The biphenyl/polychlorinated biphenyl-degradation locus (bph) of Pseudomonas sp. LB400 encodes four additional metabolic enzymes

Unraveling metabolic flexibility of rhodococci in PCB transformation

Even though the genetic attributes suggest presence of multiple degradation pathways, most of rhodococci are known to transform PCBs only via regular biphenyl (bph) pathway. Using GC-MS analysis, we monitored products formed during transformation of 2,4,4'-trichlorobiphenyl (PCB-28), 2,2',5,5'-tetrachlorobiphenyl (PCB-52) and 2,4,3'-trichlorobiphenyl (PCB-25) by previously characterized PCB-degrading rhodococci Z6, T6, R2, and Z57, with the aim to explore their metabolic pleiotropy in PCB transformations. A striking number of different transformation products (TPs) carrying a phenyl ring as a substituent, both those generated as a part of the bph pathway and an array of unexpected TPs, implied a curious transformation ability. We hypothesized that studied rhodococcal isolates, besides the regular one, use at least two alternative pathways for PCB transformation, including the pathway leading to acetophenone formation (via 3,4 (4,5) dioxygenase attack on the molecule), and a third sideway pathway that includes stepwise oxidative decarboxylation of the aliphatic side chain of the 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate. Structure of the identified chlorinated benzoic acids and acetophenones allowed us to hypothesize that the first two pathways were the outcome of a ring-hydroxylating dioxygenase with the ability to attack both the 2,3 (5,6) and the 3,4 (4,5) positions of the biphenyl ring as well as dechlorination activity at both, -ortho and -para positions. We propose that several TPs produced by the bph pathway could have caused the triggering of the third sideway pathway. In conclusion, this study proposed ability of rhodococci to use different strategies in PCB transformation, which allows them to circumvent potential negative aspect of TPs on the overall transformation pathway.

Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses

Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used ¹³C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active cells using single-cell analyses and protein–stable isotope probing. The detection of ¹³C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. The quantitative role of these microorganisms in pollutant degradation was resolved using single-cell-based uptake measurements. Our strategy advances our understanding of microbially mediated biodegradation processes and has general application potential for elucidating the ecological roles of uncultured microorganisms in their natural habitats.

Recent advances in the biodegradation of polychlorinated biphenyls

Polychlorinated biphenyls (PCBs) are typical lasting organic pollutants. Persistence and recalcitrance to biodegradation of PCBs have hampered the transformation of PCB congeners from the environment. Biological transformation of polychlorinated biphenyls could take place through anaerobic dechlorination, aerobic microbial degradation, and a combination of transformation of anaerobic dechlorination and aerobic degradation. Under anaerobic conditions, microbial dechlorination is an important degradation mode for PCBs, especially high-chlorinated congeners. The low-chlorinated compounds formed after reductive dechlorination could be further aerobically degraded and completely mineralized. This paper reviews the recent advances in biological degradation of PCBs, introduces the functional bacteria and enzymes involved in the anaerobic and aerobic degradation of PCBs, and discusses the synergistic action of anaerobic reduction and aerobic degradation. In addition, the different ways to the microbial remediation of PCBs-contaminated environments are discussed. This review provides a theoretical foundation and practical basis to use PCBs-degrading microorganisms for bioremediation.

Structural and biochemical characterization of a glutathione transferase from the citrus canker pathogen Xanthomonas

The genus Xanthomonas comprises several cosmopolitan plant-pathogenic bacteria that affect more than 400 plant species, most of which are of economic interest. Citrus canker is a bacterial disease that affects citrus species, reducing fruit yield and quality, and is caused by the bacterium Xanthomonas citri subsp. citri (Xac). The Xac3819 gene, which has previously been reported to be important for citrus canker infection, encodes an uncharacterized glutathione S-transferase (GST) of 207 amino-acid residues in length (XacGST). Bacterial GSTs are implicated in a variety of metabolic processes such as protection against chemical and oxidative stresses. XacGST shares high sequence identity (45%) with the GstB dehalogenase from Escherichia coli O6:H1 strain CFT073 (EcGstB). Here, XacGST is reported to be able to conjugate glutathione (GSH) with bromoacetate with a Km of 6.67 ± 0.77 mM, a kcat of 42.69 ± 0.32 s-1 and a kcat/Km of 6.40 ± 0.72 mM-1 s-1 under a saturated GSH concentration (3.6 mM). These values are comparable to those previously reported for EcGstB. In addition, crystal structures of XacGST were determined in the apo form (PDB entry 6nxv) and in a GSH-bound complex (PDB entry 6nv6). XacGST has a canonical GST-like fold with a conserved serine residue (Ser12) at the GSH-binding site near the N-terminus, indicating XacGST to be a serine-type GST that probably belongs to the theta-class GSTs. GSH binding stabilizes a loop of about 20 residues containing a helix that is disordered in the apo XacGST structure.

