Primary structure of xylene monooxygenase: similarities to and differences from the alkane hydroxylation system

HMDB: A curated database of genes involved in hydrocarbon monooxygenation reaction with homologous genes as background

The investigation of hydrocarbon degradation potential of environmental microorganisms is an important research topic, whether for the global carbon cycle or oil pollution remediation. Under aerobic conditions, the microorganisms employ a range of monooxygenases to use hydrocarbons substrates as a source of carbon and energy. With the explosion of sequencing data, mining genes in genomes or metagenomes has become computationally expensive and time-consuming. We proposed the HMDB, which is a professional gene database of hydrocarbon monooxygenases. HMDB contains 38 genes, which encode 11 monooxygenases responsible for the hydroxylation of 8 hydrocarbons. To reduce false positives, the strategy of using homologous genes as background noise was applied for HMDB. We added 10,095 gene sequences of homologous enzymes which took non-hydrocarbons as substrates to HMDB. The classic BLAST method and best-hit strategy were recommended for HMDB usage, but not limited. The performance of HMDB was validated using 264,402 prokaryote genomes from RefSeq and 51 metagenomes from SRA. The results showed that HMDB database had high sensitivity and low false positive rate. We release the HMDB database here, hoping to speed up the process for investigation of hydrocarbon monooxygenases in massive metagenomic data. HMDB is freely available at http://www.orgene.net/HMDB/.

Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms

Cometabolic oxidation involves the oxidation of chemicals often by monooxygenases or dioxygenases and can be a removal process for environmental contaminants such as trichloroethene (TCE) or 1,4-dioxane. Information on the occurrence of these genes and their associated microorganisms in environmental samples has the potential to enhance our understanding of contaminant removal. The overall aims were to 1) ascertain which genes encoding for monooxygenases (from methanotrophs, ammonia oxidizing bacteria and toluene/phenol oxidizers) and other key enzymes are present in soil microcosms and 2) determine which phylotypes are associated with those genes. The approach involved a predictive tool called PICRUSt2 and 16S rRNA gene amplicon datasets from two previous soil microcosm studies. The following targets from the KEGG database were examined: pmo/amo, mmo, dmp/pox/tomA, tmo/tbu/tou, bssABC (and downstream genes), tod, xylM, xylA, gst, dhaA, catE, dbfA1, dbfA2 and phenol 2-monooxygenase. A large number of phylotypes were associated with pmo/amo, while mmo was linked to only five. Several phylotypes were associated with both pmo/amo and mmo. The most dominant microorganism predicted for mmoX was Mycobacterium (also predicted for pmo/amo). A large number of phylotypes were associated with all six genes from the dmp/pox/tomA KEGG group. The taxonomic associations predicted for the tmo/tbu/tou KEGG group were more limited. In both datasets, Geobacter was a key phylotype for benzylsuccinate synthase. The dioxygenase-mediated toluene degradation pathway encoded by todC1C2BA was largely absent, as were the genes (xylM, xylA) encoding for xylene monooxygenase. All other genes investigated were predicted to be present and were associated with a number of microorganisms. Overall, the analysis predicted the genes encoding for sMMO (mmo), T3MO/T3MO/ToMO (tmo/tbu/tou) and benzylsuccinate synthase (bssABC) are present for a limited number of phylotypes compared to those encoding for pMMO/AMO (pmo/amo) and phenol monooxygenase/T2MO (dmp/poxA/tomA). These findings suggest in soils contaminant removal via pMMO/AMO or phenol monooxygenase/T2MO may be common because of the occurrence of these enzymes with a large number of phylotypes.

Sustainable production and co-immobilization of cold-active enzymes from Pseudomonas sp. for BTEX biodegradation

Toluene/o-Xylene Monooxygenase (ToMO) is equipped with a broad spectrum of aromatic substrate specificity (such as BTEX; benzene, toluene, ethylbenzene, and isomers of xylenes). TOMO has can hydroxylate more than a single position of aromatic rings in two consecutive monooxygenation reactions. Catechol 1,2-dioxygenase (C1,2D) is an iron-containing enzyme able to cleave the ring of catechol (the converted product from ToMO) for complete detoxification of BTEX. In this study, cold-active ToMO and C1,2D were produced using newly isolated psychrophilic Pseudomonas S2TR-14 in the minimal salt medium supplemented with crustacean waste and different concentrations of used motor oil (0.2-2% (v/v)). Crude ToMO and C1,2D were immobilized into micro/nano biochar-chitosan matrices and used for BTEX biodegradation. The results showed that the highest enzyme production (12 U/mg for ToMO and 22 U/mg for C1,2D) was achieved at the presence of 0.5% v/v used motor oil compared to the control group without motor oil (0.07 and 0.06 U/mg). High immobilization yield was achieved due to covalent bonding of ToMO (92.26% for micro matrix and 77.20% for nano matrix) and C1,2D (87.57% for micro matrix and 74.79% for nano matrix) with matrices. FTIR spectra confirmed the immobilization of enzymes on the surface of microbiochar and nanobiochar-chitosan matrices as proper support. The immobilization increased the storage stability of the enzymes with more than 50% residual activity after 30 days at 4 ± 1 °C, while the free form of enzymes had less than 10% of its activity. Immobilized enzymes degraded more than 80% of BTEX (~200 mg/L in groundwater and ~10,000 mg/kg in soil) at 10 ± 1 °C in groundwater and soil. Therefore, integrated use of microbiochar and nanobiochar with chitosan for co-immobilization of ToMO and C1,2D can be a potential way to remove petroleum hydrocarbons with higher efficiency from contaminated groundwater and soil.

Psychrozymes as novel tools to biodegrade p-xylene and potential use for contaminated groundwater in the cold climate

Sites contaminated by petroleum hydrocarbons in cold-climate regions have recently received significant attention due to their sensitive ecosystem and human health impacts. Two cold-adapted pseudomonas strains were isolated from contaminated groundwater and soil. As xylene monooxygenase from Pseudomonas synxantha S2TR-26 and catechol 2,3-dioxygenase from Pseudomonas mandelii S2TR-08, have a matching end product, they acted in symphony to degrade p-xylene. Their unique thermodynamic and kinetic behavior permits them to achieve rapid degradation of p-xylene at low temperatures (<15 °C). The results showed that the sequential action led to the conversion of 200 mg/l of p-xylene within 72 h and complete degradation after 120 h. The cocktail of these enzymes with a ratio of 1:1.5 (xylene monooxygenase: catechol 2, 3-dioxygenase) confirmed the complete degradation of p-xylene within 48 h at 15 °C. This approach will allow efficient biodegradation of p-xylene to minimize the bioremediation duration in cold-climate regions.

