Genome-wide definition of the CosR regulon and DNA-binding properties in Campylobacter jejuni

Authors

Chiti, E., Odorici, T., Noszka, M., Muraszko, J., Zannoni, A., Anna Zawilak-Pawlik, A., Vannini, A., Roncarati, D.

Abstract

CosR is an essential OmpR-family transcriptional regulator of Campylobacter jejuni, but its direct regulon and DNA-binding properties in vivo remain poorly defined. Here, we used ChIP-seq with a functional chromosomal CosR::3xFLAG allele to define the genome-wide CosR-binding landscape. CosR binding was strongly enriched at promoters and accumulated around transcription start sites, consistent with a primary role in transcriptional control. Functional analysis of promoter-bound targets revealed significant enrichment for translation- and transcription-related functions, identifying CosR as a regulator of core cellular processes. Motif analysis of summit-centered ChIP-seq regions identified a CosR-associated bipartite sequence signature characterized by TTAA-like elements separated by an A/T-rich spacer. DNase I footprinting confirmed direct promoter binding at nucleotide resolution and revealed heterogeneous architectures, including single, multipartite, and bidirectional binding arrangements. A footprint-derived motif was significantly similar to the ChIP-derived motif, supporting a shared recognition signature across in vivo-enriched regions and in vitro-protected segments. Footprinting also validated binding at non-coding RNA promoters and at the cosR promoter, indicating autoregulation. Hydrogen peroxide treatment differentially remodeled CosR promoter occupancy in vivo, reducing binding at translation-associated promoters while increasing enrichment at other targets. Redox-dependent footprinting showed that oxidative conditions directly impaired CosR binding at selected promoters, consistent with previously reported C218-dependent redox modulation. Despite these opposite occupancy patterns, most tested transcripts decreased after oxidative stress, indicating that CosR redox responsiveness is integrated with broader stress-dependent regulatory inputs. Together, these data define CosR as a condition-responsive regulator linking promoter recognition, core physiology and oxidative-stress-associated transcriptional remodeling.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 06 Aug 2026.

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