Journal of Bacteriology最新文献

Bacteria and phages are locked in a co-evolutionary arms race where each entity evolves mechanisms to restrict the proliferation of the other. Phage-encoded defense inhibitors have proven powerful tools to interrogate how defense systems function. A relatively common defense system is BREX (bacteriophage exclusion); however, how BREX functions to restrict phage infection remains poorly understood. A BREX system encoded by the sulfamethoxazole and trimethoprim (SXT) integrative and conjugative element, VchInd5, was recently identified in Vibrio cholerae, the causative agent of the diarrheal disease cholera. The lytic phage ICP1 (International Centre for Diarrhoeal Disease Research, Bangladesh cholera phage 1) that co-circulates with V. cholerae encodes the BREX-inhibitor OrbA, but how OrbA inhibits BREX is unclear. Here, we determine that OrbA inhibits BREX using a unique mechanism from known BREX inhibitors by directly binding to the BREX component BrxC. BrxC has a functional ATPase domain that, when mutated, not only disrupts BrxC function but also alters how BrxC multimerizes. Furthermore, we find that OrbA binding disrupts BrxC-BrxC interactions. We determine that OrbA cannot bind BrxC encoded by the distantly related BREX system encoded by the aSXT VchBan9, and thus fails to inhibit this BREX system that also circulates in epidemic V. cholerae. Lastly, we find that homologs of the VchInd5 BrxC are more diverse than the homologs of the VchBan9 BrxC. These data provide new insight into the function of the BrxC ATPase and highlight how phage-encoded inhibitors can disrupt phage defense systems using different mechanisms.IMPORTANCEWith renewed interest in phage therapy to combat antibiotic-resistant pathogens, understanding the mechanisms bacteria use to defend themselves against phages and the counter-strategies phages evolve to inhibit defenses is paramount. Bacteriophage exclusion (BREX) is a common defense system with few known inhibitors. Here, we probe how the vibriophage-encoded inhibitor OrbA inhibits the BREX system of Vibrio cholerae, the causative agent of the diarrheal disease cholera. By interrogating OrbA function, we have begun to understand the importance and function of a BREX component. Our results demonstrate the importance of identifying inhibitors against defense systems, as they are powerful tools for dissecting defense activity and can inform strategies to increase the efficacy of some phage therapies.

Cupriavidus metallidurans is able to survive exposure to high concentrations of transition metals, but is also able to grow under metal starvation conditions. A prerequisite of cellular zinc homeostasis is a flow equilibrium combining zinc uptake and efflux processes. The mutant strain ∆e4 of the parental plasmid-free strain AE104 with a deletion of all four chromosomally encoded genes of previously known efflux systems ZntA, CadA, DmeF, and FieF was still able to efflux zinc in a pulse-chase experiment, indicating the existence of a fifth efflux system. The gene cdfX, encoding a protein of the cation diffusion facilitator (CDF) family, is located in proximity to the cadA gene, encoding a P-type ATPase. Deletion of cdfX in the ∆e4 mutant resulted in a further decrease in zinc resistance. Pulse-chase experiments with radioactive ⁶⁵Zn(II) and stable-isotope-enriched ⁶⁷Zn(II) provided evidence that CdfX was responsible for the residual zinc efflux activity of the mutant strain ∆e4. Reporter gene fusions with cdfX-lacZ indicated that the MerR-type regulator ZntR, the main regulator of zntA expression, was responsible for zinc- and cadmium-dependent upregulation of cdfX expression, especially in mutant cells lacking one or both of the previously characterized efflux systems, ZntA and CadA. Expression of zntR also proved to be controlled by ZntR itself as well as by zinc and cadmium availability. These data indicate that the cdfX-cadA region provides C. metallidurans with a backup system for the zinc-cadmium-exporting P-type ATPase ZntA, with CdfX exporting zinc and CadA cadmium.IMPORTANCEBacteria have evolved the ability to supply the important trace element zinc to zinc-dependent proteins, despite external zinc concentrations varying over a wide range. Zinc homeostasis can be understood as adaptive layering of homeostatic systems, allowing coverage from extreme starvation to extreme resistance. Central to zinc homeostasis is a flow equilibrium of zinc comprising uptake and efflux reactions, which adjusts the cytoplasmic zinc content. This report describes what happens when an imbalance in zinc and cadmium concentrations impairs the central inner-membrane zinc efflux system for zinc by competitive inhibition for this exporter. The problem is solved by activation of Cd-exporting CadA or Zn-exporting CdfX as additional efflux systems.