Production of styrene oxide from styrene by a recombinant Escherichia coli with enhanced AcrAB-TolC efflux pump level in an aqueous-organic solvent two-phase system

The AcrAB-TolC efflux pump is involved in the organic solvent tolerance of Escherichia coli. Most E. coli strains are highly sensitive to organic solvents such as n-hexane and cyclohexane. Here, a recombinant E. coli transformed with an expression plasmid containing acrAB and tolC became tolerant to n-hexane and cyclohexane. The levels of AcrA, AcrB, and TolC in the recombinant increased by 3- to 5-fold compared to those in the control strain without the plasmid for acrAB or tolC. To investigate the usability of the recombinant as a biocatalyst in an aqueous-organic solvent two-phase system, we further introduced xylMA xylene monooxygenase genes from Pseudomonas putida mt-2 into the recombinant and examined the production of styrene oxide from styrene. The resulting recombinant produced 1.8 mg and 1.0 mg styrene oxide mL^-1 of medium in a medium overlaid with a 25% volume of n-hexane and cyclohexane containing 10% (wt vol^-1) styrene, respectively.

Isolation of marine xylene-utilizing bacteria and characterization of Halioxenophilus aromaticivorans gen. nov., sp. nov. and its xylene degradation gene cluster

Seven xylene-utilizing bacterial strains were isolated from seawater collected off the coast of Japan. Analysis of 16S rRNA gene sequences indicated that six isolates were most closely related to the marine bacterial genera Alteromonas, Marinobacter or Aestuariibacter. The sequence of the remaining strain, KU68FT, showed low similarity to the 16S rRNA gene sequences of known bacteria with validly published names, the most similar species being Maricurvus nonylphenolicus strain KU41ET (92.6% identity). On the basis of physiological, chemotaxonomic and phylogenetic data, strain KU68FT is suggested to represent a novel species of a new genus in the family Cellvibrionaceae of the order Cellvibrionales within the Gammaproteobacteria, for which the name Halioxenophilus aromaticivorans gen. nov., sp. nov. is proposed. The type strain of Halioxenophilus aromaticivorans is KU68FT (=JCM 19134T = KCTC 32387T). PCR and sequence analysis revealed that strain KU68FT possesses an entire set of genes encoding the enzymes for the upper xylene methyl-monooxygenase pathway, xylCMABN, resembling the gene set of the terrestrial Pseudomonas putida strain mt-2.

Shift of microbial diversity and function in high-efficiency performance biotrickling filter for gaseous xylene treatment

Xylene is the main component of many volatile industrial pollution sources, and the use of biotechnology to remove volatile organic compounds (VOCs) has become a growing trend. In this study, a biotrickling filter for gaseous xylene treatment was developed using activated sludge as raw material to study the biodegradation process of xylene. Reaction conditions were optimized, and long-term operation was performed. The optimal pH was 7.0, gas-liquid ratio was 15:1 (v/v), and temperature was 25 °C. High-throughput sequencing technique was carried out to analyze microbial communities in the top, middle, and bottom layers of the reactor. Characteristics of microbial diversity were elucidated, and microbial functions were predicted. The result showed that the removal efficiency (RE) was stable at 86%-91%, the maximum elimination capacity (EC) was 303.61 g·m^-3·hr^-1, residence time was 33.75 sec, and the initial inlet xylene concentration was 3000 mg·m^-3, which was the highest known degradation concentration reported. Kinetic analysis of the xylene degradation indicated that it was a very high-efficiency-activity bioprocess. The r_max was 1059.8 g·m^-3·hr^-1, and K_s value was 4.78 g·m^-3 in stationary phase. In addition, microbial community structures in the bottom and top layers were significantly different: Pseudomonas was the dominant genus in the bottom layer, whereas Sphingobium was dominant in the top layer. The results showed that intermediate metabolites of xylene could affect the distribution of community structure. Pseudomonas sp. can adapt to high concentration xylene-contaminated environments. Implications: We combined domesticated active sludge and reinforced microbial agent on biotrickling filter. This system performed continuously under a reduced residence time at 33.75 sec and high elimination capacity at 303.61 g·m^-3·hr^-1 in the biotrickling reactor for about 260 days. In this case, predomestication combined with reinforcing of microorganisms was very important to obtaining high-efficiency results. Analysis of microbial diversity and functional prediction indicated a gradient distribution along with the concentration of xylene. This implied a rational design of microbial reagent and optimizing the inoculation of different sites of reactor could reduce the preparation period of the technology.

Metabolic routes involved in the removal of linear alkylbenzene sulfonate (LAS) employing linear alcohol ethoxylated and ethanol as co-substrates in enlarged scale fluidized bed reactor

In this study, the microbial community characterization and metabolic pathway identification involved in the linear alkylbenzene sulfonated (LAS) degradation from commercial laundry wastewater in a fluidized bed reactor (FBR) on an increased scale were performed using the Illumina MiSeq platform. Ethanol and non-ionic surfactant (LAE, Genapol C-100) were used as co-substrates. The FBR was operated in five operational phases: (I) synthetic substrate for inoculation; (II) 7.9 ± 4.7 mg/L LAS and 11.7 ± 6.9 mg/L LAE; (III) 19.4 ± 12.9 mg/L LAS, 19.6 ± 9.2 mg/L LAE and 205 mg/L ethanol; (IV) 25.9 ± 11 mg/L LAS, 19.5 ± 9.1 mg/L LAE and 205 mg/L ethanol and (V) 43.9 ± 18 mg/L LAS, 25 ± 9.8 mg/L LAE and 205 mg/L ethanol. At all operation phases, organic matter was removed from 40.4 to 85.1% and LAS removal was from 24.7 to 56%. Sulfate-reducing bacteria (SRB) were identified in the biofilm of FBR in all operational phases. Although the LAS promoted a toxic effect on the microbiota, this effect can be reduced when using biodegradable co-substrates, such as ethanol and LAE, which was observed in Phase IV. In this phase, there was a greater microbial diversity (Shannon index) and higher microorganism richness (Chao 1 index), both for the Domain Bacteria, and for the Domain Archaea.

