Fluorescent tools for the standardized work in Gram-negative bacteria.

Standardized and thoroughly characterized genetic tools are a prerequisite for studying cellular processes to ensure the reusability and consistency of experimental results. The discovery of fluorescent proteins (FPs) represents a milestone in the development of genetic reporters for monitoring transcription or protein localization in vivo. FPs have revolutionized our understanding of cellular dynamics by enabling the real-time visualization and tracking of biological processes. Despite these advancements, challenges remain in the appropriate use of FPs, specifically regarding their proper application, protein turnover dynamics, and the undesired disruption of cellular functions. Here, we systematically compared a comprehensive set of 15 FPs and assessed their performance in vivo by focusing on key parameters, such as signal over background ratios and protein stability rates, using the Gram-negative model organism Salmonella enterica as a representative host. We evaluated four protein degradation tags in both plasmid- and genome-based systems and our findings highlight the necessity of introducing degradation tags to analyze time-sensitive cellular processes. We demonstrate that the gain of dynamics mediated by the addition of degradation tags impacts the cell-to-cell heterogeneity of plasmid-based but not genome-based reporters. Finally, we probe the applicability of FPs for protein localization studies in living cells using standard and super-resolution fluorescence microscopy. In summary, our study underscores the importance of careful FP selection and paves the way for the development of improved genetic reporters to enhance the reproducibility and reliability of fluorescence-based research in Gram-negative bacteria and beyond.

Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit.

Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively driven by sodium-dependent stator units (PomAB). However, how ion selectivity is attained, how ion transport triggers the directional rotation of the stator unit, and how the stator unit is incorporated into the flagellar rotor remained largely unclear. Here, we have determined by cryo-electron microscopy the structure of Vibrio PomAB. The electrostatic potential map uncovers sodium binding sites, which together with functional experiments and molecular dynamics simulations, reveal a mechanism for ion translocation and selectivity. Bulky hydrophobic residues from PomA prime PomA for clockwise rotation. We propose that a dynamic helical motif in PomA regulates the distance between PomA subunit cytoplasmic domains, stator unit activation, and torque transmission. Together, our study provides mechanistic insights for understanding ion selectivity and rotor incorporation of the stator unit of the bacterial flagellum.

The Novel Synthetic Antibiotic BDTL049 Based on a Dendritic System Induces Lipid Domain Formation while Escaping the Cell Envelope Stress Resistance Determinants.

The threat of antimicrobial-resistant bacteria is ever increasing and over the past-decades development of novel therapeutic counter measurements have virtually come to a halt. This circumstance calls for interdisciplinary approaches to design, evaluate and validate the mode of action of novel antibacterial compounds. Hereby, carbosilane dendritic systems that exhibit antimicrobial properties have the potential to serve as synthetic and rationally designed molecules for therapeutic use. The bow-tie type topology of BDTL049 was recently investigated against the Gram-positive model organism Bacillus subtilis, revealing strong bactericidal properties. In this study, we follow up on open questions concerning the usability of BDTL049. For this, we synthesized a fluorescent-labeled version of BDTL049 that maintained all antimicrobial features to unravel the interaction of the compound and bacterial membrane. Subsequently, we highlight the bacterial sensitivity against BDTL049 by performing a mutational study of known resistance determinants. Finally, we address the cytotoxicity of the compound in human cells, unexpectedly revealing a high sensitivity of the eukaryotic cells upon BDTL049 exposure. The insights presented here further elaborate on the unique features of BDTL049 as a promising candidate as an antimicrobial agent while not precluding that further rounds of rational designing are needed to decrease cytotoxicity to ultimately pave the way for synthetic antibiotics toward clinical applicability.

A guide for membrane potential measurements in Gram-negative bacteria using voltage-sensitive dyes.

Transmembrane potential is one of the main bioenergetic parameters of bacterial cells, and is directly involved in energizing key cellular processes such as transport, ATP synthesis and motility. The most common approach to measure membrane potential levels is through use of voltage-sensitive fluorescent dyes. Such dyes either accumulate or are excluded from the cell in a voltage-dependent manner, which can be followed by means of fluorescence microscopy, flow cytometry, or fluorometry. Since the cell's ability to maintain transmembrane potential relies upon low and selective membrane ion conductivity, voltage-sensitive dyes are also highly sensitive reporters for the activity of membrane-targeting antibacterials. However, the presence of an additional membrane layer in Gram-negative (diderm) bacteria complicates their use significantly. In this paper, we provide guidance on how membrane potential and its changes can be monitored reliably in Gram-negatives using the voltage-sensitive dye 3,3'-dipropylthiadicarbocyanine iodide [DiSC3(5)]. We also discuss the confounding effects caused by the presence of the outer membrane, or by measurements performed in buffers rather than growth medium. We hope that the discussed methods and protocols provide an easily accessible basis for the use of voltage-sensitive dyes in Gram-negative organisms, and raise awareness of potential experimental pitfalls associated with their use.

