UmuDAb: An Error-Prone Polymerase Accessory Homolog Whose N-Terminal Domain Is Required for Repression of DNA Damage Inducible Gene Expression in Acinetobacter baylyi

Repression of Acinetobacter baumannii DNA damage response requires DdrR-assisted binding of UmuDAb dimers to atypical SOS box

The DNA damage response of the multi-drug-resistant nosocomial pathogen Acinetobacter baumannii possesses multiple features that distinguish it from the commonly used LexA repression system. These include the absence of LexA in this genus, the evolution of a UmuD polymerase manager into the UmuDAb repressor of error-prone polymerases, the use of a corepressor unique to Acinetobacter (DdrR), and an unusually large UmuDAb binding site. We defined cis- and trans-acting factors required for UmuDAb DNA binding and gene repression, and tested whether DdrR directly enhances its DNA binding. We used DNA binding assays to characterize UmuDAb's binding to its proposed operator present upstream of the six co-repressed umuDC or umuC genes. UmuDAb bound tightly and cooperatively to this site with ~10-fold less affinity than LexA. DdrR enhanced the binding of both native and dimerization-deficient UmuDAb forms, but only in greater than equimolar ratios relative to UmuDAb. UmuDAb mutants unable to dimerize or effect gene repression showed impaired DNA binding, and a strain expressing the G124D dimerization mutant could not repress transcription of the UmuDAb-DdrR regulon. Competition electrophoretic mobility shift assays conducted with mutated operator probes showed that, unlike typical SOS boxes, the UmuDAb operator possessed a five-base pair central core whose sequence was more crucial for binding than the flanking palindrome. The presence of only one of the two flanking arms of the palindrome was necessary for UmuDAb binding. Overall, the data supported a model of an operator with two UmuDAb binding sites. The distinct characteristics of UmuDAb and its regulated promoters differ from the typical LexA repression model, demonstrating a novel method of repression.IMPORTANCEAcinetobacter baumannii is a gram-negative bacterium responsible for hospital-acquired infections. Its unique DNA damage response can activate multiple error-prone polymerase genes, allowing it to gain mutations that can increase its virulence and antibiotic resistance. The emergence of infectious strains carrying multiple antibiotic resistance genes, including carbapenem resistance, lends urgency to discovering and developing ways to combat infections resistant to treatment with known antibiotics. Deciphering how the regulators UmuDAb and DdrR repress the error-prone polymerases could lead to developing complementary treatments to halt this mechanism of generating resistance.

RecA levels modulate biofilm development in Acinetobacter baumannii

Infections caused by Acinetobacter baumannii, a Gram-negative opportunistic pathogen, are difficult to eradicate due to the bacterium's propensity to quickly gain antibiotic resistances and form biofilms, a protective bacterial multicellular community. The A. baumannii DNA damage response (DDR) mediates the antibiotic resistance acquisition and regulates RecA in an atypical fashion; both RecALow and RecAHigh cell types are formed in response to DNA damage. The findings of this study demonstrate that the levels of RecA can influence formation and dispersal of biofilms. RecA loss results in surface attachment and prominent biofilms, while elevated RecA leads to diminished attachment and dispersal. These findings suggest that the challenge to treat A. baumannii infections may be explained by the induction of the DDR, common during infection, as well as the delicate balance between maintaining biofilms in low RecA cells and promoting mutagenesis and dispersal in high RecA cells. This study underscores the importance of understanding the fundamental biology of bacteria to develop more effective treatments for infections.

Distinct Screening Approaches Uncover PA14_36820 and RecA as Negative Regulators of Biofilm Phenotypes in Pseudomonas aeruginosa PA14

