An unexpected gene cluster for downstream degradation of alkylphenols in Sphingomonas sp. strain TTNP3

Mechanisms of BPA Degradation and Toxicity Resistance in Rhodococcus equi

Bisphenol A (BPA) pollution poses an increasingly serious problem. BPA has been detected in a variety of environmental media and human tissues. Microbial degradation is an effective method of environmental BPA remediation. However, BPA is also biotoxic to microorganisms. In this study, Rhodococcus equi DSSKP-R-001 (R-001) was used to degrade BPA, and the effects of BPA on the growth metabolism, gene expression patterns, and toxicity-resistance mechanisms of Rhodococcus equi were analyzed. The results showed that R-001 degraded 51.2% of 5 mg/L BPA and that 40 mg/L BPA was the maximum BPA concentration tolerated by strain R-001. Cytochrome P450 monooxygenase and multicopper oxidases played key roles in BPA degradation. However, BPA was toxic to strain R-001, exhibiting nonlinear inhibitory effects on the growth and metabolism of this bacterium. R-001 bacterial biomass, total protein content, and ATP content exhibited V-shaped trends as BPA concentration increased. The toxic effects of BPA included the downregulation of R-001 genes related to glycolysis/gluconeogenesis, pentose phosphate metabolism, and glyoxylate and dicarboxylate metabolism. Genes involved in aspects of the BPA-resistance response, such as base excision repair, osmoprotectant transport, iron-complex transport, and some energy metabolisms, were upregulated to mitigate the loss of energy associated with BPA exposure. This study helped to clarify the bacterial mechanisms involved in BPA biodegradation and toxicity resistance, and our results provide a theoretical basis for the application of strain R-001 in BPA pollution treatments.

Comparative Analysis of the Genetic Basis of Branched Nonylphenol Degradation by Sphingobium amiense DSM 16289T and Sphingobium cloacae JCM 10874T

Branched nonylphenol (BNP), a degradation product of nonylphenol polyethoxylates, exerts estrogenic effects on various organisms. The genes underlying BNP degradation by Sphingobium amiense DSM 16289^T were analyzed by complete genome sequencing and compared with those of the versatile BNP-degrading Sphingobium cloacae JCM 10874^T. An opdA homolog (opdA_DSM16289) encoding BNP degradation activity was identified in DSM 16289^T, in contrast with JCM 10874^T, possessing both the opdA homolog and nmoA. The degradation profile of different BNP isomers was examined by Escherichia coli transformants harboring opdA_DSM16289, opdA_JCM10874, and nmoA_JCM10874 to characterize and compare the expression activities of these genes.

Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP

In the last decade, biological degradation and mineralization of antibiotics have been increasingly reported feats of environmental bacteria. The most extensively described example is that of sulfonamides that can be degraded by several members of Actinobacteria and Proteobacteria. Previously, we reported sulfamethoxazole (SMX) degradation and partial mineralization by Achromobacter denitrificans strain PR1, isolated from activated sludge. However, further studies revealed an apparent instability of this metabolic trait in this strain. Here, we investigated this instability and describe the finding of a low-abundance and slow-growing actinobacterium, thriving only in co-culture with strain PR1. This organism, named GP, shared highest 16S rRNA gene sequence similarity (94.6-96.9%) with the type strains of validly described species of the genus Leucobacter. This microbial consortium was found to harbor a homolog to the sulfonamide monooxygenase gene (sadA) also found in other sulfonamide-degrading bacteria. This gene is overexpressed in the presence of the antibiotic, and evidence suggests that it codes for a group D flavin monooxygenase responsible for the ipso-hydroxylation of SMX. Additional side reactions were also detected comprising an NIH shift and a Baeyer-Villiger rearrangement, which indicate an inefficient biological transformation of these antibiotics in the environment. This work contributes to further our knowledge in the degradation of this ubiquitous micropollutant by environmental bacteria.