Synthesis and mechanism-of-action of a novel synthetic antibiotic based on a dendritic system with bow-tie topology.

Over the course of the last decades, the continuous exposure of bacteria to antibiotics-at least in parts due to misprescription, misuse, and misdosing-has led to the widespread development of antimicrobial resistances. This development poses a threat to the available medication in losing their effectiveness in treating bacterial infections. On the drug development side, only minor advances have been made to bring forward novel therapeutics. In addition to increasing the efforts and approaches of tapping the natural sources of new antibiotics, synthetic approaches to developing novel antimicrobials are being pursued. In this study, BDTL049 was rationally designed using knowledge based on the properties of natural antibiotics. BDTL049 is a carbosilane dendritic system with bow-tie type topology, which has antimicrobial activity at concentrations comparable to clinically established natural antibiotics. In this report, we describe its mechanism of action on the Gram-positive model organism Bacillus subtilis. Exposure to BDTL049 resulted in a complex transcriptional response, which pointed toward disturbance of the cell envelope homeostasis accompanied by disruption of other central cellular processes of bacterial metabolism as the primary targets of BDTL049 treatment. By applying a combination of whole-cell biosensors, molecular staining, and voltage sensitive dyes, we demonstrate that the mode of action of BDTL049 comprises membrane depolarization concomitant with pore formation. As a result, this new molecule kills Gram-positive bacteria within minutes. Since BDTL049 attacks bacterial cells at different targets simultaneously, this might decrease the chances for the development of bacterial resistances, thereby making it a promising candidate for a future antimicrobial agent.

Supercoiled filaments propel them all.

In this issue of Cell, Kreutzberger and colleagues report the near-atomic-resolution, cryo-EM structures of the supercoiled filaments of both bacterial and archaeal motility machines. Despite the lack of homology, the supercoiled filament structures reveal shared fundamental features of prokaryotic locomotion and represent a prime example of convergent evolution.

Phyletic Distribution and Diversification of the Phage Shock Protein Stress Response System in Bacteria and Archaea.

Maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protein protection networks that connect stress perception, transmembrane signal transduction, and mediation of cellular responses upon cell envelope stress. The phage shock protein (Psp) stress response is one such conserved protection network. Most knowledge about the Psp response derives from studies in the Gram-negative model bacterium Escherichia coli, where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of the Proteobacteria, Actinobacteria, and Firmicutes. However, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and describe that the predicted Psp systems deviate dramatically from the known prototypes. The core proteins PspA and PspC have been integrated into various (often phylum-specifically) conserved protein networks during evolution. Based on protein domain-based and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system for Psp networks in bacteria and archaea. We validate our approach by performing a comprehensive in vivo protein interaction study of Psp domains identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected protein network. Our study highlights the diversity of Psp domain organizations and potentially diverse functions across the plethora of the microbial landscape, thus laying the ground for studies beyond known Psp functions in underrepresented organisms. IMPORTANCE The PspA protein domain is found in all domains of life, highlighting its central role in Psp networks. To date, all insights into the core functions of Psp responses derive mainly from protein network blueprints representing only three bacterial phyla. Despite large overlaps in function and regulation, the evolutionary diversity of Psp networks remains largely elusive. Here, we present an unbiased protein domain- and genomic context-centered approach that describes and classifies Psp systems. Our results suggest so-far-unknown Psp-associated roles with other protein networks giving rise to new functions. We demonstrate the applicability of our approach by dissecting the Psp protein network present in Bacillus subtilis and demonstrate Psp domains working in concert with other cell envelope stress response systems. We find that the Psp-like protein universe reflects a surprising diversity within the bacterial and archaeal microbial world.

Characterization and mode of action analysis of black soldier fly (Hermetia illucens) larva-derived hemocytes.