Headgroup hydroxylation by OlsE occurs at the C4 position of ornithine lipid and is widespread in proteobacteria and bacteroidetes

Amino acid-containing acyloxyacyl lipids are composed of a 3-hydroxy fatty acid amide-bound to the α-amino group of an amino acid. A second fatty acid is ester-linked to the 3-hydroxy group of the first fatty acid. Most commonly, ornithine is the headgroup of these lipids, but glycine, serineglycine, glutamine and lysine have also been described in bacteria. Ornithine lipids (OL) can be synthesized by about 50% of the sequenced bacterial species, and several covalent modifications of its basic structure have been described. The OL hydroxylase OlsE is widespread in Rhizobium and Agrobacterium species and is responsible for introducing a hydroxyl group at a hence unknown position within the ornithine headgroup causing the formation of the OL named S2. Using NMR on purified OL S2, we show that the OlsE-mediated hydroxylation takes place at the C-4 position of the ornithine headgroup. Furthermore, we identify a hydroxylase in the genome of Pseudopedobacter saltans, distantly related to OlsE from α-proteobacteria, able to hydroxylate the headgroup of both ornithine lipids and lysine lipids. A homology search with the amino acid sequence of this hydroxylase allows us to predict that OL headgroup hydroxylation is not restricted to a few α-proteobacteria, but is apparently also common in many genera belonging to the Cytophaga-Flavobacterium-Bacteroidetes (CFB) group of bacteria.

Biodegradation of Volatile Organic Compounds and Their Effects on Biodegradability under Co-Existing Conditions

Volatile organic compounds (VOCs) are major pollutants that are found in contaminated sites, particularly in developed countries such as Japan. Various microorganisms that degrade individual VOCs have been reported, and genomic information related to their phylogenetic classification and VOC-degrading enzymes is available. However, the biodegradation of multiple VOCs remains a challenging issue. Practical sites, such as chemical factories, research facilities, and illegal dumping sites, are often contaminated with multiple VOCs. In order to investigate the potential of biodegrading multiple VOCs, we initially reviewed the biodegradation of individual VOCs. VOCs include chlorinated ethenes (tetrachloroethene, trichloroethene, dichloroethene, and vinyl chloride), BTEX (benzene, toluene, ethylbenzene, and xylene), and chlorinated methanes (carbon tetrachloride, chloroform, and dichloromethane). We also summarized essential information on the biodegradation of each kind of VOC under aerobic and anaerobic conditions, together with the microorganisms that are involved in VOC-degrading pathways. Interactions among multiple VOCs were then discussed based on concrete examples. Under conditions in which multiple VOCs co-exist, the biodegradation of a VOC may be constrained, enhanced, and/or unaffected by other compounds. Co-metabolism may enhance the degradation of other VOCs. In contrast, constraints are imposed by the toxicity of co-existing VOCs and their by-products, catabolite repression, or competition between VOC-degrading enzymes. This review provides fundamental, but systematic information for designing strategies for the bioremediation of multiple VOCs, as well as information on the role of key microorganisms that degrade VOCs.

Comparative genomics reveals genes significantly associated with woody hosts in the plant pathogen Pseudomonas syringae

The diversification of lineages within Pseudomonas syringae has involved a number of adaptive shifts from herbaceous hosts onto various species of tree, resulting in the emergence of highly destructive diseases such as bacterial canker of kiwi and bleeding canker of horse chestnut. This diversification has involved a high level of gene gain and loss, and these processes are likely to play major roles in the adaptation of individual lineages onto their host plants. In order to better understand the evolution of P. syringae onto woody plants, we have generated de novo genome sequences for 26 strains from the P. syringae species complex that are pathogenic on a range of woody species, and have looked for statistically significant associations between gene presence and host type (i.e. woody or herbaceous) across a phylogeny of 64 strains. We have found evidence for a common set of genes associated with strains that are able to colonize woody plants, suggesting that divergent lineages have acquired similarities in genome composition that may form the genetic basis of their adaptation to woody hosts. We also describe in detail the gain, loss and rearrangement of specific loci that may be functionally important in facilitating this adaptive shift. Overall, our analyses allow for a greater understanding of how gene gain and loss may contribute to adaptation in P. syringae.

Making variability less variable: matching expression system and host for oxygenase-based biotransformations

Variability in whole-cell biocatalyst performance represents a critical aspect for stable and productive bioprocessing. In order to investigate whether and how oxygenase-catalyzed reactions are affected by such variability issues in solvent-tolerant Pseudomonas, different inducers, expression systems, and host strains were tested for the reproducibility of xylene and styrene monooxygenase catalyzed hydroxylation and epoxidation reactions, respectively. Significantly higher activity variations were found for biocatalysts based on solvent-tolerant Pseudomonas putida DOT-TIE and S12 compared with solvent-sensitive P. putida KT2440, Escherichia coli JM101, and solvent-tolerant Pseudomonas taiwanensis VLB120. Specific styrene epoxidation rates corresponded to cellular styrene monooxygenase contents. Detected variations in activity strictly depended on the type of regulatory system employed, being high with the alk- and low with the lac-system. These results show that the occurrence of clonal variability in recombinant gene expression in Pseudomonas depends on the combination of regulatory system and host strain, does not correlate with a general phenotype such as solvent tolerance, and must be evaluated case by case.

Remediation of petroleum hydrocarbon-contaminated sites by DNA diagnosis-based bioslurping technology

The application of effective remediation technologies can benefit from adequate preliminary testing, such as in lab-scale and Pilot-scale systems. Bioremediation technologies have demonstrated tremendous potential with regards to cost, but they cannot be used for all contaminated sites due to limitations in biological activity. The purpose of this study was to develop a DNA diagnostic method that reduces the time to select contaminated sites that are good candidates for bioremediation. We applied an oligonucleotide microarray method to detect and monitor genes that lead to aliphatic and aromatic degradation. Further, the bioremediation of a contaminated site, selected based on the results of the genetic diagnostic method, was achieved successfully by applying bioslurping in field tests. This gene-based diagnostic technique is a powerful tool to evaluate the potential for bioremediation in petroleum hydrocarbon contaminated soil.