Degradation Mechanism of 4-Chlorobiphenyl by Consortium of Pseudomonas sp. Strain CB-3 and Comamonas sp. Strain CD-2

Polychlorinated biphenyls (PCBs) are types of lasting environmental pollutants which are widely used in various industries. 4-chlorobiphenyl (4CBP) is a PCB which is harmful to the environment as well as humans. Two strains, CB-3 and CD-2, were isolated from the polluted soil of a chemical factory and could completely degrade 50 mg/L 4CBP within 12 h by co-culture. The consortium comprising strains CB-3 and CD-2 was effective in the degradation of 4CBP. 4CBP was degraded initially by strain CB-3 to accumulate 4-chlorobenzoate (4CBA) and further oxidised by strain CD-2. Based on 16S rRNA gene sequence analysis and phenotypic typing, strain CB-3 and strain CD-2 were identified as Pseudomonas sp. and Comamonas sp., respectively. The substrate spectra experiment showed that strain CB-3 could degrade PCBs with no more than three chlorine atoms. A gene cluster of biphenyl metabolism was found in the genome of strain CB-3. Besides, a dechlorination gene cluster and a gene cluster of protocatechuate (PCA) metabolic were found in the genome of strain CD-2. These gene clusters are supposed to be involved in 4CBP degradation. The ability of strains CB-3 and CD-2 to degrade 4CBP in soil was assessed by soil experiment, and 4CBP at the initial concentration of 10 mg/kg was 80.5% removed within 15 days.

Biodegradation of dibenzothiophene by efficient Pseudomonas sp. LKY-5 with the production of a biosurfactant

A potent bacterial strain capable of degrading dibenzothiophene (DBT) was isolated and evaluated for its characteristics. The strain, designated as LKY-5, is rod-shaped, gram-negative, and occurs mainly in clusters. It was identified as belonging to the Pseudomonas genus based on the 16S rDNA sequence and phylogenic analysis. Determination of its DBT depletion efficiency by gas chromatography revealed that the isolate was able to completely degrade up to 100 mg L^-1 DBT within 144 h. The pH values, DBT concentrations, and biomasses in the medium varied significantly in the initial 24 h. A biosurfactant produced by LKY-5 was extracted and identified as a di-rhamnolipid with the formula Rha-Rha-C₈-C_8:1 by HPLC-ESI-MS/MS. There were 26 metabolites in the DBT degradation process. Pseudomonas sp. LKY-5 exhibited unusually high DBT degradation efficiency via multiple metabolic pathways. Compared with the reported 4S and Kodama pathways, two more expanded metabolic pathways for the degradation of DBT are proposed. The polycyclic aromatic sulfur heterocycles (PASHs) in diesel, such as C₁-DBT, C₂-DBT, C₃-DBT, 4,6-DMDBT, and 2,4,6-TMDBT, can also be degraded with 28.2-42.3% efficiency. The results showed that LKY-5 is an excellent bacterial candidate for the bioremediation of PASH-contaminated sites and sediments.

Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1

The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.

Intracellular toxicity exerted by PCBs and role of VBNC bacterial strains in biodegradation

Polychlorinated biphenyls (PCBs) are xenobiotic compounds that persists in the environment for long-term, though its productivity is banned. Abatement of the pollutants have become laborious due to it's recalcitrant nature in the environment leading to toxic effects in humans and other living beings. Biphenyl degrading bacteria co-metabolically degrade low chlorinated PCBs using the active metabolic pathway. bph operon possess different genetic arrangements in gram positive and gram negative bacteria. The binding ability of the genes and the active sites were determined by PCB docking studies. The active site of bphA gene with conserved amino acid residues determines the substrate specificity and biodegradability. Accumulation of toxic intermediates alters cellular behaviour, biomass production and downturn the metabolic activity. Several bacteria in the environment attain unculturable state which is viable and metabolically active but not cultivable (VBNC). Resuscitation-promoting factor (Rpf) and Rpf homologous protein retrieve the culturability of the so far uncultured bacteria. Recovery of this adaptive mechanism against various physical and chemical stressors make a headway in understanding the functionality of both environmental and medically important unculturable bacteria. Thus, this paper review about the general aspects of PCBs, cellular toxicity exerted by PCBs, role of unculturable bacterial strains in biodegradation, genes involved and degradation pathways. It is suggested to extrapolate the research findings on extracellular organic matters produced in culture supernatant of VBNC thus transforming VBNC to culturable state.

Bacterial strategies for growth on aromatic compounds

Although the biodegradation of aromatic compounds has been studied for over 40 years, there is still much to learn about the strategies bacteria employ for growth on novel substrates. Elucidation of these strategies is crucial for predicting the environmental fate of aromatic pollutants and will provide a framework for the development of engineered bacteria and degradation pathways. In this chapter, we provide an overview of studies that have advanced our knowledge of bacterial adaptation to aromatic compounds. We have divided these strategies into three broad categories: (1) recruitment of catabolic genes, (2) expression of "repair" or detoxification proteins, and (3) direct alteration of enzymatic properties. Specific examples from the literature are discussed, with an eye toward the molecular mechanisms that underlie each strategy.

Characterization of the metabolic pathway and catabolic gene expression in biphenyl degrading marine bacterium Pseudomonas aeruginosa JP-11

Metabolic pathway of biphenyl assimilation and the catabolic gene expression in a marine bacterium Pseudomonas aeruginosa JP-11, isolated from the coastal sediments of Odisha, India have been studied. This strain utilized 98.86% ± 2.29% of biphenyl within 72 h when supplied as the sole source of carbon, however, preferential utilization of glucose was observed over catechol and biphenyl when grown in a complex medium. Combination of chromatographic and spectrophotometric techniques confirmed the catechol pathway and identified 2-Hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate as the intermediate metabolic product. Assimilation of biphenyl was initiated by its dioxygenation, forming cis-2, 3-dihydro-2, 3-dihydroxybiphenyl subsequently transformed to 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate. In the lower pathway, cis-1, 6-dihydroxy-2, 4-cyclohexadiene-1-carboxylic acid was detected which formed catechol before entering into the Krebs cycle. Detection of key enzyme catechol-1, 2-dioxygenase in the cell-free extract of P. aeruginosa JP-11 supported the proposed degradation pathway. The primary enzyme for biphenyl assimilation, biphenyl dioxygenase encoded by bphA gene was found in the genome of the isolate. On increasing biphenyl stress (50, 100, 150 and 200 mg L(-1)), bphA gene showed a significant (P < 0.01) up-regulation upto 43.5 folds. Production of biosurfactant was confirmed and the rhamnolipid synthesizing gene rhlAB was amplified. This gene also showed a significant (P < 0.01) up-regulation upto 258 folds on increasing biphenyl stress.

