OBJECTIVES:The increasing frequency of antibiotic-resistant bacterial infections is a major public health challenge, and new antibiotic drugs are urgently needed. A rapid solution to the problem is to repurpose clinically approved compounds with antibacterial properties, such as the nucleoside analogues zidovudine (azidothymidine) or 5-fluoro-2'-deoxyuridine. Here we report the in vitro and in vivo antibacterial properties of double and triple combinations of azidothymidine or 5-fluoro-2'-deoxyuridine with uridine and/or trimethoprim. METHODS:We determined MICs of azidothymidine and 5-fluoro-2'-deoxyuridine, alone or combined with uridine and/or trimethoprim, against a selection of Gram-negative and Gram-positive bacteria. We also measured MICs of a selection of antibiotics of different classes as a function of uridine concentration. The efficacy of azidothymidine and 5-fluoro-2'-deoxyuridine with uridine and/or trimethoprim was measured in a murine peritonitis infection model. RESULTS:The addition of uridine enhanced the in vitro antibacterial activity of azidothymidine and 5-fluoro-2'-deoxyuridine, against Gram-negative and Gram-positive bacteria, respectively. Uridine also enhanced the in vitro antibacterial activity of azidothymidine/trimethoprim and 5-fluoro-2'-deoxyuridine/trimethoprim combinations. Triple combinations containing azidothymidine, trimethoprim and uridine, showed antibacterial synergy against Gram-negative bacteria (Escherichia coli and Klebsiella pneumoniae) whereas the 5-fluoro-2'-deoxyuridine, trimethoprim and uridine combination showed synergy against the Gram-positive Staphylococcus aureus. The positive effect of uridine on the efficacy of azidothymidine/trimethoprim combination was also observed in vivo in a murine E. coli peritonitis model. CONCLUSIONS:Triple combinations of these clinically approved compounds warrant further investigations as therapies to combat antibiotic-resistant infections.

Introduction The Automated Quantification Algorithm (AQuA) is a rapid and efficient method for targeted NMR-based metabolomics, currently optimised for blood plasma. AQuA quantifies metabolites from 1D- 1 H NMR spectra based on the height of only one signal per metabolite, which minimises the computational time and workload of the method without compromising the quantification accuracy. Objectives To develop a fast and computationally efficient extension of AQuA for quantification of selected metabolites in highly complex samples, with minimal prior sample preparation. In particular, the method should be capable of handling interferences caused by broad background signals. Methods An automatic baseline correction function was combined with AQuA into an automated workflow, the extended AQuA, for quantification of metabolites in plant root exudate NMR spectra that contained broad background signals and baseline distortions. The approach was evaluated using simulations as well as a spike-in experiment in which known metabolite amounts were added to a complex sample matrix. Results The extended AQuA enables accurate quantification of metabolites in 1D- 1 H NMR spectra with varying complexity. The method is very fast (< 1 s per spectrum) and can be fully automated. Conclusions The extended AQuA is an automated quantification method intended for 1D- 1 H NMR spectra containing broad background signals and baseline distortions. Although the method was developed for plant root exudates, it should be readily applicable to any NMR spectra displaying similar issues as it is purely computational and applied to NMR spectra post-acquisition.

Dicer-like (DCL) proteins play a vital role in transcriptional and post-transcriptional gene silencing, also known as RNA interference (RNAi), by cleaving double-stranded RNAs or single-stranded RNAs with stem-loop structures into small RNAs. Although DCL-mediated RNAi can regulate interspecific communication between pathogenic/mutualistic organisms and their hosts, its role in parasitic fungus-fungus interactions is yet to be investigated. In this study, we deleted dcl genes in the mycoparasitic fungus Clonostachys rosea and analyzed the transcriptome and secondary metabolome to characterize the regulatory functions of DCL-dependent RNAi in mycoparasitism. Deletion of dcl2 resulted in a mutant with reduced growth rate, pigment production and antagonism towards the plant pathogenic fungus Botrytis cinerea . Moreover, the Δ dcl2 mutant displayed a reduced ability to control fusarium foot rot disease on wheat, caused by Fusarium graminearum , and reduced production of 62 secondary metabolites (SM) including yellow-coloured sorbicillinoids. Transcriptome sequencing of the in vitro interaction between the C. rosea Δ dcl2 strain and B. cinerea or F. graminearum identified downregulation of genes coding for transcription factors, membrane transporters, hydrolytic enzymes and SM biosynthesis enzymes putatively involved in antagonistic interactions, in comparison with the C. rosea wild type interaction. Sixty-one putative novel microRNA-like RNAs (milRNAs) were identified in C. rosea , and 11 was upregulated in the Δ dcl2 mutant. In addition to putative endogenous gene targets, these DCL2-dependent milRNAs were predicted to target B . cinerea and F. graminearum virulence factor genes, which showed an increased expression during interaction with the Δ dcl2 mutant incapable of producing the targeting milRNAs. This paper constitutes the first step in elucidating the role of RNAi in mycoparasitism, with important implications for biological control of plant diseases. This study further indicates a possible cross-species regulatory activity of fungal milRNAs, emphasizing a novel role of RNAi in fungal interactions and ecology. Author summary RNA interference (RNAi) is a conserved cellular mechanism mediated by small RNAs (sRNAs) regulating biological processes through the targeted destruction or modulation of RNA filaments necessary for protein synthesis. Dicer-like endoribonucleases (DCL) play a vital role in the RNAi pathway by generating sRNAs. In this study, we identified two DCL-encoding genes in the mycoparasitic fungus Clonostachys rosea and investigated a role of DCL-mediated RNAi in interference interactions between Clonostachys rosea and the two important fungal pathogens Botrytis cinerea and Fusarium graminearum (here called mycohost). Using transcriptome (sRNA and mRNA) sequencing and secondary metabolome analysis approach, we found that the dcl mutants were not able to produce 11 sRNAs predicted to finetune the regulatory network of genes known to be involved in production of hydrolytic enzymes, antifungal compounds, and membrane transporters needed for antagonistic action of C. rosea . We also found C . rosea sRNAs putatively targeting known virulence factors in the mycohost, indicating RNAi-mediated cross-species communication. Our study expanded the understanding of underlying mechanisms of cross-species communication during interference interactions and showed that DCL-mediated RNAi is an important regulator of parasitic fungus-fungus interactions. The results pose the base for future works studying the role of DCL-based cross-species RNAi in fungal interactions.

