Role of quinolinate phosphoribosyl transferase in degradation of phthalate by Burkholderia cepacia DBO1

Mechanisms and high-value applications of phthalate isomers degradation pathways in bacteria

Phthalate isomers are key intermediates in the biodegradation of pollutants including waste polyethylene terephthalate (PET) plastics and plasticizers. So far, an increasing number of phthalate isomer-degrading strains have been isolated, and their degradation pathways show significant diversity. In this paper, we comprehensively review the current status of research on the degrading bacteria, degradation characteristics, aerobic and anaerobic degradation pathways, and degradation genes (clusters) of phthalate isomers, and discuss the current shortcomings and challenges. Moreover, the degradation process of phthalate isomers produces many important aromatic precursor molecules, which can be used to produce higher-value derivative chemicals, and the modification of their degradation pathways holds good prospects. Therefore, this review also highlights the current progress made in modifying the phthalate isomer degradation pathway and explores its potential for high-value applications.

Advances in Phage Therapy: Targeting the Burkholderia cepacia Complex

The increasing prevalence and worldwide distribution of multidrug-resistant bacterial pathogens is an imminent danger to public health and threatens virtually all aspects of modern medicine. Particularly concerning, yet insufficiently addressed, are the members of the Burkholderia cepacia complex (Bcc), a group of at least twenty opportunistic, hospital-transmitted, and notoriously drug-resistant species, which infect and cause morbidity in patients who are immunocompromised and those afflicted with chronic illnesses, including cystic fibrosis (CF) and chronic granulomatous disease (CGD). One potential solution to the antimicrobial resistance crisis is phage therapy-the use of phages for the treatment of bacterial infections. Although phage therapy has a long and somewhat checkered history, an impressive volume of modern research has been amassed in the past decades to show that when applied through specific, scientifically supported treatment strategies, phage therapy is highly efficacious and is a promising avenue against drug-resistant and difficult-to-treat pathogens, such as the Bcc. In this review, we discuss the clinical significance of the Bcc, the advantages of phage therapy, and the theoretical and clinical advancements made in phage therapy in general over the past decades, and apply these concepts specifically to the nascent, but growing and rapidly developing, field of Bcc phage therapy.

Characterization and Genome Analysis of a Phthalate Esters-Degrading Strain Sphingobium yanoikuyae SHJ

A bacterium capable of utilizing dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP), and diisobuthyl phthalate (DIBP) as the sole carbon and energy source was isolated from shallow aquifer sediments. The strain was identified as Sphingobium yanoikuyae SHJ based on morphological characteristics, 16S rDNA gene phylogeny, and whole genome average nucleotide identity (ANI). The degradation half-life of DBP with substrate concentration of 8.5 and 50.0 mg/L by strain SHJ was 99.7 and 101.4 hours, respectively. The optimum degradation rate of DBP by SHJ was observed at 30°C and weak alkaline (pH 7.5). Genome sequence of the strain SHJ showed a circular chromosome and additional two circular plasmids with whole genome size of 5,669,383 bp and GC content of 64.23%. Functional annotation of SHJ revealed a total of 5,402 genes, with 5,183 protein-encoding genes, 143 pseudogenes, and 76 noncoding RNA genes. Based on genome annotation, 44 genes were identified to be involved in PAEs hydrolysis potentially. Besides, a region with size of about 6.9 kb comprised of seven ORFs, which is located on the smaller plasmid pSES189, was presumed to be responsible for the biodegradation of phthalate. These results provide insights into the genetic basis of DBP biodegradation in this strain.

RNA-Seq revealed the impairment of immune defence of tilapia against the infection of Streptococcus agalactiae with simulated climate warming

Global warming is one of the causes of disease outbreaks in fishes. Understanding its mechanisms is critical in aquaculture and fisheries. We used tilapia to study the effects of a high temperature on the infection of a bacterial pathogen Streptococcus agalactiae using RNA-Seq. We found that the dissolved oxygen level in water at 32 °C is lower than at 22 °C, and tilapia infected with the pathogen died more rapidly at 32 °C. The gene expression profiles showed significant differences in fish raised under different conditions. We identified 126 and 576 differentially expressed genes (DEGs) at 4 and 24 h post infection at 22 °C, respectively, whereas at 32 °C, the data were 312 and 1670, respectively. Almost all responding pathways at 22 °C were involved in the immune responses, whereas at 32 °C, the enriched pathways were not only involved in immune responses but also involved in oxygen and energy metabolisms. We identified significant signals of immunosuppression of immune responses at 32 °C. In addition, many of the enriched transcription factors and DEGs under positive selection were involved in immune responses, oxygen and/or energy metabolisms. Our results suggest that global warming could reduce the oxygen level in water and impair the defence of tilapia against bacterial infection.

