Search Results (476)

The modified DNA base 2,6 aminopurine (2-aminoadenine, (d)Z base) was originally found in phages to counteract host-encoded restriction systems. However, only a limited number of restriction endonucleases (REases) have been tested on dZ-modified DNA. Here, we report the activity results of 147 REases on dZ-modified PCR DNA. Among the enzymes tested, 53% are resistant or partially resistant, and 47% are sensitive when their restriction sites contain one to six modified bases. Sites with four to six dZ substitutions are most likely to resist Type II restriction. Our results support the notion that dZ-modified phage genomes evolved to combat host-encoded restriction systems. dZ-modified DNA can also reduce phage T5 exonuclease degradation, but has no effect on RecBCD digestion. When two genes for dZ biosynthesis and one gene for dATP hydrolysis from Salmonella phage PMBT28 (purZ (adenylosuccinate synthetase), datZ (dATP triphosphohydrolase), and mazZ ((d)GTP-specific diphosphohydrolase) were cloned into an E. coli plasmid, the level of dZ incorporation reached 19–20% of adenosine positions. dZ levels further increased to 29–44% with co-expression of a DNA polymerase gene from the same phage. High levels of dZ incorporation in recombinant plasmid are possible by co-expression of purZ, mazZ, datZ and phage DNA helicase, dpoZ (DNA polymerase) and ssb (single-stranded DNA binding protein SSB). This work expands our understanding of the dZ modification of DNA and opens new avenues for engineering restriction systems and therapeutic applications. Full article

This study compares the chemical composition, antimicrobial effects, and antibiotic-potentiating capacity of three Lauraceae essential oils (EO): Cryptocarya agathophylla (CAEO), Litsea cubeba (LCEO), and Laurus nobilis (LNEO). Gas chromatography–mass spectrometry (GC–MS) analysis revealed distinct chemotypes: CAEO and LCEO were dominated by oxygenated monoterpenes, while LNEO contained the highest levels of monoterpene hydrocarbons. Antibacterial testing against nine bacterial strains showed strain-dependent growth suppression trends, while true minimum inhibitory concentrations (MICs) were reached only in selected cases. EO–ampicillin interactions were evaluated using MIC-based checkerboard criteria, whereas OD-derived inhibition parameters were used exclusively to describe sub-MIC potentiation trends. In combination assays, LNEO exhibited the most pronounced potentiating effects against Streptococcus pyogenes, Shigella flexneri, and Haemophilus influenzae, while CAEO and LCEO showed moderate or strain-dependent enhancement. Hierarchical clustering highlighted distinct oil- and strain-specific interaction profiles. Overall, although CAEO displayed stronger intrinsic antibacterial effects when tested alone, LNEO emerged as the most effective potentiator of ampicillin activity in a strain-dependent manner. The effects of the major compounds identified in the Lauraceae EO were assessed in silico against protein targets of some microorganisms using the AutoDock software version 4.2.6. The docking scores revealed binding affinities of the bioactive compounds towards Dpr protein (4.3–5.8 kcal/mol), DNA gyrase (4.7–7.1 kcal/mol), mono- diacylglycerol lipase (4.4–6.2 kcal/mol), CYP51 (5.8–8.0 kcal/mol), phage-encoded quorum sensing anti-activator (5.8–8.0 kcal/mol) and Chondroitin ABC lyase I (4.8–6.3 kcal/mol). Two (2) hit compounds (α-Citral, β-Citral) were finely defined by strong hydrophobic and hydrophilic interactions with the bacterial and fungal protein targets, respectively. Full article

