Tin-carbon cleavage of organotin compounds by pyoverdine from Pseudomonas chlororaphis

iChip increases the success of cultivation of TBT-resistant and TBT-degrading bacteria from estuarine sediment

Standard methods of microbial cultivation only enable the isolation of a fraction of the total environmental bacteria. Numerous techniques have been developed to increase the success of isolation and cultivation in the laboratory, some of which derive from diffusion chambers. In a diffusion chamber, environmental bacteria in agar medium are put back in the environment to grow as close to their natural conditions as possible, only separated from the environment by semi-permeable membranes. In this study, the iChip, a device that possesses hundreds of mini diffusion chambers, was used to isolate tributyltin (TBT) resistant and degrading bacteria. IChip was shown to be efficient at increasing the number of cultivable bacteria compared to standard methods. TBT-resistant strains belonging to Oceanisphaera sp., Pseudomonas sp., Bacillus sp. and Shewanella sp. were identified from Liverpool Dock sediment. Among the isolates in the present study, only members of Pseudomonas sp. were able to use TBT as a sole carbon source. It is the first time that members of the genus Oceanisphaera have been shown to be TBT-resistant. Although iChip has been used in the search for molecules of biomedical interest here we demonstrate its promising application in bioremediation.

Metabolic reconstruction of Pseudomonas chlororaphis ATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain

Pseudomonas chlororaphis is a plant-associated bacterium with reported antagonistic activity against different organisms and plant growth-promoting properties. P. chlororaphis possesses exciting biotechnological features shared with another Pseudomonas with a nonpathogenic phenotype. Part of the antagonistic role of P. chlororaphis is due to its production of a wide variety of phenazines. To expand the knowledge of the metabolic traits of this organism, we constructed the first experimentally validated genome-scale model of P. chlororaphis ATCC 9446, containing 1267 genes and 2289 reactions, and analyzed strategies to maximize its potential for the production of phenazine-1-carboxamide (PCN). The resulting model also describes the capability of P. chlororaphis to carry out the denitrification process and its ability to consume sucrose (Scr), trehalose, mannose, and galactose as carbon sources. Additionally, metabolic network analysis suggested fatty acids as the best carbon source for PCN production. Moreover, the optimization of PCN production was performed with glucose and glycerol. The optimal PCN production phenotype requires an increased carbon flux in TCA and glutamine synthesis. Our simulations highlight the intrinsic H₂O₂ flux associated with PCN production, which may generate cellular stress in an overproducing strain. These results suggest that an improved antioxidative strategy could lead to optimal performance of phenazine-producing strains of P. chlororaphis. KEY POINTS : • This is the first publication of a metabolic model for a strain of P. chlororaphis. • Genome-scale model is worthy tool to increase the knowledge of a non model organism. • Fluxes simulations indicate a possible effect of H₂O₂ on phenazines production. • P. chlororaphis can be a suitable model for a wide variety of compounds.

Organotin compound DBDCT induces CYP3A suppression through NF-κB-mediated repression of PXR activity

Organotin anticancer agent di-n-butyl-di-(4-chlorobenzohydroxamato)tin(iv) (DBDCT) exerted an inhibitory effect on its major metabolic enzyme cytochrome CYP3A. But whether hepatic drug-metabolizing enzymes and their regulatory nuclear receptors including pregnane PXR and constitutive androstane CAR binding with retinoid receptor RXR as a heterodimer are involved in the DBDCT-mediated regulation of CYP3A remains unclear. This study was undertaken to determine the mechanisms responsible for the effects of DBDCT on CYP3A suppression, focusing on the PXR-mediated and NF-κB pathways. The results indicated DBDCT suppressed CYP3A expression by inhibiting CAR expression. But what's interesting is, both protein and mRNA of PXR increased with increasing DBDCT. A further exploration, dual luciferase reporter gene analysis, clarified that DBDCT induced CYP3A expression elevation via the PXR-mediated pathway and this induction was countered by activation of NF-κB, which played a pivotal role in suppression of CYP3A through disrupting the association of the PXR-RXRα complex with DNA sequences by EMSA. PXR-mediated CYP3A expression was similarly demonstrated by RNAi. As expected, expression of CYP3A and its mRNA levels were reduced by DBDCT only in NF-κB(+/+) but not in NF-κB(-/-) cells. The inductive effect of DBDCT on CYP3A4 mRNA was enhanced in PXR shRNA-transfected cells but weakened in the ip65 group, which showed both PXR up-regulated CYP3A expression and NF-κB p65 activation directly contributed to CYP3A inhibition. In conclusion, activated NF-κB by DBDCT interacts directly with the DNA-binding domain of PXR, and disrupts the binding between the PXR-RXR dimer, thereby affecting the regulatory process for CYP3A transcription and, therefore, leading to a decrease of the expression of the PXR-regulated CYP3A.