Sphingobium fuliginis HC3: a novel and robust isolated biphenyl- and polychlorinated biphenyls-degrading bacterium without dead-end intermediates accumulation

Biphenyl and polychlorinated biphenyls (PCBs) are typical environmental pollutants. However, these pollutants are hard to be totally mineralized by environmental microorganisms. One reason for this is the accumulation of dead-end intermediates during biphenyl and PCBs biodegradation, especially benzoate and chlorobenzoates (CBAs). Until now, only a few microorganisms have been reported to have the ability to completely mineralize biphenyl and PCBs. In this research, a novel bacterium HC3, which could degrade biphenyl and PCBs without dead-end intermediates accumulation, was isolated from PCBs-contaminated soil and identified as Sphingobium fuliginis. Benzoate and 3-chlorobenzoate (3-CBA) transformed from biphenyl and 3-chlorobiphenyl (3-CB) could be rapidly degraded by HC3. This strain has strong degradation ability of biphenyl, lower chlorinated (mono-, di- and tri-) PCBs as well as mono-CBAs, and the biphenyl/PCBs catabolic genes of HC3 are cloned on its plasmid. It could degrade 80.7% of 100 mg L -1 biphenyl within 24 h and its biphenyl degradation ability could be enhanced by adding readily available carbon sources such as tryptone and yeast extract. As far as we know, HC3 is the first reported that can degrade biphenyl and 3-CB without accumulation of benzoate and 3-CBA in the genus Sphingobium, which indicates the bacterium has the potential to totally mineralize biphenyl/PCBs and might be a good candidate for restoring biphenyl/PCBs-polluted environments.

OxyR-dependent expression of a novel glutathione S-transferase (Abgst01) gene in Acinetobacter baumannii DS002 and its role in biotransformation of organophosphate insecticides

While screening a genomic library of Acinetobacter baumannii DS002 isolated from organophosphate (OP)-polluted soils, nine ORFs were identified coding for glutathione S-transferase (GST)-like proteins. These GSTs (AbGST01-AbGST09) are phylogenetically related to a number of well-characterized GST classes found in taxonomically diverse groups of organisms. Interestingly, expression of Abgst01 (GenBank accession no. KF151191) was upregulated when the bacterium was grown in the presence of an OP insecticide, methyl parathion (MeP). The gene product, AbGST01, dealkylated MeP to desMeP. An OxyR-binding motif was identified directly upstream of Abgst01. An Abgst-lacZ gene fusion lacking the OxyR-binding site showed a drastic reduction in promoter activity. Very low β-galactosidase activity levels were observed when the Abgst-lacZ fusion was mobilized into an oxyR (GenBank accession no. KF151190) null mutant of A. baumannii DS002, confirming the important role of OxyR. The OxyR-binding sites are not found upstream of other Abgst (Abgst02-Abgst09) genes. However, they contained consensus sequence motifs that can serve as possible target sites for certain well-characterized transcription factors. In support of this observation, the Abgst genes responded differentially to different oxidative stress inducers. The Abgst genes identified in A. baumannii DS002 are found to be conserved highly among all known genome sequences of A. baumannii strains. The versatile ecological adaptability of A. baumannii strains is apparent if sequence conservation is seen together with their involvement in detoxification processes.

Cloning of three 2,3-dihydroxybiphenyl-1,2-dioxygenase genes from Achromobacter sp. BP3 and the analysis of their roles in the biodegradation of biphenyl

Three 2,3-dihydroxybiphenyl 1,2-dioxygenase genes (designated as bphC1, bphC2 and bphC3) were cloned from a biphenyl-degrading strain Achromobacter sp. BP3. The amino acid sequence of BphC1 and BphC3 had high similarity (>99%) with the reported BphCs, while BphC2 showed relatively low identity (29.51-50.17%) with the reported BphCs, which indicated that bphC2 might be a novel gene. The bphC1, bphC2 and bphC3 genes were expressed in Escherichia coli BL21 and the products were homogenously purified. BphC1, BphC2 and BphC3 displayed maximum activity at 30°C, 30°C and 40°C, respectively. Their optimal catalysis pH was 8.0, 9.0 and 9.0, respectively. BphC1 and BphC2 had higher substrate affinity and catalytic efficiency on 2,3-dihydroxybiphenyl, while BphC3 exhibited these features on aromatic monocyclic substrates. The bphC1 gene was only induced by biphenyl and bphC3 was induced by both biphenyl and toluene, while bphC2 was constitutively expressed in strain BP3. These results suggested that BphC1 and BphC3 played a role in the upstream and downstream metabolic pathways of biphenyl, respectively. However, BphC2 might play a supplementary role and contribute more to the upstream than to the downstream pathway.

Molecular characterization of 2-chlorobiphenyl degrading Stenotrophomonas maltophilia GS-103

The catabolic potential of transformer oil contaminated soil bacteria in aerobic degradation of polychlorinated biphenyls (PCB) were assessed. Transformer oil contaminated soil sample was subjected to microcosm enrichment experiments (PAS medium/biphenyl as sole carbon source). PCB-degrading activity of the enrichment cultures in PAS medium with the addition of 2-chlorobiphenyl were analysed by GC-MS indicated that, although the isolates differed in PCB-degrading capabilities, all of the enrichment cultures expressed activity toward at least some of the lower chlorinated congeners. Biphenyl-utilizing bacteria isolated from the most active PCB-degrading mixed cultures showed little taxonomic diversity and identified as Stenotrophomonas maltophilia GS-103.

Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway

2,3-Dihydroxybenzoate is the precursor in the biosynthesis of several siderophores and an important plant secondary metabolite that, in bacteria, can be degraded via meta-cleavage of the aromatic ring. The dhb cluster of Pseudomonas reinekei MT1 encodes a chimeric meta-cleavage pathway involved in the catabolism of 2,3-dihydroxybenzoate. While the first two enzymes, DhbA and DhbB, are phylogenetically related to those involved in 2,3-dihydroxy-p-cumate degradation, the subsequent steps are catalyzed by enzymes related to those involved in catechol degradation (DhbCDEFGH). Characterization of kinetic properties of DhbA extradiol dioxygenase identified 2,3-dihydroxybenzoate as the preferred substrate. Deletion of the encoding gene impedes growth of P. reinekei MT1 on 2,3-dihydroxybenzoate. DhbA catalyzes 3,4-dioxygenation with 2-hydroxy-3-carboxymuconate as the product, which is then decarboxylated by DhbB to 2-hydroxymuconic semialdehyde. This compound is then subject to dehydrogenation and further degraded to citrate cycle intermediates. Transcriptional analysis revealed genes of the dhB gene cluster to be highly expressed during growth with 2,3-dihydroxybenzoate, whereas a downstream-localized gene encoding 2-hydroxymuconic semialdehyde hydrolase, dispensable for 2,3-dihydroxybenzoate metabolism but crucial for 2,3-dihydroxy-p-cumate degradation, was only marginally expressed. This is the first report describing a gene cluster encoding enzymes for the degradation of 2,3-dihydroxybenzoate.

Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes

Bacterial aldolase-dehydrogenase complexes catalyze the last steps in the meta cleavage pathway of aromatic hydrocarbon degradation. The aldolase (TTHB246) and dehydrogenase (TTHB247) from Thermus thermophilus were separately expressed and purified from recombinant Escherichia coli. The aldolase forms a dimer, while the dehydrogenase is a monomer; these enzymes can form a stable tetrameric complex in vitro, consisting of two aldolase and two dehydrogenase subunits. Upon complex formation, the K(m) value of 4-hydroxy-2-oxopentanoate, the substrate of TTHB246, is decreased 4-fold while the K(m) of acetaldehyde, the substrate of TTHB247, is increased 3-fold. The k(cat) values of each enzyme were reduced by ~2-fold when they were in a complex. The half-life of TTHB247 at 50 °C increased by ~4-fold when it was in a complex with TTHB246. The acetaldehyde product from TTHB246 could be efficiently channelled directly to TTHB247, but the channeling efficiency for the larger propionaldehyde was ~40% lower. A single A324G substitution in TTHB246 increased the channeling efficiency of propionaldehyde to a value comparable to that of acetaldehyde. Stable and catalytically competent chimeric complexes could be formed between the T. thermophilus enzymes and the orthologous aldolase (BphI) and dehydrogenase (BphJ) from the biphenyl degradation pathway of Burkholderia xenovorans LB400. However, channeling efficiencies for acetaldehyde in these chimeric complexes were ~10%. Structural and sequence analysis suggests that interacting residues in the interface of the aldolase-dehydrogenase complex are highly conserved among homologues, but coevolution of partner enzymes is required to fine-tune this interaction to allow for efficient substrate channeling.

Metabolic characterization and genes for the conversion of biphenyl in Dyella ginsengisoli LA-4

A complete bph gene cluster (bphLA-4) containing 12,186 bp was amplified from Dyella ginsengisoli LA-4. The bphLA-4 was composed of bphABCXD, and an additional gene encoding a meta-fission product hydrolase was located in the bphX region. BphLA-4 was independently transcribed by the two operons, bphA1A2orf1A3A4BCX0 and bphX1orf2X2X3D, and significantly differed from bphKF707. Both benzoate and catechol induced the expression of both operons. 2-Hydroxypenta-2,4-dienoate was identified as the intermediate of the biphenyl degradation by strain LA-4. This finding suggested that there existed a novel lower pathway of biphenyl degradation in strain LA-4.

MDC1 collaborates with TopBP1 in DNA replication checkpoint control

The DNA damage checkpoint protein MDC1 also interacts with TopBP1 to promote DNA replication checkpoint control.

Human TopBP1 is a major player in the control of the DNA replication checkpoint. In this study, we identified MDC1, a key checkpoint protein involved in the cellular response to DNA double-strand breaks, as a TopBP1-associated protein. The specific TopBP1–MDC1 interaction is mediated by the fifth BRCT domain of TopBP1 and the Ser-Asp-Thr (SDT) repeats of MDC1. In addition, we demonstrated that TopBP1 accumulation at stalled replication forks is promoted by the H2AX/MDC1 signaling cascade. Moreover, MDC1 is important for ATR-dependent Chk1 activation in response to replication stress. Collectively, our data suggest that MDC1 facilitates several important steps in both cellular DNA damage response and the DNA replication checkpoint.

[Advance in bioremediation of polychlorinated biphenyls]

As one of the persistent organic pollutants, polychlorinated biphenyls are harmful to the environment and humans. Biodegradation is the most potential way to remove PCBs. Biodegradation can mainly be divided into microbial degradation, phytoremediation, plant and microbial combined remediation. Here, we introduced isolation of the PCBs-degrading strains, cloning and modification of the related degradation genes. Additionally, on the other hand, the natural remediation of plant, plant and microbial combined remediation, plant transgenic remediation were described.

