What makes a bacterium pathogenic? Since the early days of germ theory, researchers have categorized bacteria as pathogens or non-pathogens, those that cause harm and those that do not, but this binary view is not always accurate. Vibrio fischeri is an exclusive mutualistic symbiont found within the light organs of Hawaiian bobtail squid. This symbiotic interaction requires V. fischeri to utilize a range of behaviors and produce molecules that are often associated with pathogenicity. This juxtaposition of employing "pathogenic" behaviors for a symbiotic relationship led the field to focus on how V. fischeri establishes a beneficial association with its host. In this study, we observe that V. fischeri induces mortality in zebrafish embryos and Artemia nauplii. Non-lethal doses of V. fischeri lead to zebrafish growth delays and phenotypes indicative of disease. Our data also provide evidence that the conserved type VI secretion system on chromosome I (T6SS1) plays a role in the V. fischeri-induced mortality of zebrafish embryos and Artemia nauplii. These results support the hypothesis that the V. fischeri T6SS1 is involved in eukaryotic cell interactions. Despite its traditional view as a beneficial symbiont, we provide evidence that V. fischeri is capable of harming aquatic organisms, indicating its potential to be pathogenic toward non-symbiotic hosts.IMPORTANCEVibrio fischeri is best known for its beneficial partnership with the Hawaiian bobtail squid, where it uses molecular tools often associated with disease-causing bacteria. Our research shows that V. fischeri can also cause harm, killing zebrafish embryos and brine shrimp larvae. We pinpoint one of V. fischeri's two type VI secretion systems (T6SS1) as a key factor in this pathogenicity. These findings reveal that V. fischeri is not strictly a mutualistic microbe but can act like a pathogen under certain conditions. This broadens our understanding of how V. fischeri could interact with different hosts and offers new insights into the dual roles bacteria can play in nature.

Two component system bacterial response regulators are typically DNA-binding proteins which enable the genetic regulation of many adaptive bacterial behaviors. Despite structural similarity across response regulator families, there is a diverse array of DNA-binding mechanisms. Bacteria usually encode several dozen two-component system response regulators, but Francisella tularensis only encodes three. Due to their simplified response regulatory network, Francisella species are a model for studying the role of response regulator proteins in virulence. Here, we show that Francisella response regulators QseB, KdpE, and BfpR all utilize different DNA-binding mechanisms. Our evidence suggests that QseB follows a simple mechanism whereby it binds a single inverted repeat sequence with a higher affinity upon phosphorylation. This behavior is independent of whether QseB is a positive or negative regulator of the gene as demonstrated by qseB and priM promoter sequences, respectively. Similarly, KdpE binds DNA more tightly upon phosphorylation, but also exhibits a cooperative binding isotherm. While we propose a KdpE binding site, it is possible that KdpE has a complex DNA-binding mechanism potentially involving multiple copies of KdpE being recruited to a promoter region. Finally, we show that BfpR appears to bind a region of its own promoter sequence with a lower affinity upon phosphorylation. Further structural and enzymatic work will need to be performed to deconvolute the KdpE and BfpR binding mechanisms.

Anti-sigma factor antagonists SpoIIAA and RsbV from Bacillus subtilis are the archetypes for single-domain STAS proteins in bacteria. The structures and mechanisms of these proteins along with their cognate anti-sigma factors have been well studied. SpoIIAA and RsbV utilize a partner-switching mechanism to regulate gene expression through protein-protein interactions to control the activity of their downstream anti-sigma factor partners. The Vibrio fischeri STAS domain protein SypA is also proposed to employ a partner-switching mechanism with its partner SypE, a serine kinase/phosphatase that controls SypA's phosphorylation state. However, this regulation appears opposite to the canonical pathway, with SypA being the more downstream component rather than SypE. Here we explore the commonalities and differences between SypA and the canonical single-domain STAS proteins SpoIIAA and RsbV. We use a combination of AlphaFold 2 structure predictions and computational modeling to investigate the SypA-SypE binding interface. We then test a subset of our predictions in V.fischeri by generating and expressing SypA variants. Our findings suggest that, while SypA shares many sequence and structural traits with anti-sigma factor antagonist STAS domain proteins, there are significant differences that may account for SypA's distinct regulatory output.