Species of the Vibrio genus occupy diverse aquatic environments ranging from brackish water to warm equatorial seas to salty coastal regions. More than 80 species of Vibrio have been identified, many of them as pathogens of marine organisms, including fish, shellfish, and corals, causing disease and wreaking havoc on aquacultures and coral reefs. Moreover, many Vibrio species associate with and thrive on chitinous organisms abundant in the ocean. Among the many diverse Vibrio species, the most well-known and studied is Vibrio cholerae, discovered in the 19th century to cause cholera in humans when ingested. The V. cholerae field blossomed in the late 20th century, with studies broadly examining V. cholerae evolution as a human pathogen, natural competence, biofilm formation, and virulence mechanisms, including toxin biology and virulence gene regulation. This review discusses some of the historic discoveries of V. cholerae biology and ecology as one of the fundamental model systems of bacterial genetics and pathogenesis.

Type IVa pili (T4aP) are widespread and enable bacteria to translocate across surfaces. T4aP engage in cycles of extension, surface adhesion, and retraction, thereby pulling cells forward. Accordingly, the number and localization of T4aP are critical to efficient translocation. Here, we address how T4aP formation is regulated in Myxococcus xanthus, which translocates with a well-defined leading and lagging cell pole using T4aP at the leading pole. This localization is orchestrated by the small GTPase MglA and its downstream effector SgmX that both localize at the leading pole and recruit the PilB extension ATPase to the T4aP machinery at this pole. Here, we identify the previously uncharacterized protein SopA and show that it interacts directly with SgmX, localizes at the leading pole, stimulates polar localization of PilB, and is important for T4aP formation. We corroborate that MglA also recruits FrzS to the leading pole, and FrzS stimulates SgmX recruitment. In addition, FrzS and SgmX separately recruit SopA. Precise quantification of T4aP-formation and T4aP-dependent motility in various mutants supports a model whereby the main pathway for stimulating T4aP formation is the MglA/SgmX pathway. FrzS stimulates this pathway by recruiting SgmX and SopA. SopA stimulates the MglA/SgmX pathway by stimulating the function of SgmX, likely by promoting the SgmX-dependent recruitment of PilB to the T4aP machinery. The architecture of the MglA/SgmX/FrzS/SopA protein interaction network for orchestrating T4aP formation allows for combinatorial regulation of T4aP levels at the leading cell pole resulting in discrete levels of T4aP-dependent motility.

Importance: Type IVa pili (T4aP) are widespread bacterial cell surface structures with important functions in translocation across surfaces, surface adhesion, biofilm formation, and virulence. T4aP-dependent translocation crucially depends on the number of pili. To address how the number of T4aP is regulated, we focused on M. xanthus, which assembles T4aP at the leading cell pole and is a model organism for T4aP biology. Our results support a model whereby the four proteins MglA, SgmX, FrzS, and the newly identified SopA protein establish a highly intricate interaction network for orchestrating T4aP formation at the leading cell pole. This network allows for combinatorial regulation of the number of T4aP resulting in discrete levels of T4aP-dependent motility.

Enterococci are Gram-positive bacteria that colonize the gastrointestinal tract. Clinically relevant enterococci are intrinsically resistant to antibiotics in the cephalosporin family, and prior therapy with cephalosporins is a major risk factor for the acquisition of an enterococcal infection. One important determinant of intrinsic cephalosporin resistance in enterococci is the two-component signal transduction system CroS/R. The CroS sensor kinase senses cephalosporin-induced cell wall stress to become activated and phosphorylates its cognate response regulator CroR, thereby enhancing CroR-dependent gene expression to drive cephalosporin resistance. CroS possesses a short (~30 amino acids) extracellular segment between its two transmembrane domains near the N-terminus, but whether this extracellular segment is important for sensing cephalosporin stress, or possesses any other function, has remained unknown. Here, we explored the role of the CroS extracellular segment through mutagenesis and functional studies. We found that mutations in the CroS extracellular segment biased CroS to adopt a more active state during ceftriaxone stress, which led to an increase in CroR-dependent gene expression and hyper-resistance to ceftriaxone. Importantly, these mutants still responded to ceftriaxone-mediated stress by enhancing CroS activity, indicating that the extracellular segment of CroS does not directly bind a regulatory ligand. Overall, our results suggest that although the extracellular segment of CroS does not directly bind a regulatory ligand, it can modulate the magnitude of CroS signaling for phosphorylation of CroR to regulate cephalosporin resistance through the resulting changes in CroR-dependent gene expression.