With the growing importance of the black soldier fly (Hermetia illucens) for both sustainable food production and waste management as well as for science, a great demand of understanding its immune system arises. Here, we present the first description of the circulating larval hemocytes with special emphasis on uptake of microorganisms and distinguishing hemocyte types. With histological, zymographic, and cytometric methods and with a set of hemocyte binding lectins and antibodies, the hemocytes of H. illucens are identified as plasmatocytes, crystal cells, and putative prohemocytes. Total hemocyte counts (THC) are determined, and methods for THC determination are compared. Approximately 1100 hemocytes per microliter hemolymph are present in naive animals, while hemocyte density decreases dramatically shortly after wounding, indicating a role of hemocytes in response to wounding (and immune response in general). The determination of the relative abundance of each hemocyte type (differential hemocyte count, DHC) revealed that plasmatocytes are highly abundant, whereas prohemocytes and crystal cells make up only a small percentage of the circulating cells. Plasmatocytes are not only the most abundant but also the professional phagocytes in H. illucens. They rapidly engulf and take up bacteria both in vivo and in vitro, indicating a very potent cellular defense against invading pathogens. Larger bioparticles such as yeasts are also removed from circulation by phagocytosis, but slower than bacteria. This is the first analysis of the potent cellular immune response in the black soldier fly, and a first toolbox that helps to identify hemocyte (types) is presented.

The Epipeptide Biosynthesis Locus epeXEPAB Is Widely Distributed in Firmicutes and Triggers Intrinsic Cell Envelope Stress.

The epeXEPAB (formerly yydFGHIJ) locus of Bacillus subtilis encodes a minimalistic biosynthetic pathway for a linear antimicrobial epipeptide, EpeX, which is ribosomally produced and post-translationally processed by the action of the radical-SAM epimerase, EpeE, and a membrane-anchored signal 2 peptide peptidase, EpeP. The ABC transporter EpeAB provides intrinsic immunity against self-produced EpeX, without conferring resistance against extrinsically added EpeX. EpeX specifically targets, and severely perturbs the integrity of the cytoplasmic membrane, which leads to the induction of the Lia-dependent envelope stress response. Here, we provide new insights into the distribution, expression, and regulation of the minimalistic epeXEPAB locus of B. subtilis, as well as the biosynthesis and biological efficiency of the produced epipeptide EpeX*. A comprehensive comparative genomics study demonstrates that the epe-locus is restricted to but widely distributed within the phylum Firmicutes. The gene products of epeXEP are necessary and sufficient for the production of the mature antimicrobial peptide EpeX*. In B. subtilis, the epeXEPAB locus is transcribed from three different promoters, one upstream of epeX (PepeX) and two within epeP (PepeA1 and PepeA2). While the latter two are mostly constitutive, PepeX shows a growth phase-dependent induction at the onset of stationary phase. We demonstrate that this regulation is the result of the antagonistic action of two global regulators: The transition state regulator AbrB keeps the epe locus shut off during exponential growth by direct binding. This tight repression is relieved by the master regulator of sporulation, Spo0A, which counteracts the AbrB-dependent repression of epeXEPAB expression during the transition to stationary phase. The net result of these three -promoters is an expression pattern that ensures EpeAB-dependent autoimmunity prior to EpeX* production. In the absence of EpeAB, the general envelope stress response proteins LiaIH can compensate for the loss of specific autoimmunity by providing sufficient protection against the membrane-perturbating action of EpeX*. Hence, the transcriptional regulation of epe expression and the resulting intrinsic induction of the two corresponding resistance functions, encoded by epeAB and liaIH, are well balanced to provide a need-based immunity against mature EpeX*.

With or without you: crosstalk between cell division and flagellum assembly.

In this issue of Developmental Cell, Siwach et al. describe a novel mechanism found in α-proteobacteria that links flagellar biosynthesis and cell division via a regulator that senses proper flagellar assembly. This spatial and temporal checkpoint control helps ensure inheritance of a flagellum during cell division.

Silver (I) N-Heterocyclic Carbenes Carbosilane Dendritic Systems and Their Imidazolium-Terminated Analogues as Antibacterial Agents: Study of Their Mode of Action.

Spherical dendrimers and dendrons containing silver(I) N-heterocyclic carbenes (Ag(I)-NHC) and additionally bow-tie metal-free dendritic systems were synthesized in a simple and straightforward synthetic procedure and subsequently characterized. The antibacterial activity was evaluated, and in parallel, a comparative study with the cationic analogue precursors was performed to explore the effect of silver ions in the dendritic structure. Other parameters, such as topology, generation, and hydrophobicity, of the imidazole substituents were also studied. All these dendritic systems presented antibacterial activity against three different bacterial strains, two Gram-positive (Staphylococcus aureus and Bacillus subtilis) and one Gram-negative (Escherichia coli). Several assays were conducted to elucidate their mechanism of action against Bacillus subtilis, by using bacterial biosensors or specific probes and fluorescent proteins sensitive to changes in the cell membrane potential. These studies are specially focused on the role of the polyvalence of our systems containing silver atoms, which may provoke interesting effects in the mode of action.

