Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [ChIP-Seq]

Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome also may play an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutant and ambient stimuli (acetic acid and furfural, derived from lignocellulosic hydrolysate). We find that genomic mutation only influences the local chromosome contacts, whereas stress of acetic acid and furfural restrict the long-range contacts and change the chromosome organization at domain scales significantly. Further deciphering the domain feature unveils the important transcription factors, Ferric uptake regulation (Fur) proteins, which act as nucleoid-associated proteins to promote long-range (> 200 kb) chromosomal communications and regulate the expression of genes involved in stress response. Our work suggests that ubiquitous transcription factors in prokaryotes mediate chromosome organization and regulate stress-resistance genes in bacterial adaptation. ChIP-seq analysis of Fur proteins binding in the genome of ZM532. Binding sites of Fur and Zur in strain Zymomonas mobilis ZM532 under RM condition