Endoplasmic reticulum microenvironment and conserved histidines govern ELOVL4 fatty acid elongase activity

Autosomal dominant Stargardt-like macular dystrophy (STGD3) in humans results from mutations in elongation of very long chain FAs-like 4 (ELOVL4), which leads to vision loss in young adults. ELOVL4 is an integral endoplasmic reticulum (ER) protein that mediates the elongation of very long chain (VLC) FAs. Mutations in ELOVL4 lead to truncation and mislocalization of the translated protein from the ER, the site of FA elongation. Little is known about the enzymatic elongation of VLC-FAs by ELOVL4. We over-expressed full-length mouse ELOVL4, an N-glycosylation-deficient mutant, an ER-retention mutant, and mutants of active site histidines to parse their individual roles in VLC-FA elongation. ELOVL4 elongated appropriate precursors to the corresponding VLC-FA species ≥28 carbons. Active site histidine mutants of ELOVL4 did not elongate appropriate precursors, establishing ELOVL4 as the elongase. Displacing ELOVL4 from the ER was sufficient to cause loss of condensation activity, while absence of N-glycosylation was irrelevant for enzyme function. This study shows that ELOVL4 enzymatic activity is governed by individual histidines in its active site and the ER microenvironment, both of which are essential for elongation of VLC-FAs.

Whole-cell biocatalysis for selective and productive C-O functional group introduction and modification

During the last decades, biocatalysis became of increasing importance for chemical and pharmaceutical industries. Regarding regio- and stereospecificity, enzymes have shown to be superior compared to traditional chemical synthesis approaches, especially in C-O functional group chemistry. Catalysts established on a process level are diverse and can be classified along a functional continuum starting with single-step biotransformations using isolated enzymes or microbial strains towards fermentative processes with recombinant microorganisms containing artificial synthetic pathways. The complex organization of respective enzymes combined with aspects such as cofactor dependency and low stability in isolated form often favors the use of whole cells over that of isolated enzymes. Based on an inventory of the large spectrum of biocatalytic C-O functional group chemistry, this review focuses on highlighting the potentials, limitations, and solutions offered by the application of self-regenerating microbial cells as biocatalysts. Different cellular functionalities are discussed in the light of their (possible) contribution to catalyst efficiency. The combined achievements in the areas of protein, genetic, metabolic, and reaction engineering enable the development of whole-cell biocatalysts as powerful tools in organic synthesis.

Deciphering mutant ELOVL4 activity in autosomal-dominant Stargardt macular dystrophy

Autosomal-dominant Stargardt-like macular dystrophy [Stargardt3 (STGD3)] results from single allelic mutations in the elongation of very-long-chain fatty acids-like 4 (ELOVL4), whereas recessive mutations lead to skin and brain dysfunction. ELOVL4 protein localizes to the endoplasmic reticulum, where it mediates the condensation reaction catalyzing the formation of very-long-chain (VLC) (C-28 to C-40) fatty acids, saturated and polyunsaturated (PUFA). The defective gene product is truncated at the C terminus, leading to mislocalization and aggregation in other organelles. We hypothesized that the STGD3 truncated mutant may generate mislocalized, and therefore toxic, keto intermediates of fatty acid elongation, thereby contributing to the disease process. Using cell-based and cell-free microsome assays, we found that the truncated protein lacked innate condensation activity. Coexpression of different forms of wild-type and mutant ELOVL4 revealed a large dominant-negative effect of mutant protein on ELOVL4 localization and enzymatic activity, resulting in reduced VLC-PUFA synthesis. The reduction in VLC-PUFA levels in STGD3 and age-related macular degeneration may be a contributing factor to their retinal pathology.

Ornithine lipids and their structural modifications: from A to E and beyond

Ornithine lipids (OLs) are phosphorus-free membrane lipids that are widespread in eubacteria, but absent from archaea and eukaryotes. They contain a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of the amino acid ornithine. A second fatty acyl group is ester-linked to the 3-hydroxy position of the first fatty acid. About 25% of the bacterial species whose genomes have been sequenced are predicted to have the capacity to form OLs. Distinct OL hydroxylations have been described in the ester-linked fatty acid, the amide-linked fatty acid, and the ornithine moiety. These modifications often seem to form part of a bacterial stress response to changing environmental conditions, allowing the bacteria to adjust membrane properties by simply modifying already existing membrane lipids without the need to synthesize new lipids.

Isolation and characterization of a 4-nitrotoluene-oxidizing enzyme from activated sludge by a metagenomic approach

To isolate a biocatalytic enzyme, metagenomic libraries were constructed in fosmids from samples of activated sludge used to treat coke plant wastewater. Six indigo-producing clones were isolated from approximately 40,000 metagenomic clones in the search for the oxygenase responsible. In vitro mutagenesis and whole-sequencing revealed one open reading frame to be responsible for the production of indigo in the fosmid clones. The deduced sequence of the gene product showed 60% identity with 2-naphthoate monooxygenase from Burkholderia sp. JT1500. Subclones carrying this open reading frame (icpA) retained indigo production, and indigo-producing enzymes expressed from subclones catalyzed the oxidization of 4-nitrotoluene to form 4-nitrobenzyl alcohol. These results suggested that the icp product is an enzyme involved in catalyzing 4-nitrotoluene's oxygenation.

Hydroxylated ornithine lipids increase stress tolerance in Rhizobium tropici CIAT899

Ornithine lipids (OLs) are widespread among Gram-negative bacteria. Their basic structure consists of a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of ornithine and a second fatty acyl group ester-linked to the 3-hydroxy position of the first fatty acid. OLs can be hydroxylated within the secondary fatty acyl moiety and this modification has been related to increased stress tolerance. Rhizobium tropici, a nodule-forming α-proteobacterium known for its stress tolerance, forms four different OLs. Studies of the function of these OLs have been hampered due to lack of knowledge about their biosynthesis. Here we describe that OL biosynthesis increases under acid stress and that OLs are enriched in the outer membrane. Using a functional expression screen, the OL hydroxylase OlsE was identified, which in combination with the OL hydroxylase OlsC is responsible for the synthesis of modified OLs in R. tropici. Unlike described OL hydroxylations, the OlsE-catalysed hydroxylation occurs within the ornithine moiety. Mutants deficient in OlsE or OlsC and double mutants deficient in OlsC/OlsE were characterized. R. tropici mutants deficient in OlsC-mediated OL hydroxylation are more susceptible to acid and temperature stress. All three mutants lacking OL hydroxylases are affected during symbiosis.

