Complete Biochemical Characterization of Pantaphos Biosynthesis Highlights an Unusual Role for a SAM-Dependent Methyltransferase

Pantaphos is small molecule virulence factor made by the plant pathogen Pantoea ananatis. An 11 gene operon, designated hvr for high virulence, is required for production of this phosphonic acid natural product, but the metabolic steps used in its production have yet to be established. Herein, we determine the complete biosynthetic pathway using a combination of bioinformatics, in vitro biochemistry and in vivo heterologous expression. Only 6 of the 11 hvr genes are needed to produce pantaphos, while a seventh is likely to be required for export. Surprisingly, the pathway involves a series of O-methylated intermediates, which are then hydrolyzed to produce the final product. The methylated intermediates are produced by an irreversible S-adenosylmethione (SAM)-dependent methyltransferase that is required to drive a thermodynamically unfavorable dehydration in the preceding step, a function not previously attributed to members of this enzyme class. Methylation of pantaphos by the same enzyme is also likely to limit its toxicity in the producing organism. The pathway also involves a novel flavin-dependent monooxygenase that differs from homologous proteins due to its endogenous flavin-reductase activity. Heterologous production of pantaphos by Escherichia coli strains expressing the minimal gene set strongly supports the in vitro biochemical data.     

A secretome-based methodology may provide a better characterization of the virulence of Listeria monocytogenes: preliminary results

Four strains of Listeria monocytogenes with different levels of virulence were studied. Two strains were consistently evaluated as virulent (strain 3077) and of low virulence (strain 3993), whereas the other two strains (3006 and 3049) originated conflicting results in what the evaluation tests were concerned: both were shown to exhibit low virulence when evaluated by in vitro assays, but virulent when the analyses were performed under in vivo conditions.To clarify the virulence potential of the selected strains, a proteomic approach was used after incubating L. monocytogenes cultures under conditions favoring the expression of virulence factors (minimal medium, at 37 °C). Bacterial proteins present in the liquid culture media were precipitated from late exponential phase cultures, fractionated by SDS-PAGE and identified by MALDI-TOF-MS.Three virulence factors differentially expressed were detected: protein p60, listeriolysin O (LLO) and internalin C (InlC). Clustering analysis of the four L. monocytogenes strains based on their secretome profiles allowed their categorization in two groups: the virulent group, composed by strains 3077 and 3049, and the low virulence group, containing strains 3993 and 3006. The results presented in this work suggest that the virulent potential of a particular L. monocytogenes strain may be predicted from the levels of both listeriolysin O (LLO) and internalin C (InlC) present in its secretome when the bacterium is grown under conditions favoring the expression of virulence factors. Following validation of this proposal through the analysis of a large array of strains, this methodology exhibits a great potential to be developed into an accurate and rapid method to characterize L. monocytogenes strain virulence.     

Different iron-chelating properties of pyochelin diastereoisomers revealed by LC/MS

Pyochelin is a siderophore and virulence factor common to Burkholderia cepacia and several Pseudomonas strains. It is isolated from bacterial media as a mixture of two epimers, which readily equilibrate in most solvents. Experiments based on high-performance liquid chromatography/electrospray ionization mass spectrometry are reported here, allowing the investigation of the different Fe(III)-chelating properties of pyochelin diastereomers in solution without the need for labourious isolation. It is demonstrated in this study that only one of the two pyochelin diastereomers is able to chelate Fe(III); no Fe(III) complexes of the other diastereomer could be detected. The Fe(III)–pyochelin complex exhibited a 1:1 metal-to-siderophore ratio and no evidence for other stoichiometries was found.      

On the analysis of the virulence nature of TIGR4 and R6 strains of Streptococcus pneumoniae using genome comparison tools

Comparative genome sequence analysis is a powerful technique for gaining insights into any genome of interest. Streptococcus pneumoniae is a human pathogen, which causes life-threatening diseases, such as pneumoniae, bacteremia, meningitis, etc. After the whole genome of two strains of S. pneumoniae, the virulent TIGR4 and non-pathogenic R6 were sequenced; there is a hope that comparing the genomes will allow an identification of the genes responsible for its virulence and thus the development of treatment and control. Many antimicrobial drugs have diminished the risk from pneumococcal disease because of its multi-drug resistance nature. Several pneumococcal proteins are also being investigated, as virulence factors as potential vaccine or drug targets. Structural and biochemical studies of these pneumococcal virulence factors have facilitated the development of novel antibiotics or protein antigen-based vaccines for the treatment of pneumococcal disease. Here we describe the comparison between the genomes of two strains of S. pneumoniae with few existing genomics databases and tools available in the public domain websites. By comparing nucleotide and protein sequences of the two strains, we investigate the existing differences and similarities. Mainly we focus on the virulence factors and its encoding genes in TIGR4 and how do they differ from R6 strain.     

