Evolution of the T4 phage virion is driven by selection pressure from non-bacterial factors

Bacteriophages colonize animal and human bodies, propagating on sensitive bacteria that are symbionts, commensals, or pathogens of animals and humans. T4-like phages are dependent on abundant symbionts such as Escherichia coli, commonly present in animal and human gastrointestinal (GI) tracts. Bacteriophage T4 is one of the most complex viruses, and its intricate structure, particularly the capsid head protecting the phage genome, likely contributes substantially to the overall phage fitness in diverse environments. We investigated how individual head proteins-gp24, Hoc, and Soc-affect T4 phage survival under pressure from non-bacterial factors. We constructed a panel of T4 phage variants defective in these structural proteins: T4∆Soc, T4∆24byp24, T4∆Hoc∆Soc, T4∆Hoc∆24byp24, T4∆Soc∆24byp24, and T4∆Hoc∆Soc∆24byp24 (byp = bypass). These variants were investigated for their sensitivity to selected environmental conditions relevant to the microenvironment of the GI tract, including pH, temperature, and digestive enzymes. The simple and "primitive" structure of the phage capsid (∆24byp24) was significantly less stable at low pH and more sensitive to inactivation by digestive enzymes, and the simultaneous lack of gp24 and Soc resulted in a notable decrease in phage activity at 37°C. Gp24 was also found to be highly resistant to thermal and chemical denaturation. Thus, gp24, which was acquired relatively late in evolution, seems to play a key role in T4 withstanding environmental conditions, including those related to the animal/human GI tract, and Soc is a molecular glue that enhances this protective effect. IMPORTANCE Bacteriophages are important components of animal and human microbiota, particularly in the gastrointestinal tract, where they dominate the viral community and contribute to shaping microbial balance. However, interactions with bacterial hosts are not the only element of the equation in phage survival-phages inhabiting the GI tract are constantly exposed to increased temperature, pH fluctuations, or digestive enzymes, which raises the question of whether and how the complex structure of phage capsids contributes to their persistence in the specific microenvironment of human/animal bodies. Here we address this phage-centric perspective, identifying the role of individual head proteins in T4 phage survival in GI tract conditions. The selection pressure driving the evolution of T4-like phages could have come from the external environment that affects phage virions with increased temperature and variable pH; it is possible that in the local microenvironment along the GI tract, the phage benefits from stability-protecting proteins.

Polysaccharide BAP1 of Bifidobacterium adolescentis CCDM 368 is a biologically active molecule with immunomodulatory properties

Bifidobacteria are among the most common bacteria used for their probiotic properties and their impact on the maturation and function of the immune system has been well-described. Recently, scientific interest is shifting from live bacteria to defined bacteria-derived biologically active molecules. Their greatest advantage over probiotics is the defined structure and the effect independent of the viability status of the bacteria. Here, we aim to characterize Bifidobacterium adolescentis CCDM 368 surface antigens that include polysaccharides (PSs), lipoteichoic acids (LTAs), and peptidoglycan (PG). Among them, Bad368.1 PS was observed to modulate OVA-induced cytokine production in cells isolated from OVA-sensitized mice by increasing the production of Th1-related IFN-γ and inhibition of Th2-related IL-5 and IL-13 cytokines (in vitro). Moreover, Bad368.1 PS (BAP1) is efficiently engulfed and transferred between epithelial and dendritic cells. Therefore, we propose that the Bad368.1 PS (BAP1) can be used for the modulation of allergic diseases in humans. Structural studies revealed that Bad368.1 PS has an average molecular mass of approximately 9,99 × 10⁶ Da and it consists of glucose, galactose, and rhamnose residues that are creating the following repeating unit: →2)-β-D-Glcp-1→3-β-L-Rhap-1→4-β-D-Glcp-1→3-α-L-Rhap-1→4-β-D-Glcp-1→3-α-D-Galp-(1→_n.

