Search bioRxiv⌕ Search

Biology subjects

Meyer, R. L.

Publications and source records attributed to Meyer, R. L..

15 recordsLinked to original sources

Spatial organization of self-assembled G-quadruplex nucleic acids tunes extracellular electron transfer in pathogenic biofilms

Extracellular electron transfer (EET) allows bacteria to sustain metabolism when soluble electron acceptors such as oxygen are scarce, a situation typical of the biofilm interior. These mechanisms are well characterised in environmental metal-reducing bacteria but poorly defined in the biofilms of pathogens, where they may contribute to persistence at infection sites. We previously found that synthetic guanine-quadruplex (G4) nucleic acids bound to hemin can conduct electrons1, yet whether bacteria self-assemble such structures in electroactive form was unknown. Here we show that Staphylococcus aureus biofilms naturally assemble G4-rich extracellular nucleic acids that bind hemin to form a catalytically active, electron-conducting complex, without exogenous G4 addition. Nutrient starvation, rather than biofilm age or cell density, triggers extracellular G4 accumulation, and as biofilms develop, the G4 reorganise from intercellular networks to being primarily located at the cell-envelope. Using electrochemistry, peroxidase imaging and different types of nucleases, we show that these architectures impose distinct modes of electron transfer through the matrix or at the cell surface. Degradation of G4 abolishes electroactivity whereas removing canonical B-DNA does not. S. aureus thus builds and organises its own electroactive nucleic-acid network, identifying biofilm architecture as a tunable determinant of extracellular electron flow.

microbiology↗

Unmasking the diversity of extracellular nucleic acids in the biofilm matrix using nucleic acid-binding dyes

Extracellular nucleic acids (eNA) are central components of bacterial biofilms, contributing to structural integrity, antibiotic tolerance, and emerging functions such as extracellular electron transfer and peroxidase-like catalysis. While extracellular DNA has traditionally been assumed to adopt the canonical B-DNA conformation, biofilms are now known to contain non-canonical structures, including Z-DNA/RNA (Z-NA), G-quadruplex DNA/RNA (G4-NA), and substantial amounts of extracellular RNA. Conventional nucleic acid-binding dyes are widely used for rapid eNA detection, yet their specificity for these diverse structures has not been systematically evaluated. Here, we compare the fluorescence properties of eleven membrane-impermeant dyes (TOTO, BOBO, YOYO, and POPO series, SYTOX Green, SYTOX Red, and propidium iodide) against synthetic B-DNA, Z-DNA, G4-DNA, A-RNA, Z-RNA, and G4-RNA oligonucleotides, with Z-NA stabilised through brominated guanosine analogues synthesised in-house. A clear pattern emerged: green-fluorescent dyes preferentially bound canonical B-DNA, whereas red-fluorescent counterparts displayed broader specificity that extended to non-canonical structures. TOTO-3 and SYTOX Red bound G4-NA with higher fluorescence than B-DNA, and propidium iodide showed an unexpected preference for A-RNA over B-DNA. These observations were validated in Staphylococcus aureus biofilms by parallel immunolabelling with structure-specific antibodies. TOTO-3, YOYO-3, BOBO-3, POPO-3, and propidium iodide reproduced the eNA distribution at the bacterial cell surface. Finally, we introduce poly-A tailing with fluorescently labelled ATP as a stringent, RNA-specific imaging method for biofilms. Together, these results provide practical guidelines for visualising the structural diversity of eNA in biofilms. HIGHLIGHTS- Biofilms contain non-canonical structures of extracellular DNA and RNA - This study tests the ability of DNA-binding dyes to visualise such structures - Propidium iodide visualises RNA with brighter fluorescence than DNA - Red-fluorescent dyes were more versatile than green-fluorescent dyes - Combining several dyes enabled the detection of non-canonical structures

microbiology↗

Secret life of prophages: template-directed synthesis of DNA superstructures via prophage activation and rolling circle replication in bacterial biofilms

