Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria

The molecular basis for DNA-binding by competence T4P is distinct in a representative Gram-positive and Gram-negative species

Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.

Host-dependent alteration of the gut microbiota: the role of luminal microRNAs

MicroRNAs (miRNAs) are short, non-coding RNAs that play gene expression regulatory roles in eukaryotes. MiRNAs are also released in body fluids, and in the intestine, they are found in the lumen and feces. Here, together with exogenous dietary-derived miRNAs, they constitute the fecal miRNome. Several miRNAs were identified in the feces of healthy adults, including, as shown here, core miRNAs hsa-miR-21-5p and hsa-miR-1246. These miRNAs are important for intestinal homeostasis. Recent evidence suggests that miRNAs may interact with gut bacteria. This represents a new avenue to understand host-bacteria crosstalk in the gut and its role in health and disease. This review provides a comprehensive overview of current knowledge on fecal miRNAs, their representation across individuals, and their effects on the gut microbiota. It also discusses existing evidence on potential mechanisms of uptake and interaction with bacterial genomes, drawing from knowledge of prokaryotic small RNAs (sRNAs) regulation of gene expression. Finally, we review in silico and experimental approaches for profiling miRNA-mRNA interactions in bacterial species, highlighting challenges in target validation. This work emphasizes the need for further research into host miRNA-bacterial interactions to better understand their regulatory roles in the gut ecosystem and support their exploitation for disease prevention and treatment.

The molecular basis for DNA-binding by competence T4P is distinct in Gram-positive and Gram-negative species

Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.

AUTHOR SUMMARY

Diverse bacteria use extracellular structures called competence type IV pili (T4P) to take up DNA from their environment. The uptake of DNA by T4P is the first step of natural transformation, a mode of horizontal gene transfer that contributes to the spread of antibiotic resistance and virulence traits in diverse clinically relevant Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA binding by competence T4P in diderms has been an area of recent study, relatively little is known about how monoderm competence T4P bind DNA. Here, we explore how monoderm competence T4P bind DNA using Streptococcus pneumoniae as a model system. Our results indicate that while monoderm T4P and diderm T4P likely have conserved structural features, the DNA-binding mechanism of each system is distinct.

pH-responsive antibacterial emulsion gel based on cinnamaldehyde and carboxymethyl chitosan for fruits preservation applications

Although the natural antibacterial agent, cinnamaldehyde, has been extensively studied in the field of food packaging, its water solubility and instability limit its further applications. The controllable responsive release can be achieved through encapsulation in responsive emulsion systems based on carboxymethyl chitosan. Herein, a pH-responsive antibacterial emulsion gel was constructed from cinnamaldehyde-loaded oil-in-water emulsion templates. The interfacial imidization between carboxymethyl chitosan and cinnamaldehyde forms a pH-responsive Schiff base and further stabilizes the emulsion. To immobilize the droplets, acrylamide was subsequently added and polymerized. Such a double network design gives materials adjustable mechanical strength in addition to sealing off the cinnamaldehyde droplets in the network to postpone their release. According to the results of the tensile and compressive cycle, this material has good fatigue resistance. Furthermore, the antibacterial results showed that this material has a 15-day antibacterial cycle and long-lasting antibacterial qualities. In practical applications, acidic moisture from the fruits' respiration decomposes Schiff base bonds and accelerates the release of cinnamaldehyde. The results of cinnamaldehyde release proved that the emulsion gel was pH-responsive, and the dynamic covalent network and emulsion encapsulation technology prolonged the release period of cinnamaldehyde. The mechanical test results proved that the acrylamide network structure gave the material good mechanical properties. Using longan and citrus fruits as examples, we found emulsion gel can significantly prolong the life of fruits by two to three times.

An Extracellular, Ca2+-Activated Nuclease (EcnA) Mediates Transformation in a Naturally Competent Archaeon

Transformation, the uptake of DNA directly from the environment, is a major driver of gene flow in microbial populations. In bacteria, DNA uptake requires a nuclease that processes dsDNA to ssDNA, which is subsequently transferred into the cell and incorporated into the genome. However, the process of DNA uptake in archaea is still unknown. Previously, we cataloged genes essential to natural transformation in Methanococcus maripaludis, but few homologs of bacterial transformation-associated genes were identified. Here, we characterize one gene, MMJJ_16440 (named here as ecnA), to be an extracellular nuclease. We show that EcnA is Ca2+-activated, present on the cell surface, and essential for transformation. While EcnA can degrade several forms of DNA, the highest activity was observed with ssDNA as a substrate. Activity was also observed with circular dsDNA, suggesting that EcnA is an endonuclease. This is the first biochemical characterization of a transformation-associated protein in a member of the archaeal domain and suggests that both archaeal and bacterial transformation initiate in an analogous fashion.