New Phage-Derived Antibacterial Enzyme PolaR Targeting Rothia spp

Rothia is an opportunistic pathogen, particularly life-threatening for the immunocompromised. It is associated with pneumonia, endocarditis, peritonitis and many other serious infections, including septicemia. Of note, Rothia mucilaginousa produces metabolites that support and increase overgrowth of Pseudomonas aeruginosa, one of the ESKAPE bacteria. Endolysins are considered as antibacterial enzymes derived from bacteriophages that selectively and efficiently kill susceptible bacteria without harming human cells or the normal microbiome. Here, we applied a computational analysis of metagenomic sequencing data of the gastric mucosa phageome extracted from human patients' stomach biopsies. A selected candidate anti-Rothia sequence was produced in an expression system, purified and confirmed as a Rothia mucilaginosa- and Rothia dentocariosa-specific endolysin PolaR, able to destroy bacterial cells even when aggregated, as in a biofilm. PolaR had no cytotoxic or antiproliferative effects on mammalian cells. PolaR is the first described endolysin selectively targeting Rothia species, with a high potential to combat infections caused by Rothia mucilaginosa and Rothia dentocariosa, and possibly other bacterial groups. PolaR is the first antibacterial enzyme selected from the gastric mucosa phageome, which underlines the biological complexity and probably underestimated biological role of the phageome in the human gastric mucosa.

φYeO3-12 phage tail fiber Gp17 as a promising high specific tool for recognition of Yersinia enterocolitica pathogenic serotype O:3

Yersiniosis is an infectious zoonotic disease caused by two enteropathogenic species of Gram-negative genus Yersinia: Yersinia enterocolitica and Yersinia pseudotuberculosis. Pigs and other wild and domestic animals are reservoirs for these bacteria. Infection is usually spread to humans by ingestion of contaminated food. Yersiniosis is considered a rare disease, but recent studies indicate that it is overlooked in the diagnostic process therefore the infections with this bacterium are not often identified. Reliable diagnosis of Yersiniosis by culturing is difficult due to the slow growth of the bacteria easily overgrown by other more rapidly growing microbes unless selective growth media is used. Phage adhesins recognizing bacteria in a specific manner can be an excellent diagnostic tool, especially in the diagnosis of pathogens difficult for culturing. In this study, it was shown that Gp17, the tail fiber protein (TFP) of phage φYeO3-12, specifically recognizes only the pathogenic Yersinia enterocolitica serotype O:3 (YeO:3) bacteria. The ELISA test used in this work confirmed the specific interaction of this protein with YeO:3 and demonstrated a promising tool for developing the pathogen recognition method based on phage adhesins.

Immune Response to Therapeutic Staphylococcal Bacteriophages in Mammals: Kinetics of Induction, Immunogenic Structural Proteins, Natural and Induced Antibodies

Bacteriophages are able to affect the human immune system. Phage-specific antibodies are considered as major factors shaping phage pharmacokinetics and bioavailability. So far, general knowledge of phage antigenicity nevertheless remains extremely limited. Here we present comparative studies of immunogenicity in two therapeutic bacteriophages, A3R and 676Z, active against Staphylococcus aureus, routinely applied in patients at the Phage Therapy Unit, Poland. Comparison of the overall ability of whole phages to induce specific antibodies in a murine model revealed typical kinetics of IgM and IgG induction by these two phages. In further studies we identified the location of four phage proteins in the virions, with the focus on the external capsid head (Mcp) or tail sheath (TmpH) or an unidentified precise location (ORF059 and ORF096), and we confirmed their role as structural proteins of these viruses. Next, we compared the immune response elicited by these proteins after phage administration in mice. Similar to that in T4 phage, Mcp was the major element of the capsid that induced specific antibodies. Studies of protein-specific sera revealed that antibodies specific to ORF096 were able to neutralize antibacterial activity of the phages. In humans (population level), none of the studied proteins plays a particular role in the induction of specific antibodies; thus none potentially affects in a particular way the effectiveness of A3R and 676Z. Also in patients subjected to phage therapy, we did not observe increased specific immune responses to the investigated proteins.