Background: Shiga toxin (Stx), produced by enterohemorrhagic Escherichia coli (EHEC), is a highly potent exotoxin responsible for severe complications such as hemolytic uremic syndrome (HUS). Among its isoforms, Stx2 exhibits stronger cytotoxicity and poses greater clinical risk, yet no effective therapy currently exists. Methods: In this study, two human monoclonal antibodies, YG12-1 and YG12-2, were identified from a phage display library and systematically characterized using an integrated modeling–validation workflow. Results: Structural modeling with ImmuneBuilder and Rosetta revealed that YG12-2 possessed a longer CDRH3 topology, more short-range hydrogen bonds, and stronger electrostatic complementarity, corresponding to lower binding energy and higher apparent affinity in ELISA and SPR. Although YG12-2 had a better affinity, YG12-1 shows better protective activity in a murine model of acute peritoneal infection. This paradox highlights a non-linear relationship between structural affinity and biological efficacy, emphasizing the importance of functional epitope accessibility and pharmacokinetic behavior in determining neutralization outcomes. Conlusions: Overall, these results indicated that targeting Stx2 with YG12-1 and YG12-2 could serve as a promising protective strategy against E. coli O157:H7 infection. Full article

The rapid evolution of SARS-CoV-2, particularly the emergence of Omicron subvariants, has significantly reduced the efficacy of existing vaccines and monoclonal antibodies. This study investigates the phenomenon of immune imprinting by comparing two phage display antibody libraries derived from early 2020 wild-type SARS-CoV-2 convalescents (WT-AbLib) and early 2023 Omicron convalescents (Omi-AbLib). The capacity and diversity of both antibody libraries were systematically evaluated. The libraries were screened using BF.7 and XBB.1.5 antigens. WT-AbLib showed markedly reduced diversity after Omicron antigen selection, with dominant clones shifting from IGHV3-66-class broadly neutralizing antibodies (bnAbs) targeting the receptor-binding motif to IGHV1-46-class broadly non-neutralizing antibodies targeting conserved lateral receptor-binding domain (RBD) sites. Omi-AbLib maintained higher diversity, but dominant antibodies were also non-neutralizing and targeted the same conserved lateral region. These findings suggest that immune imprinting drives the dominance of broadly non-neutralizing antibodies following Omicron breakthrough or reinfection. This phenomenon provides a mechanistic explanation for persistent viral evasion and recurrent infection, and highlights major challenges for the development of next-generation broadly neutralizing therapeutics. Full article

Tetanus is a zoonotic disease posing significant threats to both humans and animals, particularly horses, sheep, and ruminants. Current antitoxin therapies rely on animal-derived immunoglobulins, presenting challenges including animal welfare concerns, pathogen contamination risks, and manufacturing complexity. Alpaca-derived nanobodies (VHH) are promising alternatives owing to their high antigen-binding affinity, thermostability, and potential for microbial production. We developed highly active trivalent VHH antibodies (tVHH) that target multiple epitopes of tetanus neurotoxin (TeNT). Following alpaca immunization with tetanus toxoid, 41 VHH clones were isolated using phage display. Six VHH clones were selected through in vivo neutralization assays, from which three clones of VHH (8, 11, 36) were selected to construct tVHH-8/11/36 and tVHH-8/36/11. Using an improved 21-day mouse neutralization assay, tVHH-8/11/36 demonstrated exceptional neutralizing activity of approximately 1580 IU/mg against 4000 LD₅₀ of toxin, substantially exceeding current human and veterinary anti-tetanus immunoglobulin preparations. Surface plasmon resonance and ELISA confirmed that each VHH recognizes different TeNT domains, producing synergistic neutralizing effects through multimerization. Since antitoxin therapy challenges are common to both animals and humans, this tVHH technology supports One Health by providing a unified therapeutic platform applicable across species through sustainable microbial production. Full article

To identify pancoronaviral inhibitors, we sought to identify peptides that bound the evolutionarily conserved SARS-CoV-2 spike fusion peptide (FP). We screened the NEB PhD-7-mer random combinatorial phage display library against FP, synthesised as a D-peptide, to identify peptides from the L-library to be synthesised as proteolytically resistant D peptides. We selected the top ten peptides that were not seen in another published screen with this library, as these were more likely to be specific. All ten D-peptides had no impact on the infection of Vero-E6/TMPRSS2 cells by SARS-CoV-2. Screening of a proteomic-derived phage display library from the disordered regions of human proteins identified two overlapping 14mer peptides from a region of OTUD1. While a synthetic peptide based on their sequences failed to markedly inhibit viral entry, molecular dynamics structural modelling highlighted a stable binding mode where positive residues on one side of the OTUD1 helix interacted with hydrophobic residues of the FP triple-helical wedge. Thus, while the two phage display strategies failed to yield peptide sequences that are themselves strong inhibitors of viral infection, they led to the development of a computational model that can underpin future designs of potential pancoronaviral FP disruptors. Full article