Methylation and dealkykation of tin compounds by sulfate- and nitrate-reducing bacteria

In this study, axenic cultures of sulfate-reducing (SRB) and nitrate-reducing (NRB) bacteria were examined for their ability to methylate inorganic tin and to methylate or dealkylate butyltin compounds. Environmentally relevant concentrations of natural abundance tributyltin (TBT) and ¹¹⁶Sn-enriched inorganic tin were added to bacterial cultures to identify bacterial-mediated methylation and dealkylation reactions. The results show that none of the Desulfovibrio strains tested was able to induce any transformation process. In contrast, Desulfobulbus propionicus strain DSM-6523 degraded TBT either under sulfidogenic or non-sulfidogenic conditions. In addition, it was able to alkykate ¹¹⁶Sn-enriched inorganic tin leading to the formation of more toxic dimethyltin and trimethyltin. A similar capacity was observed for incubations of Pseudomonas but with a much greater dealkykation of TBT. As such, Pseudomonas sp. ADR42 degraded 61% of the initial TBT under aerobic conditions and 35% under nitrate-reducing conditions. This is the first work reporting a simultaneous TBT degradation and a methylation of both inorganic tin species and TBT dealkykation products by SRB and NRB under anoxic conditions. These reactions are environmentally relevant as they can control the mobility of these compounds in aquatic ecosystems; as well as their toxicity toward resident organisms.

Draft Genome Sequence of Pseudomonas chlororaphis ATCC 9446, a Nonpathogenic Bacterium with Bioremediation and Industrial Potential

Pseudomonas chlororaphis strain ATCC 9446 is a biocontrol-related organism. We report here its draft genome sequence assembled into 35 contigs consisting of 6,783,030 bp. Genome annotation predicted a total of 6,200 genes, 6,128 coding sequences, 81 pseudogenes, 58 tRNAs, 4 noncoding RNAs (ncRNAs), and 41 frameshifted genes.

Bio-Electron-Fenton (BEF) process driven by microbial fuel cells for triphenyltin chloride (TPTC) degradation

The intensive use of triphenyltin chloride (TPTC) has caused serious environmental pollution. In this study, an effective method for TPTC degradation was proposed based on the Bio-Electron-Fenton process in microbial fuel cells (MFCs). The maximum voltage of the MFC with graphite felt as electrode was 278.47% higher than that of carbon cloth. The electricity generated by MFC can be used for in situ generation of H₂O₂ to a maximum of 135.96μmolL^-1 at the Fe@Fe₂O_3(*)/graphite felt composite cathode, which further reacted with leached Fe²⁺ to produce hydroxyl radicals. While 100μmolL^-1 TPTC was added to the cathodic chamber, the degradation efficiency of TPTC reached 78.32±2.07%, with a rate of 0.775±0.021μmolL^-1h^-1. This Bio-Electron-Fenton driving TPTC degradation might involve in SnC bonds breaking and the main process is probably a stepwise dephenylation until the formation of inorganic tin and CO₂. This study provides an energy saving and efficient approach for TPTC degradation.

Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin (TBT): Unravelling the effects from the molecular level to the organism

Aeromonas molluscorum Av27 cells were exposed to 0, 5 and 50 μM of TBT and the respective transcriptomes were obtained by pyrosequencing. Gene Ontology revealed that exposure to 5 μM TBT results in a higher number of repressed genes in contrast with 50 μM of TBT, where the number of over-expressed genes is greater. At both TBT concentrations, higher variations in gene expression were found in the functional categories associated with enzymatic activities, transport/binding and oxidation-reduction. A number of proteins are affected by TBT, such as the acriflavin resistance protein, several transcription-related proteins, several Hsps, ABC transporters, CorA and ZntB and other outer membrane efflux proteins, all of these involved in cellular metabolic processes, important to maintain overall cell viability. Using the STRING tool, several proteins with unknown function were related with others involved in degradation processes, such as the pyoverdine chromophore biosynthetic protein, that has been described as playing a role in the Sn-C cleavage of organotins. This approach has allowed a better understanding of the molecular effects of exposure of bacterial cells to TBT. Furthermore it contributes to the knowledge of the functional genomic aspects of bacteria exposed to this pollutant. Furthermore, the transcriptomic data gathered, and now publically available, constitute a valuable resource for comparative genome analysis.

Tributyltin chloride (TBTCl)-enhanced exopolysaccharide and siderophore production in an estuarine Alcaligenes faecalis strain

Tributyltin chloride (TBTCl) has been used extensively as an antifouling agent in ship paints, which results in the contamination of aquatic sites. These contaminated sites serve as enrichment areas for TBTCl-resistant bacterial strains. One TBTCl-resistant bacterial strain was isolated from the sediments of Zuari estuary, Goa, India, which is a major hub of various ship-building activities. Based on biochemical characteristics and 16S rDNA sequence analysis, this bacterial strain was identified as Alcaligenes faecalis and designated as strain SD5. It could degrade ≥3 mM TBTCl by using it as a sole carbon source and transform it into the less toxic dibutyltin chloride, which was confirmed by nuclear magnetic resonance and mass spectroscopy. Interestingly, this bacterial strain also showed enhanced exopolysaccharide and siderophore production when cells were exposed to toxic levels of TBTCl, suggesting their involvement in conferring resistance to this antifouling biocide as well as degradative capability respectively.

Denitration of 2,4,6-trinitrotoluene in aqueous solutions using small-molecular-weight catalyst(s) secreted by Pseudomonas aeruginosa ESA-5

The denitration of 2,4,6-trinitrotoluene (TNT) can produce mono- or dinitro aromatic compounds susceptible to microbial mineralization. In the present study, denitration of TNT and other nitro aromatic compounds was investigated with a solid-phase extract obtained from the culture supernatant of Pseudomonas aeruginosa ESA-5 grown on a chemically defined aerobic medium. When the C18 solid-phase extract containing extracellular catalysts (EC) was incubated with TNT and NAD(P)H, we observed a significant release of nitrite. The concentration of nitrite released in the reaction medium was strongly dependent on the concentration of NAD(P)H and EC. Denitration also occurred with two TNT-related molecules, 2,4,6-trinitrobenzaldehyde, and 2,4,6-trinitrobenzyl alcohol. The release of nitrite was coupled with the formation of two polar metabolites, and mass spectrometry analyses indicated that each of these compounds had lost two nitro groups from the trinitro aromatic parent molecule. During this process, the production of toxic reduced TNT metabolites was minimal. The incubation of EC with TNT, NAD(P)H, and specific scavengers of reactive oxygen species suggested the involvement of superoxide radicals (O2*-) and hydrogen peroxide in the denitration process. Results obtained in this study reveal for the first time that extracellular small-molecular-weight substance(s) of bacterial origin can serve as green catalyst(s) to initiate TNT denitration. In addition, this study gives clear evidence for the production of a TNT metabolite bearing a single nitro groupfollowing a denitration reaction with catalyst(s) of biotic origin.

Siderophores in fluorescent pseudomonads: new tricks from an old dog

Iron is an essential nutrient for almost all bacteria; however, at neutral pH its bioavailability is limited. Siderophores are iron-binding compounds of low molecular weight that enable the microorganisms that produce them to obtain the necessary iron from the environment. Fluorescent pseudomonads include those that are plant growth promoting, human and plant pathogens, as well as bacteria involved in the biodegradation of xenobiotics. Although pyoverdine is the main siderophore produced by different fluorescent pseudomonads, other siderophores produced by fluorescent pseudomonads include pyochelin, (thio)quinolobactin and pyridine-2, 6-bis thiocarboxylic acid. Research on siderophores continues to reveal new information on their regulation, biosynthesis, function and properties. In this review, we focus on recent advances in the field, particularly on newly characterized siderophores produced by fluorescent pseudomonads and their biotechnological potential.