Heterobasidion annosum s.s. and H. parviporum are severe pathogens of conifers causing butt rot and root rot thus reducing the economic value of timber. Here, the antifungal activity of Bacillus subtilis isolate A18 against these two Heterobasidion species was investigated. Five different culture media with different culture age were investigated to study the effect of substrate composition and culture age for metabolite production. Bacterial cultures and cell-free culture filtrates were tested for antifungal activity. Inhibition of fungal growth was analysed using the agar disc-diffusion method. MALDI-TOF and LC-HRMS analyses were used to identify the antifungal metabolites. Substrate composition and age of culture were found to be active variables with direct effect on the antifungal activity of bacterial culture extracts. High anti-fungal activity was observed when B. subtilis was cultured in PDB, SGB and LB media for four days. Mass-spectrometry analysis showed the presence of lipopeptides in culture filtrates identified as members of the surfactins, polymixins, kurstakins and fengycins. A culture filtrate containing fengycin-type lipopeptides showed the highest bioactivity against Heterobasidion species. Bacterial cultures had higher bioactivity compared to their respective cell free culture filtrates. The results of the present study suggest that B. subtilis A18 is a powerful biocontrol agent against Heterobasidion infections of tree wounds and stumps.

Phytophthora niederhauserii, P. pisi, P. sojae and P. vignae are closely related species that are pathogenic to various legume plants. While P. sojae and P. vignae are reported to specifically infect soybean and cowpea, respectively, P. pisi is reported to attack pea and faba bean. Phytophthora niederhauserii is considered to have a broad host range. Zoospores of some Phytophthora species are chemotactically attracted to the isoflavones that are secreted by their host plants. The focus of the current study was to determine the chemotaxic behaviour of zoospores from closely related legume‐root infecting Phytophthora species and to investigate the correlation, if any, to host preference as determined by greenhouse pathogenicity tests. The results showed that P. sojae and P. vignae were attracted to the non‐soybean isoflavone prunetin as well as to the soybean isoflavones genistein and daidzein, which is in contrast with their host specificity on soybean and cowpea, respectively. On the other hand, P. pisi and P. niederhauserii were only attracted to prunetin, previously reported to be produced by pea, but not to the isoflavones associated with the non‐host soybean. The lack of responsiveness to genistein and daidzein in P. pisi may represent a recent adaptation to the host specialization towards pea. However, the affinity of P. niederhauserii to prunetin shows that this trait can also be present in taxa not specifically associated with legume hosts.