High stability and fast recovery of expression of the TOL plasmid-carried toluene catabolism genes of Pseudomonas putida mt-2 under conditions of oxygen limitation and oscillation

Pseudomonas putida mt-2 harbors the TOL plasmid (pWWO), which contains the genes encoding the enzymes necessary to degrade toluene aerobically. The xyl genes are clustered in the upper operon and encode the enzymes of the upper pathway that degrade toluene to benzoate, while the genes encoding the enzymes of the lower pathway (meta-cleavage pathway) that are necessary for the conversion of benzoate to tricarboxylic acid cycle intermediates, are encoded in a separate operon. In this study, the effects of oxygen availability and oscillation on the expression of catabolic genes for enzymes involved in toluene degradation were studied by using P. putida mt-2 as model bacterium. Quantitative reverse transcription-PCR was used to detect and quantify the expression of the catabolic genes xylM (a key gene of the upper pathway) and xylE (a key gene of the lower pathway) in cultures of P. putida mt-2 that were grown with toluene as a carbon source. Toluene degradation was shown to have a direct dependency on oxygen concentration, where gene expression of xylM and xylE decreased due to oxygen depletion during degradation. Under oscillating oxygen concentrations, P. putida mt-2 induced or downregulated xylM and xylE genes according to the O₂ availability in the media. During anoxic periods, P. putida mt-2 decreased the expression of xylM and xylE genes, while the expression of both xylM and xylE genes was immediately increased after oxygen became available again in the medium. These results suggest that oxygen is not only necessary as a cosubstrate for enzyme activity during the degradation of toluene but also that oxygen modulates the expression of the catabolic genes encoded by the TOL plasmid.

Redox biocatalysis and metabolism: molecular mechanisms and metabolic network analysis

Whole-cell biocatalysis utilizes native or recombinant enzymes produced by cellular metabolism to perform synthetically interesting reactions. Besides hydrolases, oxidoreductases represent the most applied enzyme class in industry. Oxidoreductases are attributed a high future potential, especially for applications in the chemical and pharmaceutical industries, as they enable highly interesting chemistry (e.g., the selective oxyfunctionalization of unactivated C-H bonds). Redox reactions are characterized by electron transfer steps that often depend on redox cofactors as additional substrates. Their regeneration typically is accomplished via the metabolism of whole-cell catalysts. Traditionally, studies towards productive redox biocatalysis focused on the biocatalytic enzyme, its activity, selectivity, and specificity, and several successful examples of such processes are running commercially. However, redox cofactor regeneration by host metabolism was hardly considered for the optimization of biocatalytic rate, yield, and/or titer. This article reviews molecular mechanisms of oxidoreductases with synthetic potential and the host redox metabolism that fuels biocatalytic reactions with redox equivalents. The tools discussed in this review for investigating redox metabolism provide the basis for studies aiming at a deeper understanding of the interplay between synthetically active enzymes and metabolic networks. The ultimate goal of rational whole-cell biocatalyst engineering and use for fine chemical production is discussed.

Oxidation of naphthenoaromatic and methyl-substituted aromatic compounds by naphthalene 1,2-dioxygenase

Oxidation of acenaphthene, acenaphthylene, and fluorene was examined with recombinant strain Pseudomonas aeruginosa PAO1(pRE695) expressing naphthalene dioxygenase genes cloned from plasmid NAH7. Acenaphthene underwent monooxygenation to 1-acenaphthenol with subsequent conversion to 1-acenaphthenone and cis- and trans-acenaphthene-1,2-diols, while acenaphthylene was dioxygenated to give cis-acenaphthene-1,2-diol. Nonspecific dehydrogenase activities present in the host strain led to the conversion of both of the acenaphthene-1,2-diols to 1,2-acenaphthoquinone. The latter was oxidized spontaneously to naphthalene-1,8-dicarboxylic acid. No aromatic ring dioxygenation products were detected from acenaphthene and acenaphthylene. Mixed monooxygenase and dioxygenase actions of naphthalene dioxygenase on fluorene yielded products of benzylic 9-monooxygenation, aromatic ring dioxygenation, or both. The action of naphthalene dioxygenase on a variety of methyl-substituted aromatic compounds, including 1,2,4-trimethylbenzene and isomers of dimethylnaphthalene, resulted in the formation of benzylic alcohols, i.e., methyl group monooxygenation products, which were subsequently converted to the corresponding carboxylic acids by dehydrogenase(s) in the host strain. Benzylic monooxygenation of methyl groups was strongly predominant over aromatic ring dioxygenation and essentially nonspecific with respect to the substitution pattern of the aromatic substrates. In addition to monooxygenating benzylic methyl and methylene groups, naphthalene dioxygenase behaved as a sulfoxygenase, catalyzing monooxygenation of the sulfur heteroatom of 3-methylbenzothiophene.

Monitoring aromatic hydrocarbon biodegradation by functional marker genes

The development of biological treatment technologies for contaminated environments requires tools for obtaining direct information about the biodegradation of specific contaminants. The potential of functional gene array analysis to monitor changes in the amount of functional marker genes as indicators of contaminant biodegradation was investigated. A prototype functional gene array was developed for targeting key functions in the biodegradation of naphthalene, toluene and xylenes. Internal standard probe based normalization was introduced to facilitate comparison across multiple samples. Coupled with one-colour hybridization, the signal normalization improved the consistency among replicate hybridizations resulting in better discrimination for the differences in the amount of target DNA. During the naphthalene biodegradation in a PAH-contaminated soil slurry microcosm, the normalized hybridization signals in naphthalene catabolic gene probes were in good agreement with the amount of naphthalene-degradation genes and the production of 14CO2. Gene arrays provide efficient means for monitoring of contaminant biodegradation in the environment.