Bacterial biofilms are notorious for their ability to protect bacteria from environmental challenges, most importantly the action of antibiotics. Bacillus subtilis is an extensively studied model organism used to understand the process of biofilm formation. A complex network of principal regulatory proteins including Spo0A, AbrB, AbbA, Abh, SinR, SinI, SlrR, and RemA, work in concert to transition B. subtilis from the free-swimming planktonic state to the biofilm state. In this review, we explore, connect, and summarize decades worth of structural and biochemical studies that have elucidated this protein signaling network. Since structure dictates function, unraveling aspects of protein molecular mechanisms will allow us to devise ways to exploit critical features of the biofilm regulatory pathway, such as possible therapeutic intervention. This review pools our current knowledge base of B. subtilis biofilm regulatory proteins and highlights potential therapeutic intervention points.

Acinetobacter baumannii is a common nosocomial pathogen that utilizes numerous mechanisms to aid its survival in both the environment and the host. Coordination of such mechanisms requires an intricate regulatory network. We report here that A. baumannii can directly regulate several stress-related pathways via the two-component regulatory system BfmRS. Similar to previous studies, results from transcriptomic analysis showed that mutation of the BfmR response regulator causes dysregulation of genes required for the oxidative stress response, the osmotic stress response, the misfolded protein/heat shock response, Csu pilus/fimbria production, and capsular polysaccharide biosynthesis. We also found that the BfmRS system is involved in controlling siderophore biosynthesis and transport, and type IV pili production. We provide evidence that BfmR binds to various stress-related promoter regions and show that BfmR alone can directly activate transcription of some stress-related genes. Additionally, we show that the BfmS sensor kinase acts as a BfmR phosphatase to negatively regulate BfmR activity. This work highlights the importance of the BfmRS system in promoting survival of A. baumannii. IMPORTANCE Acinetobacter baumannii is a nosocomial pathogen that has extremely high rates of multidrug resistance. This organism's ability to endure stressful conditions is a key part of its ability to spread in the hospital environment and cause infections. Unlike other members of the gammaproteobacteria, A. baumannii does not encode a homolog of the RpoS sigma factor to coordinate its stress response. Here, we demonstrate that the BfmRS two-component system directly controls the expression of multiple stress resistance genes. Our findings suggest that BfmRS is central to a unique scheme of general stress response regulation by A. baumannii.

Multidrug-resistant bacteria cause immense public health concerns as once effective antibiotics no longer work against even common infections. Concomitantly, there has been a decline in the discovery of new antibiotics, and the current global clinical pipeline is woefully inadequate, especially against resistant Gram-negative bacteria. One major contribution to Gram-negative resistance is the presence of a protective outer membrane. Consequently, an appealing option for tackling resistance is to adversely affect that outer membrane. With that in mind, we define the response regulator PhoP as a target for new 2-aminoimidazole compounds and show that they affect the integrity of the outer membrane in resistant strains of Escherichia coli and Klebsiella pneumoniae. We also provide empirical evidence for the 2-aminoimidazole mechanism of action.

Acinetobacter baumannii is an insidious emerging nosocomial pathogen that has developed resistance to all available antimicrobials, including the last resort antibiotic, colistin. Colistin resistance often occurs due to mutations in the PmrAB two-component regulatory system. To better understand the regulatory mechanisms contributing to colistin resistance, we have biochemically characterized the A. baumannii PmrA response regulator. Initial DNA-binding analysis shows that A. baumannii PmrA bound to the Klebsiella pneumoniae PmrA box motif. This prompted analysis of the putative A. baumannii PmrAB regulon that indicated that the A. baumannii PmrA consensus box is 5'-HTTAAD N5 HTTAAD. Additionally, we provide the first structural information for the A. baumannii PmrA N-terminal domain through X-ray crystallography and we present a full-length model using molecular modelling. From these studies, we were able to infer the effects of two critical PmrA mutations, PmrA::I13M and PmrA::P102R, both of which confer increased colistin resistance. Based on these data, we suggest structural and dynamic reasons for how these mutations can affect PmrA function and hence encourage resistive traits. Understanding these mechanisms will aid in the development of new targeted antimicrobial therapies. Graphical Abstract.