pPSX: a novel vector for the cloning and heterologous expression of antitumor antibiotic gene clusters

A cosmid cloning vector has been constructed that demonstrates high levels of segregational stability in Escherichia coli K12. pPSX is a 14-kilobase vector derived from the IncW plasmid pR388. pPSX is highly stable in E. coli in the absence of antibiotic selection, even while expressing the toxic indolocarbazole antitumor antibiotic violacein. The incorporation of the lambdacos sequence enables construction of cosmid libraries with inserts ranging from 24 to 36kb. The inclusion of a lacZalpha multiple cloning site (MCS) allows blue/white screening. pPSX cosmids can be extracted from the host cell with commercial plasmid extraction kits facilitating downstream analysis, sequencing and sub-cloning. pPSX can be transferred to a variety of heterologous hosts by either electroporation or mobilization from E. coli S17-1. While it is unstable in non-E. coli hosts without antibiotic selection, heterologous host strains such as Rhodobacter sphaeroides and Pseudomonas stutzeri will maintain the plasmid under antibiotic selection to allow screening of expressed inserts. pPSX provides the benefits of large insert sizes with high stability to allow cloning of chemotherapeutic gene clusters in E. coli and a range of other heterologous hosts.

Organotin decomposition by pyochelin, secreted by Pseudomonas aeruginosa even in an iron-sufficient environment

A triphenyltin (TPT)-decomposing strain, Pseudomonas aeruginosa CGMCC 1.860, was screened out. It secreted an unknown TPT-decomposing factor into the medium, later shown to be pyochelin, even in the presence of 100 muM iron. To our knowledge, this is the first report of organotin decomposition by pyochelin.

Mechanism of augmentation of organotin decomposition by ferripyochelin: formation of hydroxyl radical and organotin-pyochelin-iron ternary complex

Pyochelin (PCH), a kind of siderophore secreted by Pseudomonas aeruginosa, was recently found to have triphenyltin (TPT)-decomposing capacity. In this work, significant augmentation of TPT decomposition by ferripyochelin (FePCH), the chelating compound of PCH with iron, was demonstrated in Tris-HCl buffer (pH 8.0). The generation of hydroxyl radical (HO.) in the presence of FePCH was observed. Inhibition of HO. generation by adding catalase and HO. scavengers (methanol and dimethyl sulfoxide) decreased TPT decomposition, while an increase in HO. formation in the presence of H(2)O(2) enhanced its decomposition. Our findings indicated that HO. generated in the reaction system was responsible for the enhanced TPT decomposition by FePCH versus PCH. The existence of the TPT-pyochelin-iron ternary complex was demonstrated by electron spray ionization-mass spectrometry, tandem mass spectrometry, and (1)H nuclear magnetic resonance. On the basis of the above results, HO. produced in the presence of FePCH was deduced to be in close proximity to TPT and has more opportunity to attack the Sn-C bond, which resulted in the enhanced organotin decomposition. The information obtained may have considerable environmental significance.

Degradation of tributyltin in microcosm using Mekong River sediment

The degradation of tributyltin (TBT) and changes of bacterial number and community structures were investigated in microcosms using the sediment collected from the Mekong River, Vietnam. Concentrations of TBT in sediments were less than 0.62 ng/g (dry wt), lower than those reported from other areas. TBT-resistant bacteria were found in the three sampling sites, and the occurrence rates were 11-16% out of the total viable count. In this microcosm experiment, initial concentration of TBT [1.0-1.4 microg/g (dry wt)] decreased to 0.6 microg/g (dry wt) during 150 days, whereas that in the control microcosm with autoclaved sediment did not change, indicating that Mekong River sediment contains high TBT-degrading activity by microorganisms. The occurrence of TBT-resistant bacteria and the bacterial community structures monitored by denaturing gradient gel electrophoresis were almost the same between test and control groups, indicating that the addition of TBT had little influence on microbial community structure. Mekong River sediment seems to have a stable microbial community against TBT pollution.