Transcriptional and proteomic insights into phytotoxic activity of interspecific potato hybrids with low glycoalkaloid contents

BACKGROUND

Glycoalkaloids are bioactive compounds that contribute to the defence response of plants against herbivore attack and during pathogenesis. Solanaceous plants, including cultivated and wild potato species, are sources of steroidal glycoalkaloids. Solanum plants differ in the content and composition of glycoalkaloids in organs. In wild and cultivated potato species, more than 50 steroidal glycoalkaloids were recognized. Steroidal glycoalkaloids are recognized as potential allelopathic/phytotoxic compounds that may modify the growth of target plants. There are limited data on the impact of the composition of glycoalkaloids on their phytotoxic potential.

RESULTS

The presence of α-solasonine and α-solamargine in potato leaf extracts corresponded to the high phytotoxic potential of the extracts. Among the differentially expressed genes between potato leaf bulks with high and low phytotoxic potential, the most upregulated transcripts in sample of high phytotoxic potential were anthocyanin 5-aromatic acyltransferase-like and subtilisin-like protease SBT1.7-transcript variant X2. The most downregulated genes were carbonic anhydrase chloroplastic-like and miraculin-like. An analysis of differentially expressed proteins revealed that the most abundant group of proteins were those related to stress and defence, including glucan endo-1,3-beta-glucosidase acidic isoform, whose expression level was 47.96× higher in potato leaf extract with low phytotoxic.

CONCLUSIONS

The phytotoxic potential of potato leaf extract possessing low glycoalkaloid content is determined by the specific composition of these compounds in leaf extract, where α-solasonine and α-solamargine may play significant roles. Differentially expressed gene and protein profiles did not correspond to the glycoalkaloid biosynthesis pathway in the expression of phytotoxic potential. We cannot exclude the possibility that the phytotoxic potential is influenced by other compounds that act antagonistically or may diminish the glycoalkaloids effect.

Hydroxyethylcellulose as a methotrexate carrier in anticancer therapy

Clinical and experimental cancer therapy is multifaceted; one such facet is the use of drug carriers. Drug carriers are various nano- and macromolecules, e.g., oligosaccharides, proteins, and liposomes. The present study aimed to verify the suitability of cellulose as a carrier for methotrexate (MTX). Hydroxyethylcellulose, with a molecular weight of 90 kDa and soluble in water, was used. Methotrexate was linked to cellulose by methyl ester bonds. A conjugate containing on average 9.5 molecules of MTX per molecule of cellulose was developed. Gel filtration HPLC analysis showed that the conjugate contained approximately 2% free drug. Dynamic light scattering analysis showed an increase in the polydispersity of the conjugate. The degradation of the conjugate in phosphate buffer and plasma followed first-order kinetics. The conjugate showed the lowest stability (half-life 154 h) in plasma. The conjugate showed 10-fold lower cytotoxicity to the 4 T1 mammary tumour cell line than the free drug. In the in vivo experiment to treat orthotopically implanted mammary tumours, the conjugate and the free drug, both applied intravenously, showed maximum inhibition of tumour growth of 48.4% and 11.2%, respectively. In conclusion, cellulose, which is a non-biodegradable chain glucose polymer, can be successfully used as a drug carrier, which opens up new research perspectives.

An Antibody Specific for the Dog Leukocyte Antigen DR (DLA-DR) and Its Novel Methotrexate Conjugate Inhibit the Growth of Canine B Cell Lymphoma

Canine B-cell lymphoma (CBL) is an incurable, spontaneous lymphoid malignancy constituting an accurate animal model for testing novel therapeutic strategies in human medicine. Resources of available species-specific therapeutic monoclonal antibodies (mAbs) targeting CBL are scarce. The aim of the present study was to evaluate the therapeutic potential of mAb B5, specific for the dog leukocyte antigen DR (DLA-DR) and its antibody-drug conjugate with methotrexate (B5-MTX). B5 induced caspase-dependent apoptosis of DLA-DR-expressing canine B cell lymphoma/CLBL1 and CLB70 leukemia lines, but not the GL-1 line not expressing DLA-DR. The cytotoxicity of B5-MTX to sensitive cells was further potentiated by a payload of MTX, but without any substantial off-target effects. The infusion of B5 and B5-MTX in a murine model of disseminated, advanced canine lymphoma, mediated >80% and >90% improvement in survival, respectively, and was well tolerated by the animals. Interestingly, the concentrations of soluble DLA-DR (sDLA-DR) antigens present in the blood serum of tumor-bearing mice were found proportional to the tumor burden. On this basis, sDLA-DR levels were evaluated as a potential biomarker using samples from canine lymphoma patients. In summary, the action of B5 and B5-MTX holds promise for further development as an alternative/complementary option for the diagnosis and treatment of canine lymphoma.