SIRT1 regulates autoacetylation and histone acetyltransferase activity of TIP60

The histone acetyltransferase TIP60, a frequent target of monoallelic loss in human carcinomas, can acetylate many substrates, including histones and p53, and thus promote apoptosis following UV radiation. Here we showed that TIP60 is autoacetylated in response to UV damage, which is critically important for TIP60 activation. Mechanistically we demonstrated that TIP60 autoacetylation leads to the dissociation of TIP60 oligomer and enhances its interaction with substrates. Moreover, we identified SIRT1 that specifically deacetylates TIP60 and negatively regulates TIP60 activity in vivo. Taken together, our data reveal TIP60 autoacetylation as a key step in the control of its histone acetyltransferase activity and function in response to DNA damage.

A novel LZAP-binding protein, NLBP, inhibits cell invasion

LXXLL/leucine zipper-containing alternative reading frame (ARF)-binding protein (LZAP) was recently shown to function as a tumor suppressor through inhibition of the NF-kappaB signaling pathway. LZAP is also known as a negative regulator of cell invasion, and its expression was demonstrated to be reduced in several tumor tissues. However, the molecular mechanism of the negative effect of LZAP on cell invasion is unclear. In this study, we identify NLBP as a novel LZAP-binding protein using tandem affinity purification. We demonstrate the negative effects of NLBP on cell invasion and the NF-kappaB signaling pathway. NLBP expression was not detected in hepatocellular carcinoma cells with strong invasive activity, whereas its expression was detected in a hepatocellular carcinoma cell line with no invasive activity. We also demonstrate that these two proteins mutually affect the stability of each other by inhibiting ubiquitination of the other protein. Based on these results, we suggest that NLBP may act as a novel tumor suppressor by inhibiting cell invasion, blocking NF-kappaB signaling, and increasing stability of the LZAP protein.

Characterization of an aldolase-dehydrogenase complex that exhibits substrate channeling in the polychlorinated biphenyls degradation pathway

An aldolase and dehydrogenase complex from the polychlorinated biphenyl degradation pathway of the bacterium Burkholderia xenovorans LB400 was purified. The aldolase, BphI, had the highest activity with Mn(2+) as the cofactor and was able to transform 4-hydroxy-2-oxopentanoate and 4-hydroxy-2-oxohexanoate to pyruvate and acetaldehyde or propionaldehyde with similar specificity constants. Aldolase activity was competitively inhibited by the pyruvate enolate analogue, oxalate, with a K(ic) of 0.93 microM. The pH-rate profiles suggested the involvement of a pK(a) 7.7 catalytic base in the reaction mechanism. BphI activity was activated 15-fold when substrate turnover was occurring in the dehydrogenase, BphJ, which can be attributed partially to nicotinamide coenzyme binding to BphJ. BphJ had similar specificity constants for acetaldehyde or propionaldehyde and was able to utilize aliphatic aldehydes from two to five carbons in length as substrates, although K(m) values for these aldehyes were >20 mM. When 4-hydroxy-2-oxopentanoate was provided as a substrate to the BphI-BphJ complex in a coupled enzyme assay, no lag in the progress curve of BphJ was observed. When 1 mM propionaldehyde was added exogenously to a reaction mixture containing 0.1 mM 4-hydroxy-2-oxopentanoate, 95% of the CoA esters produced was acetyl CoA. Conversely, 99% of the CoA esters produced was propionyl CoA when a 10-fold molar excess of exogenous acetaldehyde was added in a reaction mixture containing 4-hydroxy-2-oxohexanoate. These results demonstrate that acetaldehyde and propionaldehyde, products of the BphI reaction, are not released in the bulk solvent but are channeled directly to the dehydrogenase.

RAD18 transmits DNA damage signalling to elicit homologous recombination repair

To maintain genome stability, cells respond to DNA damage by activating signalling pathways that govern cell-cycle checkpoints and initiate DNA repair. Cell-cycle checkpoint controls should connect with DNA repair processes, however, exactly how such coordination occurs in vivo is largely unknown. Here we describe a new role for the E3 ligase RAD18 as the integral component in translating the damage response signal to orchestrate homologous recombination repair (HRR). We show that RAD18 promotes homologous recombination in a manner strictly dependent on its ability to be recruited to sites of DNA breaks and that this recruitment relies on a well-defined DNA damage signalling pathway mediated by another E3 ligase, RNF8. We further demonstrate that RAD18 functions as an adaptor to facilitate homologous recombination through direct interaction with the recombinase RAD51C. Together, our data uncovers RAD18 as a key factor that orchestrates HRR through surveillance of the DNA damage signal.

Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation

The extradiol dioxygenase diversity of a site highly contaminated with aliphatic and aromatic hydrocarbons under air-sparging treatment was assessed by functional screening of a fosmid library in Escherichia coli with catechol as substrate. The 235 positive clones from inserts of DNA extracted from contaminated soil were equivalent to one extradiol dioxygenase-encoding gene per 3.6 Mb of DNA screened, indicating a strong selection for genes encoding this function. Three subfamilies were identified as being predominant, with 72, 55 and 43 fosmid inserts carrying genes, related to those encoding TbuE of Ralstonia pickettii PK01 (EXDO-D), IpbC of Pseudomonas sp. JR1 (EXDO-K2) or DbtC of Burkholderia sp. DBT1 (EXDO-Dbt), respectively, whereas genes encoding enzymes related to XylE of Pseudomonas putida mt-2 were not observed. Genes encoding oxygenases related to isopropylbenzene dioxygenases were usually colocalized with genes encoding EXDO-K2 dioxygenases. Functional analysis of representative proteins indicated a subcluster of EXDO-D proteins to show exceptional high affinity towards different catecholic substrates. Based on V_max/K_m specificity constants, a task-sharing between different extradiol dioxygenases in the community of the contaminated site can be supposed, attaining a complementary and community-balanced catalytic power against diverse catecholic derivatives, as necessary for effective degradation of mixtures of aromatics.