Application of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry for the study of Helicobacter pylori

The characteristics of matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry based investigation of extremely variable bacteria such as Helicobacter pylori were studied. H. pylori possesses a very high natural variability. Accurate tools for species identification and epidemiological characterization could help the scientific community to better understand the transmission pathways and virulence mechanisms of these bacteria. Seventeen clinical as well as two laboratory strains of H. pylori were analyzed by the MALDI Biotyper method for rapid species identification. Mass spectra collected were found containing 7–13 significant peaks per sample, and only six protein signals were identical for more than half of the strains. Four of them could be assigned to ribosomal proteins RL32, RL33, RL34, and RL36. The reproducible peak with m/z 6948 was identified as a histidine‐rich metal‐binding polypeptide by tandem mass spectrometry (MS/MS). In spite of the evident protein heterogeneity of H. pylori the mass spectra collected for a particular strain under several cultivations were highly reproducible. Moreover, all clinical strains were perfectly identified as H. pylori species through comparative analysis using the MALDI Biotyper software (Bruker Daltonics, Germany) by pattern matching against a database containing mass spectra from different microbial strains (n = 3287) including H. pylori 26695 and J99. The results of this study allow the conclusion that the MALDI‐TOF direct bacterial profiling is suited for H. pylori identification and could be supported by mass spectra fragmentation of the observed polypeptide if necessary. Copyright © 2010 John Wiley & Sons, Ltd.     

Distribution and Degradation of 14C-Ethyl Prothiofos in a Potato Plant and the Effect of Processing

Prothiofos and some of its degradation products have been synthesized in our laboratory for investigation purposes. The residual fate of ¹⁴ C-ethyl prothiofos in different parts of potato plant was studied. The highest level of insecticide residues was detected in and on the leaves of potato plants. The residues of prothiofos insecticide were mainly located in the peels of potato tubers (peeling process removed 85% of the total residue after one month of the treatment), small amount penetrated into the pulp of potato tubers. The degradation products in the extracts of both peel and pulp of potato tubers were identified as prothiofos, prothiofos oxon, desethyl prothiofos, O-ethyl-S-propyl phosphorodithioate, O-ethyl phosphorothioate, O-ethyl-S-propyl phosphoric acid, O-ethyl phosphoric acid, despropylthio prothiofos, and prothiofos oxon sulfoxide. In addition 2,4-dichlorophenol was identified as such and in conjugated metabolites.

Potatoes are processed in three ways: frying, boiling, and baking, which is simulated in home preparation. The amount of prothiofos residues was found to decrease on boiling (70%) and further on baking (82%) and frying (100%). The results indicated that frying process is the most effective method for reducing the amount of pesticide residues. Detectable residues were found in boiled potatoes (2.64 ppm), in the boiling water (0.24 ppm), and in the frying oil (0.71 ppm). From these results we concluded that the processed potatoes are safely used for human consumption.     

Analysis of volatiles emitted by potato plants by means of a Colorado beetle electroantennographic detector

An electroantennographic detector based on the antenna of the Colorado potato beetle (Leptinotarsa decemlineata Say, 1824) was used to investigate volatile organic compounds emitted by injured potato plants (Solanum tuberosum L., 1753). Samples were collected on charcoal traps using the CLSA method. Analyses were performed with a GC-EAD-FID setup as well as a GC-MS system. The experiments revealed that several groups of compounds are perceptible to the Colorado potato beetle. The ability of the Colorado potato beetle to detect green leaf odours (e.g. (Z)-3-hexen-1-ol and (E)-2-hexenal), linalool and some terpenes has been noticed before [Visser et al., J. Chem. Ecol. 5 (1979) 13]. In this work the presence of (Z)-3-hexen-1-ol, (E)-2-hexenal and linalool in the potato odour could be confirmed. Moreover, β-myrcene, benzeneethanol, and several sesquiterpenes (e.g. caryophyllene and germacrene-D) were identified. The GC-EAD experiments reveal that apart from the green leaf odours and linalool prominent reactions of the Colorado bettle antenna are induced by benzeneethanol and the sesquiterpene fraction.     