Extracellular DNA (eDNA) plays crucial roles in biofilm formation and function, yet the role of bacteriophages (phages) in controlling eDNA synthesis, structure and activity remains obscure. Here, we demonstrate that phages harbored by environmental bacteria can be exploited for programmable synthesis of functional eDNA superstructures. We designed a 112-nucleotide circular template (T1) and used it to direct rolling circle replication (RCR) of G-quadruplex (GQ) motifs in Shewanella oneidensis and Bacillus subtilis. Under nutrient-limiting conditions, prophage activation triggered cell lysis and subsequent extracellular DNA synthesis, producing multimeric GQ concatemers that self-assembled into distinct morphologies: spherical structures ([≤]10 m) in S. oneidensis and wire-like structures (>50 m) in B. subtilis. Real-time monitoring using fluorescent reporter strains revealed that DNA synthesis occurred predominantly after bacterial lysis, coinciding with prophage replication. The resulting DNA superstructures exhibited peroxidase activity through GQ-hemin DNAzyme formation and enhanced the electrochemical properties of S. oneidensis biofilms, showing a 3-fold increase in current density. This work unveils a previously unknown mechanism by which prophages contribute to biofilm architecture and establishes a biotechnological platform for engineering functional DNA materials in living bacterial communities, with potential applications in biotechnology and synthetic biology. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/691978v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@aec065org.highwire.dtl.DTLVardef@d94709org.highwire.dtl.DTLVardef@c6c228org.highwire.dtl.DTLVardef@f4f465_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

The host environment activates multiple stress responses which correlate with antibiotic tolerance in Staphylococcus aureus

Introduction. Antibiotic tolerance allows genetically susceptible bacteria to survive antibiotic exposure and contributes to treatment failure and recurrent infection. In Staphylococcus aureus, tolerance is closely associated with biofilm infections, and this association is conventionally explained by the biofilm mode of growth itself, in which mass transfer limitation is presumed to starve and arrest cells in the deeper layers. Gap Statement. That explanation rests largely on biofilms grown in rich laboratory media, and it has rarely been tested against the alternative that the host environment, rather than the biofilm architecture, drives the underlying physiological change. Furthermore, because transcriptomic and bulk fluorescence methods average across the population, they cannot establish whether stress responses are activated uniformly in all cells or strongly in a minority. Aim. To determine, at single-cell resolution, whether bacterial stress responses are activated by biofilm growth, by the host environment, or by both, and whether such activation coincides with a reduced rate of antibiotic killing. Methodology. Promoter regions of recA, katA, relQ, ilvleu and groESL were fused to a stable green fluorescent protein variant to report the SOS, oxidative stress, cell wall stress- and starvation-activated stringent, and heat shock responses. Reporter activation was quantified by confocal microscopy in exponential and stationary cultures, after defined chemical and physical stresses, in biofilms grown in tryptic soy broth, in diluted and undiluted human serum, in heat-inactivated serum, and in S. aureus internalised by human neutrophils. Tolerance was assessed as the rate of killing in time-kill assays. Results. Biofilms grown in laboratory media or in diluted serum showed minimal stress response activation, whereas biofilms of the same strain grown in undiluted human serum activated all five responses, uniformly across the population. Heat inactivation of the serum did not abolish this effect, indicating that complement and heat-labile serum enzymes are not required. One hour of serum exposure activated the stringent response via both starvation and cell wall stress, and it abolished detectable killing by ciprofloxacin, while producing only small changes in killing by vancomycin and rifampicin and none by daptomycin or dicloxacillin. Pre-treatments that activated the stringent or heat shock responses likewise arrested growth and slowed ciprofloxacin killing. Neutrophil phagocytosis activated the oxidative stress response and both stringent response branches. The host environment, rather than the biofilm mode of growth, is the dominant driver of stress response activation in S. aureus. Activation is population-wide and coincides with population-wide ciprofloxacin tolerance. Laboratory biofilm models that omit host components are therefore likely to underestimate the tolerance encountered during infection.