Glutathione transferases in bacteria

Bacterial glutathione transferases (GSTs) are part of a superfamily of enzymes that play a key role in cellular detoxification. GSTs are widely distributed in prokaryotes and are grouped into several classes. Bacterial GSTs are implicated in a variety of distinct processes such as the biodegradation of xenobiotics, protection against chemical and oxidative stresses and antimicrobial drug resistance. In addition to their role in detoxification, bacterial GSTs are also involved in a variety of distinct metabolic processes such as the biotransformation of dichloromethane, the degradation of lignin and atrazine, and the reductive dechlorination of pentachlorophenol. This review article summarizes the current status of knowledge regarding the functional and structural properties of bacterial GSTs.

Structure of bacterial glutathione-S-transferase maleyl pyruvate isomerase and implications for mechanism of isomerisation

Maleyl pyruvate isomerase (MPI) is a bacterial glutathione S-transferase (GST) from the pathway for degradation of naphthalene via gentisate that enables the bacterium Ralstonia to use polyaromatic hydrocarbons as a sole carbon source. Genome sequencing projects have revealed the presence of large numbers of GSTs in bacterial genomes, often located within gene clusters encoding the degradation of different aromatic compounds. This structure is therefore an example of this under-represented class of enzymes. Unlike many glutathione transferases, the reaction catalysed by MPI is an isomerisation of an aromatic ring breakdown product, and glutathione is a true cofactor rather than a substrate in the reaction. We have solved the structure of the enzyme in complex with dicarboxyethyl glutathione, an analogue of a proposed reaction intermediate, at a resolution of 1.3 A. The structure provides direct evidence that the glutathione thiolate attacks the substrate in the C2 position, with the terminal carboxylate buried at the base of the active site cleft. Our structures suggest that the C1-C2 bond remains fixed so when rotation occurs around the C2-C3 bond the atoms from C4 onwards actually move. We identified a conserved arginine that is likely to stabilize the enolate form of the substrate during the isomerisation. Arginines at either side of the active site cleft can interact with the end of the substrate/product and preferentially stabilise the product. MPI has significant sequence similarity to maleylacetoacetate isomerase (MAAI), which performs an analogous reaction in the catabolism of phenylalanine and tyrosine. The proposed mechanism therefore has relevance to the MAAIs. Significantly, whilst the overall sequence identity is 40% only one of the five residues from the Zeta motif in the active site is conserved. We re-examined the roles of the residues in the active site of both enzymes and the Zeta motif itself.

Microbial transformation and degradation of polychlorinated biphenyls

This paper reviews the potential of microorganisms to transform polychlorinated biphenyls (PCBs). In anaerobic environments, higher chlorinated biphenyls can undergo reductive dehalogenation. Meta- and para-chlorines in PCB congeners are more susceptible to dechlorination than ortho-chlorines. Anaerobes catalyzing PCB dechlorination have not been isolated in pure culture but there is strong evidence from enrichment cultures that some Dehalococcoides spp. and other microorganisms within the Chloroflexi phylum can grow by linking the oxidation of H(2) to the reductive dechlorination of PCBs. Lower chlorinated biphenyls can be co-metabolized aerobically. Some aerobes can also grow by utilizing PCB congeners containing only one or two chlorines as sole carbon/energy source. An example is the growth of Burkholderia cepacia by transformation of 4-chlorobiphenyl to chlorobenzoates. The latter compounds are susceptible to aerobic mineralization. Higher chlorinated biphenyls therefore are potentially fully biodegradable in a sequence of reductive dechlorination followed by aerobic mineralization of the lower chlorinated products.

VprBP targets Merlin to the Roc1-Cul4A-DDB1 E3 ligase complex for degradation

Inactivation of the neurofibromatosis type 2 (NF2) tumor suppressor gene function has been observed not only in familial schwannomas and other central nervous system tumors, but also in malignant tumors unrelated to the NF2 syndrome, indicating a broader role of NF2 in human tumorigenesis. The NF2-encoded protein Merlin is closely related to the Ezrin-Radixin-Moesin family of membrane/cytoskeleton linker proteins, and has been demonstrated to suppress tumor growth by inhibiting extracellular signal-regulated kinase (ERK) and Rac1 activation. Interestingly, serum deprivation has been shown to regulate Merlin at the protein level, however, exactly how such condition affects Merlin remains elusive. In this study, we provide evidence to show that Merlin is regulated in a Roc1-Cullin4A-DDB1-dependent manner. Following serum stimulation, Merlin is recruited to the E3 ligase complex through a direct interaction with the WD40-containing adaptor protein VprBP. Loading of Merlin to the E3 ubiquitin ligase complex resulted in its polyubiquitination, and consequently its proteasome-mediated degradation. Consistently, VprBP depletion abolished the in vivo interaction of Merlin and Roc1-Cullin4A-DDB1, which resulted in Merlin stabilization and inhibited ERK and Rac activation. Together, our data revealed a novel regulatory mechanism for the tumor suppressor function of Merlin.

