CYP201A2, a cytochrome P450 from Rhodopseudomonas palustris, plays a key role in the biodegradation of tributyl phosphate

Anoxygenic phototrophic purple non-sulfur bacteria: tool for bioremediation of hazardous environmental pollutants

The extraordinary metabolic flexibility of anoxygenic phototrophic purple non-sulfur bacteria (PNSB) has been exploited in the development of various biotechnological applications, such as wastewater treatment, biohydrogen production, improvement of soil fertility and plant growth, and recovery of high-value compounds. These versatile microorganisms can also be employed for the efficient bioremediation of hazardous inorganic and organic pollutants from contaminated environments. Certain members of PNSB, especially strains of Rhodobacter sphaeroides and Rhodopseudomonas palustris, exhibit efficient remediation of several toxic and carcinogenic heavy metals and metalloids, such as arsenic, cadmium, chromium, and lead. PNSB are also known to utilize diverse biomass-derived lignocellulosic organic compounds and xenobiotics. Although biodegradation of some substituted aromatic compounds by PNSB has been established, available information on the involvement of PNSB in the biodegradation of toxic organic pollutants is limited. In this review, we present advancements in the field of PNSB-based bioremediation of heavy metals and organic pollutants. Furthermore, we highlight that the potential role of PNSB as a promising bioremediation tool remains largely unexplored. Thus, this review emphasizes the necessity of investing extensive research efforts in the development of PNSB-based bioremediation technology.

Mechanisms of flame retardant tris (2-ethylhexyl) phosphate biodegradation via novel bacterial strain Ochrobactrum tritici WX3-8

Tris (2-ethylhexyl) phosphate (TEHP) is a common organophosphorus flame retardant analog with considerable ecological toxicity. Here, novel strain Ochrobactrum tritici WX3-8 capable of degrading TEHP as the sole C source was isolated. Our results show that the strain's TEHP degradation efficiency reached 75% after 104 h under optimal conditions, i.e., 30 °C, pH 7, bacterial inoculum 3%, and Collapse

Key Words

• Biodegradation
• Metabolic pathway
• Ochrobactrum tritici
• Organic pollutants

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Affiliation(s)

Jiamei He College of Environment, Zhejiang University of Technology, Hangzhou, 310032, China
Zeyu Wang Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, 310015, China
Fengzhen Zhen College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310015, China
Zhaoyun Wang College of Environment, Zhejiang University of Technology, Hangzhou, 310032, China
Zhongdi Song Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, 310015, China
Jun Chen Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, 310015, China.
Dzmitry Hrynsphan Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk, 220030, Belarus
Savitskaya Tatsiana Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk, 220030, Belarus

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Rhodopseudomonas palustris: A biotechnology chassis

Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production. This review provides a holistic summary of the commercial applications for R. palustris as a biotechnology chassis and suggests future perspectives for research and engineering.

Degradation of the mixed organic solvents of tributyl phosphate and n-dodecane by heterogeneous Fenton-like oxidation using nanoscale zero-valent iron as the catalyst

The treatment and disposal of spent radioactive organic solvents, i.e., tributyl phosphate (TBP) and diluent (such as kerosene, n-dodecane, etc.), produced in the reprocessing of spent fuel in the closed cycle are crucial for the sustainable development of the nuclear industry. In this study, the synthesized nanoscale zero-valent iron (nZVI) was used as the heterogeneous Fenton-like catalyst to promote the generation of hydroxyl radicals (•OH) by reacting with H₂O₂ to degrade the mixed organic solvents of TBP and n-dodecane. nZVI was characterized by scanning electron microscopy (SEM), nitrogen adsorption/desorption isotherms, and X-ray photoelectron spectroscopy (XPS) to investigate the micro-morphology, nano-particle size, and surface valence state. The change of Fe²⁺/Fe³⁺ concentration ratio during the reaction was measured to clarify the performance of nZVI. The effects of temperature, catalyst dosage, H₂O₂ dosage, and acidifier concentration on the degradation of TBP and n-dodecane were studied, and the results were complemented by the COD of the aqueous solution and the volume reduction rate of the organic phase. The mixed organic solvents of TBP and n-dodecane containing Co²⁺ were used to simulate the spent radioactive organic solvents and to study the distribution of nuclides after the reaction. The results showed that most of the radioactivity was in the residual solution, and the condensate contained almost no radioactivity. The degradation of TBP and n-dodecane was carried out separately, which showed that n-dodecane was more difficult to degrade. Density functional theory (DFT) calculations were applied to determine the adsorption energy of organic solvents and nZVI. According to the Fourier transform infrared spectra (FTIR) and their corresponding DFT calculations, liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) of the sample after the reaction, the possible intermediates were analyzed, and the degradation mechanism was speculated.

