In Vivo Dissection of theHelicobacter pyloriFur Regulatory Circuit by Genome-Wide Location Analysis

Abstract

Iron homeostasis is particularly important in pathogenic bacteria, which need to compete with the host for this essential cofactor. In Helicobacter pylori, a causative agent of several gastric pathologies, iron uptake and storage genes are regulated at the transcriptional level by the ferric uptake regulator Fur. The regulatory circuit of Fur has recently come under focus because of an intimate interlink with a broader regulatory network governing metal homeostasis, acidic response, and virulence. To dissect the Fur regulatory circuit and identify in vivo targets of regulation, we developed a genome-wide location analysis protocol which allowed the identification of 200 genomic loci bound by Fur as well as the investigation of the binding efficiency of the protein to these loci in response to iron. Comparative analysis with transcriptomes of wild-type and fur deletion mutant strains allowed the distinction between targets associated with Fur regulation and genes indirectly influenced by the fur mutation. The Fur regulon includes 59 genes, 25 of which appear to be positively regulated. A case study conducted by primer extension analysis of two oppositely regulated genes, hpn2 and flaB, suggests that negative regulation as well as positive regulation occurs at the transcriptional level. Furthermore, the results revealed the existence of 13 Fur targeted loci within polycistronic operons, which were associated with transcript deregulation in the fur mutant strain. This study provides a systematic insight of Fur regulation at the genome-wide level in H. pylori and points to regulatory functions extending beyond the classical Fur repression paradigm.

A Comparative Analysis of Perturbations Caused by a Gene Knock-out, a Dominant Negative Allele, and a Set of Peptide Aptamers

“…5A), thus confirming the identity of the samples, the proper expression of the transgenes, and the strong Fur basal activity under our experimental conditions. 75 of the 196 selected genes have already been identified in previous transcriptome studies as Fur-and/or iron-regulated genes in E. coli (17,42), Helicobacter pylori (38,(43)(44)(45), Neisseria meningitidis (46,47), Pseudomonas aeruginosa (48,49), Campylobacter jejuni (50), Shewanella oneidensis (51,52), and Pasteurella multicoda (53). Conversely we unveiled 121 genes that have not been reported by previous studies.…”

Iron deficiency accelerates Helicobacter pylori–induced carcinogenesis in rodents and humans

“…The ferric uptake regulator (Fur) is a master H. pylori regulator that controls expression of a large repertoire of genes by acting as a repressor under iron-replete conditions (21). To define the role of fur in H. pylori-induced injury in this model, wild-type H. pylori strain 7.13 and a 7.13 fur -isogenic mutant were used to infect Mongolian gerbils under iron-replete conditions (Supplemental Figure 3A).…”

Characterization of Key Helicobacter pylori Regulators Identifies a Role for ArsRS in Biofilm Formation

“…Examination of these transcriptome studies en masse demonstrates the vast and overlapping nature of the Fur, NikR, and ArsRS regulons. Furthermore, evidence suggests that these regulators affect expression of each other; nikR and arsR are part of the Fur regulon (23,24), whereas NikR appears to regulate fur (20,25). Given the overlapping nature of these regulatory cascades, it is likely not surprising that the role of each of these factors appears to be expanded compared to what is seen in other bacteria.…”