Dibutylphthalate and Tween 80 alter ultrastructure inCandida albicans: implications for peroxisome proliferation

Phthalates are ubiquitous environmental pollutants associated with endocrine disruption and peroxisome proliferation in experimental animals. In yeasts exposed to environmental chemicals, including phthalates, alterations in cell growth, cellular morphology, and H2O2detoxification occur. Nutrient availability also influences diverse cellular processes. Differences in responses to environmental stress between Candida albicans and the model yeast, Saccharomyces cerevesiae , have been reported. In this study, we chose C. albicans as an alternate model for testing estrogen-like chemicals because of its high affinity estrogen-binding protein and, in contrast to S. cerevesiae, estrogens are not growth inhibitory for C. albicans. Cultures were grown in either yeast nitrogen dextrose (YND; phosphate limiting) or YNDP (YND plus 100 mmol/L inorganic phosphate). For chemical testing, 0.5% dibutylphthalate (DBP), 0.05% Tween 80, or a combination of the two (DBPT) were incorporated in growth media to investigate the effects of these estrogenic agents on cell proliferation, morphology, and catalase demonstration. We observed significant differences in cell growth related to DBP and changes in cell wall thickness related to both Tween 80 and phosphate. We describe ultrastructural changes including detachment of the outer yeast cell wall layer and presence of putative peroxisomes. Our findings support the proposal that C. albicans may be particularly suitable for use in studies involving cellular responses associated with exposure to estrogenic chemicals contained in complex mixtures.

Comparative metabolomic analysis of Sinorhizobium sp. C4 during the degradation of phenanthrene

Comparative metabolic responses of Sinorhizobium sp. C4 were investigated. Comprehensive metabolites profiles, including polar metabolites, fatty acids, and polyhydroxyalkanoates were evaluated through untargeted metabolome analyses. Intracellular metabolomes during the degradation of phenanthrene were compared with those from natural carbon sources. Principal component analysis showed a clear separation of metabolomes of phenanthrene degradation from other carbon sources. Shift to more hydrophobic fatty acid was observed from the analysis of fatty acid methyl ester. Polyhydroxyalkanoate from strain C4 was composed mainly with 3-hydroxybutyric acid and small amount of 3-hydroxypentanoic acid, while the monomeric composition was independent on carbon sources. However, the amount of polyhydroxyalkanoates during degradation of phenanthrene was 50–210% less than those from other carbon sources. Among 207 gas chromatography–mass spectrometry peaks from the polar metabolite fraction, 60% of the peaks were identified and compared. Several intermediates in tricarboxylic acid cycles and glycolysis were increased during phenanthrene degradation. Accumulation of trehalose was also evident in the phenanthrene-treated bacterium. Some amino acid, including branched amino acids, glycine, homoserine, and valine, were also increased, while more than 70% of identified metabolites were decreased during the phenanthrene metabolism. Accumulation of sulfur amino acids and nicotinic acid suggested the possible oxidative stress conditions during phenanthrene metabolism.

Bacterial degradation of phthalate isomers and their esters

Phthalate isomers and their esters are used heavily in various industries. Excess use and leaching from the product pose them as major pollutants. These chemicals are toxic, teratogenic, mutagenic and carcinogenic in nature. Various aspects like toxicity, diversity in the aerobic bacterial degradation, enzymes and genetic organization of the metabolic pathways from various bacterial strains are reviewed here. Degradation of these esters proceeds by the action of esterases to form phthalate isomers, which are converted to dihydroxylated intermediates by specific and inducible phthalate isomer dioxygenases. Metabolic pathways of phthalate isomers converge at 3,4-dihydroxybenzoic acid, which undergoes either ortho- or meta- ring cleavage and subsequently metabolized to the central carbon pathway intermediates. The genes involved in the degradation are arranged in operons present either on plasmid or chromosome or both, and induced by specific phthalate isomer. Understanding metabolic pathways, diversity and their genetic regulation may help in constructing bacterial strains through genetic engineering approach for effective bioremediation and environmental clean up.