Response regulators are a critical part of the two-component system of gene expression regulation in bacteria, transferring a signal from a sensor kinase into DNA binding activity resulting in alteration of gene expression. In this study, we investigated a previously uncharacterized response regulator in Francisella novicida, FTN_1452 that we have named BfpR (Biofilm-regulating Francisella protein Regulator, FTN_1452). In contrast to another Francisella response regulator, QseB/PmrA, BfpR appears to be a negative regulator of biofilm production, and also a positive regulator of antimicrobial peptide resistance in this bacterium. The protein was crystallized and X-ray crystallography studies produced a 1.8 Å structure of the BfpR N-terminal receiver domain revealing interesting insight into its potential interaction with the sensor kinase. Structural analysis of BfpR places it in the OmpR/PhoP family of bacterial response regulators along with WalR and ResD. Proteomic and transcriptomic analyses suggest that BfpR overexpression affects expression of the critical Francisella virulence factor iglC, as well as other proteins in the bacterium. We demonstrate that mutation of bfpR is associated with an antimicrobial peptide resistance phenotype, a phenotype also associated with other response regulators, for the human cathelicidin peptide LL-37 and a sheep antimicrobial peptide SMAP-29. F. novicida with mutated bfpR replicated better than WT in intracellular infection assays in human-derived macrophages suggesting that the down-regulation of iglC expression in bfpR mutant may enable this intracellular replication to occur. Response regulators have been shown to play important roles in the regulation of bacterial biofilm production. We demonstrate that F. novicida biofilm formation was highly increased in the bfpR mutant, corresponding to altered glycogen synthesis. Waxworm infection experiments suggest a role of BfpR as a negative modulator of iglC expression with de-repression by Mg2+. In this study, we find that the response regulator BfpR may be a negative regulator of biofilm formation, and a positive regulator of antimicrobial peptide resistance in F. novicida.

Bacteria have developed numerous protection strategies to ensure survival in harsh environments, with perhaps the most robust method being the formation of a protective biofilm. In biofilms, bacterial cells are embedded within a matrix that is composed of a complex mixture of polysaccharides, proteins, and DNA. The gram-positive bacterium Bacillus subtilis has become a model organism for studying regulatory networks directing biofilm formation. The phenotypic transition from a planktonic to biofilm state is regulated by the activity of the transcriptional repressor, SinR, and its inactivation by its primary antagonist, SinI. In this work, we present the first full-length structural model of tetrameric SinR using a hybrid approach combining high-resolution solution nuclear magnetic resonance (NMR), chemical cross-linking, mass spectrometry, and molecular docking. We also present the solution NMR structure of the antagonist SinI dimer and probe the mechanism behind the SinR-SinI interaction using a combination of biochemical and biophysical techniques. As a result of these findings, we propose that SinI utilizes a residue replacement mechanism to block SinR multimerization, resulting in diminished DNA binding and concomitant decreased repressor activity. Finally, we provide an evidence-based mechanism that confirms how disruption of the SinR tetramer by SinI regulates gene expression.