Near-infrared laser-assisted Ag@Chi-PB nanocompounds for synergistically eradicating multidrug-resistant bacteria and promoting diabetic abscess healing

Chronic wound infections, particularly multidrug-resistant microbe-caused infections, have imposed severe challenges in clinical administration. The therapeutic effectiveness of the current strategy using conventional antibiotics is extremely unsatisfactory. The development of novel treatment strategies to inhibit the infections caused by multidrug-resistant bacteria is highly desired. In this work, based on the combination of nanocompounds with the assistance of NIR laser, an antibacterial strategy was designed for MRSA-infected abscesses in diabetic mice. The nanocompounds named Ag@Chi-PB were prepared by using chitosan-coated Prussian blue (PB) as a nanocarrier for silver nanoparticles anchoring. Combined with near-infrared (NIR) laser, the nanocompounds were more efficient at killing Escherichia coli (E. coli) and Methicillin-resistant staphyllococcus aureus (MRSA) in vitro. Notably, MRSA was significantly removed in vivo and promoted diabetic abscess healing by the combined therapy of this nanocompound and NIR laser, owing to the synergistic antibacterial effect of photothermal therapy and release of Ag+. Meanwhile, the nanocompound showed satisfactory biocompatibility and superior biosafety. Collectively, the combination therapy of this nanocompound with the assistance of NIR laser may represent a promising strategy for clinical anti-infection.

Self-supporting noncovalent Choline Alginate/Tannic acid/Ag antibacterial films for strawberry preservation

Packaging materials with peculiar antibacterial properties can shield off and inhibit microorganism proliferation, thus achieving packaging goals such as fresh-keeping, good hygiene, and biosafety. Especially, antibacterial films made of biocompatible substances have received wide attentions, which could effectively extend the shelf life, enhance food security, and guarantee economic benefits. Herein, a self-supporting hybrid antibacterial film was prepared based on non-covalently linked choline hydroxide (ChOH) and alginic acid (HAlg). Then tannic acid (TA) and silver ions were added to improve the mechanical and antimicrobial properties of this hybrid film. The rich hydroxyl groups from TA not only form multiple hydrogen bonds with ChAlg, but can also in situ reduce silver ions to silver nanoparticles, which were confirmed with various characterizations. In addition, the quantitative antibacterial test proved that the antibacterial rate was significantly improved after adding silver ions, reaching >60 %. In an actual storage test, we found that choline cation (Ch+) captured in antibacterial film by electrostatic interaction could achieve sustained release, i.e. sustainable bacteriostasis, and keep strawberries fresh for 48 h at room temperature. This work offers a new strategy for preparing antibacterial films via non-covalent weak interactions, explored an alternative antibacterial film for food packaging applications.

Chemically Tailored Single Atoms for Targeted and Light-Controlled Bactericidal Activity

Single-atom (SA) nanoparticles exhibit considerable potential in terms of photothermal properties for bactericidal applications. Nevertheless, the restricted efficacy of their targeted and controlled antibacterial activity has hindered their practical implementation. This study aims to overcome this obstacle by employing chemical modifications to tailor SAs, thereby achieving targeted and light-controlled antimicrobial effects. By conducting atomic-level modifications on palladium SAs using glutathione (GSH) and mercaptophenylboronic acid (MBA), their superior targeted binding capabilities toward Escherichia coli cells are demonstrated, surpassing those of SAs modified with cysteine (Cys). Moreover, these modified SAs effectively inhibit wound bacteria proliferation and promote wound healing in rats, without inducing noticeable toxicity to major organs under 808 nm laser irradiation. This study highlights the significance of chemical engineering in tailoring the antibacterial properties of SA nanoparticles, opening avenues for combating bacterial infections and advancing nanoparticle-based therapies.