N6-methyladenosine (m⁶A) constitutes the most prevalent nucleotide modification within eukaryotic messenger RNA (mRNA). Variations in m⁶A levels are associated with numerous human diseases and health conditions, including various forms of cancer, diabetes, neurological disorders, male infertility, and obesity. Nevertheless, the molecular mechanisms underpinning the recognition of m⁶A by different ‘reader’ proteins remain incompletely elucidated. In this study, we used phage display to identify key sequence features that methyl readers recognize in m⁶A. This study shows that m⁶A modifications affect the mRNA interactome. A peptide motif recognizing m⁶A in DRACH sequences suggests a common recognition mechanism, though proteins may use different methods to detect m⁶A in less accessible areas. The sequence of the hnRNP A1 RRM domain that aligns with the newly discovered m⁶A-binding peptide, m1p1, is crucial for the binding of m⁶A-modified RNAs, indicating a strong link between the m1p1 sequence and m⁶A recognition, which is key for recognizing m⁶A-modified, unstructured RNAs. Gaining a comprehensive understanding of the evolutionary influence of m⁶A on its reader proteins may facilitate the identification of additional m⁶A readers. These signature peptides could enhance theranostic approaches across cancers, enabling more targeted therapies. Full article

Bacteriophage therapy, which employs bacterial viruses to selectively eliminate pathogenic bacteria, has re-emerged as a promising strategy in the face of increasing antimicrobial resistance. However, its widespread clinical implementation is constrained by concerns regarding safety, standardisation, and predictable efficacy. In this review, we examine the key role of genomics in transforming phage therapy from an empirical practice into a standardised and personalised modality of contemporary medicine. We describe how whole-genome sequencing (WGS) provides a basis for safety assessment by enabling systematic screening to exclude virulence factors, antibiotic resistance genes, and markers of lysogeny. WGS also facilitates the prediction of therapeutic efficacy and supports more rational phage selection by identifying receptor-binding proteins and characterising bacterial defence systems. In clinical settings, WGS data are increasingly used to monitor the evolution of bacterial populations and to adapt phage cocktails during treatment, thereby supporting personalised, adaptive phage therapy. Looking ahead, further progress is likely to come from integrating synthetic biology and artificial intelligence to engineer phage-based therapeutics with programmable specificity and predictable properties. Together, these developments are shaping a new paradigm of phage therapy as a scientifically grounded, standardised and controlled strategy to treat infections caused by antibiotic-resistant bacteria. Full article

Background/Objectives. Antibiotic resistance is an escalating global health concern, highlighting the need for innovative antibacterial strategies beyond traditional drugs. GroEL, a highly conserved bacterial chaperonin essential for protein folding and stress tolerance, represents a promising but underexplored therapeutic target. This study aimed to identify short peptides capable of binding GroEL monomers and potentially altering their function, with the long-term goal of disrupting bacterial survival mechanisms. Methods. A phage display screening of a 12-mer peptide library was performed against purified GroEL monomers, yielding five candidate peptides (G1–G5). Their interactions with GroEL were analyzed through molecular docking and molecular dynamics simulations using three-dimensional GroEL structures (1MNF, 1XCK, 8S32). Stability of binding and interaction profiles were assessed through molecular dynamics-based analyses and MM/GBSA free energy calculations. Results. Peptides G4 and G5 displayed the most stable and energetically favorable interactions, with G4–8S32 showing the strongest binding (−116.68 kcal/mol). These peptides localized near inter-subunit interfaces, suggesting potential interference with GroEL oligomerization or allosteric transitions, which are critical for its biological function. Conclusions. Our findings demonstrate that short peptides can stably bind GroEL and potentially modulate its activity. Peptides G4 and G5 represent at our knowledge the first promising scaffolds for developing a novel class of peptide-based antibacterial agents targeting conserved chaperonin systems. This work introduces a new avenue that warrants further experimental validation. Full article