Pseudomonas aeruginosa commonly infects hospitalized patients and the lungs of individuals with cystic fibrosis. This species is known for forming biofilms, which are communities of bacterial cells held together and encapsulated by a self-produced extracellular matrix. The matrix provides extra protection to the constituent cells, making P. aeruginosa infections challenging to treat. We previously identified a gene, PA14_16550, which encodes a DNA-binding TetR-type repressor and whose deletion reduced biofilm formation. Here, we assessed the transcriptional impact of the 16550 deletion and found six differentially regulated genes. Among them, our results implicated PA14_36820 as a negative regulator of biofilm matrix production, while the remaining 5 had modest effects on swarming motility. We also screened a transposon library in a biofilm-impaired ΔamrZ Δ16550 strain for restoration of matrix production. Surprisingly, we found that disruption or deletion of recA increased biofilm matrix production, both in biofilm-impaired and wild-type strains. Because RecA functions both in recombination and in the DNA damage response, we asked which function of RecA is important with respect to biofilm formation by using point mutations in recA and lexA to specifically disable each function. Our results implied that loss of either function of RecA impacts biofilm formation, suggesting that enhanced biofilm formation may be one physiological response of P. aeruginosa cells to loss of either RecA function. IMPORTANCE Pseudomonas aeruginosa is a notorious human pathogen well known for forming biofilms, communities of bacteria that protect themselves within a self-secreted matrix. Here, we sought to find genetic determinants that impacted biofilm matrix production in P. aeruginosa strains. We identified a largely uncharacterized protein (PA14_36820) and, surprisingly, RecA, a widely conserved bacterial DNA recombination and repair protein, as negatively regulating biofilm matrix production. Because RecA has two main functions, we used specific mutations to isolate each function and found that both functions influenced matrix production. Identifying negative regulators of biofilm production may suggest future strategies to reduce the formation of treatment-resistant biofilms.

The DdrR Coregulator of the Acinetobacter baumannii Mutagenic DNA Damage Response Potentiates UmuDAb Repression of Error-Prone Polymerases

Acinetobacter baumannii is a nosocomial pathogen that acquires antibiotic resistance genes through conjugative transfer and carries out a robust mutagenic DNA damage response. After exposure to conditions typically encountered in health care settings, such as antibiotics, UV light, and desiccation, this species induces error-prone UmuD′ 2 C polymerases.

Locking down SOS Mutagenesis Repression in a Dynamic Pathogen

The article "The DdrR coregulator of the Acinetobacter baumannii mutagenic DNA damage response potentiates UmuDAb repression of error-prone polymerases" in this issue of the J Bacteriol, (D. Cook, M. D. Flannigan, B. V. Candra, K. D. Compton, and J. M. Hare., J Bacteriol 204:e00165-22, 2022, https://doi.org/10.1128/jb.00165-22) reveals a more detailed understanding of the regulatory mechanism of the SOS response in Acinetobacter baumannii. This information provides novel targets for development of antimicrobial therapies against this ESKAPE pathogen and new insight into the complex regulation of the SOS stress-response.

The small DdrR protein directly interacts with the UmuDAb regulator of the mutagenic DNA damage response in Acinetobacter baumannii

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.

Homodimerization and heterodimerization requirements of Acinetobacter baumannii SOS response coregulators UmuDAb and DdrR revealed by two-hybrid analyses

The multidrug-resistant pathogen Acinetobacter baumannii displays unusual control of its SOS mutagenesis genes, as it does not encode a LexA repressor, but instead employs the UmuDAb repressor and a small protein, DdrR, that is uniquely found in Acinetobacter species. We used bacterial adenylate cyclase two-hybrid analyses to determine if UmuDAb and DdrR coregulation might involve physical interactions. Neither quantitative nor qualitative assays showed UmuDAb interaction with DdrR. DdrR hybrid proteins, however, demonstrated modest head-to-tail interactions in a qualitative assay. The similarity of UmuDAb to the homodimer-forming polymerase manager UmuD and LexA repressor proteins suggested that it may form dimers, which we observed. UmuDAb homodimerization required a free C terminus, and either small truncations or addition of a histidine tag at the C terminus abolished this homodimerization. The amino acid N100, crucial for UmuD dimer formation, was dispensable if both C termini were free to interact. However, mutation of the amino acid G124, necessary for LexA dimerization, yielded significantly less UmuDAb dimerization, even if both C termini were free. This suggests that UmuDAb forms dimers like LexA does, but may not coregulate gene expression involving a physical association with DdrR. The homodimerization of these coregulators provides insight into a LexA-independent, coregulatory process of controlling a conserved bacterial action such as the mutagenic DNA damage response.