Comparative Transcriptome Analysis Reveals the Mechanism Underlying 3,5-Dibromo-4-Hydroxybenzoate Catabolism via a New Oxidative Decarboxylation Pathway

The compound 3,5-dibromo-4-hydroxybenzoate (DBHB) is both anthropogenically released into and naturally produced in the environment, and its environmental fate is of great concern. Aerobic and anaerobic reductive dehalogenations are the only two reported pathways for DBHB catabolism. In this study, a new oxidative decarboxylation pathway for DBHB catabolism was identified in a DBHB-utilizing strain, Pigmentiphaga sp. strain H8. The genetic determinants underlying this pathway were elucidated based on comparative transcriptome analysis and subsequent experimental validation. A gene cluster comprising orf420 to orf426, with transcripts that were about 33- to 4,400-fold upregulated in DBHB-induced cells compared with those in uninduced cells, was suspected to be involved in DBHB catabolism. The gene odcA (orf420), which is essential for the initial catabolism of DBHB, encodes a novel NAD(P)H-dependent flavin monooxygenase that mediates the oxidative decarboxylation of DBHB to 2,6-dibromohydroquinone (2,6-DBHQ). The substrate specificity of the purified OdcA indicated that the 4-hydroxyl group and its ortho-halogen(s) are important for hydroxylation of the C-1 site carboxyl group by OdcA. 2,6-DBHQ is then ring cleaved by the dioxygenase OdcB (Orf425) to 2-bromomaleylacetate, which is finally transformed to β-ketoadipate by the maleylacetate reductase OdcC (Orf426). These results provide a better understanding of the molecular mechanism underlying the catabolic diversity of halogenated para-hydroxybenzoates.IMPORTANCE Halogenated hydroxybenzoates (HBs), which are widely used synthetic precursors for chemical products and common metabolic intermediates from halogenated aromatics, exert considerable adverse effects on human health and ecological security. Microbial catabolism plays key roles in the dissipation of halogenated HBs in the environment. In this study, the discovery of a new catabolic pathway for 3,5-dibromo-4-hydroxybenzoate (DBHB) and clarification of the genetic determinants underlying the pathway broaden our knowledge of the catabolic diversity of halogenated HBs in microorganisms. Furthermore, the NAD(P)H-dependent flavin monooxygenase OdcA identified in Pigmentiphaga sp. strain H8 represents a novel 1-monooxygenase for halogenated para-HBs found in prokaryotes and enhances our knowledge of the decarboxylative hydroxylation of (halogenated) para-HBs.

PnpM, a LysR-Type Transcriptional Regulator Activates the Hydroquinone Pathway in para-Nitrophenol Degradation in Pseudomonas sp. Strain WBC-3

A LysR-type transcriptional regulator (LTTR), PnpR, has previously been shown to activate the transcription of operons pnpA, pnpB, and pnpCDEFG for para-nitrophenol (PNP) degradation in Pseudomonas sp. strain WBC-3. Further preliminary evidence suggested the possible presence of an LTTR additional binding site in the promoter region of pnpCDEFG. In this study, an additional LTTR PnpM, which shows 44% homology to PnpR, was determined to activate the expression of pnpCDEFG. Interestingly, a pnpM-deleted WBC-3 strain was unable to grow on PNP but accumulating hydroquinone (HQ), which is the catabolic product from PNP degradation by PnpAB and the substrate for PnpCD. Through electrophoretic mobility shift assays (EMSAs) and promoter activity detection, only PnpR was involved in the activation of pnpA and pnpB, but both PnpR and PnpM were involved in the activation of pnpCDEFG. DNase I footprinting analysis suggested that PnpR and PnpM shared the same DNA-binding regions of 27 bp in the pnpCDEFG promoter. In the presence of PNP, the protection region increased to 39 bp by PnpR and to 38 bp by PnpM. Our data suggested that both PnpR and PnpM were involved in activating pnpCDEFG expression, in which PNP rather than the substrate hydroquinone for PnpCD is the inducer. Thus, during the PNP catabolism in Pseudomonas sp. strain WBC-3, pnpA and pnpB operons for the initial two reactions were controlled by PnpR, while the third operon (pnpCDEFG) for HQ degradation was activated by PnpM and PnpR. This study builds upon our previous findings and shows that two LTTRs PnpR and PnpM are involved in the transcriptional activation of these three catabolic operons. Specifically, our identification that an LTTR, PnpM, regulates pnpCDEFG expression provides new insights in an intriguing regulation system of PNP catabolism that is controlled by two regulators.