Surfactin production from potato process effluent by Bacillus subtilis in a chemostat

The biosurfactant surfactin has potential to aid in the recovery of energy resources (oil recovery) or subsurface organic contaminants (environmental remediation). However, high medium and purification costs limit its use in these high-volume applications. In previous work, we showed that surfactin could be produced from an inexpensive low-solids potato process effluent with minimal amendments or pretreatments. Previous research has also shown that surfactin can be both produced in Bacillus subtilis cultures and recovered by foam fractionation in an airlift reactor. Results using both purified potato starch and unamended low-solids potato process effluent as substrates for surfactin production indicate that the process is oxygen limited and that recalcitrant indigenous bacteria in the potato process effluent hamper continuous surfactin production. The research reported here features the use of a chemostat operated in batch mode for producing surfactin with concomitant use of antifoam to prevent surfactant loss. The antifoam did not interfere with surfactin recovery by acid precipitation or its efficacy. Initial trials took about 48 h to produce 0.9 g/L of surfactin from potato process effluent. Increasing the oxygen mass transfer by increasing the stirring speed and adding a baffle decreased production time to 12–24 h and produced about 0.6 g/L of surfactin from two different potato-processing facilities.     

Construction of recombinant Bacillus subtilis for production of polyhydroxyalkanoates

Polyhydroxyalkanoates (PHAs) are polyesters of hydroxyalkanoates synthesized by numerous bacteria as intracellular carbon and energy storage compounds and accumulated as granules in the cytoplasm of cells. In this work, we constructed two recombinant plasmids, pBE2C1, and pBE2C1AB, containing one or two PHA synthse, genes, respectively. The two plasmids were inserted into Bacillus subtilis DB104 to generate modified strains, B. subtilis/pBE2C1 and B. subtilis/pBE2C1AB. The two recombinants strains were subjected to fermentation and showed PHA accumulation, the first reported example of mcl-PHA production in B. subtilis. Gas Chromatography analysis identified the compound produced by B. subtilis/pBE2C1 to be a hydroxydecanoate-co-hydroxydodecanoate (HD-co-HDD) polymer whereas that produced by B. subtilis/pBE2C1AB was a hydroxybutyrate-co-hydroxyde-canoate-co-hydroxydodecanoate (HB-HD-HDD) polymer.     

Characterization of different food‐isolated Enterococcus strains by MALDI‐TOF mass fingerprinting

Enterococcus is a controversial genus due to its great variability; this genus includes pathogenic strains, spoilage strains, and apparently safe strains including some probiotic strains. Previous studies focused on the characterization of strains of Enterococcus spp. involved in nosocomial infections. However, little research has been conducted on Enterococcus strains in foodstuffs. In the present work, 36 strains of different species of Enterococcus have been characterized by means of MALDI‐TOF MS, resulting in highly specific mass spectral fingerprints. Characteristic peak masses common to certain bacterial species of Enterococcus have been identified. Thus, a peak at m/z 4426 ± 1 was assigned as a genus‐specific biomarker. In addition, phyloproteomic relationships based on the mass spectral data were compared to the results of a phylogenetic analysis based on the 16S rRNA gene sequence. A better grouping at the species level was observed in the phyloproteomic tree, especially for the Enterococcus faecium group. Presumably, the assortment of some strains or ecotypes could be related to their ecological niche specialization. The approach described in this study leads the way toward the rapid and specific identification of different strains and species of Enterococcus in food based on molecular protein markers, aiming at the early detection of pathogenic strains and strains implicated in food poisoning or food spoilage.     

Cyclopropanol Warhead in Malleicyprol Confers Virulence of Human‐ and Animal‐Pathogenic Burkholderia Species

Burkholderia species such as B. mallei and B. pseudomallei are bacterial pathogens causing fatal infections in humans and animals (glanders and melioidosis), yet knowledge on their virulence factors is limited. While pathogenic effects have been linked to a highly conserved gene locus (bur/mal) in the B. mallei group, the metabolite associated to the encoded polyketide synthase, burkholderic acid (syn. malleilactone), could not explain the observed phenotypes. By metabolic profiling and molecular network analyses of the model organism B. thailandensis, the primary products of the cryptic pathway were identified as unusual cyclopropanol‐substituted polyketides. First, sulfomalleicyprols were identified as inactive precursors of burkholderic acid. Furthermore, a highly reactive upstream metabolite, malleicyprol, was discovered and obtained in two stabilized forms. Cell‐based assays and a nematode infection model showed that the rare natural product confers cytotoxicity and virulence.     