Crystallization and preliminary X-ray diffraction analysis of a glutathione S-transferase from Xylella fastidiosa

Glutathione S-transferases (GSTs) form a group of multifunctional isoenzymes that catalyze the glutathione-dependent conjugation and reduction reactions involved in the cellular detoxification of xenobiotic and endobiotic compounds. GST from Xylella fastidiosa (xfGST) was overexpressed in Escherichia coli and purified by conventional affinity chromatography. In this study, the crystallization and preliminary X-ray analysis of xfGST is described. The purified protein was crystallized by the vapour-diffusion method, producing crystals that belonged to the triclinic space group P1. The unit-cell parameters were a = 47.73, b = 87.73, c = 90.74 A, alpha = 63.45, beta = 80.66, gamma = 94.55 degrees. xfGST crystals diffracted to 2.23 A resolution on a rotating-anode X-ray source.

c-Myc interacts with TRF1/PIN2 and regulates telomere length

Telomere, the end of linear chromosome, is protected by DNA-protein complexes. These complexes cap the linear chromosome and play an important role in the maintenance of genomic stability. TRF1/PIN2, a double-stranded DNA-binding protein is known to regulate telomere length by not only protecting telomere but also blocking the access of telomerase to telomere in cis. To better understand the mechanism through which TRF1/PIN2 regulates telomere length, we performed the yeast two-hybrid screening and identified the transcriptional activator c-Myc as a TRF1/PIN2-binding protein. The c-Myc-TRF1/PIN2 interaction was observed both in vitro and in vivo. This interaction is mediated by the basic helix-loop-helix (bHLH) domain of c-Myc. Importantly, overexpression of this TRF1/PIN2-interacting domain of c-Myc leads to telomere elongation in vivo. Together, these results suggest that c-Myc may be involved in the regulation of telomere length through its direct binding with TRF1/PIN2.

CCDC98 is a BRCA1-BRCT domain-binding protein involved in the DNA damage response

The product of the breast cancer-1 gene, BRCA1, plays a crucial part in the DNA damage response through its interactions with many proteins, including BACH1, CtIP and RAP80. Here we identify a coiled-coil domain-containing protein, CCDC98, as a BRCA1-interacting protein. CCDC98 colocalizes with BRCA1 and is required for the formation of BRCA1 foci in response to ionizing radiation. Moreover, like BRCA1, CCDC98 has a role in radiation sensitivity and damage-induced G2/M checkpoint control. Together, these results suggest that CCDC98 is a mediator of BRCA1 function involved in the mammalian DNA damage response.

Structures of Ternary Complexes of BphK, a Bacterial Glutathione S-Transferase That Reductively Dechlorinates Polychlorinated Biphenyl Metabolites

Prokaryotic glutathione S-transferases are as diverse as their eukaryotic counterparts but are much less well characterized. BphK from Burkholderia xenovorans LB400 consumes two GSH molecules to reductively dehalogenate chlorinated 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (HOPDAs), inhibitory polychlorinated biphenyl metabolites. Crystallographic structures of two ternary complexes of BphK were solved to a resolution of 2.1A. In the BphK-GSH-HOPDA complex, GSH and HOPDA molecules occupy the G- and H-subsites, respectively. The thiol nucleophile of the GSH molecule is positioned for SN2 attack at carbon 3 of the bound HOPDA. The respective sulfur atoms of conserved Cys-10 and the bound GSH are within 3.0A, consistent with product release and the formation of a mixed disulfide intermediate. In the BphK-(GSH)2 complex, a GSH molecule occupies each of the two subsites. The three sulfur atoms of the two GSH molecules and Cys-10 are aligned suitably for a disulfide exchange reaction that would regenerate the resting enzyme and yield disulfide-linked GSH molecules. A second conserved residue, His-106, is adjacent to the thiols of Cys-10 and the GSH bound to the G-subsite and thus may stabilize a transition state in the disulfide exchange reaction. Overall, the structures support and elaborate a proposed dehalogenation mechanism for BphK and provide insight into the plasticity of the H-subsite.

A glutathione S-transferase catalyzes the dehalogenation of inhibitory metabolites of polychlorinated biphenyls

BphK is a glutathione S-transferase of unclear physiological function that occurs in some bacterial biphenyl catabolic (bph) pathways. We demonstrated that BphK of Burkholderia xenovorans strain LB400 catalyzes the dehalogenation of 3-chloro 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (HOPDAs), compounds that are produced by the cometabolism of polychlorinated biphenyls (PCBs) by the bph pathway and that inhibit the pathway's hydrolase. A one-column protocol was developed to purify heterologously produced BphK. The purified enzyme had the greatest specificity for 3-Cl HOPDA (kcat/Km, approximately 10(4) M(-1) s(-1)), which it dechlorinated approximately 3 orders of magnitude more efficiently than 4-chlorobenzoate, a previously proposed substrate of BphK. The enzyme also catalyzed the dechlorination of 5-Cl HOPDA and 3,9,11-triCl HOPDA. By contrast, BphK did not detectably transform HOPDA, 4-Cl HOPDA, or chlorinated 2,3-dihydroxybiphenyls. The BphK-catalyzed dehalogenation proceeded via a ternary-complex mechanism and consumed 2 equivalents of glutathione (GSH) (Km for GSH in the presence of 3-Cl HOPDA, approximately 0.1 mM). A reaction mechanism consistent with the enzyme's specificity is proposed. The ability of BphK to dehalogenate inhibitory PCB metabolites supports the hypothesis that this enzyme was recruited to facilitate PCB degradation by the bph pathway.

