Genetic footprinting in bacteria.

Interaction between ArgR and AhrC controls regulation of arginine metabolism in Lactococcus lactis.

The expression of arginine metabolism in Lactococcus lactis is controlled by the two homologous transcriptional regulators ArgR and AhrC. Genome sequence analyses have shown that the occurrence of multiple homologues of the ArgR family of transcriptional regulators is a common feature of many low-G + C Gram-positive bacteria. Detailed studies of ArgR type regulators have previously only been ca...

Genomic Identification of SinR Transcription Factor Binding Sites in Nitrogen Fixing Bacterium Bradyrhizobium japonicum

SinR is a transcription factor which controls expression of stress tolerance sin genes related to alternate development processes under stress condition. Identification of genome wide SinR-box motif and their regulated genes has not been worked out yet in Bradyrhizobium japonicum. For this, a weight matrix of 9 bp was developed from the known promoter sequences of Bacillus subtilis, which was t...

Identification by In Vivo Genomic Footprinting of a Transcriptional Switch Containing NF-kB and Sp1 That Regulates the IkBa Promoter

Catching RNA polymerase in the act of binding: intermediates in transcription illuminated by synchrotron footprinting.

T he article by Sclavi et al. (1) in this issue of PNAS addresses ‘‘initiation,’’ the first step in transcription. Gene transcription is catalyzed in cells by large multisubunit proteins called RNA polymerases (RNAP). The eubacteria holoenzyme of RNAP is composed of five core subunits ( , 2, , , and ) that contain the amino acid residues required for the enzyme’s catalytic activity. A sixth sub...

Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals

UNLABELLED Phylogenetic footprinting is an efficient approach for revealing potential transcription factor binding sites in promoter sequences. The idea is based on an assumption that functional sites in promoters should evolve much slower then other regions that do not bear any conservative function. Therefore, potential transcription factor (TF) binding sites that are found in the evolutional...