Ancient Bacterial Class Alphaproteobacteria Cytochrome P450 Monooxygenases Can Be Found in Other Bacterial Species

Cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins, are well-known players in the generation of chemicals valuable to humans and as a drug target against pathogens. Understanding the evolution of P450s in a bacterial population is gaining momentum. In this study, we report comprehensive analysis of P450s in the ancient group of the bacterial class Alphaproteobacteria. Genome data mining and annotation of P450s in 599 alphaproteobacterial species belonging to 164 genera revealed the presence of P450s in only 241 species belonging to 82 genera that are grouped into 143 P450 families and 214 P450 subfamilies, including 77 new P450 families. Alphaproteobacterial species have the highest average number of P450s compared to Firmicutes species and cyanobacterial species. The lowest percentage of alphaproteobacterial species P450s (2.4%) was found to be part of secondary metabolite biosynthetic gene clusters (BGCs), compared other bacterial species, indicating that during evolution large numbers of P450s became part of BGCs in other bacterial species. Our study identified that some of the P450 families found in alphaproteobacterial species were passed to other bacterial species. This is the first study to report on the identification of CYP125 P450, cholesterol and cholest-4-en-3-one hydroxylase in alphaproteobacterial species (Phenylobacterium zucineum) and to predict cholesterol side-chain oxidation capability (based on homolog proteins) by P. zucineum.

Using high-throughput transcriptome sequencing to investigate the biotransformation mechanism of hexabromocyclododecane with Rhodopseudomonas palustris in water

We discovered one purple photosynthetic bacterium, Rhodopseudomonas palustris YSC3, which has a specific ability to degrade 1, 2, 5, 6, 9, 10-hexabromocyclododecane (HBCD). The whole transcriptome of R. palustris YSC3 was analyzed using the RNA-based sequencing technology in illumina and was compared as well as discussed through Multi-Omics onLine Analysis System (MOLAS, http://molas.iis.sinica.edu.tw/NTUIOBYSC3/) platform we built. By using genome based mapping approach, we can align the trimmed reads on the genome of R. palustris and estimate the expression profiling for each transcript. A total of 341 differentially expressed genes (DEGs) in HBCD-treated R. palustris (RPH) versus control R. palustris (RPC) was identified by 2-fold changes, among which 305 genes were up-regulated and 36 genes were down-regulated. The regulated genes were mapped to the database of Gene Ontology (GO) and Genes and Genomes Encyclopedia of Kyoto (KEGG), resulting in 78 pathways being identified. Among those DEGs which annotated to important functions in several metabolic pathways, including those involved in two-component system (13.6%), ribosome assembly (10.7%), glyoxylate and dicarboxylate metabolism (5.3%), fatty acid degradation (4.7%), drug metabolism-cytochrome P450 (2.3%), and chlorocyclohexane and chlorobenzene degradation (3.0%) were differentially expressed in RPH and RPC samples. We also identified one transcript annotated as dehalogenase and other genes involved in the HBCD biotransformation in R. palustris. Furthermore, the putative HBCD biotransformation mechanism in R. palustris was proposed.

Halogen-free organophosphorus flame retardants caused oxidative stress and multixenobiotic resistance in Asian freshwater clams (Corbicula fluminea)

Halogen-free organophosphorus flame retardants are widespread in aquatic environments. Although it has been documented that they affect the behavior and reproduction of aquatic species, researches investigating cellular detoxification and the defense system in bivalves are scarce. In this study, adult Asian clams (C. fluminea) were exposed to tris (2-butoxyethyl) phosphate (TBEP) and tributyl phosphate (TBP) at 20, 200, and 2000 μg/L for 28 d. The results showed no noticeable difference in siphoning behavior. However, the siphoning behavior displayed a trend toward a slight decrease in the treatment groups. GR activity was markedly reduced compared with the control groups, whereas the levels of cyp4 significantly increased following the 2000 μg/L TBP treatments (p < 0.05). Moreover, the levels of gsts1 and gstm1 significantly decreased following all TBEP treatments and were significantly inhibited by 20 μg/L TBP (p < 0.05). The adverse effects on antioxidant enzymes suggested that C. fluminea mainly relies on the antioxidant system to reduce damage without an increase in MDA levels following exposure to a low concentration. Moreover, mRNA expression levels of heat shock proteins (hsp 22, 40, 60, 70, and 90) were significantly down-regulated with TBEP and TBP treatments lower than 200 μg/L (p < 0.05), whereas significant up-regulations were observed for hsp 22 and hsp 70 in response to 2000 μg/L TBP treatment (p < 0.05). Up-regulation of ATP-binding cassette (ABC) transporter genes (abcb1 and abcc1) showed that TBEP and TBP could activate the multixenobiotic resistance (MXR) system to discharge xenobiotics in C. fluminea, which kept its shell closed at high concentrations to prevent xenobiotic entry. Our results provide a new insight into the different mechanisms of cellular detoxification and the MXR system of C. fluminea in response to low and high concentrations of TBEP and TBP.