Bacillus subtilis is one of the most well studied bacterial species, serving as an archetype model organism which has been used in numerous genetic and biochemical studies. Unfortunately, B. subtilis also has a dark side. Strains have been identified in hospitals which are highly resistant to cleaning agents. Bacteria have developed numerous protection strategies to survive in harsh environments, but the most robust method is through the formation of biofilm. Pathogenic bacteria, such as Staphylococcus aureus, can hide in B. subtilis biofilms, taking shelter from extensive disinfecting techniques. B. subtilis is also able to transfer antibiotic resistance genes to serious human health threats such as Clostridium difficile. With these behaviors coming to light, new interest has emerged in what was once thought to be a harmless bacterium.The transition into a biofilm state in B. subtilis is regulated by the transcriptional repressor SinR, through inactivation by its primary antagonist, SinI. Extensive work has been undertaken over the years to understand the interactions between SinR and SinI, but many gaps in knowledge remain. In this work, we present the first full‐length structural models of tetrameric SinR and dimeric SinI using a hybrid approach, combining solution NMR, chemical crosslinking, mass spectrometry, and molecular docking. Our molecular dynamics studies highlight the highly flexible nature of these proteins, which appears to play a critical role in the ability of SinR to recognize a wide range of DNA binding sites. We also probe the mechanism behind the SinR‐SinI interaction using a combination of biochemical and biophysical techniques. As a result of these findings, we conclude that SinI utilizes a residue replacement mechanism to block SinR multimerization, resulting in decreased repressor activity. Finally, building on decades of work, we provide the first biochemical evidence to support the ability of SinR to bend DNA by binding significantly separated binding sites. The bending of a DNA promoter site is likely the key mechanism for gene repression by SinR, and is facilitated by the formation of the flexible SinR tetramer. SinI disrupts the SinR tetramers, inhibiting SinR from effectively binding DNA. Since derepression of SinR by SinI induces a biofilm state, targeting the SinR‐SinI protein interaction could be a viable therapeutic intervention point. Inhibition of the SinR‐SinI interaction would impede biofilm formation, making B. subtilis more vulnerable and unable to harbor dangerous pathogens.Support or Funding InformationThis work was supported by NIH grant RO1 GM055769 and the V Foundation for Cancer Research.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

2-aminoimidazole (2-AI) compounds inhibit the formation of bacterial biofilms, disperse preformed biofilms, and re-sensitize multidrug resistant bacteria to antibiotics. 2-AIs have previously been shown to interact with bacterial response regulators, but the mechanism of interaction is still unknown. Response regulators are one part of two-component systems (TCS). TCSs allow cells to respond to changes in their environment, and are used to trigger quorum sensing, virulence factors, and antibiotic resistance. Drugs that target the TCS signaling process can inhibit pathogenic behavior, making this a potent new therapeutic approach that has not yet been fully exploited. We previously laid the groundwork for the interaction of the Acinetobacter baumannii response regulator BfmR with an early 2-AI derivative. Here, we further investigate the response regulator/2-AI interaction and look at a wider library of 2-AI compounds. By combining molecular modeling with biochemical and cellular studies, we expand on a potential mechanism for interaction between response regulators and 2-AIs. We also establish that Francisella tularensis/novicida, encoding for only three known response regulators, can be a model system to study the interaction between 2-AIs and response regulators. We show that knowledge gained from studying Francisella can be applied to the more complex A. baumannii system, which contains over 50 response regulators. Understanding the impact of 2-AIs on response regulators and their mechanism of interaction will lead to the development of more potent compounds that will serve as adjuvant therapies to broad-range antibiotics.

Many of the currently available antibiotics target a narrow spectrum of metabolic processes required for cellular growth. The rate at which bacteria are developing resistance leads to traditional approaches no longer offering long‐term protection. Bacteria often avoid antibiotics through the use of biofilms. Biofilms act as a protective barrier against harsh environments and leave bacteria resistant to antibiotic treatments. As such, understanding how biofilms are formed and developing small molecule therapies are vital steps in combating antibiotic resistance. Formation of biofilms is controlled in part by transcription factors known as response regulators. Response regulators are part of two‐component systems which allow the cell to detect and respond to changes in its environment and are used to trigger quorum sensing and virulence factors. Response regulators have been highly sought after as drug targets. Knocking out function with drug therapies would likely inhibit pathogenic behavior, making response regulators a potent new approach that has not yet been exploited. The dynamic nature of response regulators makes structure based drug design challenging. Fortunately, a class of 2‐aminoimidazole (2‐AI) compounds can bind bacterial response regulators, inhibiting biofilm formation and resensitize multidrug resistant bacteria to antibiotics. This work highlights the interactions between 2‐AIs and the biofilm response regulators BfmR from Acinetobacter baumannii and QseB from Francisella tularensis. These studies have led to a model for response regulator inhibition by 2‐AIs. Understanding the impact of 2AIs on response regulators and their mechanism of interaction will lead to the development of more potent compounds that will serve as adjuvant therapies with broad‐range antibiotics.Support or Funding InformationThis project has been funded in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272201500010C, grant R01‐GM055769 and by the V Foundation for Cancer Research.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Biofilms provide protection for many bacterial species against a variety of physical and chemical assaults. Bacteria utilize universal cell-signaling modules known as two-component systems (TCS) to detect and respond to environmental changes, control quorum sensing, and initiate biofilm formation. Acinetobacter baumannii is an opportunistic human pathogen prevalent in hospitals that possesses extensive multi-drug resistance. The TCS response regulator BfmR from A. baumannii controls biofilm adhesion through the csu operon. BfmR is considered an attractive drug target since it plays a critical role in the survival and antibiotic resistance of A. baumannii in humans. Recent structural information has shed some light on the mechanism of BfmR DNA binding. Here, we further investigate the DNA-binding properties of BfmR. Response regulators typically form dimers upon activation through phosphorylation. The presence of DNA promotes dimerization of unphosphorylated BfmR. We have also narrowed down the minimum DNA required for BfmR binding to just beyond the perfect inverted repeat in the putative BfmR promotor region. Understanding how BfmR recognizes and interacts with DNA will help further develop novel therapeutics and expand our understanding of bacterial communication and biofilm formation.