Amphotericin B Specifically Induces the Two-Component System LnrJK: Development of a Novel Whole-Cell Biosensor for the Detection of Amphotericin-Like Polyenes.

The rise of drug-resistant fungal pathogens urges for the development of new tools for the discovery of novel antifungal compounds. Polyene antibiotics are potent agents against fungal infections in humans and animals. They inhibit the growth of fungal cells by binding to sterols in the cytoplasmic membrane that subsequently causes pore formation and eventually results in cell death. Many polyenes are produced by Streptomycetes and released into the soil environment, where they can then target fungal hyphae. While not antibacterial, these compounds could nevertheless be also perceived by bacteria sharing the same habitat and serve as signaling molecules. We therefore addressed the question of how polyenes such as amphotericin B are perceived by the soil bacterium, Bacillus subtilis. Global transcriptional profiling identified a very narrow and specific response, primarily resulting in strong upregulation of the lnrLMN operon, encoding an ABC transporter previously associated with linearmycin resistance. Its strong and specific induction prompted a detailed analysis of the lnrL promoter element and its regulation. We demonstrate that the amphotericin response strictly depends on the two-component system LnrJK and that the target of LnrK-dependent gene regulation, the lnrLMN operon, negatively affects LnrJK-dependent signal transduction. Based on this knowledge, we developed a novel whole-cell biosensor, based on a P lnrL -lux fusion reporter construct in a lnrLMN deletion mutant background. This highly sensitive and dynamic biosensor is ready to be applied for the discovery or characterization of novel amphotericin-like polyenes, hopefully helping to increase the repertoire of antimycotic and antiparasitic polyenes available to treat human and animal infections.

Development of a novel heterologous ß-lactam-specific whole-cell biosensor in Bacillus subtilis.

BACKGROUND: Whole-cell biosensors are a powerful and easy-to-use screening tool for the fast and sensitive detection of chemical compounds, such as antibiotics. ß-Lactams still represent one of the most important antibiotic groups in therapeutic use. They interfere with late stages of the bacterial cell wall biosynthesis and result in irreversible perturbations of cell division and growth, ultimately leading to cell lysis. In order to simplify the detection of these antibiotics from solutions, solid media or directly from producing organisms, we aimed at developing a novel heterologous whole-cell biosensor in Bacillus subtilis, based on the ß-lactam-induced regulatory system BlaR1/BlaI from Staphylococcus aureus. RESULTS: The BlaR1/BlaI system was heterologously expressed in B. subtilis and combined with the luxABCDE operon of Photorhabdus luminescens under control of the BlaR1/BlaI target promoter to measure the output of the biosensor. A combination of codon adaptation, constitutive expression of blaR1 and blaI and the allelic replacement of penP increased the inducer spectrum and dynamic range of the biosensor. ß-Lactams from all four classes induced the target promoter P blaZ in a concentration-dependent manner, with a dynamic range of 7- to 53-fold. We applied our biosensor to a set of Streptomycetes soil isolates and demonstrated its potential to screen for the production of ß-lactams. In addition to the successful implementation of a highly sensitive ß-lactam biosensor, our results also provide the first experimental evidence to support previous suggestions that PenP functions as a ß-lactamase in B. subtilis. CONCLUSION: We have successfully established a novel heterologous whole-cell biosensor in B. subtilis that is highly sensitive for a broad spectrum of ß-lactams from all four chemical classes. Therefore, it increases the detectable spectrum of compounds with respect to previous biosensor designs. Our biosensor can readily be applied for identifying ß-lactams in liquid or on solid media, as well as for identifying potential ß-lactam producers.

The Epipeptide YydF Intrinsically Triggers the Cell Envelope Stress Response of Bacillus subtilis and Causes Severe Membrane Perturbations.

