The Small DdrR Protein Directly Interacts with the UmuDAb Regulator of the Mutagenic DNA Damage Response in Acinetobacter baumannii

Abstract

Acinetobacter baumannii poses a great threat in healthcare settings worldwide with clinical isolates displaying an ever-evolving multidrug-resistance. In strains of A. baumannii , expression of multiple error-prone polymerase genes is co-repressed by UmuDAb, a member of the LexA superfamily, and a small protein, DdrR. It is currently unknown how DdrR establishes this repression. Here, we use surface plasmon resonance spectrometry to show that DdrR forms a stable complex with the UmuDAb regulator. Our results indicate that the carboxy-terminal dimerization domain of UmuDAb forms the interaction interface with DdrR. Our in vitro data also show that RecA-mediated inactivation of UmuDAb is inhibited when this transcription factor is bound to its target DNA. In addition, we show that DdrR interacts with a putative prophage repressor, homologous to LexA superfamily proteins. These data suggest that DdrR modulates DNA damage response and prophage induction in A. baumannii by binding to LexA-like regulators. Importance We previously identified a 50-residue bacteriophage protein, gp7, which interacts with and modulates the function of the LexA transcription factor from Bacillus thuringiensis . Here we present data that indicates that the small DdrR protein from A. baumannii likely coordinates the SOS response and prophage processes by also interacting with LexA superfamily members. We suggest that similar small proteins that interact with LexA-like proteins to coordinate DNA repair and bacteriophage functions may be common to many bacteria that mount the SOS response.

DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

“…Although it affects the expression of many genes, the mechanism of action of ddrR has not yet been elucidated. It co-regulates the error-prone polymerases, umuDAb and itself ( Peterson et al., 2020 ) by enhancing the repression activity of the LexA-like repressor, UmuDAb ( Cook et al., 2022 ), and DdrR has been shown to interact with UmuDAb protein in vitro ( Pavlin et al., 2022 ). DdrR actions resemble in some ways those of the small bacteriophage protein, gp7, found in Bacillus thuringiensis , which binds to the bacterial LexA protein and increases its repression ( Fornelos et al., 2015 ).…”

“…DdrR actions resemble in some ways those of the small bacteriophage protein, gp7, found in Bacillus thuringiensis , which binds to the bacterial LexA protein and increases its repression ( Fornelos et al., 2015 ). However, DdrR is not prophage-encoded, shares no sequence similarity with gp7 ( Cook et al., 2022 ; Pavlin et al., 2022 ), and interacts with the non-canonical UmuDAb repressor, not LexA. Nevertheless, its corepressor activities allow speculation that it may interact with other repressors or activators to modulate their regulatory activity.…”

A small bacteriophage protein determines the hierarchy over co-residential jumbo phage in Bacillus thuringiensis serovar israelensis

“…In E. coli , an as-yet-unidentified factor is required for LexA to bind noncanonical sequence motifs 27 , and in the multidrug-resistant pathogen Acinetobacter baumanii , the LexA-like repressor UmuDAb controls the DNA-damage-inducible genes through a direct interaction with the ~9-kDa co-repressor DdrR, although the mechanism is not yet fully understood 35 , 36 . Similar to the narrow distribution of gp7 homologs across the tectivirus genomes, DdrR is only found in the chromosomes of Acinetobacter spp.…”