microbiology↗

Extracellular RNA drives Electromethanogenesis in a Methanogenic Archaeon

Methanogenic archaea account for two-thirds of global methane emissions. Some species, including Methanosarcina barkeri, reduce CO2 by directly acquiring electrons from solid substrates. However, the mechanism of electron acquisition in M. barkeri has remained unclear because this archaeon lacks the multiheme c-type cytochromes that drive extracellular electron transfer in many other microbes. Here we show that M. barkeri releases abundant extracellular nucleic acids during early growth, primarily short RNAs (78%). These extracellular nucleic acids assemble into G-quadruplexes (G4s) and B-DNA architectures that decorate cell surfaces and link aggregates. Surface-associated G4s are folded in vivo in a conformation compatible with cofactor binding and redox chemistry. Enzymatic degradation of extracellular nucleic acids abolished electron uptake and electromethanogenesis, whereas addition of synthetic G4-RNAs doubled methane yields and lowered cell-electrode interfacial resistance. These effects were not observed when cells were grown on soluble substrates. Together, these findings identify eRNA as a previously unrecognized electron conduit in methanogens, raising the possibility that RNA-based electron transfer may predate more elaborate protein-based electron conduits, with implications for models of early earth metabolism and for the design of next-generation bioenergy systems.

microbiology↗

Hemin-binding DNA structures on the surface of bacteria promote extracellular electron transfer

Recent research has shown that bacteria in anoxic layers of Pseudomonas aeruginosa biofilms can respire by transferring electrons to oxygen via extracellular DNA (eDNA) and DNA-binding redox mediators that are unique to this species1. In this study, we propose a similar but generic mechanism by which bacteria can transfer electrons via DNA in biofilms, using hemin as a redox-mediator and hemin-binding G-quadruplex (G4) DNA structures in the extracellular matrix. Using Staphylococcus epidermidis as a model organism, voltammetry showed that eDNA and hemin were needed for extracellular electron transfer (EET). Surface-associated G4-DNA formed a complex with hemin, which transferred electrons from the bacteria to an electrode under anoxic conditions. Addition of G4-DNA and hemin to growing biofilms promoted EET which was stable for days. G4-DNA/hemin is also a peroxidase-like DNAzyme, capable of transferring electrons from bacteria to H2O2. G4-DNA were only recently discovered to be abundant in the extracellular matrix of biofilms2,3. We now show that hemin turns these structures into conduits for EET. The study opens the door to new and generic mechanisms for bacterial energy conservation under oxygen-limiting conditions, and for tackling H2O2, a common host defense mechanism against bacterial infections.

microbiology↗

Mitomycin C Retains Efficacy after Adaptive Laboratory Evolution of Staphylococcus aureus

Antibiotic resistance is one of the greatest threats against human health and the misuse and overuse of antibiotics is a key factor driving resistance development. During prolonged antibiotic treatment of chronic infections, the antimicrobial pressure facilitates selection of antibiotic resistance mutations. It has been suggested that using antibiotics in combinations may reduce the emergence of resistance. Furthermore, antibiotic tolerant persister cells may be a reservoir for resistance development, so targeting persister cells with anti-persister drugs could also reduce the emergence of resistance. In this study, we conducted a 42-day adaptive laboratory evolution experiment using Staphylococcus aureus exposed to common antibiotics and the anti-persister drug mitomycin C, either alone or in combination. We monitored susceptibility daily and assessed phenotypic changes in growth and biofilm formation in evolved strains. Whole-genome sequencing revealed mutations linked to antibiotic resistance and phenotypic shifts. Resistance developed rapidly against rifampicin, while ciprofloxacin and daptomycin showed slower resistance emergence. Treatments with vancomycin or mitomycin C resulted in minimal changes in susceptibility. Combination therapies generally delayed resistance, though resistance was not fully prevented. Notably, mitomycin C combined with rifampicin effectively suppressed rifampicin resistance. Sub-inhibitory antibiotic concentrations were associated with both known and novel mutations, including in the nucleotide excision repair system and azoreductase, following mitomycin C treatment--mutations not previously reported. While combination therapy delayed resistance, mitomycin Cs efficacy and ability to prevent rifampicin resistance highlights its potential in combating antibiotic resistance. Further investigation is needed to evaluate the broader application of anti-persister drugs in resistance prevention.