Visualizing dynamic competence pili and DNA capture throughout the long axis of Bacillus subtilis

The first step in the process of bacterial natural transformation is DNA capture. Although long hypothesized based on genetics and functional experiments, the pilus structure responsible for initial DNA binding had not yet been visualized for Bacillus subtilis. Here, we visualize functional competence pili in Bacillus subtilis using fluorophore-conjugated maleimide labeling in conjunction with epifluorescence microscopy. In strains that produce pilin monomers within tenfold of wild-type levels, the median length of detectable pili is 300 nm. These pili are retractile and associate with DNA. The analysis of pilus distribution at the cell surface reveals that they are predominantly located along the long axis of the cell. The distribution is consistent with localization of proteins associated with subsequent transformation steps, DNA binding, and DNA translocation in the cytosol. These data suggest a distributed model for B. subtilis transformation machinery, in which initial steps of DNA capture occur throughout the long axis of the cell and subsequent steps may also occur away from the cell poles. IMPORTANCE This work provides novel visual evidence for DNA translocation across the cell wall during Bacillus subtilis natural competence, an essential step in the natural transformation process. Our data demonstrate the existence of natural competence-associated retractile pili that can bind exogenous DNA. Furthermore, we show that pilus biogenesis occurs throughout the cell long axis. These data strongly support DNA translocation occurring all along the lateral cell wall during natural competence, wherein pili are produced, bind to free DNA in the extracellular space, and finally retract to pull the bound DNA through the gap in the cell wall created during pilus biogenesis.

Characterization and quantification of adeno-associated virus capsid-loading states by multi-wavelength analytical ultracentrifugation with UltraScan

Aim: We present multi-wavelength (MW) analytical ultracentrifugation (AUC) methods offering superior accuracy for adeno-associated virus characterization and quantification. Methods: Experimental design guidelines are presented for MW sedimentation velocity and analytical buoyant density equilibrium AUC. Results: Our results were compared with dual-wavelength AUC, transmission electron microscopy and mass photometry. In contrast to dual-wavelength AUC, MW-AUC correctly quantifies adeno-associated virus capsid ratios and identifies contaminants. In contrast to transmission electron microscopy, partially filled capsids can also be detected and quantified. In contrast to mass photometry, first-principle results are obtained. Conclusion: Our study demonstrates the improved information provided by MW-AUC, highlighting the utility of several recently integrated UltraScan programs, and reinforces AUC as the gold-standard analysis for viral vectors.

A spectral decomposition quality assessment tool for multi-wavelength AUC experiments with UltraScan

Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recently developed technique that has proven to be a promising tool to investigate mixtures of molecules containing multiple chromophores. It provides an orthogonal separation approach by distinguishing molecules based on their spectral and hydrodynamic properties. Existing software implementations do not permit the user to assess the integrity of the spectral decomposition. To address this shortcoming, we developed a new spectral decomposition residual visualization module, which monitors the accuracy of the spectral decomposition. This module assists the user by providing visual and statistical feedback from the decomposition. The software has been integrated into the UltraScan software suite and an example of a mixture containing thyroglobulin and DNA is presented for illustration purposes.

Investigation of dynamic solution interactions between NET-1 and UNC-5B by multi-wavelength analytical ultracentrifugation

NET-1 is a key chemotropic ligand that signals commissural axon migration and change in direction. NET-1 and its receptor UNC-5B switch axon growth cones from attraction to repulsion. The biophysical properties of the NET-1 + UNC-5B complex have been poorly characterized. Using multi-wavelength-AUC by adding a fluorophore to UNC-5B, we were able to separate the UNC-5B sedimentation from NET-1. Using both multi-wavelength- and single-wavelength AUC, we investigated NET-1 and UNC-5B hydrodynamic parameters and complex formation. The sedimentation velocity experiments show that NET-1 exists in a monomer-dimer equilibrium. A close study of the association shows that NET-1 forms a pH-sensitive dimer that interacts in an anti-parallel orientation. UNC-5B can form equimolar NET-1 + UNC-5B heterocomplexes with both monomeric and dimeric NET-1.

Visualizing dynamic competence pili and DNA capture throughout the long axis of Bacillus subtilis

The first step in the process of bacterial natural transformation is DNA capture. Although long-hypothesized based on genetics and functional experiments, the pilus structure responsible for initial DNA-binding had not yet been visualized for Bacillus subtilis. Here, we visualize functional competence pili in Bacillus subtilis using fluorophore-conjugated maleimide labeling in conjunction with epifluorescence microscopy. In strains that produce pilin monomers within ten-fold of wild type levels, the median length of detectable pili is 300nm. These pili are retractile and associate with DNA. Analysis of pilus distribution at the cell surface reveals that they are predominantly located along the long axis of the cell. The distribution is consistent with localization of proteins associated with subsequent transformation steps, DNA-binding and DNA translocation in the cytosol. These data suggest a distributed model for B. subtilis transformation machinery, in which initial steps of DNA capture occur throughout the long axis of the cell and subsequent steps may also occur away from the cell poles.