The rise of drug-resistant bacterial infections coupled with decreasing antibiotic efficacy poses a significant challenge to global health care. Acinetobacter baumannii is an insidious, emerging bacterial pathogen responsible for severe nosocomial infections aided by its ability to form biofilms. The response regulator BfmR, from the BfmR/S two-component system, is the master regulator of biofilm initiation in A. baumannii and is a tractable therapeutic target. Here we present the structure of A. baumannii BfmR using a hybrid approach combining X-ray crystallography, nuclear magnetic resonance spectroscopy, chemical crosslinking mass spectrometry, and molecular modeling. We also show that BfmR binds the previously proposed bfmRS promoter sequence with moderate affinity. While BfmR shares many traits with other OmpR/PhoB family response regulators, some unusual properties were observed.Most importantly, we observe that when phosphorylated, BfmR binds this promoter sequence with a lower affinity than when not phosphorylated. All other OmpR/PhoB family members studied to date show an increase in DNA-binding affinity upon phosphorylation. Understanding the structural and biochemical mechanisms of BfmR will aid in the development of new antimicrobial therapies.

Biofilms provide cells with protection against numerous physical and chemical assaults. Bacteria utilize biofilms to avoid antibiotics, leaving the bacteria resistant to antibiotic treatments. The rise of antibiotic resistance and lack of new viable treatments threaten to usher in a post‐antibiotic era if new approaches towards drug development are not made. Many of the currently available antibiotics target a narrow spectrum of metabolic processes required for cellular growth. These traditional approaches no longer offer long‐term protection due to the acquisition rate of resistance; new mechanisms must be pursued. One such mechanism is through the two‐component systems (TCSs) used in bacterial communication. TCSs allow the cell to detect and respond to changes in its environment and are used to trigger quorum sensing and virulence factors. Drugs that target the TCS signaling process could inhibit pathogenic behavior, making them a potent new approach that has not yet been exploited. The TCS response regulator BfmR from Acinetobacter baumannii is the master controller of biofilm formation, making BfmR an attractive drug target. BfmR is targeted by 2‐aminoimidazoles (2AIs), compounds that inhibit and disperse biofilms in Gram‐negative and Gram‐positive bacteria. This work focuses on the interactions between 2AI based compounds and the response regulators BfmR and PmrA/QseB, from Fancisella tularensis, which also regulates biofilm development. Understanding the impact of 2AIs on response regulators and their mechanism of interaction will lead to the development of more potent inhibitors.

With antibiotic resistance increasing at alarming rates, targets for new antimicrobial therapies must be identified. A particularly promising target is the bacterial two-component system. Two-component systems allow bacteria to detect, evaluate and protect themselves against changes in the environment, such as exposure to antibiotics and also to trigger production of virulence factors. Drugs that target the response regulator portion of two-component systems represent a potent new approach so far unexploited. Here, we focus efforts on the highly virulent bacterium Francisella tularensis tularensis. Francisella contains only three response regulators, making it an ideal system to study. In this study, we initially present the structure of the N-terminal domain of QseB, the response regulator responsible for biofilm formation. Subsequently, using binding assays, computational docking and cellular studies, we show that QseB interacts with2-aminoimidazole based compounds that impede its function. This information will assist in tailoring compounds to act as adjuvants that will enhance the effect of antibiotics.

