Mode of action of AraR, the key regulator of L-arabinose metabolism in Bacillus subtilis

Mol Microbiol. 1999 Aug;33(3):476-89. doi: 10.1046/j.1365-2958.1999.01484.x.


The AraR protein is a negative regulator involved in L-arabinose-inducible expression of the Bacillus subtilis araABDLMNPQ-abfA metabolic operon and of the araE/araR genes that are organized as a divergent transcriptional unit. The two ara gene clusters are found at different positions in the bacterial chromosome. AraR was overproduced in Escherichia coli and purified to more than 95% homogeneity. AraR binds specifically to DNA fragments carrying the promoter region of the ara genes. DNase I protection assays showed that AraR binds to two sequences within the promoters of the araABDLMNPQ-abfA operon and the araE gene, and to one sequence in the araR promoter. The AraR target sequences are palindromic and share high identity, defining a 16 bp AraR consensus operator sequence showing half-symmetry, ATTTGTAC. Binding of AraR to DNA was inhibited by L-arabinose but not by other sugars. The two operator sites within the araABDLMNPQ-abfA operon and araE promoters are located on the same side of the DNA helix, and a pattern of enhanced and diminished DNase I cleavage was observed between them, but not in the araR promoter. Quantitative DNase I footprinting in DNA templates containing one, two or three AraR binding sites showed that the repressor binds cooperatively to the two operator sites within the metabolic operon and araE promoters but not to the site located in the araR promoter. These results are consistent with two modes for AraR transcriptional repression that might correlate with different physiological requirements: a high level of repression is achieved by DNA bending requiring two in-phase operator sequences (metabolic operon and araE transport gene), whereas binding to a single operator, which autoregulates araR expression, is 10-fold less effective.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • AraC Transcription Factor
  • Arabinose / metabolism*
  • Bacillus subtilis / genetics*
  • Bacterial Proteins*
  • Base Sequence
  • Consensus Sequence
  • DNA Footprinting
  • DNA-Binding Proteins / chemistry
  • Deoxyribonuclease I
  • Escherichia coli
  • Escherichia coli Proteins
  • Gene Expression Regulation, Bacterial / genetics
  • Molecular Sequence Data
  • Oligodeoxyribonucleotides
  • Operon / genetics
  • Promoter Regions, Genetic
  • Protein Binding
  • Recombinant Proteins / chemistry
  • Repressor Proteins / chemistry*
  • Sequence Alignment
  • Transcription Factors*


  • AraC Transcription Factor
  • AraC protein, E coli
  • Bacterial Proteins
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Oligodeoxyribonucleotides
  • Recombinant Proteins
  • Repressor Proteins
  • Transcription Factors
  • Arabinose
  • Deoxyribonuclease I