microbiology↗

Dental biofilms contain DNase I-resistant Z-DNA and G-quadruplexes

eDNA is a major component of the extracellular matrix of bacterial biofilms, and recent studies have shown that biofilms from many pathogens contain both Z-DNA and G-quadruplex (G4) structures in addition to the canonical B-DNA double helix. These secondary DNA structures provide new emergent functions to the biofilm, most notably by making biofilms more resilient by protecting them from nucleases. In dental biofilms, it is largely unknown what conformation eDNA adopts, and the aim of this study was to determine if dental biofilms contain non-canonical secondary DNA structures. In this study, we visualised B-DNA, G4, and Z-DNA in dental biofilms from 10 healthy subjects and from 10 caries-active subjects using fluorescence immunolabeling and confocal microscopy. eDNA formed large structures surrounding clusters of microorganisms that contained B-DNA, G4, and Z-DNA in the majority of the samples. We also identified microorganisms outside of these large eDNA structures that contained smaller G4 and Z-DNA structures associated to cell surfaces. G4 and Z-DNA are resistant to degradation by the commonly used mammalian DNase I. We verified this resistance in dental biofilms, and we suggest that these structures present a novel target for improved enzyme formulations for controlling oral biofilms and, more broadly, any biofilm that contains G4 and Z-DNA.

microbiology↗

Bacterial efflux pumps excrete SYTO-TM dyes from bacteria and lead to false-negative staining results

Multidrug efflux pumps excrete a range of small molecules from bacterial cells. In this study, we show that bacterial efflux pumps have affinity for a range of SYTO dyes that are commonly used to label bacteria. Efflux pump activity will there lead to false negative results from bacterial staining and SYTO dyes should be used with caution on live samples. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/560001v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1b8bab4org.highwire.dtl.DTLVardef@e9a84forg.highwire.dtl.DTLVardef@291058org.highwire.dtl.DTLVardef@1f0245d_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Extracellular G-quadruplex and Z-DNA protect biofilms from DNase I and forms a DNAzyme with peroxidase activity

Many bacteria form biofilms to protect themselves from predators or stressful environmental conditions. In the biofilm, bacteria are embedded in a protective extracellular matrix composed of polysaccharides, proteins and extracellular DNA (eDNA). eDNA most often arises from lysed cells, and it is the only matrix component most biofilms appear to have in common. However, little is known about the form DNA takes in the extracellular space, and how different non-canonical DNA structures such as Z-DNA or G-quadruplex formation might contribute to its function in the biofilm. The aim of this study was to determine if non-canonical DNA structures form in eDNA-rich staphylococcal biofilms, and if these structures protect the biofilm from degradation by nucleases. We grew Staphylococcus epidermidis biofilms in laboratory media amended with hemin and NaCl to stabilize secondary DNA structures and visualized their location by immunolabelling and fluorescence microscopy. We furthermore visualized the macroscopic biofilm structure by optical coherence tomography. We developed assays to quantify degradation of Z-DNA and G-quadruplex DNA oligos by different nucleases, and subsequently investigated how these enzymes affected eDNA in the biofilms. Z-DNA and G-quadruplex DNA were abundant in the biofilm matrix, and were often present in a web-like structure in biofilms grown in vitro and in vivo using a murine implant-associated osteomyelitis model. In vitro, the structures did not form in the absence of NaCl or mechanical shaking during biofilm growth, or in bacterial strains deficient in eDNA or exopolysaccharide production. We thus infer that eDNA and polysaccharides interact, leading to non-canonical DNA structures under mechanical stress when stabilized by salt, and we confirmed that G-quadruplex DNA and Z-DNA was also present in biofilms from infected implants. Mammalian DNase I lacked activity against Z-DNA and G-quadruplex DNA, while Micrococcal nuclease could degrade G-quadruplex DNA and S1 Aspergillus nuclease could degrade Z-DNA. Micrococcal nuclease, which originates from Staphylococcus aureus, may thus be key for dispersal of biofilm in staphylococci. In addition to its structural role, we show for the first time that the eDNA in biofilms forms a DNAzyme with peroxidase-like activity in the presence of hemin. While peroxidases are part of host defenses against pathogens, we now show that biofilms can possess intrinsic peroxidase activity in the extracellular matrix. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/541711v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@c32012org.highwire.dtl.DTLVardef@6e8c7eorg.highwire.dtl.DTLVardef@1c9cc6corg.highwire.dtl.DTLVardef@18be51e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