A rapid and eco-friendly method for determination of the main components of gamma-oryzanol in equestrian dietary and nutritional supplements by liquid chromatography-Tandem mass spectrometry

Gamma-oryzanol (GO) has gained special attention in the equine sports industry in recent years due to its touted properties, including the fact that it may cause anabolic effects on muscle growth and reduce fatigue. Many manufactures offer supplements containing GO as a naturally occurring anabolic substance; however, some producers do not declare its presence in product compositions. Taking into consideration the touted properties of GO, its ambiguous effectiveness and the open character of the Prohibited Substances List established by the Fédération Equestre Internationale, there is an urgent need to elaborate procedures for the estimation of horse exposure to GO during supplementation, as well as during routine analysis of supplements. This work describes the development and validation of the method for determination of the four main GO components, i.e., cycloartenyl ferulate, 24-methylenecycloartanyl ferulate, campesteryl ferulate and β-sitosteryl ferulate, in equestrian supplements based on LC-MS/MS after a simple ultrasound-assisted extraction (Eco-Scale score value of 76). The analytical performance achieved satisfactory results in terms of linearity (R² > 0.9910), sensitivity (LODs ranged from 0.4 to 1.9 ng/mL), intra- and interday accuracy (from 90.4-115.8%), precision (CV < 9.6%) and recovery (from 87.6-108.6%) for all of the investigated compounds. The method was successfully applied to the analysis of thirty equestrian supplements.

New diaryl ω-(isothiocyanato)alkylphosphonates and their mercapturic acids as potential antibacterial agents

Thirty-four novel, diaryl ω-(isothiocyanato)alkylphosphonates with chlorine atom and methoxy, dimethoxy, methylsulfanyl, or methoxycarbonyl groups at ortho, meta, or para positions of the phenyl ring, and with an unbranched alkyl chain (n = 2-6) were designed and synthesized in a one-pot reaction in 11-76% yields. All isothiocyanates thus generated were evaluated for the first time for antibacterial activity on Pseudomonas aeruginosa and Staphylococcus aureus bacterial strains, and had satisfactory antibacterial activity in most cases. The highest activity, similar to that of reference gentamicin activity against S. aureus, was seen in compounds 9 and 13 (1.5 ± 0.1 and 2.5 ± 0.2 μM, respectively), whereas for P. aeruginosa more than half of tested compounds proved to be more effective than gentamicin. Additionally, selected isothiocyanates (9, 13, 18, and 23) were transformed in 52-73% yields into mercapturic acids 42-45, which also exhibited satisfactory antibacterial effect against S. aureus strain.

Epitope Mapping of Streptococcus agalactiae Elongation Factor Tu Protein Recognized by Human Sera

The elongation factor Tu has been identified as one of the most immunoreactive proteins that was recognized by human sera of GBS (group B streptococcus) positive patients. In this paper, we present the polypeptide-specific epitopes of the bacterial protein that are recognized by human antibodies: ²⁸LTAAITTVLARRLP⁴¹ (peptide no. 3) and ²⁹⁴GQVLAKPGSINPHTKF³⁰⁹ (peptide no. 21). To determine the shortest amino acid sequence recognized by antibodies, truncation peptide libraries were prepared using the PEPSCAN method. The analysis of immunoreactivity of peptides with sera of GBS positive and negative women revealed that the most immunoreactive sequence was ³⁰⁶HTKF³⁰⁹. Moreover, we observed that this sequence also showed the highest specificity which was based on ratio of reactivity with sera of GBS positive relative to sera of GBS negative patients. Epitope was synthetized on Wang resin with the Fmoc strategy. Our results open the possibility to use ³⁰⁶HTKF³⁰⁹ peptide in diagnostic assays to determine Streptococcus agalactiae infection in humans.