Importance: Clinically relevant enterococci are intrinsically resistant to antibiotics in the cephalosporin family. The CroS sensor kinase senses cephalosporin-induced cell wall stress to trigger signaling that drives cephalosporin resistance, but the mechanism by which CroS senses stress is unknown. We report the first functional characterization of the CroS extracellular segment, revealing that mutations in the extracellular segment did not prevent CroS from responding to cell wall stress but instead biased CroS to adopt a more active state during cephalosporin stress that led to an increase in CroR-dependent gene expression and hyper-resistance to ceftriaxone. Overall, our results suggest that the extracellular segment of CroS does not directly bind to a regulatory ligand but that it can modulate the magnitude of CroS signaling.

Staphylococcus aureus is a Gram-positive, opportunistic human pathogen that is a leading cause of skin and soft tissue infections and invasive disease worldwide. Virulence in this bacterium is tightly controlled by a network of regulatory factors. One such factor is the global regulatory protein CodY. CodY links branched-chain amino acid sufficiency to the production of surface-associated and secreted factors that facilitate immune evasion and subversion. Our previous work revealed that CodY regulates virulence factor gene expression indirectly in part by controlling the activity of the SaeRS two-component system (TCS). While this is correlated with an increase in membrane anteiso-15:0 and -17:0 branched-chain fatty acids (BCFAs) derived from isoleucine, the true mechanism of control has remained elusive. Herein, we report that CodY-dependent regulation of SaeS sensor kinase activity requires BCFA synthesis. During periods of nutrient sufficiency, BCFA synthesis and Sae TCS activity are kept relatively low by CodY-dependent repression of the ilv-leu operon and the isoleucine-specific permease gene brnQ2. In a codY null mutant, which simulates extreme nutrient limitation, de-repression of ilv-leu and brnQ2 directs the synthesis of enzymes in redundant de novo and import pathways to upregulate production of BCFA precursors. Overexpression of brnQ2, independent of CodY, is sufficient to increase membrane anteiso BCFAs, Sae-dependent promoter activity, and SaeR ~P levels. Our results further clarify the molecular mechanisms by which CodY controls virulence in S. aureus.IMPORTANCEExpression of bacterial virulence genes often correlates with the exhaustion of nutrients, but how the signaling of nutrient availability and the resulting physiological responses are coordinated is unclear. In S. aureus, CodY controls the activity of two major regulators of virulence-the Agr and Sae two-component systems (TCSs)-by unknown mechanisms. This work identifies a mechanism by which CodY controls the activity of the sensor kinase SaeS by modulating the levels of anteiso branched-chain amino acids that are incorporated into the membrane. Understanding the mechanism adds to our understanding of how bacterial physiology and metabolism are linked to virulence and underscores the role virulence in maintaining homeostasis. Understanding the mechanism also opens potential avenues for targeted therapeutic strategies against S. aureus infections.

We have previously shown that the nucleoid-associated protein, HU, uses its DNA-binding surfaces to bind to bacterial outer-membrane lipopolysaccharide (LPS), causing HU to act as a glue aiding the adherence of DNA to bacteria, e.g., in biofilms. We have also previously shown that HU and DNA coacervate into a state of liquid-liquid phase separation (LLPS), within bacterial cells and also in vitro. Here, we show that HU and free LPS (which is ordinarily shed by bacteria) also condense into a state of phase separation. Coacervates of HU, DNA, and free LPS are less liquid-like than coacervates of HU and DNA. Escherichia coli cells bearing LPS on their surfaces are shown to adhere to (as well as advance into) coacervates of HU and DNA. HU appears to play a role, therefore, in maintaining both intracellular and extracellular states of phase separation with DNA that are compatible with LPS and LPS-bearing E. coli, with LPS determining the liquidity of the biofilm-simulating coacervate.

Importance: Understanding the constitution and behavior of biofilms is crucial to understanding how to deal with persistent biofilms. This study, together with other recent studies from our group, elucidates a novel aspect of the extracellular polymeric substance (EPS) of Escherichia coli biofilms, by creating a simulacrum of the EPS and then demonstrating that its formation involves liquid-liquid phase separation (LLPS) of HU, DNA, and lipopolysaccharide (LPS) components, with LPS determining the liquidity of this EPS simulacrum. The findings provide insight into the nature of biofilms and into how the interplay of HU, DNA, and LPS could modulate the structural integrity and functional dynamics of biofilms.