Functional gene abundances (nahAc, alkB, xylE) in the assessment of the efficacy of bioremediation

In this study, we compared the mineralization rates of three selected (14)C-labeled hydrocarbon compounds, octacosane, toluene, and naphthalene, with the presence of the corresponding functional genes (alkB, xylE, nahAc) in a large number of soil samples representing different types of soil and petroleum hydrocarbon contamination. Functional genes were enumerated by the replicate limited dilution (RLD) polymerase chain reaction (PCR) technique. RLD-PCR was further compared to real-time PCR measurements for nahAc and xylE for some samples. At a heating oil-contaminated site, octacosane mineralization rates were higher (on average 0.0015 day(-1)) when compared to aerobic naphthalene and toluene mineralization (on average 0.00003 and 0.0007 day(-1)). The corresponding gene abundances measured by RLD-PCR were on average 0.95, 0.3, and 0.13 x 10(3) gene copies g(-1) soil for alkB, nahAc, and xylE, respectively. At a site contaminated with gasoline, the situation was the opposite: Toluene mineralization was the highest (on average 0.0031 day(-1)), and only xylE genes could be detected (on average 0.13 x 10(3) gene copies g(-1) soil by RLD-PCR). XylE and nahAc gene abundances were correlated with the (14)C-toluene and naphthalene mineralization activities, respectively, in samples from aerobic layers. AlkB gene abundances were not correlated with the octacosane mineralization. Real-time PCR was a more sensitive method than RLD-PCR by a factor of 1,200 for nahAc and 300 for xylE. In conclusion, functional gene abundances seemed to reflect the type of the contamination. With optimized assays, the gene abundances can be used to assess bioremediation efficacy.

Evaluating the biodegradation of aromatic hydrocarbons by monitoring of several functional genes

Various microbial activities determine the effectiveness of bioremediation processes. In this work, we evaluated the feasibility of gene array hybridization for monitoring the efficiency of biodegradation processes. Biodegradation of 14C-labelled naphthalene and toluene by the aromatic hydrocarbon-degrading Pseudomonas putida F1, P. putida mt-2 and P. putida G7 was followed in mixed liquid culture microcosm by a preliminary, nylon membrane-based gene array. In the beginning of the study, toluene was degraded rapidly and increased amount of toluene degradation genes was detected by the preliminary gene array developed for the study. After toluene was degraded, naphthalene mineralization started and the amount of naphthalene degradation genes increased as biodegradation proceeded. The amount of toluene degradation genes decreased towards the end of the study. The hybridization signal intensities determined by preliminary gene array were in good agreement with mineralization of naphthalene and toluene and with the amount of naphthalene dioxygenase and toluene dioxygenase genes quantified by dot blot hybridization. The clear correlation between the results obtained by the preliminary array and the biodegradation process suggests that gene array methods can be considered as a promising tool for monitoring the efficiency of biodegradation processes.

Identification of Rv3230c as the NADPH oxidoreductase of a two-protein DesA3 acyl-CoA desaturase in Mycobacterium tuberculosis H37Rv

DesA3 is a membrane-bound stearoyl-CoA Delta(9)-desaturase that produces oleic acid, a precursor of mycobacterial membrane phospholipids and triglycerides. The sequence of DesA3 is homologous with those of other membrane desaturases, including the presence of the eight-His motif proposed to bind the diiron center active site. This family of desaturases function as multicomponent complexes and thus require electron transfer proteins for efficient catalytic turnover. Here we present evidence that Rv3230c from Mycobacterium tuberculosis H37Rv is a biologically relevant electron transfer partner for DesA3 from the same pathogen. For these studies, Rv3230c was expressed as a partially soluble protein in Escherichia coli; recombinant DesA3 was expressed in Mycobacterium smegmatis as a catalytically active membrane protein. The addition of E. coli lysates containing Rv3230c to lysates of M. smegmatis expressing DesA3 gave strong conversion of [1-(14)C]-18:0-CoA to [1-(14)C]-cis-Delta(9)-18:1-CoA and of [1-(14)C]-16:0-CoA to [1-(14)C]-cis-Delta(9)-16:1-CoA. Both M. tuberculosis proteins were required for reconstitution of activity, as various combinations of control lysates lacking either Rv3230c or DesA3 gave minimal or no activity. Furthermore, the specificity of interaction between Rv3230c and DesA3 was implied by the inability of other related redox systems to substitute for Rv3230c. The reconstituted activity was dependent upon the presence of NADPH, could be saturated by increasing the amount of Rv3230c added, and was also sensitive to the salt concentration in the buffer. The results are consistent with the formation of a protein-protein complex, possibly with electrostatic character. This work defines a multiprotein, acyl-CoA desaturase complex from M. tuberculosis H37Rv to minimally consist of a soluble Rv3230c reductase and integral membrane DesA3 desaturase. Further implications of this finding relative to the properties of other multiprotein iron-enzyme complexes are discussed.

Flow-cytometric detection of changes in the physiological state of E. coli expressing a heterologous membrane protein during carbon-limited fedbatch cultivation

The key to optimizing productivity during industrial fermentations is the ability to rapidly monitor and interpret the physiological state of single microbial cells in a population and to recognize and characterize different sub-populations. Here, a flow cytometry-based method for the reproducible detection of changes in membrane function and/or structure of recombinant E. coli JM101 (pSPZ3) expressing xylene monooxygenase (XMO), was developed. XMO expression led to compromised but not permeabilized cell membranes. This was deduced from the fact that recombinant cells only stained with ethidium bromide (EB) and not with propidium iodide (PI). During the glucose-limited fedbatch cultivation, an increase from 25% to 95% of EB-stained cells was observed, occurring between 2 and 5 h after induction. Control experiments confirmed that this increase was due to the recombinant protein production and not caused by any possible effects of varying substrate availability, high cell density, plasmid replication or the presence of the inducing agent. We hypothesize that the integration of the recombinant protein into the cell membrane physically disrupted the functionality of the efflux pumps, thus resulting in EB-staining of the recombinant cells. This method enabled us to detect changes in the physiological state of single cells 2-4 h before other indications of partial cell damage, such as unbalanced growth, acetate accumulation and an increased CO(2) production rate, were observed. This method therefore shows promise with respect to the further development of an early-warning system to prevent sudden productivity decreases in processes with recombinant E. coli expressing heterologous membrane proteins.