A novel high-throughput assay identifies small molecules with activity against persister cells

Persister cells are a subpopulation of transiently antibiotic tolerant bacteria, which are believed to be the main cause of relapsing bacterial infections. Due to the importance of persister cells in human infections, there is a need for new antibiotics that kill bacteria independently of their activity. However, high-throughput assays to screen for drugs with such activity are missing. This is partly due to the transient nature of the phenotype, which makes it is difficult to prepare a concentrated population of persister cells that remain inactive during incubation with antibiotics in standard growth media. The purpose of this study was to develop a simple and high-throughput assay to identify compounds with antimicrobial activity against persister cells during a 24 h incubation period. Subsequently, this assay was used to screen a selection of small molecules with hypothesized antimicrobial activity. The fraction of S. aureus that tolerate bactericidal concentrations of ciprofloxacin were defined as persister cells. We first quantified how the cell concentration, growth phase, antibiotic concentration, duration of antibiotic exposure, and presence/absence of nutrients during antibiotic exposure affected the fraction of persister cells in a population. After optimizing these parameters, we compared our approach to generate persister cells, to a process that generated persister cells by a short exposure to rifampicin. Finally, we used the optimised protocol to identify molecular structures that have anti-persister activity by performing screening on initially compound fragments and then selecting compounds that incorporated the fragments that displayed activity. We show that exponential- and stationary-phase cultures transferred to nutrient-rich media only contain a small fraction (0.001 to 0.07 %) of persister cells that tolerated 10, 50 and 100 x MIC ciprofloxacin. Exponential-phase cultures displayed a bi-phasic time-kill curve, which plateaued after 5 h exposure, while stationary phase cultures displayed a low, but constant death rate at 50 and 100 x MIC ciprofloxacin. Inducing the persister phenotype with a short rifampicin treatment resulted in 100% persister cells when evaluated after [≤]5 h exposure to ciprofloxacin. However, after longer incubation times, cells resumed activity and lost their tolerance to ciprofloxacin. Tolerance was only maintained in the majority of the population for the full 24 h incubation period if cells were transferred to a carbon-free minimal medium before exposure to ciprofloxacin. We conclude that keeping cells starved in a carbon-free medium enables generation of high concentrations of S. aureus cells that tolerate 50 x MIC ciprofloxacin, and we find this protocol easily applicable for rapid screening of anti-persister drugs that act on dormant or non-dividing cells.

microbiology↗

Polyether ionophore antibiotics target drug-resistant clinical isolates, persister cells, and biofilms

Polyether ionophores are complex natural products known to transport various cations across biological membranes. While several members of this family are used in agriculture, e.g. as anti-coccidiostats, and have potent antibacterial activity, they are not currently pursued as antibiotics for human use. Polyether ionophores are typically grouped as having similar functions, despite the fact that they differ significantly in structure, and for this reason, it remains unclear how structure and activity are related. To triage whether certain members of the family constitute particularly interesting springboards for in-depth investigations, and future synthetic optimization, we here conduct a systematic comparative study of nine different polyether ionophores for their potential as antibiotics. This includes clinical isolates from bloodstream infections and studies of the compounds effects on bacterial biofilms and persister cells. We uncover distinct differences within the compound class and identify the compounds lasalocid, calcimycin, and nanchangmycin as having particularly interesting activity profiles for further development.

