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- Title
Definition of the Binding Architecture to a Target Promoter of HP1043, the Essential Master Regulator of Helicobacter pylori.
- Authors
Zannoni, Annamaria; Pelliciari, Simone; Musiani, Francesco; Chiappori, Federica; Roncarati, Davide; Scarlato, Vincenzo
- Abstract
HP1043 is an essential orphan response regulator of Helicobacter pylori orchestrating multiple crucial cellular processes. Classified as a member of the OmpR/PhoB family of two-component systems, HP1043 exhibits a highly degenerate receiver domain and evolved to function independently of phosphorylation. Here, we investigated the HP1043 binding mode to a target sequence in the hp1227 promoter (Php1227). Scanning mutagenesis of HP1043 DNA-binding domain and consensus sequence led to the identification of residues relevant for the interaction of the protein with a target DNA. These determinants were used as restraints to guide a data-driven protein-DNA docking. Results suggested that, differently from most other response regulators of the same family, HP1043 binds in a head-to-head conformation to the Php1227 target promoter. HP1043 interacts with DNA largely through charged residues and contacts with both major and minor grooves of the DNA are required for a stable binding. Computational alanine scanning on molecular dynamics trajectory was performed to corroborate our findings. Additionally, in vitro transcription assays confirmed that HP1043 positively stimulates the activity of RNA polymerase.
- Subjects
HELICOBACTER pylori; MOLECULAR dynamics; PROTEIN-protein interactions; DNA-protein interactions; PHOSPHORYLATION; RNA polymerases
- Publication
International Journal of Molecular Sciences, 2021, Vol 22, Issue 15, p7848
- ISSN
1661-6596
- Publication type
Article
- DOI
10.3390/ijms22157848