Plasmodium falciparum , the primary cause of malaria in humans, contains a plastid‐like organelle called the apicoplast. The apicoplast exists in most parasitic members of the phylum Apicomplexa and has its own genome along with organelle‐specific enzymes for DNA replication and repair. The only DNA polymerase in the apicoplast, apPOL, is an atypical A‐family polymerase. We solved the crystal structure of P. falciparum apPOL, the first atypical A‐family polymerase to be structurally characterized. apPOL diverges from typical members in two of three previously identified signature motifs and a region not implicated by sequence. Moreover, apPOL has an additional N‐terminal subdomain that may bind DNA, participate in protein‐protein interactions, and/or stabilize its DNA proofreading domain. These structural variances may account for functional differences in polymerase activity. The structure of apPOL also provides a point of departure for structure‐based antimalarial drug design and these atypical regions could be targeted for potent and specific inhibitors. Since apPOL has no direct orthologs to mammalian polymerases, P. falciparum apPOL is an attractive anti‐malarial drug target that provides structural and biochemical insight into a poor characterized subgroup of A‐family polymerases.

Members of the phylum Apicomplexa are responsible for many devastating diseases including malaria (Plasmodium spp.), toxoplasmosis (Toxoplasma gondii), babesiosis (Babesia bovis), and cyclosporiasis (Cyclospora cayetanensis). Most Apicomplexans contain a unique and essential organelle called the apicoplast. Derived from an ancient chloroplast, the apicoplast replicates and maintains a 35 kilobase (kb) circular genome. Due to its essential nature within the parasite, drugs targeted to proteins involved in DNA replication and repair of the apicoplast should be potent and specific. This review summarizes the current knowledge surrounding the replication and repair of the Plasmodium falciparum apicoplast genome and identifies several putative proteins involved in replication and repair pathways.

Plasmodium falciparum, the primary cause of malaria, contains a non-photosynthetic plastid called the apicoplast. The apicoplast exists in most members of the phylum Apicomplexa and has its own genome along with organelle-specific enzymes for its replication. The only DNA polymerase found in the apicoplast (apPOL) was putatively acquired through horizontal gene transfer from a bacteriophage and is classified as an atypical A-family polymerase. Here, we present its crystal structure at a resolution of 2.9Å. P. falciparum apPOL, the first structural representative of a plastidic A-family polymerase, diverges from typical A-family members in two of three previously identified signature motifs and in a region not implicated by sequence. Moreover, apPOL has an additional N-terminal subdomain, the absence of which severely diminishes its 3' to 5' exonuclease activity. A compound known to be toxic to Plasmodium is a potent inhibitor of apPOL, suggesting that apPOL is a viable drug target. The structure provides new insights into the structural diversity of A-family polymerases and may facilitate structurally guided antimalarial drug design.

Infection by the parasite Plasmodium falciparum is the leading cause of malaria in humans. The parasite has a unique and essential plastid-like organelle called the apicoplast. The apicoplast contains a genome that undergoes replication and repair through the action of a replicative polymerase (apPOL). apPOL has no direct orthologs in mammalian polymerases and is therefore an attractive antimalarial drug target. No structural information exists for apPOL, and the Klenow fragment of Escherichia coli DNA polymerase I, which is its closest structural homolog, shares only 28% sequence identity. Here, conditions for the crystallization of and preliminary X-ray diffraction data from crystals of P. falciparum apPOL are reported. Data complete to 3.5 Å resolution were collected from a single crystal (2 × 2 × 5 µm) using a 5 µm beam. The space group P6522 (unit-cell parameters a = b = 141.8, c = 149.7 Å, α = β = 90, γ = 120°) was confirmed by molecular replacement. Refinement is in progress.