Effects of enrichment with phthalate on polycyclic aromatic hydrocarbon biodegradation in contaminated soil

The effect of enrichment with phthalate on the biodegradation of polycyclic aromatic hydrocarbons (PAH) was tested with bioreactor-treated and untreated contaminated soil from a former manufactured gas plant (MGP) site. Soil samples that had been treated in a bioreactor and enriched with phthalate mineralized (14)C-labeled phenanthrene and pyrene to a greater extent than unenriched samples over a 22.5-h incubation, but did not stimulate benzo[a]pyrene mineralization. In contrast to the positive effects on (14)C-labeled phenanthrene and pyrene, no significant differences were found in the extent of biodegradation of native PAH when untreated contaminated soil was incubated with and without phthalate amendment. Denaturing-gradient gel electrophoresis (DGGE) profiles of bacterial 16S rRNA genes from unenriched and phthalate-enriched soil samples were substantially different, and clonal sequences matched to prominent DGGE bands revealed that beta-Proteobacteria related to Ralstonia were most highly enriched by phthalate addition. Quantitative real-time PCR analyses confirmed that, of previously determined PAH-degraders in the bioreactor, only Ralstonia-type organisms increased in response to enrichment, accounting for 89% of the additional bacterial 16S rRNA genes resulting from phthalate enrichment. These findings indicate that phthalate amendment of this particular PAH-contaminated soil did not significantly enrich for organisms associated with high molecular weight PAH degradation or have any significant effect on overall degradation of native PAH in the soil.

Fluoranthene metabolism and associated proteins in Mycobacterium sp. JS14

Fluoranthene is a polycyclic aromatic hydrocarbon (PAH) commonly present in PAH-contaminated soils. We studied fluoranthene catabolism and associated proteins in Mycobacterium sp. JS14, a bacterium isolated from a PAH-contaminated soil in Hilo (HI, USA). Fluoranthene degrades in at least three separated pathways via 1-indanone, 2',3'-dihydroxybiphenyl-2,3,-dicarboxylic acid, and naphthalene-1,8-dicarboxylic acid. Part of the diverse catabolism is converged into phthalate catabolism. An increased expression of 25 proteins related to fluoranthene catabolism is found with 1-D PAGE or 2-DE and nano-LC-MS/MS. Detection of fluoranthene catabolism associated proteins coincides well with its multiple degradation pathways that are mapped via metabolites identified. Among the up-regulated proteins, PAH ring-hydroxylating dioxygenase alpha-subunit and beta-subunit and 2,3-dihydroxybiphenyl 1,2-dioxygenase are notably induced. The up-regulation of trans-2-carboxybenzalpyruvate hydratase suggests that some of fluoranthene metabolites may be further degraded through aromatic dicarboxylic acid pathways. Catalase and superoxide dismutase were up-regulated to control unexpected oxidative stress during the fluoranthene catabolism. The up-regulation of chorismate synthase and nicotine-nucleotide phosphorylase may be necessary for sustaining shikimate pathway and pyrimidine biosynthesis, respectively. A fluoranthene degradation pathway for Mycobacterium sp. JS14 was proposed and confirmed by proteomic study by identifying almost all the enzymes required during the initial steps of fluoranthene degradation.

Diethyl phthalate in compost: ecotoxicological effects and response of the microbial community

There is a great need to understand the environmental impacts of organic pollutants on soil health. Phthalates are widely used in consumables and can be found extensively. We studied the toxicity of diethyl phthalate (DEP), spiked in a compost plant growth substrate, by means of the acute toxicity Flash test and on the basis of the germination and plant growth of radish seedlings. The response of the microbial community to DEP in the growth substrate was studied by PCR-DGGE (denaturing gradient gel electrophoresis). In the acute toxicity test, DEP was found to be less toxic as a pure compound than when mixed with the compost mixture. This suggests the synergistic effect of unknown toxic compounds or the release of compounds due to DEP addition. The same DEP concentration level in compost substrate induced toxic response in both plant test and microbial community analysis. The diversity of the major microbial community was reduced from a broad community to only 10 major species at toxic concentrations of DEP. Several of the identified microbial species are known to be able to degrade phthalates, which means that the suppression of other microbial species might be due to the substrate availability and toxicity. The major species identified included Sphingomonas sp., Pseudomonas sp., Actinomycetes sp.

