gluconeogenic at the middle logarithmic phase of growth in a nutrient sporulation medium, which remained repressed by the addition of glucose. We also examined whether or not glucose repression of these genes was mediated by CcpA, the catabolite control protein of this bacterium. The wild-type and ccpA1 cells were grown with and without glucose, and their proteomes and transcriptomes were compared. 2D gel electrophoresis allowed us to identify 11 proteins, the synthesis of which was under glucose repression. Of these proteins, the synthesis of four (IolA, I, S and PckA) was under CcpA-independent control. Microarray analysis enabled us to detect 66 glucose-repressive genes, 22 of which (glmS, acoA, C, yisS, speD, gapB, pckA, yvdR, yxeF, iolA, B, C, D, E, F, G, H, I, J, R, S and yxbF ) were at least partially under CcpA-independent control. Furthermore, we found that CcpA and IolR, a repressor of the iol divergon, were involved in the glucose repression of the synthesis of inositol dehydrogenase encoded by iolG included in the above list. The CcpA-independent glucose repression of the iol genes appeared to be explained by inducer exclusion.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacillus subtilis / drug effects*
  • Bacillus subtilis / genetics
  • Bacillus subtilis / metabolism
  • Bacterial Proteins / drug effects
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Cell Division / drug effects
  • Cell Division / genetics
  • Culture Media / pharmacology
  • DNA-Binding Proteins / drug effects
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Electrophoresis, Gel, Two-Dimensional
  • Gene Expression Regulation, Bacterial / drug effects*
  • Glucose / pharmacology*
  • L-Iditol 2-Dehydrogenase / drug effects
  • L-Iditol 2-Dehydrogenase / genetics
  • L-Iditol 2-Dehydrogenase / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Proteome*
  • Repressor Proteins / drug effects
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism
  • Transcription, Genetic

Substances

  • Bacterial Proteins
  • Culture Media
  • DNA-Binding Proteins
  • Proteome
  • Repressor Proteins
  • catabolite control proteins, bacteria
  • L-Iditol 2-Dehydrogenase
  • Glucose