Steroidal glycoalkaloids (SGA) are toxic secondary metabolites naturally occurring in the potato, as well as in certain other Solanaceous plant species, such as tomato, eggplant and pepper. To investigate the steroidal origin of SGA biosynthesis, cut potato shoots were fed cholesterol labelled with deuterium (D) in the sterol ring structure (D5- or D6-labelled), or side chain (D7-labelled), and analysed after three or five weeks. The labelled cholesterol and presence of D-labelled SGA were analysed by GC-MS and LC-MS/MS, respectively. When feeding D-labelled cholesterol solubilised in Tween-80, labelled cholesterol in free form became present in both leaves and stems, although the major part was recovered as steryl esters. Minor amounts of D-labelled SGA (α-solanine and α-chaconine) were identified in cholesterol-treated shoots, but not in blank controls, or in shoots fed D6-27-hydroxycholesterol. Solubilising the labelled cholesterol in methyl-β-cyclodextrin instead of Tween-80 increased the levels of labelled SGA up to 100-fold, and about 1 mole% of the labelled cholesterol was recovered as labelled SGA in potato leaves. Both side chain and ring structure D labels were retained in SGA, showing that the entire cholesterol molecule is converted to SGA. However, feeding side chain D7-labelled cholesterol resulted in D5-labelled SGA, indicating that two hydrogen atoms were released during formation of the SGA nitrogen-containing ring system. Feeding with D7-sitosterol did not produce any labelled SGA, indicating that cholesterol is a specific SGA precursor. In conclusion, we have demonstrated a superior performance of methyl-β-cyclodextrin for delivery of cholesterol in plant tissue feeding experiments, and given firm evidence for cholesterol as a specific sterol precursor of SGA in potato.

The structures of several enzymatic hydrolysis products of Nothogenia erinacea seaweed xylan, a linear homopolymer with mixed beta-(1-->3)/beta-(1-->4) linkages, were analysed by physicochemical and biochemical techniques. With the glycoside hydrolase family 10 beta-(1-->4)-xylanase from Cryptococcus adeliae, hydrolysis proceeds to a final mixture of products containing a mixed linkage-type triose as a major compound, whereas with the family 11 xylanase from Thermomyces lanuginosus this is a mixed linkage tetraose. The Cryptococcus xylanase is shown to be capable of also catalysing the hydrolysis of beta-(1-->3) linkages, that is this of a mixed type tetraose intermediary formed, in accordance with the broader substrate specificity of family 10 enzymes. From a partial degradation experiment with the T. lanuginosus xylanase, a series of higher mixed oligosaccharides were isolated and identified. The observed oligosaccharide intermediates and splicing pattern indicate an irregular beta-(1-->3)/beta-(1-->4) linkage distribution within the linear d-xylose polymer. Similar results were obtained with rhodymenan, the seaweed xylan from Palmares palmata.

Xanthomonas campestris pv. vitians is a Gram-negative plant-associated bacterium that acts as causative agent of bacterial leaf spot and headrot in lettuce. The lipopolysaccharide of this bacterium is suspected to be an important molecule for adhesion to and infection of the plants. The lipopolysaccharide has been isolated from the phenol phase and the O-specific chain characterized by compositional analysis, high field NMR and MALDI-TOF MS. It consists of a nonrepetitive branched polysaccharide with a rhamnan backbone to which Fuc3NAc is linked. The NMR and MS approach led to the characterization of the fine structure of the polymer, which is randomly assembled. The rhamnan backbone is built up of beta-Rhap and alpha-Rhap, this last is present in one, two or three adjacent units and branched by an alpha-Fucp3NAc unit. This is a real case of a random constituted O-specific chain, therefore biosynthetic studies towards the comprehension of this irregular biosynthesis are needed.

The ascomycetous yeast Pichia anomala J121, inhibits mould growth in malfunctioning airtight storage systems for moist animal feed grain. Extensive studies of P. anomala J121 have given detailed kn ...

A sensitive and selective method for detection and quantification of 1,5-anhydro-D-fructose, microthecin, and 4-deoxy-glycero-hexo-2, 3-diulose using GC-MS in selected ion monitoring mode has been developed. These compounds, which occur in many biological systems, have here been quantified in the red alga Gracilariopsis lemaneiformis. A screening of other algae showed the occurrence of 1, 5-anhydro-D-fructose in several other species of red algae as well as in some green and brown algae.

4-Deoxy-glycero-hexo-2,3-diulose was formed from microthecin [2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one] in neutral water solutions by a Michael addition. The compound was determined by NMR spectroscopy, MS and polarimetry to be a racemic mixture of d-and l-forms and existing mainly as two furanosidic C-2 epimers in equilibrium with microthecin. GC–MS analysis showed that 4-deoxy-glycero-hexo-2,3-diulose and microthecin were present in extracts of the red alga Gracilariopsis lemaneiformis.

The content of low-molecular-weight compounds in the red alga Gracilariopsis lemaneiformis [(Bory) Dawson, Acleto, et Foldvik] has been analysed in-situ using high-resolution magic angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy. The major heteroside was shown to be floridoside, but digeneaside and isofloridoside were also detected in the alga. Other major components were isethionic acid and the amino acids taurine and citrulline. The results from the HR-MAS NMR analysis were confirmed with high-resolution NMR spectroscopy, high-resolution fast atom bombardment mass spectrometry (FABMS) and GC-MS, on material isolated from the studied alga, but also on authentic samples.

Microthecin, a pyrone isolated from Gracilariopsis lemaneiformis, is formed from 1,5-anhydro-D-fructose through two sequential elimination reactions; presumably by the action of a single enzyme.