An RNA pseudoknot mediates toxin translation and antitoxin inhibition.

Type I toxin-antitoxin systems (T1TAs) are bipartite bacterial loci encoding a growth-inhibitory toxin and an antitoxin small RNA (sRNA). In many of these systems, the transcribed toxin mRNA is translationally inactive, but becomes translation-competent upon ribonucleolytic processing. The antitoxin sRNA targets the processed mRNA to inhibit its translation. This two-level control mechanism prevents cotranscriptional translation of the toxin and allows its synthesis only when the antitoxin is absent. Contrary to this, we found that the timP mRNA of the timPR T1TA locus does not undergo enzymatic processing. Instead, the full-length timP transcript is both translationally active and can be targeted by the antitoxin TimR. Thus, tight control in this system relies on a noncanonical mechanism. Based on the results from in vitro binding assays, RNA structure probing, and cell-free translation experiments, we suggest that timP mRNA adopts mutually exclusive structural conformations. The active form uniquely possesses an RNA pseudoknot structure which is essential for translation initiation. TimR preferentially binds to the active conformation, which leads to pseudoknot destabilization and inhibited translation. Based on this, we propose a model in which "structural processing" of timP mRNA enables tight inhibition by TimR in nonpermissive conditions, and TimP synthesis only upon TimR depletion.

A taxonomically representative strain collection to explore xenobiotic and secondary metabolism in bacteria.

Bacteria employ secondary metabolism to combat competitors, and xenobiotic metabolism to survive their chemical environment. This project has aimed to introduce a bacterial collection enabling comprehensive comparative investigations of those functions. The collection comprises 120 strains (Proteobacteria, Actinobacteria and Firmicutes), and was compiled on the basis of the broad taxonomic range of isolates and their postulated biosynthetic and/or xenobiotic detoxification capabilities. The utility of the collection was demonstrated in two ways: first, by performing 5144 co-cultures, recording inhibition between isolates and employing bioinformatics to predict biosynthetic gene clusters in sequenced genomes of species; second, by screening for xenobiotic sensitivity of isolates against 2-benzoxazolinone and 2-aminophenol. The co-culture medium of Bacillus siamensis D9 and Lysinibacillus sphaericus DSM 28T was further analysed for possible antimicrobial compounds, using liquid chromatography-mass spectrometry (LC-MS), and guided by computational predictions and the literature. Finally, LC-MS analysis demonstrated N-acetylation of 3,4-dichloroaniline (a toxic pesticide residue of concern) by the actinobacterium Tsukamurella paurometabola DSM 20162T which is highly tolerant of the xenobiotic. Microbial collections enable "pipeline" comparative screening of strains: on the one hand, bacterial co-culture is a promising approach for antibiotic discovery; on the other hand, bioremediation is effective in combating pollution, but requires knowledge of microbial xenobiotic metabolism. The presented outcomes are anticipated to pave the way for studies that may identify bacterial strains and/or metabolites of merit in biotechnological applications.

Plasmonic Coupling in Silver Nanoparticle Aggregates and Their Polymer Composite Films for Near-Infrared Photothermal Biofilm Eradication.

Plasmonic nanoparticles with near-IR (NIR) light absorption are highly attractive in biomedicine for minimally invasive photothermal treatments. However, these optical properties are typically exhibited by plasmonic nanostructures with complex, nonspherical geometries that may prohibit their broad commercialization and further integration into photothermal devices. Herein, we present the single-step aerosol self-assembly of plasmonic nanoaggregates that consisted of spherical silver nanoparticles with tunable extinction from visible to NIR wavelengths. This tunable extinction was achieved by the addition of SiO2 during the flame synthesis of the nanoparticles, which acted as a dielectric spacer between the spherical silver nanoparticles and was also computationally validated by simulating the extinction spectra of similar silver nanoaggregates. These plasmonic nanoaggregates were easily deposited on silicone polymeric surfaces and further encased with a top polymer layer, forming plasmonic photothermal nanocomposite films. The photothermal properties of the NIR nanocomposite films were utilized to eradicate the established biofilms of clinically relevant Escherichia coli and Staphylococcus aureus, with a relationship observed between the final surface temperature and biofilm eradication.