Isolation and characterization of o-xylene oxygenase genes from Rhodococcus opacus TKN14

o-Xylene is one of the most difficult-to-degrade environmental pollutants. We report here Rhodococcus genes mediating oxygenation in the first step of o-xylene degradation. Rhodococcus opacus TKN14, isolated from soil contaminated with o-xylene, was able to utilize o-xylene as the sole carbon source and to metabolize it to o-methylbenzoic acid. A cosmid library from the genome of this strain was constructed in Escherichia coli. A bioconversion analysis revealed that a cosmid clone incorporating a 15-kb NotI fragment had the ability to convert o-xylene into o-methylbenzyl alcohol. The sequence analysis of this 15-kb region indicated the presence of a gene cluster significantly homologous to the naphthalene-inducible dioxygenase gene clusters (nidABCD) that had been isolated from Rhodococcus sp. strain I24. Complementation studies, using E. coli expressing various combinations of individual open reading frames, revealed that a gene (named nidE) for rubredoxin (Rd) and a novel gene (named nidF) encoding an auxiliary protein, which had no overall homology with any other proteins, were indispensable for the methyl oxidation reaction of o-xylene, in addition to the dioxygenase iron-sulfur protein genes (nidAB). Regardless of the presence of NidF, the enzyme composed of NidABE was found to function as a typical naphthalene dioxygenase for converting naphthalene and various (di)methylnaphthalenes into their corresponding cis-dihydrodiols. All the nidABEF genes were transcriptionally induced in R. opacus TKN14 by the addition of o-xylene to a mineral salt medium. It is very likely that these genes are involved in the degradation pathways of a wide range of aromatic hydrocarbons by Rhodococcus species as the first key enzyme.

Characterization of four Rhodococcus alcohol dehydrogenase genes responsible for the oxidation of aromatic alcohols

Four genes were isolated and characterized for alcohol dehydrogenases (ADHs) catalyzing the oxidation of aromatic alcohols such as benzyl alcohol to their corresponding aldehydes, one from o-xylene-degrading Rhodococcus opacus TKN14 and the other three from n-alkane-degrading Rhodococcus erythropolis PR4. Various aromatic alcohols were bioconverted to their corresponding carboxylic acids using Escherichia coli cells expressing each of the four ADH genes together with an aromatic aldehyde dehydrogenase gene (phnN) from Sphingomonas sp. strain 14DN61. The ADH gene (designated adhA) from strain TKN14 had the ability to biotransform a wide variety of aromatic alcohols, i.e., 2-hydroxymethyl-6-methylnaphthalene, 2-hydroxymethylnaphthalene, xylene-alpha,alpha'-diol, 3-chlorobenzyl alcohol, and vanillyl alcohol, in addition to benzyl alcohol with or without a hydroxyl, methyl, or methoxy substitution. In contrast, the three ADH genes of strain PR4 (designated adhA, adhB, and adhC) exhibited lower ability to degrade these alcohols: these genes stimulated the conversion of the alcohol substrates by only threefold or less of the control value. One exception was the conversion of 3-methoxybenzyl alcohol, which was stimulated sevenfold by adhB. A phylogenetic analysis of the amino acid sequences of these four enzymes indicated that they differed from other Zn-dependent ADHs.

Characterization of Sphingomonas aldehyde dehydrogenase catalyzing the conversion of various aromatic aldehydes to their carboxylic acids

An aldehyde dehydrogenase gene, designated phnN, was isolated from a genome library of the 1,4-dimethylnaphthalene-utilizing soil bacterium, Sphingomonas sp. 14DN61. Escherichia coli expressing the phnN gene converted 1,4-dihydroxymethylnaphthalene to 1-hydroxymethyl-4-naphthoic acid. The putative amino acid sequence of the phnN gene product had 31-42% identity with those of NAD(+)-dependent short-chain aliphatic aldehyde dehydrogenases and a secondary alcohol dehydrogenase. The NAD(P)(+)-binding site and two consensus sequences involved in the active site for aldehyde dehydrogenase are conserved among these proteins. The PhnN enzyme purified from recombinant E. coli showed broad substrate specificity towards various aromatic aldehydes, i.e., 1- and 2-naphaldehydes, cinnamaldehyde, vanillin, syringaldehyde, benzaldehyde and benzaldehydes substituted with a hydroxyl, methyl, methoxy, chloro, fluoro, or nitro group were converted to their corresponding carboxylic acids. Interestingly, E. coli expressing phnN was able to biotransform a variety of not only aromatic aldehydes, but also aromatic alcohols to carboxylic acids.

Process implementation aspects for biocatalytic hydrocarbon oxyfunctionalization

Oxidoreductases catalyze a large variety of regio-, stereo-, and chemoselective hydrocarbon oxyfunctionalizations, reactions, which are important in industrial organic synthesis but difficult to achieve by chemical means. This review summarizes process implementation aspects for the in vivo application of the especially versatile enzyme class of oxygenases, capable of specifically introducing oxygen from molecular oxygen into a large range of organic molecules. Critical issues such as reaching high enzyme activity and specificity, product degradation, cofactor recycling, reactant toxicity, and substrate and oxygen mass transfer can be overcome by biochemical process engineering and biocatalyst engineering. Both strategies provide a growing toolset to facilitate process implementation, optimization, and scale-up. Major advances were achieved via heterologous overexpression of oxygenase genes, directed evolution, metabolic engineering, and in situ product removal. Process examples from industry and academia show that the combined use of different concepts enables efficient oxygenase-based whole-cell catalysis of various commercially interesting reactions such as the biosynthesis of chiral compounds, the specific oxyfunctionalization of complex molecules, and also the synthesis of medium-priced chemicals. Better understanding of the cell metabolism and future developments in both biocatalyst and bioprocess engineering are expected to promote the implementation of many and various industrial biooxidation processes.