Chemical characterization and immunomodulatory properties of polysaccharides isolated from probiotic Lactobacillus casei LOCK 0919

The Lactobacillus casei strain, LOCK 0919, is intended for the dietary management of food allergies and atopic dermatitis (LATOPIC® BIOMED). The use of a probiotic to modulate immune responses is an interesting strategy for solving imbalance problems of gut microflora that may lead to various disorders. However, the exact bacterial signaling mechanisms underlying such modulations are still far from being understood. Here, we investigated variations in the chemical compositions and immunomodulatory properties of the polysaccharides (PS), L919/A and L919/B, which are produced by L. casei LOCK 0919. By virtue of their chemical features, such PS can modulate the immune responses to third-party antigens. Our results revealed that L919/A and L919/B could both modulate the immune response to Lactobacillus planatarum WCFS1, but only L919/B could alter the response of THP-1 cells (in terms of tumor necrosis factor alpha production) to L. planatarum WCFS1 and Escherichia coli Nissle 1917. The comprehensive immunochemical characterization is crucial for the understanding of the biological function as well as of the bacteria-host and bacteria-bacteria cross-talk.

Applying the prodrug strategy to α-phosphonocarboxylate inhibitors of Rab GGTase--synthesis and stability studies

Fourteen novel prodrug-like analogs of two highly ionic phosphonocarboxylate inhibitors of Rab geranylgeranyl transferase were synthesized and preliminary assessment of their chemical and enzymatic stability was evaluated in buffers (pH 6.5 and 7.4) and rat intestinal homogenate (pH 6.5). Both acidic groups in phosphonocarboxylates were subject to modification. Phosphonic acid was protected either as bis(acyloxyalkyl) ester or phosphonodiamidate derived from amino acids. The carboxylic acid group was either left unchanged or was studied as ethyl ester. The compounds exhibited favorable stability in physiologically relevant pH (t1/2 above 18 h), while in intestinal homogenate they showed a large variety of half-lives (from 5 minutes to over 150 hours). LC MS studies have shown that the main product of decomposition under studied conditions resulted from cleavage of one of the ester (for acyloxyalkyl analogs) or amide (for phosphonodiamidate) bonds with phosphorus.

Methods for preliminary determination of pemetrexed in macromolecular drug-carrier systems

Pemetrexed (PMX) is an antifolate drug utilized in the treatment of non-small cell lung cancer. For studies of potential macromolecular carriers for PMX, fast and precise methods were developed to determine the bound and free drug contained in investigated conjugate preparations. The analysis of the total amount of PMX in conjugates was based on absorption spectrophotometry. The linearity was found in the range of 4.697-46.97 μmol L(-1) PMX. The limit of quantitation was 1.070 μmol L(-1). The method for the analysis of unbound PMX was based on size-exclusion chromatography and detection at 225 nm. This method shows linear range of 2.230-223.0 μmol L(-1). LOQ was 0.539 μmol L(-1). The proposed methods can be used both for the characterization of the polysaccharide based conjugates of PMX and for the determination of conjugate drug release profiles.

Oral Application of T4 Phage Induces Weak Antibody Production in the Gut and in the Blood

A specific humoral response to bacteriophages may follow phage application for medical purposes, and it may further determine the success or failure of the approach itself. We present a long-term study of antibody induction in mice by T4 phage applied per os: 100 days of phage treatment followed by 112 days without the phage, and subsequent second application of phage up to day 240. Serum and gut antibodies (IgM, IgG, secretory IgA) were analyzed in relation to microbiological status of the animals. T4 phage applied orally induced anti-phage antibodies when the exposure was long enough (IgG day 36, IgA day 79); the effect was related to high dosage. Termination of phage treatment resulted in a decrease of IgA again to insignificant levels. Second administration of phage induces secretory IgA sooner than that induced by the first administrations. Increased IgA level antagonized gut transit of active phage. Phage resistant E. coli dominated gut flora very late, on day 92. Thus, the immunological response emerges as a major factor determining phage survival in the gut. Phage proteins Hoc and gp12 were identified as highly immunogenic. A low response to exemplary foreign antigens (from Ebola virus) presented on Hoc was observed, which suggests that phage platforms can be used in oral vaccine design.

