Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

Abstract

We determined the genome-wide distribution of the nucleoid-associated protein Fis in Escherichia coli using chromatin immunoprecipitation coupled with high-resolution whole genome-tiling microarrays. We identified 894 Fis-associated regions across the E. coli genome. A significant number of these binding sites were found within open reading frames (33%) and between divergently transcribed transcripts (5%). Analysis indicates that A-tracts and AT-tracts are an important signal for preferred Fis-binding sites, and that A6-tracts in particular constitute a high-affinity signal that dictates Fis phasing in stretches of DNA containing multiple and variably spaced A-tracts and AT-tracts. Furthermore, we find evidence for an average of two Fis-binding regions per supercoiling domain in the chromosome of exponentially growing cells. Transcriptome analysis shows that ∼21% of genes are affected by the deletion of fis; however, the changes in magnitude are small. To address the differential Fis bindings under growth environment perturbation, ChIP-chip analysis was performed using cells grown under aerobic and anaerobic growth conditions. Interestingly, the Fis-binding regions are almost identical in aerobic and anaerobic growth conditions—indicating that the E. coli genome topology mediated by Fis is superficially identical in the two conditions. These novel results provide new insight into how Fis modulates DNA topology at a genome scale and thus advance our understanding of the architectural bases of the E. coli nucleoid.

Reconstruction of novel transcription factor regulons through inference of their binding sites

“…8) which corresponds to the consensus half-site sequence of the Fis motif. This is in accord with the findings in [13], where the different Fis motif subtypes (non-palindromic and palin- dromic) share the most common bases in their consensus half-site. In fact, motif comparison of our estimate with the SwissRegulon database resulted in a significant hit to one of the Fis weight matrices, i.e., Fis_26-32 (Table 8).…”

“…To validate our approach's sensitivity for recovering such rare binding motifs, we reconstructed E. coli's Fis motif, and compared our results with those that are deduced by the ChIP-chip binding data in [13]. We used the gene expression data set in [29], and estimated a highconfidence set of 100 genes by using the proposed biclustering method and Algorithm 1 (see Additional file 1).…”

DnaA binding locus datA promotes DnaA-ATP hydrolysis to enable cell cycle-coordinated replication initiation

“…The procedures for ChIP and replication synchronization were performed as previously described (40). For details, see SI Material and Methods.…”

Development of a 3-hydroxypropionate resistantEscherichia colistrain

“…The Fis protein can organize and maintain the nucleoid structure through direct DNA binding and by modulating synthesis of gyrase, topoisomerase I and other proteins, and transcription of approximately 21% of E. coli genes is modulated directly or indirectly by Fis. 31 The twocomponent system ArcAB and the regulatory protein Fnr are both related with gene expression under anaerobic conditions. Some Arc-and Fnr-repressed genes were up-regulated in this study, implying that the oxidative level was elevated under 3HP stress.…”