Effects of surface hydrophobicity on the catalytic iron ion retention in the active site of two catechol 1,2-dioxygenase isoenzymes

The different behaviour of two isozymes (IsoA and IsoB) of catechol 1,2-dioxygenase (C 1,20) from Acinetobacter radioresistens S13 on a hydrophobic interaction, Phenyl-Sepharose chromatographic column, prompted us to investigate the role of superficial hydrophobicity on structural-functional aspects for such class of enzymes. The interaction of 8-anilino-1-naphtalenesulphonate (ANS), a fluorescent probe known to bind to hydrophobic sites in proteins, revealed that the two isoenzymes have a markedly different hydrophobicity degree although a similar number of hydrophobic superficial sites were estimated (2.65 for IsoA and 2.18 for IsoB). ANS is easily displaced by adding the substrates catechol or 3-methylcatechol to the adduct, suggesting that the binding sites are in the near surroundings of the catalytic clefts. The analysis of the hydropathy profiles and the possible superficial cavities allowed to recognize the most feasible region for ANS binding. The lower hydrophobicity detected in the near surroundings of the catalytic pocket of IsoB supports its peculiarity to lose the catalytic metal ions more easily than IsoA. As previously suggested for other metalloenzymes, the presence of more hydrophilic and/or smaller residues near to the active site of IsoB is expected to increase the metal ligands mobility thus increasing the metal ion dissociation rate constants, estimated to be 0.078 h(-1) and 0.670 h(-1) for IsoA and IsoB respectively.

Evolution of the soluble diiron monooxygenases

Based on structural, biochemical, and genetic data, the soluble diiron monooxygenases can be divided into four groups: the soluble methane monooxygenases, the Amo alkene monooxygenase of Rhodococcus corallinus B-276, the phenol hydroxylases, and the four-component alkene/aromatic monooxygenases. The limited phylogenetic distribution of these enzymes among bacteria, together with available genetic evidence, indicates that they have been spread largely through horizontal gene transfer. Phylogenetic analyses reveal that the alpha- and beta-oxygenase subunits are paralogous proteins and were derived from an ancient gene duplication of a carboxylate-bridged diiron protein, with subsequent divergence yielding a catalytic alpha-oxygenase subunit and a structural beta-oxygenase subunit. The oxidoreductase and ferredoxin components of these enzymes are likely to have been acquired by horizontal transfer from ancestors common to unrelated diiron and Rieske center oxygenases and other enzymes. The cumulative results of phylogenetic reconstructions suggest that the alkene/aromatic monooxygenases diverged first from the last common ancestor for these enzymes, followed by the phenol hydroxylases, Amo alkene monooxygenase, and methane monooxygenases.

Xylene monooxygenase, a membrane-spanning non-heme diiron enzyme that hydroxylates hydrocarbons via a substrate radical intermediate

The non-heme diiron enzyme xylene monooxygenase (XylM) has been shown to hydroxylate hydrocarbons via a hydrogen abstraction-carbon radical recombination mechanism (oxygen rebound). Using the radical clock bicyclo[4.1.0]heptane (norcarane) in a whole-cell assay, and observing the ratio of rearranged 3-(hydroxymethyl)cyclohexene and unrearranged 2-norcaranol products, the lifetime of the substrate radical was determined to be approximately 0.2 ns. The wild-type organism Pseudomonas putida mt-2 and two separate Escherichia coli clones expressing xylMA genes gave similar results. One clone produced the Pseudomonas putida mt-2 XylMA hydroxylase and the other produced Sphingomonas yanoikuyae B1 XylMA hydroxylase. Clones were constructed by inserting genes for xylene monooxygenase and xylene monooxygenase reductase downstream from an IPTG-inducible T7 promoter. Mechanistic investigations using whole-cell assays will facilitate more rapid screening of structure-function relationships and the identification of novel oxygenases. This approach should enable the construction of a picture of the key metalloenzymes and the mechanisms they use in selected parts of the global carbon cycle without requiring the isolation of every protein involved.

Evidence linking the Pseudomonas oleovorans alkane omega-hydroxylase, an integral membrane diiron enzyme, and the fatty acid desaturase family

Pseudomonas oleovorans alkane omega-hydroxylase (AlkB) is an integral membrane diiron enzyme that shares a requirement for iron and oxygen for activity in a manner similar to that of the non-heme integral membrane desaturases, epoxidases, acetylenases, conjugases, ketolases, decarbonylase and methyl oxidases. No overall sequence similarity is detected between AlkB and these desaturase-like enzymes by computer algorithms; however, they do contain a series of histidine residues in a similar relative positioning with respect to hydrophobic regions thought to be transmembrane domains. To test whether these conserved histidine residues are functionally equivalent to those of the desaturase-like enzymes we used scanning alanine mutagenesis to test if they are essential for activity of AlkB. These experiments show that alanine substitution of any of the eight conserved histidines results in complete inactivation, whereas replacement of three non-conserved histidines in close proximity to the conserved residues, results in only partial inactivation. These data provide the first experimental support for the hypotheses: (i) that the histidine motif in AlkB is equivalent to that in the desaturase-like enzymes and (ii) that the conserved histidine residues play a vital role such as coordinating the Fe ions comprising the diiron active site.

Use of the two-liquid phase concept to exploit kinetically controlled multistep biocatalysis

The two-liquid phase concept was used to develop a whole cell biocatalytic system for the efficient multistep oxidation of pseudocumene to 3,4-dimethylbenzaldehyde. Recombinant Escherichia coli cells were employed to express the Pseudomonas putida genes encoding xylene monooxygenase, which catalyzes the multistep oxygenation of one methyl group of toluene and xylenes to corresponding alcohols, aldehydes, and acids. A fed-batch based two-liquid phase bioconversion was established with bis(2-ethylhexyl)- phthalate as organic carrier solvent and a phase ratio of 0.5; the product formation pattern, the impact of the nutrient feeding strategy, and the partitioning behavior of the reactants were studied. On the basis of the favorable conditions provided by the two-liquid phase system, engineering of the initial pseudocumene concentration allowed exploiting the complex kinetics of the multistep reaction for the exclusive production of 3,4-dimethyl- benzaldehyde. Further oxidation of the product to 3,4-dimethylbenzoic acid could be inhibited by suitable concentrations of pseudocumene or 3,4-dimethylbenzyl alcohol. The optimized biotransformation setup includes a completely defined medium with high iron content and a nutrient feeding strategy that avoids severe glucose limitation as well as high inhibitory glucose levels. Using such a system on a 2-liter scale, we were able to produce, within 14.5 h, 30 g of 3,4-dimethylbenzaldehyde as predominant reactant in the organic phase and reached a maximal productivity of 1.6 g per liter liquid volume per hour. The present study implicates that the two-liquid phase concept is an efficient tool to exploit the kinetics of multistep biotransformations in general.