microbiology↗

Antibody-drug conjugates to treat bacterial biofilms

Implant-associated infections remain a grand unmet medical need because they involve biofilms that protect bacteria from the immune system and harbour antibiotic-tolerant persister cells. There is an urgent need for new biofilm-targeting therapies with antimicrobials, to treat these infections via a non-surgical way. In this work, we address this urgent medical need and engineer antibody-drug conjugates (ADC) that kill bacteria in suspension and in biofilms, in vitro and in vivo. The ADC contains an anti-neoplastic drug mitomycin C, which is also a potent antimicrobial against biofilms. While most ADCs are clinically validated as anti-cancer therapeutics where the drug is released after internalisation of the ADC in the target cell, the ADCs designed herein release the conjugated drug without cell entry. This is achieved with a novel mechanism of drug, which likely involves an interaction of ADC with thiols on the bacterial cell surface. ADC targeted towards bacteria were superior by the afforded antimicrobial effects compared to the non-specific counterpart, in suspension and within biofilms, in vitro and in vivo. An implant-associated murine osteomyelitis model was then used to demonstrate the ability of the antibody to reach the infection, and the superior antimicrobial efficacy compared to standard antibiotic treatment in vivo. Our results illustrate the development of ADCs into a new area of application with a significant translational potential.

microbiology↗

The giant Staphylococcus epidermidis surface protein Embp binds selectively to fibrillated fibronectin through a Velcro-like mechanism

Staphylococcus epidermidis causes some of the most hard-to-treat clinical infections by forming biofilms: Multicellular communities of bacteria encased in a protective matrix, supporting immune evasion and tolerance against antibiotics. Biofilms occur most commonly on medical implants, and a key event in implant colonization is the robust adherence to the surface, facilitated by interactions between bacterial surface proteins and host matrix components. S. epidermidis is equipped with a giant adhesive protein, Embp, which facilitates bacterial interactions with surface-deposited, but not soluble fibronectin. The structural basis behind this selective binding process has remained obscure. Using a suite of single-cell and single-molecule analysis techniques, we show that S. epidermidis is capable of such distinction because Embp binds specifically to fibrillated fibronectin on surfaces, while ignoring globular fibronectin in solution. S. epidermidis adherence is critically dependent on multi-valent interactions involving 50 fibronectin-binding repeats of Embp. This unusual, Velcro-like interaction proved critical for colonization of surfaces under high flow, making this newly identified attachment mechanism particularly relevant for colonization of intravascular devices, such as prosthetic heart valves or vascular grafts. Other biofilm-forming pathogens, such as Staphylococcus aureus, express homologs of Embp and likely deploy the same mechanism for surface colonization. Our results may open for a novel direction in efforts to combat devastating, biofilm-associated infections, as the development of implant materials that steer the conformation of adsorbed proteins is a much more manageable task than avoiding protein adsorption altogether. Graphical abstractFibronectin exists in two different conformations in the body. It circulates in the bodily fluids in globular conformation, however, it become fibrillated once adsorbed to an implant surface. S. epidermidis possess a giant 1 MDa receptor known as Embp bind specifically to fibrillated Fn but not to the globular Fn. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/446437v2_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1999895org.highwire.dtl.DTLVardef@f0717corg.highwire.dtl.DTLVardef@1aa8773org.highwire.dtl.DTLVardef@a2991b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Novel prosthecate bacteria from the candidate phylum Acetothermia revealed by culture-independent genomics and advanced microscopy

Members of the candidate phylum Acetothermia are globally distributed and detected in various habitats. However, little is known about their physiology and ecological importance. In this study, an OTU belonging to Acetothermia was detected at high abundance in two full-scale anaerobic digesters. The first closed genome from this phylum was obtained by differential coverage binning of metagenomes and scaffolding with nanopore data. Genome annotation and metabolic reconstruction suggested an anaerobic chemoheterotrophic lifestyle in which the bacterium obtain energy and carbon via fermentation of peptides, amino acids, and simple sugars to acetate, formate, and hydrogen. The morphology was unusual and composed of a central rod-shaped cell with bipolar prosthecae as revealed by fluorescence in situ hybridization combined with confocal laser scanning microscopy, Raman microspectroscopy and atomic force microscopy. We hypothesize that these prosthecae allow for increased nutrient uptake by greatly expanding the cell surface area, providing a competitive advantage under nutrient-limited conditions.

microbiology↗