Type II thioesterase ScoT is required for coelimycin production by the modular polyketide synthase Cpk of Streptomyces coelicolor A3(2)

Type II thioesterases were shown to maintain efficiency of modular type I polyketide synthases and nonribosomal peptide synthetases by removing acyl residues blocking extension modules. We found that thioesterase ScoT from Streptomyces coelicolor A3(2) is required for the production of the yellow-pigmented coelimycin by the modular polyketide synthase Cpk. No production of coelimycin was observed in cultures of scoT disruption mutant. Polyketide production was restored upon complementation with an intact copy of the scoT gene. An enzymatic assay showed that ScoT thioesterase can hydrolyse a 12-carbon acyl chain but the activity is too low to play a role in product release from the polyketide synthase. We conclude that ScoT is an editing enzyme necessary to maintain the activity of polyketide synthase Cpk. We provide a HPLC based method to measure the amount of coelimycin P2 in a culture medium.

Type II thioesterase ScoT is required for coelimycin production by the modular polyketide synthase Cpk of Streptomyces coelicolor A3(2)

Type II thioesterases were shown to maintain efficiency of modular type I polyketide synthases and nonribosomal peptide synthetases by removing acyl residues blocking extension modules. We found that thioesterase ScoT from Streptomyces coelicolor A3(2) is required for the production of the yellow-pigmented coelimycin by the modular polyketide synthase Cpk. No production of coelimycin was observed in cultures of scoT disruption mutant. Polyketide production was restored upon complementation with an intact copy of the scoT gene. An enzymatic assay showed that ScoT thioesterase can hydrolyse a 12-carbon acyl chain but the activity is too low to play a role in product release from the polyketide synthase. We conclude that ScoT is an editing enzyme necessary to maintain the activity of polyketide synthase Cpk. We provide a HPLC based method to measure the amount of coelimycin P2 in a culture medium.

Comparison of microbiological and physicochemical methods for enumeration of microorganisms

Determination of the number of cultured bacteria is essential for scientific and industrial practice. A spread plate technique is the most common and accurate method for counting of microorganisms. However, time consuming incubation does not allow for a quick estimation of the number of bacteria in a growing culture. In the present study, the results of photometric measurements: direct optical density method (OD at 585 nm), UV absorbance at 260 and/or 280 nm of separated and lysed bacteria by sodium hydroxide and surfactant with the spread plate technique were compared. The linear regression model for bacterial strains Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli was used to compare these three methods. The UV measurement method enabled determination of the number of bacteria with similar precision. The procedure for solubilized bacteria UV measurement is robust, and is not influenced by dispersions in the original culture medium.

Methods for methotrexate determination in macromolecular conjugates drug carrier

In this paper, two simple, cost-effective and fast methods for quantification of methotrexate (MTX) in the macromolecular conjugates are presented. The method for analysis of total MTX in preparations was based on absorption spectrophotometry. Validation was performed by measuring absorbance at 372 nm of the sodium bicarbonate solution. Curve describing drug concentration against absorption had a linear character in the range of 1.204-40.13 microM. The reproducibility and precision of method was 0.1558 to 3.086%. The recovery of the method was between 99.56 and 104.7%. The limit of quantitation method was 1.050 microM. The method for free MTX determination was based on size exclusion chromatography and UV-VIS detection at the wavelength of 302 nm. Superdex Peptide column (150 x 4.6 mm) and a mobile phase 0.1 M sodium bicarbonate with a flow rate of 0.4 mL/min was used. In the free drug determination method, the curve had a linear character in the range of 2.006-200.6 microM. The reproducibility and precision of method was 0.3761 to 2.452%. The recovery of the method was between 93.18 and 104.5%. The limit of quantitation method was 0.9203 microM.