The Gram-positive model organism and soil bacterium Bacillus subtilis naturally produces a variety of antimicrobial peptides (AMPs), including the ribosomally synthesized and post-translationally modified AMP YydF, which is encoded in the yydFGHIJ locus. The yydF gene encodes the pre-pro-peptide, which is, in a unique manner, initially modified at two amino acid positions by the radical SAM epimerase YydG. Subsequently, the membrane-anchored putative protease YydH is thought to cleave and release the mature AMP, YydF, to the environment. The AMP YydF, with two discreet epimerizations among 17 residues as sole post-translational modification, defines a novel class of ribosomally synthesized and post-translationally modified peptides (RiPPs) called epipeptides, for which the mode-of-action (MOA) is unknown. The predicted ABC transporter encoded by yydIJ was previously postulated as an autoimmunity determinant of B. subtilis against its own AMP. Here, we demonstrate that extrinsically added YydF* kills B. subtilis cells by dissipating membrane potential via membrane permeabilization. This severe membrane perturbation is accompanied by a rapid reduction of membrane fluidity, substantiated by lipid domain formation. The epipeptide triggers a narrow and highly specific cellular response. The strong induction of liaIH expression, a marker for cell envelope stress in B. subtilis, further supports the MOA described above. A subsequent mutational study demonstrates that LiaIH-and not YydIJ-represents the most efficient resistance determinant against YydF* action. Unexpectedly, none of the observed cellular effects upon YydF* treatment alone are able to trigger liaIH expression, indicating that only the unique combination of membrane permeabilization and membrane rigidification caused by the epipetide, leads to the observed cell envelope stress response.

Coordinated Cell Death in Isogenic Bacterial Populations: Sacrificing Some for the Benefit of Many?

Antibiotics are classically perceived as biological weapons that bacteria produce to hold their ground against competing species in their natural habitat. But in the context of multicellular differentiation processes, antimicrobial compounds sometimes also play a role in intraspecies competition, resulting in the death of a sub-population of genetically identical siblings for the benefit of the population. Such a strategy is based on the diversification and hence phenotypic heterogeneity of an isogenic bacterial population. This review article will address three such phenomena. In Bacillus subtilis, cannibalism is a differentiation strategy that enhances biofilm formation, prolongs or potentially even prevents full commitment to endospore formation under starvation conditions, and protects cells within the biofilm against competing species. The nutrients released by lysed cells can be used by the toxin producers, thereby delaying the full activation of the master regulator of sporulation. A related strategy is associated with the initiation of competence development under nutrient excess in Streptococcus pneumoniae. This process, termed fratricide, causes allolysis in a sub-population and is thought to enhance genetic diversity within the species. In Myxococcus xanthus, a large fraction of the population undergoes programmed cell death during the formation of fruiting bodies. This sacrifice ensures the survival of the sporulating sub-population by providing nutrients and hence energy to complete this differentiation process. The biological relevance and underlying regulatory mechanisms of these three processes will be discussed in order to extract common features of such strategies. Moreover, open questions and future challenges will be addressed.

Genetically Engineered Bacterial Biohybrid Microswimmers for Sensing Applications.

Bacterial biohybrid microswimmers aim at exploiting the inherent motion capabilities of bacteria (carriers) to transport objects (cargoes) at the microscale. One of the most desired properties of microswimmers is their ability to communicate with their immediate environment by processing the information and producing a useful response. Indeed, bacteria are naturally equipped with such communication skills. Hereby, two-component systems (TCSs) represent the key signal transducing machinery and enable bacteria to sense and respond to a variety of stimuli. We engineered a natural microswimmer based on the Gram-positive model bacterium Bacillus subtilis for the development of biohybrids with sensing abilities. B. subtilis naturally adhered to silica particles, giving rise to different motile biohybrids systems with variable ratios of carrier(s)-to-cargo(es). Genetically engineered TCS pathways allowed us to couple the binding to the inert particles with signaling the presence of antibiotics in their surroundings. Activation of the antibiotic-induced TCSs resulted in fluorescent bacterial carriers as a response readout. We demonstrate that the genetically engineered TCS-mediated signaling capabilities of B. subtilis allow for the custom design of bacterial hybrid microswimmers able to sense and signal the presence of target molecules in the environment. The generally recognized as safe (GRAS) status of B. subtilis makes it a promising candidate for human-related applications of these novel biohybrids.

The Bacillus BioBrick Box 2.0: expanding the genetic toolbox for the standardized work with Bacillus subtilis.

Standardized and well-characterized genetic building blocks allow the convenient assembly of novel genetic modules and devices, ensuring reusability of parts and reproducibility of experiments. In the first Bacillus subtilis-specific toolbox using the BioBrick standard, we presented integrative vectors, promoters, reporter genes and epitope tags for this Gram-positive model bacterium. With the Bacillus BioBrick Box 2.0, we significantly expand the range of our toolbox by providing new integrative vectors, introducing novel tools for fine-tuning protein expression, and carefully evaluating codon-adapted fluorescence proteins in B. subtilis, which cover the whole spectrum of visible light. Moreover, we developed new reporter systems to allow evaluating the strength of promoters and ribosome binding sites. This well-evaluated extension of our BioBrick-based toolbox increases the accessibility of B. subtilis and will therefore promote the use of this model bacterium and biotechnological workhorse as a host for fundamental and applied Synthetic Biology projects.