A corepressor participates in LexA-independent regulation of error-prone polymerases in Acinetobacter

The DNA damage response of the multidrug-resistant pathogen Acinetobacter baumannii, which induces mutagenic UmuD'2C error-prone polymerases, differs from that of many bacteria. Acinetobacter species lack a LexA repressor, but induce gene transcription after DNA damage. One regulator, UmuDAb, binds to and represses the promoters of the multiple A. baumannii ATCC 17978 umuDC alleles and the divergently transcribed umuDAb and ddrR genes. ddrR is unique to the genus Acinetobacter and of unknown function. 5' RACE (rapid amplification of cDNA ends) PCR mapping of the umuDAb and ddrR transcriptional start sites revealed that their -35 promoter elements overlapped the UmuDAb binding site, suggesting that UmuDAb simultaneously repressed expression of both genes by blocking polymerase access. This coordinated control of ddrR and umuDAb suggested that ddrR might also regulate DNA damage-inducible gene transcription. RNA-sequencing experiments in 17 978 ddrR- cells showed that ddrR regulated approximately 25 % (n=39) of the mitomycin C-induced regulon, with umuDAb coregulating 17 of these ddrR-regulated genes. Eight genes (the umuDC polymerases, umuDAb and ddrR) were de-repressed in the absence of DNA damage, and nine genes were uninduced in the presence of DNA damage, in both ddrR and umuDAb mutant strains. These data suggest ddrR has multiple roles, both as a co-repressor and as a positive regulator of DNA damage-inducible gene transcription. Additionally, 57 genes were induced by mitomycin C in the ddrR mutant but not in wild-type cells. This regulon contained multiple genes for DNA replication, recombination and repair, transcriptional regulators, RND efflux, and transport. This study uncovered another regulator of the atypical DNA damage response of this genus, to help describe how this pathogen acquires drug resistance through its expression of the error-prone polymerases under DdrR and UmuDAb control.

Betulinic Acid Prevents the Acquisition of Ciprofloxacin-Mediated Mutagenesis in Staphylococcus aureus

The occurrence of damage on bacterial DNA (mediated by antibiotics, for example) is intimately associated with the activation of the SOS system. This pathway is related to the development of mutations that might result in the acquisition and spread of resistance and virulence factors. The inhibition of the SOS response has been highlighted as an emerging resource, in order to reduce the emergence of drug resistance and tolerance. Herein, we evaluated the ability of betulinic acid (BA), a plant-derived triterpenoid, to reduce the activation of the SOS response and its associated phenotypic alterations, induced by ciprofloxacin in Staphylococcus aureus. BA did not show antimicrobial activity against S. aureus (MIC > 5000 µg/mL), however, it (at 100 and 200 µg/mL) was able to reduce the expression of recA induced by ciprofloxacin. This effect was accompanied by an enhancement of the ciprofloxacin antimicrobial action and reduction of S. aureus cell volume (as seen by flow cytometry and fluorescence microscopy). BA could also increase the hyperpolarization of the S. aureus membrane, related to the ciprofloxacin action. Furthermore, BA inhibited the progress of tolerance and the mutagenesis induced by this drug. Taken together, these findings indicate that the betulinic acid is a promising lead molecule in the development helper drugs. These compounds may be able to reduce the S. aureus mutagenicity associated with antibiotic therapies.

Mechanisms of Bacterial Tolerance and Persistence in the Gastrointestinal and Respiratory Environments

Pathogens that infect the gastrointestinal and respiratory tracts are subjected to intense pressure due to the environmental conditions of the surroundings. This pressure has led to the development of mechanisms of bacterial tolerance or persistence which enable microorganisms to survive in these locations. In this review, we analyze the general stress response (RpoS mediated), reactive oxygen species (ROS) tolerance, energy metabolism, drug efflux pumps, SOS response, quorum sensing (QS) bacterial communication, (p)ppGpp signaling, and toxin-antitoxin (TA) systems of pathogens, such as Escherichia coli, Salmonella spp., Vibrio spp., Helicobacter spp., Campylobacter jejuni, Enterococcus spp., Shigella spp., Yersinia spp., and Clostridium difficile, all of which inhabit the gastrointestinal tract. The following respiratory tract pathogens are also considered: Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Burkholderia cenocepacia, and Mycobacterium tuberculosis Knowledge of the molecular mechanisms regulating the bacterial tolerance and persistence phenotypes is essential in the fight against multiresistant pathogens, as it will enable the identification of new targets for developing innovative anti-infective treatments.

On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations

Background

Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations.

Results

Analysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic–pituitary–thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors.

Conclusions

We show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0258-1) contains supplementary material, which is available to authorized users.