Inhibitory effects of tributyl phosphate on algal growth, photosynthesis, and fatty acid synthesis in the marine diatom Phaeodactylum tricornutum

The widely used solvent extractant, tributyl phosphate (TBP), primarily used as a solvent for the conventional processing of nuclear fuel, has come under scrutiny recently due to concerns surrounding potential environmental contamination and toxicity. In this study, we found that, in Phaeodactylum tricornutum, administration of TBP severely inhibited algal cell growth by reducing photosynthetic efficiency and inducing oxidative stress. We further explored the effect of TBP by examining the gene expression of the photosynthetic electron transport chain and its contribution to reactive oxygen species (ROS) burst. Our data revealed that TBP affected both fatty acid content and profile by regulating the transcription of genes related to glycolysis, fatty acid biosynthesis, and β-oxidation. These results demonstrated that TBP did in fact trigger the synthesis of ROS, disrupting the subcellular membrane structure of this aquatic organism. Our study brings new insight into the fundamental mechanism of toxicity exerted by TBP on the marine alga P. tricornutum.

Biodegradation of tributyl phosphate, an organosphate triester, by aerobic granular biofilms

Tributyl phosphate (TBP) is commercially used in large volumes for reprocessing of spent nuclear fuel. TBP is a very stable compound and persistent in natural environments and it is not removed in conventional wastewater treatment plants. In this study, cultivation of aerobic granular biofilms in a sequencing batch reactor was investigated for efficient biodegradation of TBP. Enrichment of TBP-degrading strains resulted in efficient degradation of TBP as sole carbon or along with acetate. Complete biodegradation of 2mM of TBP was achieved within 5h with a degradation rate of 0.4 μmol mL(-1) h(-1). TBP biodegradation was accompanied by release of inorganic phosphate in stoichiometric amounts. n-Butanol, hydrolysed product of TBP was rapidly biodegraded. But, dibutyl phosphate, a putative intermediate of TBP degradation was only partially degraded pointing to an alternative degradation pathway. Phosphatase activity was 22- and 7.5-fold higher in TBP-degrading biofilms as compared to bioflocs and acetate-fed aerobic granules. Community analysis by terminal restriction length polymorphism revealed presence of 30 different bacterial strains. Seven bacterial stains, including Sphingobium sp. a known TBP degrader were isolated. The results show that aerobic granular biofilms are promising for treatment of TBP-bearing wastes or ex situ bioremediation of TBP-contaminated sites.

Heterologous expression of membrane proteins: choosing the appropriate host

Background

Membrane proteins are the targets of 50% of drugs, although they only represent 1% of total cellular proteins. The first major bottleneck on the route to their functional and structural characterisation is their overexpression; and simply choosing the right system can involve many months of trial and error. This work is intended as a guide to where to start when faced with heterologous expression of a membrane protein.

Methodology/Principal Findings

The expression of 20 membrane proteins, both peripheral and integral, in three prokaryotic (E. coli, L. lactis, R. sphaeroides) and three eukaryotic (A. thaliana, N. benthamiana, Sf9 insect cells) hosts was tested. The proteins tested were of various origins (bacteria, plants and mammals), functions (transporters, receptors, enzymes) and topologies (between 0 and 13 transmembrane segments). The Gateway system was used to clone all 20 genes into appropriate vectors for the hosts to be tested. Culture conditions were optimised for each host, and specific strategies were tested, such as the use of Mistic fusions in E. coli. 17 of the 20 proteins were produced at adequate yields for functional and, in some cases, structural studies. We have formulated general recommendations to assist with choosing an appropriate system based on our observations of protein behaviour in the different hosts.

Conclusions/Significance

Most of the methods presented here can be quite easily implemented in other laboratories. The results highlight certain factors that should be considered when selecting an expression host. The decision aide provided should help both newcomers and old-hands to select the best system for their favourite membrane protein.

Biodegradation of tributyl phosphate by novel bacteria isolated from enrichment cultures

Tributyl phosphate (TBP) is an organophosphorous compound, used extensively (3000-5000 tonnes/annum) as a solvent for nuclear fuel processing and as a base stock in the formulation of fire-resistant aircraft hydraulic fluids and other applications. Because of its wide applications and relative stability in the natural environment TBP poses the problem of pollution and health hazards. In the present study, fifteen potent bacterial strains capable of using tributyl phosphate (TBP) as sole carbon and phosphorus source were isolated from enrichment cultures. These isolates were identified on the basis of biochemical and morphological characteristics and 16S rRNA gene sequence analysis. Phylogenetic analysis of 16S rRNA gene sequences revealed that two isolates belonged to class Bacilli and thirteen to β and γ-Proteobacteria. All these isolates were found to be members of genera Alcaligenes, Providencia, Delftia, Ralstonia, and Bacillus. These isolates were able to tolerate and degrade up to 5 mM TBP, the highest concentration reported to date. The GC-MS method was developed to monitor TBP degradation. Two strains, Providencia sp. BGW4 and Delftia sp. BGW1 showed respectively, 61.0 ± 2.8% and 57.0 ± 2.0% TBP degradation within 4 days. The degradation rate constants, calculated by first order kinetic model were between 0.0024 and 0.0099 h(-1). These bacterial strains are novel for TBP degradation and could be used as an important bioresource for efficient decontamination of TBP polluted waste streams.