Requirement of duplicated operons for maximal metabolism of phthalate by Rhodococcus sp. strain DK17

The operons encoding the transformation of phthalate to protocatechuate are duplicated and present on two different megaplasmids [pDK2 (330 kb) and pDK3 (750 kb)] in Rhodococcus sp. strain DK17. RT-PCR experiments using gene-specific primers showed that both the pDK2- and the pDK3-encoded dihydroxyphthalate decarboxylase genes are simultaneously expressed during growth on phthalate. The doubling time of the pDK2-cured mutant strain DK176 in minimal liquid medium with 5mM phthalate is 52.5% of that of the wild-type strain DK17. The data indicate that both copies of the phthalate operon are equally functional in DK17, and gene dosage is the main reason for slower growth of DK176 on phthalate.

Burkholderia spp. alter Pseudomonas aeruginosa physiology through iron sequestration

Pseudomonas aeruginosa and members of the Burkholderia cepacia complex often coexist in both the soil and the lungs of cystic fibrosis patients. To gain an understanding of how these different species affect each other's physiology when coexisting, we performed a screen to identify P. aeruginosa genes that are induced in the presence of Burkholderia: A random gene fusion library was constructed in P. aeruginosa PA14 by using a transposon containing a promoterless lacZ gene. Fusion strains were screened for their ability to be induced in the presence of Burkholderia strains in a cross-streak assay. Three fusion strains were induced specifically by Burkholderia species; all three had transposon insertions in genes known to be iron regulated. One of these fusion strains, containing a transposon insertion in gene PA4467, was used to characterize the inducing activity from Burkholderia: Biochemical and genetic evidence demonstrate that ornibactin, a siderophore produced by nearly all B. cepacia strains, can induce P. aeruginosa PA4467. Significantly, PA4467 is induced early in coculture with an ornibactin-producing but not an ornibactin-deficient B. cepacia strain, indicating that ornibactin can be produced by B. cepacia and detected by P. aeruginosa when the two species coexist.

Molecular characterization of quinolinate phosphoribosyltransferase (QPRtase) in Nicotiana

Quinolate acid phosphoribosyltransferase (QPRTase), a key enzyme in nicotinamide adenine dinucleotide (NAD) biosynthesis, also plays an important role in ensuring nicotinic acid is available for the synthesis of defensive pyridine alkaloids in Nicotiana species. In this study, cDNAs for QPRTase were characterized from N. rustica and N. tabacum. Deduced proteins from both cDNAs are almost identical and contain a 24 amino acid N-terminal extension, not reported in other QPRTases, that has characteristics of a mitochondrial targeting sequence. In N. tabacum and N. sylvestris, both of which contain nicotine as the major pyridine alkaloid, QPRTase transcript was detected in roots, the site of nicotine synthesis, but not in leaves. QPRTase transcript levels increased markedly in roots of both species 12-24 h after damage to aerial tissues, with a concomitant rise in transcript levels of putrescine N-methyltransferase (PMT), another key enzyme in nicotine biosynthesis. In N. glauca, however, in which anabasine represents the major pyridine alkaloid, QPRTase transcript was detected in both leaf and root tissues. Moreover, wound induction of QPRTase but not PMT was observed in leaf tissues, and not in roots, 12-24 h after wounding. Southern analysis of genomic DNA from the Nicotiana species noted above, and also several others from within the genus, suggested that QPRTase is encoded by a small gene family in all the species investigated.

Characterization of the phthalate permease OphD from Burkholderia cepacia ATCC 17616

The ophD gene, encoding a permease for phthalate transport, was cloned from Burkholderia cepacia ATCC 17616. Expression of the gene in Escherichia coli results in the ability to transport phthalate rapidly into the cell. Uptake inhibition experiments show that 4-hydroxyphthalate, 4-chlorophthalate, 4-methylphthalate, and cinchomeronate compete for the phthalate permease. An ophD knockout mutant of 17616 grows slightly more slowly on phthalate but is still able to take up phthalate at rates equivalent to that of the wild-type strain. This means that 17616 must have a second phthalate-inducible phthalate uptake system.