This study characterizes two novel Bacillus phages, B450T and B450C, isolated from Bacillus thuringiensis VKM B-450 via mitomycin C induction, along with their endolysin, PlyC19. Both phages, siphoviruses with 41,205 bp genomes, lysed 38% of the tested Bacillus cereus sensu lato strains, with B450C showing enhanced lytic activity due to mutations in the repressor protein. PlyC19 lysed 56% of the strains tested, including Priestia flexa, demonstrating broader efficacy. Its Amidase_2 domain and dual SH3 cell wall-binding domains enable targeted peptidoglycan hydrolysis, with optimal activity at pH 9.0 and thermal stability up to 40 °C. We propose the taxonomic designation Bquatquinnuvirus eskimopiis for these phages, with B450T and B450C representing distinct strains, based on genomic divergence in the repressor protein’s HTH_Xre domain, consistent with their turbid and clear plaque morphologies, respectively. PlyC19′s broad specificity underscores its potential as an enzybiotic against multidrug-resistant Bacillus cereus group strains in food safety and medicine. Full article

Shiga toxin-producing Escherichia coli (STEC) pose a significant threat to public health and effective methods of detection are needed. The use of naturally occurring bacteriophages (phages) to detect E. coli has been well documented. However, detecting multiple serotypes at the same time often required multiple phages specific to individual serotypes. To limit the burden of complex cocktails, this study aimed to engineer phages with an expanded host range that allows each phage to contribute to detection across multiple STEC serogroups. Kutterviruses, in the Ackermannviridae family, contain four tailspike proteins (TSPs), each of which confers tropism to a different bacterial strain. The modular nature of TSPs allows for mixing receptor-binding domains from diverse phage types. The host range of the Kuttervirus CBA120 was modified by replacing its native tailspike proteins (TSPs) with chimeric versions incorporating receptor-binding domains from related and unrelated phages. A structure-guided approach was utilized to overcome minimal sequence similarity between donor and recipient phages and achieve novel functional TSP chimeras. Two engineered phage variants were created that collectively detect five STEC serogroups: O26, O45, O103, O111, and O157. Spotting and luciferase assays confirmed that the replacement TSPs were functional and the phages had acquired new host ranges. This study demonstrates the feasibility of engineering Ackermannviridae phages with customized host ranges for detecting multiple STEC strains. This approach has potential applications in developing improved phage-based bacterial detection, therapy, and biocontrol. Full article

Background: Antibodies that cross the blood–brain barrier (BBB) by targeting receptor-mediated transport (RMT) systems can allow efficient drug delivery to the central nervous system (CNS). In order to improve brain uptake of antibodies, their binding properties have been engineered, but it is not always clear what antibody properties dictate BBB transport efficiency. In this study, we therefore developed and employed an in vitro phenotypic screen and a quantitative transcytosis assay in an attempt to identify improved variants of a previously identified BBB transcytosing antibody known as 46.1. Methods: First, a random mutagenic 46.1 antibody phage display library was screened for improved transcytosis through a human induced pluripotent stem cell (iPSC)-derived BBB model. These screens yielded antibody variants that enriched over multiple screening rounds; however, when produced as soluble antibodies, the variants did not display improved in vitro transcytosis over the wild-type (WT) 46.1 antibody. As a second strategy, we performed a targeted histidine point mutation of a solvent-exposed residue in each complementarity-determining region (CDR) and evaluated the in vitro transcytosis capacity of the variants. Results and Conclusions: In this way, we identified a 46.1 variant, R162H, with modestly improved in vitro transcytosis properties. These results show that the iPSC-derived BBB screening insights and evaluation strategies presented here could facilitate the engineering and optimization of lead antibodies for CNS delivery. Full article

