While extracellular vesicles (EVs) are established mediators of intra-species signaling, their contribution to cross-kingdom communication remains incompletely understood. Here, we investigate the EV-mediated interactions between human colon epithelial cells and both Gram-positive and Gram-negative gut bacteria. We show that bacterial EVs (BEVs) derived from Lacticaseibacillus casei, Enterococcus faecalis, and Proteus mirabilis induce distinct transcriptomic changes in Caco-2 cells depending on the bacterial species, with up to ~6,000 differentially expressed genes, including CCL20, CXCL8, or CXCL10. Transfection of BEV-derived RNA independently induces a subset of similar effects, indicating that the EV-mediated communication is partially driven by the RNA cargo. Conversely, we demonstrate that bacteria interact with Caco-2-derived EVs and miR-192-5p, which is highly abundant (~36.4-fold higher) in EVs isolated from conditioned medium compared with EVs from unconditioned medium, with modest effects on bacterial growth. Furthermore, we show that lipid-based packaging of miR-192-5p modulates its association with the bacteria. Our findings support a conceptual model in which EVs and their RNA cargo contribute to species-dependent host-microbe interactions. This study introduces a framework for understanding EVs as cross-kingdom regulators and underscores the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in microbiome-host homeostasis and disease.
In this study, we introduce DockM8, an innovative open-source platform designed for consensus virtual screening in drug design. Leveraging various docking algorithms and scoring functions, DockM8 provides a highly customizable workflow for structure-based virtual screening. In rigorous evaluations across the DEKOIS 2.0, DUD-E, and Lit-PCBA datasets, DockM8 not only met but frequently surpassed state-of-the-art methods. Achieving average enrichments of 27%, 47.5%, and 13% respectively, DockM8 has proven its exceptional adaptability and generalizability across a variety of targets. Our study emphasizes the importance of tailoring the virtual screening strategy to specific targets, suggesting that no single pose selection or consensus method universally outperforms others. DockM8's user-friendly interface and minimal programming requirements make advanced virtual screening accessible to a broader scientific community. DockM8 is freely available at https://github.com/DrugBud-Suite/DockM8.
A targeted sequencing and genome mining approach for delftibactin-like biosynthetic pathways revealed three distinct biosynthetic gene cluster architectures (BGC del, dlc and dlp) encoded in genomes of members of the genus Delftia. Comparative metabolomic analysis guided the isolation and characterization of a yet unreported metallophore, delftichelin A from Delftia deserti DSM1621 (previously named Delftia acidovorans DSM1621). Prediction of BGC architecture and A domain specificity was in line with the structure analysis uncovering previously unreported differences in amino acid composition and modifications. Analysis of bioactivity and metal-binding characteristics demonstrated that delftichelin A shows a preferential affinity for ferric iron, while also exhibiting heavy metal detoxification mechanisms via oxidative degradation, analogous to those reported for the delftibactin family of compounds.
Effects of dihydroxybenzene additives on liquid crystal properties of nematic 4-n-pentyl-4′-cyanobiphenyl (5CB) were studied. While pyrocatechol, as a non-mesogenic dopant, duly lowered the isotropic transition temperature, and hydroquinone showed rather poor solubility, resorcinol induced substantial (by up to ∼16 °C) increase in the temperature stability of the nematic phase. At the same time, FTIR spectra of all three diols indicated similar features characteristic for hydrogen bonds. Though formation of 2:1 complex 5CB-resorcinol could be expected (and supported by UV spectra in solutions), the maximum increase of the isotropic transition temperature suggested the composition close to the 3:1 ratio. A tentative model is proposed, involving a combination of steric factors and dipole-dipole interactions favoring attachment of additional 5CB molecules to the stoichiometric complex. Further implications for other liquid crystal systems are discussed, including helically twisted phases with partial substitution of chiral isomer CB15 for 5CB. In the latter case, the temperature range of the blue phase was shifted upwards upon addition of resorcinol in a good accordance with the isotropic transition in 5CB-based mixtures. A possibility is considered of resorcinol mitigating 5CB cytotoxicity in human fibroblasts. Resorcinol release was shown to be largely decelerated by the 5CB matrix. A mathematical model is developed to describe drug release from 5CB matrix into water medium.
Cyanobacteria have long been recognized as a prolific source of bioactive natural products (NPs). Among these are the furanolides, a structurally diverse class of compounds first discovered in the 1980s. Furanolides are characterized by a γ-butyrolactone core bearing aromatic or aliphatic substituents at the α- and β-positions and an aromatic substituent at the γ-position. Recent advances in understanding the genetic basis of furanolide biosynthesis have enabled genome mining approaches to discover related cryptic furanolide biosynthetic gene clusters (BGCs). In this work, we identified and cloned a cryptic BGC (15.5 kb) from Nodularia sp. NIES-3585 using the Direct Pathway Cloning (DiPaC) strategy and heterologously expressed it in E. coli BAP1. Through isolation and structural elucidation, we characterized the known compounds maculalactone B and deoxyenhygrolide A and discovered the novel analogue maculalactone N, featuring a 4-hydroxyphenyl substituent at the β-position. Application of Global Natural Product Social Molecular Networking (GNPS) analysis of high-resolution LCMS data enabled the identification of 25 maculalactone-related molecules. Further, a MS/MS fragmentation rationale for furanolides was developed and used to probe for maculalactone-like molecules that were too low in abundance for isolation. The fragmentation analysis suggests the β-substituent displays remarkable diversity, accommodating phenolic, aliphatic, or indole moieties. Additionally, structural diversity occurs through various hydroxylations. These results demonstrate the substrate promiscuity of the maculalactone biosynthetic enzymes and their capacity to generate considerable structural diversity, while highlighting DiPaC as an effective strategy to access cyanobacterial NPs from cryptic BGCs.