Complete Genome Sequence of the Nonylphenol-Degrading Bacterium Sphingobium cloacae JCM 10874T

Sphingobium cloacae JCM 10874^T can degrade phenolic endocrine-disrupting chemicals, nonylphenol, and octylphenol. Here, we report the complete genome sequence of the JCM 10874^T strain.

Degradation of sulfonamide antibiotics by Microbacterium sp. strain BR1 - elucidating the downstream pathway

Microbacterium sp. strain BR1 is among the first bacterial isolates which were proven to degrade sulfonamide antibiotics. The degradation is initiated by an ipso-substitution, initiating the decay of the molecule into sulfur dioxide, the substrate specific heterocyclic moiety as a stable metabolite and benzoquinone imine. The latter appears to be instantaneously reduced to p-aminophenol, as that in turn was detected as the first stable intermediate. This study investigated the downstream pathway of sulfonamide antibiotics by testing the strain's ability to degrade suspected intermediates of this pathway. While p-aminophenol was degraded, degradation products could not be identified. Benzoquinone was shown to be degraded to hydroquinone and hydroquinone in turn was shown to be degraded to 1,2,4-trihydroxybenzene. The latter is assumed to be the potential substrate for aromatic ring cleavage. However, no products from the degradation of 1,2,4-trihydroxybenzene could be identified. There are no signs of accumulation of intermediates causing oxidative stress, which makes Microbacterium sp. strain BR1 an interesting candidate for industrial waste water treatment.

Emerging chemicals and the evolution of biodegradation capacities and pathways in bacteria

The number of new chemicals produced is increasing daily by the thousands, and it is inevitable that many of these chemicals will reach the environment. Current research provides an understanding of how the evolution of promiscuous enzymes and the recruitment of enzymes available from the metagenome allows for the assembly of these pathways. Nevertheless, physicochemical constraints including bioavailability, bioaccessibility, and the structural variations of similar chemicals limit the evolution of biodegradation pathways. Similarly, physiological constraints related to kinetics and substrate utilization at low concentrations likewise limit chemical-enzyme interactions and consequently evolution. Considering these new data, the biodegradation decalogue still proves valid while at the same time the underlying mechanisms are better understood.

Exploring the potential of applying proteomics for tracking bisphenol A and nonylphenol degradation in activated sludge

A significant percentage of bisphenol A and nonylphenol removal in municipal wastewater treatment plants relies on biodegradation. Nonetheless, incomplete information is available concerning their degradation pathways performed by microbial communities in activated sludge systems. Hydroquinone dioxygenase (HQDO) is a specific degradation marker enzyme, involved in bisphenol A and nonylphenol biodegradation, and it can be produced by axenic cultures of the bacterium Sphingomonas sp. strain TTNP3. Proteomics, a technique based on the analysis of microbial community proteins, was applied to this strain. The bacterium proteome map was obtained and a HQDO subunit was successfully identified. Additionally, the reliability of the applied proteomics protocol was evaluated in activated sludge samples. Proteins belonging to Sphingomonas were searched at decreasing biomass ratios, i.e. serially diluting the bacterium in activated sludge. The protein patterns were compared and Sphingomonas proteins were discriminated against the ones from sludge itself on 2D-gels. The detection limit of the applied protocol was defined as 10(-3) g TTNP3 g(-1) total suspended solids (TSSs). The results proved that proteomics can be a promising methodology to assess the presence of specific enzymes in activated sludge samples, however improvements of its sensitivity are still needed.