Bacteriophage receptor-binding proteins are often attached to the tail via a conserved N-terminal adapter/anchor domain, presumed to function independently from the distal receptor-binding/catalytic domain. Using synthetic phage technology, we demonstrated that the N-terminal domain in Przondovirus phages KP192 and KP195 substantially modulates the receptor-binding and hydrolytic activities of their type A tailspikes. A bioinformatics analysis of related proteins revealed a high correlation between the N-terminal domain and the distal receptor-binding region. Furthermore, it was shown that an imperfect structural fit between the N-terminal domain and the adjacent tail proteins (gatekeeper and nozzle proteins) can reduce virion assembly efficiency, thereby impairing phage fitness. These results underscore the importance of selecting an appropriate N-terminal domain of receptor-binding proteins when engineering bacteriophages with altered host specificity. Full article

Streptococcus agalactiae (GBS) has emerged as one of the most prevalent bacterial pathogens causing severe economic losses in tilapia aquaculture due to its highly contagious and lethal nature. Nanobodies (Nbs), characterized by their small molecular size, enhanced tissue penetration, high tolerance, and exceptional antigen-binding affinity, represent a promising green alternative to conventional antibiotics. In the present study, the objective was to explore the potential of specific Nbs in the treatment of tilapia GBS disease. We first screened specific Nbs targeting the surface immunogenic (Sip) protein of GBS from a naïve phage display library, and a novel nanobody Nb30 was obtained. Nb30 was expressed in Escherichia coli and purified using the Ni-NTA Agarose column. Indirect ELISA showed that Nb30 had a high affinity against Sip and GBS in vitro. Moreover, Nb30 significantly reduced GBS colonization in the liver, spleen, and brain of GBS-infected tilapia. The survival rate in the control groups was 53%, whereas it was increased to 86% after treatment with 100 mg/kg Nb30. Transcriptome profiling revealed that Nb30 could modulate critical biological processes, including antioxidant defense, immune regulation, amino acid/protein synthesis, and energy metabolism in the liver tissues of GBS-infection tilapia. Notably, the expression levels of antioxidant enzymes (cat and gpx) were significantly up-regulated, and the TLR/MyD88/NF-κB pathway-related genes (tlr5, myd88, irak4, traf6, Rela, and NF-κB2) were significantly down-regulated after treatment with Nb30. Collectively, these findings establish a novel therapeutic strategy for controlling GBS infection in tilapia and provide evidence supporting the application of nanobodies as sustainable alternatives to antibiotics in aquaculture disease management. Full article

Although phage@nanozymes have proven to be a rapid, precise, and cost-effective method for detecting pathogens in food, the basis of phage and nanozyme selection remains poorly understood. In this study, a novel colourimetric biosensor utilising the temperate phage SapYZUs891 and an Fe/Mn-MOF nanozyme was constructed and assessed for its efficacy in detecting Staphylococcus aureus in food products. Notably, SapYZUs891 exhibited a high titre, broad host range, and strong pH and thermal stability. Moreover, the bimetallic Fe/Mn-MOF nanozyme exhibited an enhanced oxidase-mimicking ability, greater affinity, and a higher reaction rate. The biosensor had a detection time of 19 min, a detection limit of 69 CFU/mL, and a recovery rate between 92.52% and 121.48%, signifying its high reliability and accuracy in identifying S. aureus. This sensor distinguishes between viable and non-viable bacteria and demonstrates resistance to interferent bacterial and food compounds, likely attributable to the particular receptor-binding proteins of SapYZUs891 that bind to the teichoic acid wall on the S. aureus. These results indicated that the SapYZUs891@Fe/Mn-MOF is suitable for the rapid visual assessment of S. aureus. Moreover, the highly sensitive and specific detection system holds significant potential for extended application in on-site screening of S. aureus contamination within food processing environments. Full article