A potential bacterial carrier for bioremediation

One of the limiting factors to the effectiveness of biostimulation and bioremediation is the loss of inoculated material from the site. This can occur by a number of pathways, but is particularly problematic in open water systems where the inoculated material is simply lost in the water. It is desirable to develop new material, a matrix, within which bacteria and/or biostimulants can be incorporated. We have investigated the basic physical properties of insoluble potato starch to eventually evaluate its use as such a matrix. Insoluble starch fibers were prepared from white potato (Solanum tuberosum) and sweet potato (Ipomoea batatas) and were compared for their melting temperature by DSC and their ability to bind/aggregate bacteria. The DSC curves for white and sweet potato showed that the melting temperature is 127.34 and 133.05°C for white and sweet potato fibers, respectively. The TG curves for white and sweet potato starches exhibited one main mass loss step corresponding to the DTG peak temperature at 323.39 and 346.93°C, respectively. The two types of fibers, however, showed different binding/aggregation capacities for bacteria, with white potato approximately twice as many cells of Burkholderia cepacia (22.6 billion/g) as cells of Pseudomonas putida. The reverse was true for fibers from sweet potato, binding twice as many cells of Pseudomonas putida (23 billion/g) as cells of Burkholderia cepacia.     

Degradation of bisphenol A by <Emphasis Type="Italic">Bacillus pumilus</Emphasis> isolated from kimchi,a traditionally fermented food

Novel bisphenol A (BPA)-degrading bacterial strains, designated as BP-2CK, BP-21DK, and BP-22DK, were isolated from kimchi, a traditionally fermented food. These isolates were identified as Bacillus pumilus and efficiently degraded BPA in a medium supplemented with nutrients such as peptone, beef extract, and yeast extract. Strains BP-2CK, BP-21DK, and BP-22DK successfully degraded 25, 25, and 50 ppm of BPA, respectively, and all strains exhibited BPA-degrading activity in the presence of 10% NaCl. Accumulation of the metabolites including 4-hydroxyacetophenone, one of the intermediates produced by the other BPA-degrading bacteria, was not observed in BPA degradation by the isolated strains. These results indicate that the isolated food-derived bacteria are applicable for the construction of efficient and safer systems for the removal of BPA.     

A LecA Ligand Identified from a Galactoside‐Conjugate Array Inhibits Host Cell Invasion by Pseudomonas aeruginosa

Lectin LecA is a virulence factor of Pseudomonas aeruginosa involved in lung injury, mortality, and cellular invasion. Ligands competing with human glycoconjugates for LecA binding are thus promising candidates to counteract P. aeruginosa infections. We have identified a novel divalent ligand from a focused galactoside(Gal)‐conjugate array which binds to LecA with very high affinity (K_d=82 nM ). Crystal structures of LecA complexed with the ligand together with modeling studies confirmed its ability to chelate two binding sites of LecA. The ligand lowers cellular invasiveness of P. aeruginosa up to 90 % when applied in the range of 0.05–5 μM . Hence, this ligand might lead to the development of drugs against P. aeruginosa infection.     

Gold‐Catalyzed Cyclization Leads to a Bridged Tetracyclic Indolenine that Represses β‐Lactam Resistance

A gold‐catalyzed desilylative cyclization was developed for facile synthesis of bridged tetracyclic indolenines, a common motif in many natural indole alkaloids. An antimicrobial screen of the cyclization products identified one compound which selectively potentiates β‐lactam antibiotics in methicillin‐resistant S. aureus (MRSA), and re‐sensitizes a variety of MRSA strains to β‐lactams.     