Genetic organization of a plasmid from an industrial wastewater bioreactor

Pseudomonas strain CT14 was isolated from activated sludge. Strain CT14 contained a 55, 216 bp plasmid that was characterized by sequence analysis. The plasmid had a modular structure with 51 open reading frames (ORFs) that were distributed between two clearly demarcated domains. Domain I primarily contained genes for plasmid-related functions and a novel origin of replication. Domain II bore evidence of extensive transposition and recombination. Domain II contained several genes from a meta-cleavage pathway for aromatic rings. These genes appeared to have been recruited from different hosts. This observation suggests that sequencing pCT14 may have revealed an intermediate stage in the evolution of a new assemblage of meta-cleavage pathway genes.

Directed evolution of extradiol dioxygenase by a novel in vivo DNA shuffling

RecA-dependent homologous recombination in Escherichia coli is a very effective way to construct chimeras between two homologous genes. The disadvantage of in vivo method is a small library size of chimeric genes in comparison with in vitro DNA shuffling. In order to overcome the disadvantage, we have developed novel in vivo DNA shuffling methods with successive homologous recombinations. Linearized DNA molecules with two homologous genes were made with ligation rather than the conventional restriction enzyme cleavage between two genes. The three-way ligation of a vector and two homologous bphC genes encoding 2,3-dihydroxybiphenyl 1,2-dioxygenases or the two-way ligation of the donor bphC gene and an acceptor plasmid carrying the homologous bphC gene generated a variety of linearized DNA molecules. The homologous recombination between the genes on the linearized DNA molecules created the large chimeric bphC gene libraries in a recBC sbcA E. coli strain. After three rounds of recombinations, chimeric bphC genes with four-part gene fragments by triple-crossover were easily obtained. By employing a 96-well microtiter plate high-throughput screening, thermally stable chimeric 2,3-dihydroxybiphenyl 1,2-dioxygenases were selected from chimeric bphC gene libraries. This opens up a new way for directed evolution of proteins in vivo.

Pathways in the Degradation of Hydrolyzed Alcohols of Butyl Benzyl Phthalate in Metabolically Diverse Gordonia sp.Strain MTCC 4818

In the present study, the metabolic pathways involved in the degradation of benzyl alcohol and 1-butanol, the hydrolyzed products of butyl benzyl phthalate, were investigated by the Gordonia sp. strain MTCC 4818. The strain can utilize both benzyl alcohol and 1-butanol individually as sole carbon sources, where benzyl alcohol was found to be metabolized via benzaldehyde, benzoic acid and catechol, which was further degraded by ortho-cleavage dioxygenase to cis,cis-muconic acid and subsequently to muconolactone leading to tricarboxylic acid cycle. On the other hand, 1-butanol was metabolized via butyraldehyde and butyric acid, which was channeled into the tricarboxylic acid cycle via the beta-oxidation pathway. Numbers of dehydrogenases, both NAD+-dependent and NAD+-independent, were found to be involved in the degradation of benzyl alcohol and 1-butanol, where several dehydrogenases exhibited relaxed substrate specificity. Both 2,3- and 3,4-dihydroxybenzoic acids were utilized by the test organism for growth and metabolized by the ortho-cleavage pathway by the cell-free extract of benzoate-grown cells, similar to catechol, suggesting possible broad substrate specificity of the ring cleavage dioxygenase. Moreover, the test organism can utilize various primary and secondary alcohols, aliphatic aldehydes and acids in the C2-C5 range besides n-hexadecane, 1,4-butanediol and cyclohexanol individually as the sole carbon sources indicating metabolic diversity in the Gordonia sp. strain MTCC 4818.

Identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in Comamonas testosteroni TA441

Comamonas testosteroni TA441 utilizes testosterone via aromatization of the A ring followed by meta-cleavage of the ring. The product of the meta-cleavage reaction, 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-dien-4-oic acid, is degraded by a hydrolase, TesD. We directly isolated and identified two products of TesD as 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid and (2Z,4Z)-2-hydroxyhexa-2,4-dienoic acid. The latter was a pure 4Z isomer. 2-Hydroxyhexa-2,4-dienoic acid was converted by a hydratase, TesE, and the product isolated from the reaction solution was identified as 2-hydroxy-4-hex-2-enolactone, indicating the direct product of TesE to be 4-hydroxy-2-oxohexanoic acid.

Engineering a hybrid pseudomonad to acquire 3,4-dioxygenase activity for polychlorinated biphenyls

We constructed a hybrid strain that acquired 3,4-dioxygenase activity for polychlorinated biphenyls (PCBs). This strain, KF707-D34, possessed a chimeric biphenyl dioxygenase gene, of which a portion of bphA1 (coding for a large subunit of biphenyl dioxygenase) of Pseudomonas pseudoalcaligenes KF707 was replaced with that of a PCB-degrader, Burkholderia cepacia LB400 by homologous recombination. KF707-D34 retained the ability to degrade 4,4'-dichlorobiphenyl via 2,3-dioxygenation in a fashion identical to that of KF707 and gained novel capability to degrade 2,5,4'-trichlorobiphenyl and 2,5,2',5'-tetrachlorobiphenyl via 3,4-dioxygenation in a fashion identical to that of LB400. Sequence analysis of bphA1 from KF707-D34 revealed that three nucleotides in the 3'-terminal region of KF707 bphA1 were changed to correspond to those in LB400 bphA1. The resulting BphA1 protein in KF707-D34 was changed at position 376 from threonine (Thr) to asparagine (Asn). The results demonstrate that a minor alteration of the amino acid sequence in BphA1 improved the PCB degradation capability in biphenyl-utilizing bacteria.