Plant pathogenic bacteria encounter a drastic increase in apoplastic pH during the early stages of plant immunity. The effects of alkalization on pathogen-host interactions have not been comprehensively characterized. Here, we used a global transcriptomic approach to assess the impact of environmental alkalization on Pseudomonas syringae pv. tomato DC3000 in vitro. In addition to the Type 3 Secretion System, we found expression of genes encoding other virulence factors such as iron uptake and coronatine biosynthesis to be strongly affected by environmental alkalization. We also found that the activity of AlgU, an important regulator of virulence gene expression, was induced at pH 5.5 and suppressed at pH 7.8, which are pH levels that this pathogen would likely experience before and during pattern-triggered immunity, respectively. This pH-dependent control requires the presence of periplasmic proteases, AlgW and MucP, that function as part of the environmental sensing system that activates AlgU in specific conditions. This is the first example of pH-dependency of AlgU activity, suggesting a regulatory pathway model where pH affects the proteolysis-dependent activation of AlgU. These results contribute to deeper understanding of the role apoplastic pH has on host-pathogen interactions.IMPORTANCEPlant pathogenic bacteria, like Pseudomonas syringae, encounter many environmental changes including oxidative stress and alkalization during plant immunity, but the ecological effects of the individual responses are not well understood. In this study, we found that transcription of many previously characterized virulence factors in P. syringae pv. tomato DC3000 is downregulated by the level of environmental alkalization these bacteria encounter during the early stages of plant immune activation. We also report for the first time the sigma factor AlgU is post-translationally activated by low environmental pH through its natural activation pathway, which partially accounts for the expression Type 3 Secretion System virulence genes at acidic pH. The results of this study demonstrate the importance of extracellular pH on global regulation of virulence-related gene transcription in plant pathogenic bacteria.

Cobamides (Cbas) are cobalt-containing cyclic tetrapyrroles used by cells from all domains of life as co-catalyst of diverse reactions. There are several structural features that distinguish Cbas from one another. The most relevant of those features discussed in this review is the lower ligand, which is the nucleobase of a ribotide located in the lower face of the cyclic tetrapyrrole ring. The above-mentioned ribotide is known as the nucleotide loop, which is attached to the ring by a short linker. In Cbas, the nucleobase of the ribotide can be benzimidazole or derivatives of it, purine or derivatives of it, or phenolic compounds. Given the importance of Cbas in prokaryotic metabolism, it is not surprising that prokaryotes have evolved enzymes that cleave part or the entire nucleotide loop. This function is advantageous when Cbas contain nucleobases that somehow interfere with the function of Cba-dependent enzymes in the organism. After cleavage, Cbas are rebuilt via the nucleotide loop assembly (NLA) pathway, which includes enzymes that activate the nucleobase and the ring intermediate, followed by condensation of activated intermediates and a final dephosphorylation reaction. This exchange of nucleobases is known as Cba remodeling. The NLA pathway is used to salvage Cba precursors from the environment.

Although the development of disinfection technologies with novel mechanisms has stagnated, we demonstrate the bactericidal effects and mechanisms of high-speed nanodroplet generation technology. The first development of this technology in 2017 gushes out a water droplet of 10 nm in size at 50 m/s; however, the target surface does not become completely wet. Nanodroplets were exposed to biofilm models of Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Serratia marcescens. This phenomenon was verified when the nanodroplets collide with the surface of the bacteria at an impact pressure of ~75 MPa. S. aureus was exposed to nanodroplets for 30 seconds at 75 MPa, which exploded the bacterial body and completely sterilized. Eighteen MPa damaged the bacterial surface, causing peptidoglycan leakage. S. aureus was repaired and survives in this state. In contrast, in Gram-negative bacteria, nanodroplets with 18 MPa penetrated some biofilm-forming bacteria but did not hit all of them, and the viable count was not significantly reduced. Although all three bacterial species were completely sterilized at 75 MPa, the disinfectant effect was affected by the biomass of the biofilm formed. In summary, our findings prove that nanodroplets at 18 MPa on the bacterial surface were ineffective in killing bacteria, whereas at 75 MPa, all four bacterial species were completely sterilized. The disinfection mechanism involved a high-velocity collision of nanodroplets with the bacteria, physically destroying them. Our results showed that disinfection using this technology could be an innovative method that is completely different from existing disinfection techniques.

Importance: Although existing disinfection techniques demonstrate bactericidal effects through chemical reactions, concerns regarding human toxicity and environmental contamination have been raised. To the best of our knowledge, this study is the first in the world to reveal that the use of this technology, with nanodroplets of less than 100 nm, can destroy and sterilize bacterial cells by colliding with biofilm-forming bacteria at 75 MPa. Furthermore, because this technology uses only water, it can solve the problems of human toxicity and environmental contamination caused by existing disinfection techniques. Because of its minimal water usage, it can be employed for sanitation worldwide without being limited to specific regions. Our report proposes an unprecedented physical disinfection approach that utilizes a high-speed nanodroplet generation technology.