Treatment of dairy wastewater using a selected bacterial isolate, Alcaligenes sp. MMRR7

Physicochemical and biologic analysis of dairy wastewater showed that the effluent had a high organic load (chemical oxygen demand [COD]: 5095 mg/L), an acidic pH (6.4), and a high probability of coliforms (most probable number [MPN]>1100). The various bacterial strains isolated and purified were identified as Sporolactobacillus sp., Citrobacter sp., Pseudomonas sp., Alcaligenes sp., Bacillus sp., Staphylococcus sp., and Proteus sp., as per the Bergey’s manual of systematic bacteriology. Among the five selected bacterial strains, the strain designated as MMRR₇ and identified as Alcaligenes sp. was found to give a maximum reduction in COD (62%) in 5 d of incubation. Chemical coagulation using alum at a concentration of 0.5 g/100 mL was found to be effective in the primary treatment of the effluent. Studies on free-cell treatment of the coagulated effluent with the selected bacterial strain Alcaligenes sp. MMRR₇ gave a maximum COD reduction of 91% in 120 h. This study clearly indicates the possibility of using Alcaligenes sp. MMRR₇ for the effective treatment of dairy wastewater.     

Enzymatic Thioamide Formation in a Bacterial Antimetabolite Pathway

6‐Thioguanine (6TG) is a DNA‐targeting therapeutic used in the treatment of various cancers. While 6TG was rationally designed as a proof of concept for antimetabolite therapy, it is also a rare thioamide‐bearing bacterial natural product and critical virulence factor of Erwinia amylovorans, plant pathogens that cause fire blight. Through gene expression, biochemical assays, and mutational analyses, we identified a specialized bipartite enzyme system, consisting of an ATP‐dependent sulfur transferase (YcfA) and a sulfur‐mobilizing enzyme (YcfC), that is responsible for the peculiar oxygen‐by‐sulfur substitution found in the biosynthesis of 6TG. Mechanistic and phylogenetic studies revealed that YcfA‐mediated 6TG biosynthesis evolved from ancient tRNA modifications that support translational fidelity. The successful in vitro reconstitution of 6TG thioamidation showed that YcfA employs a specialized sulfur shuttle that markedly differs from universal RNA‐related systems. This study sheds light on underexplored enzymatic C?S bond formation in natural product biosynthesis.     

Extraction and determination of the potato glycoalkaloid α -solanine in soil

The toxic glycoalkaloids α-solanine and α-chaconine are produced in all parts of the potato plant, and post-harvest potato tubers may represent a source of soil and water contamination. A new method was developed for extraction and purification of α-solanine in soil samples. Soil samples were extracted with THF?:?H₂O?:?ACN?:?CH₃COOH (50?:?30?:?20?:?1) and the extract purified by SPE before HPLC determination of α-solanine. The limit of detection was 2.4?mg of α-solanine?kg^?1 soil. The new procedure was used for determination of α-solanine in spiked soils with varying content of organic matter and texture. Recovery for soil samples spiked with α-solanine 1?h before extraction was 61–68% for soils low in organic carbon (<2.2% C), and to 47% for soil high in organic carbon. Similar recoveries were obtained for α-chaconine. The reproducibility of the method shown by the relative standard deviation varied from 1.7 to 10.1%, depending on the soil type. No decrease in extractable α-solanine was observed until day 17 for soil samples spiked with pure α-solanine kept at 5°C, while the content in samples spiked with potato materials showed a faster decline. This indicates that the degradation and/or ageing processes proceed relatively slowly for glycoalkaloids in soil matrices. This is the first method reported for determination of potato glycoalkaloids in soil.     

Identification and differentiation of dragon's blood in works of art using gas chromatography/mass spectrometry

Dragon's blood is a common but non-specific name for red-coloured resins that are produced by various plants, particularly exudations from plant species belonging to the genera Dracaena and Daemonorops. Although dragon's blood is mentioned in historic sources as a colourant, it has hardly ever been identified in real artworks. This paper reports the identification and discrimination of dragon's blood produced by Dracaena cinnabari, Dracaena draco as well as Daemonorops draco and Daemonorops micracantha by means of gas chromatography/mass spectrometry (GC/MS) within the context of a routine analysis of binding media used in works of art. The detection of specific flavonoid marker compounds in both underivatised and methylated methanol extracts provided the first evidence for the use of dragon's blood from all four species in various works of art from the fifteenth to nineteenth centuries. Dragon's blood was mainly used as a red colourant in gold lacquers as well as translucent glazes and paints, e.g. in reverse-glass paintings (Hinterglasmalerei).