Cloning of three Alnus sieboldiana type III polyketide synthases and formation of polyketides in recombinant Escherichia coli using cinnamic acid analogs as substrates.

Alnus sieboldiana is an actinorhizal plant that coexists with the nitrogen-fixing actinomycete Frankia via nodules. It produces a variety of polyketides, including flavonoids, stilbenoids, and diarylheptanoids. These compounds have beneficial biological activities. Plant polyketides are produced by type III polyketide synthases (PKSIII). In this study, three A. sieboldiana PKSIIIs (AsPKSIII1, AsPKSIII2, and AsPKSIII3) predicted from next-generation sequencing analysis of A. sieboldiana seedling RNA were amplified and cloned. Phylogenetic tree analysis classified AsPKSIII2 and AsPKSIII3 into the chalcone synthase (CHS) group, whereas AsPKSIII1 was not classified into this group. We attempted to produce polyketides by adding cinnamic acid analogs to the culture medium of Escherichia coli, in which the respective PKSIII gene and the acetyl-CoA carboxylase (ACC) and 4-coumarate: CoA ligase (4CL) genes were simultaneously recombined. AsPKSIII1 is an enzyme that condensed only one molecule of malonyl-CoA to cinnamoyl-CoAs. In contrast, AsPKSIII2 and AsPKSIII3 produced chalcones as shown in a phylogenetic tree analysis, but also produced triketide pyrone. The ratio of these products differed between the two enzymes. We determined the gene and amino acid sequences as well as the substrate specificities of the two enzymes involved in flavonoid production and one enzyme potentially involved in diarylheptanoid production in A. sieboldiana.

Cloning and characterization of NADPH-dependent double-bond reductases from Alnus sieboldiana that recognize linear diarylheptanoids as substrates.

Diarylheptanoids are secondary metabolites of plants that comprise a C6-C7-C6 scaffold. They can be broadly classified into linear-type and cyclic-type diarylheptanoids based on their chemical structures. Actinorhizal trees, such as Casuarina, Alnus, and Myrica, which form nodule symbiosis with actinomycetes Frankia, produce cyclic diarylheptanoids (CDHs); in Alnus sieboldiana Matsum. in particular, we have reported that the addition of CDHs leads to an increase in the number of nodules. However, the information available on the biosynthesis of CDHs is scarce. A greater number of plants CDHs (including those isolated from actinorhizal trees) with a saturated heptane chain have been isolated compared with linear, non-cyclic diarylheptanoids. To identify the genes involved in the synthesis of these compounds, genes with significant sequence similarity to existing plant double-bond reductases were screened in A. sieboldiana. This report describes the isolation and characterization of two A. sieboldiana double-bond reductases (AsDBR1 and AsDBR2) that catalyze the NADPH-dependent reduction of bisdemethoxycurcumin and curcumin. The optimum pH for the two enzymes was 5.0. The apparent Km values for bisdemethoxycurcumin and NADPH were 4.24 and 3.53 µM in the case of AsDBR1, and 2.55 and 2.13 µM for AsDBR2. The kcat value was 9.4-fold higher for AsDBR1 vs. AsDBR2 when using the bisdemethoxycurcumin substrate. Interestingly, the two AsDBRs failed to reduce the phenylpropanoid monomer.

Two O-Methyltransferases from Phylogenetically Unrelated Cow Parsley (Anthriscus sylvestris) and Hinoki-Asunaro (Thujopsis dolabrata var. hondae) as a Signature of Lineage-Specific Evolution in Lignan Biosynthesis.

O-Methyltransferases (OMTs) play important roles in antitumor lignan biosynthesis. To date, six OMTs catalyzing the methylation of dibenzylbutyrolactone lignans as biosynthetic precursors of antitumor lignans have been identified. However, there is still no systematic understanding of the diversity and regularity of the biosynthetic mechanisms among various plant lineages. Herein, we report the characterization of two OMTs from Anthriscus sylvestris and Thujopsis dolabrata var. hondae [designated as AsSecoNorYatein (SNY) OMT and TdSNYOMT] together with the six known OMTs to evaluate their diversity and regularity. Although A. sylvestris 5-O-methylthujaplicatin (SecoNorYatein) and 4-O-demethylyatein (NorYatein) OMT (AsSNYOMT) and TdSNYOMT accept 5-O-methylthujaplicatin and 4-O-demethylyatein as substrates, phylogenetic analysis indicated that these two OMTs shared low amino acid sequence identity, 33.8%, indicating a signature of parallel evolution. The OMTs and the six previously identified OMTs were found to be diverse in terms of their substrate specificity, regioselectivity and amino acid sequence identity, indicating independent evolution in each plant species. Meanwhile, two-entropy analysis detected four amino acid residues as being specifically acquired by dibenzylbutyrolactone lignan OMTs. Site-directed mutation of AsSNYOMT indicated that two of them contributed specifically to 5-O-methylthujaplicatin methylation. The results provide a new example of parallel evolution and the diversity and regularity of OMTs in plant secondary (specialized) metabolism.

Cyclic diarylheptanoids as potential signal compounds during actinorhizal symbiosis between Alnus sieboldiana and Frankia.

The nitrogen-fixing actinomycete Frankia coexists with actinorhizal plants via nodules and supplies nitrogen compounds to the plants. Although communication has been suggested to exist through chemical substances in this nodule symbiosis, the details underlying this mechanism remain elusive. The biphenyl-type diarylheptanoids (BP-CDHs), alnusonol, and alnusdione, previously isolated from the actinorhizal plant A. sieboldiana branch wood, are secondary metabolites that accumulate in a limited number of plant species. However, since relatively widely distributed in actinorhizal plants, we investigated whether adding A. sieboldiana root extracts and these BP-CDHs could affect plant seedlings inoculated with Frankia. The results showed that the addition of root extract or alnusonol significantly increased the number of nodules and lobes more than two times compared with that upon Frankia supplementation only. We also proved that the extracted components of this plant affected nodule symbiosis. Finally, we confirmed through LC-MS that the root extract component contained BP-CDH, alnusonol. The above-described results indicate that BP-CDHs, at leaset alnusonol, might function as signal compounds from the plant side of the actinorhizal symbiosis between A. sieboldiana and Frankia.

Complete Genome Sequence of Halomonas meridiana Strain Eplume2, Isolated from a Hydrothermal Plume in the Northeast Pacific Ocean.

Halomonas meridiana strain Eplume2 (ATCC BAA-804) is a Gram-negative bacterium isolated from hydrothermal plume seawater in the Northeast Pacific Ocean at a depth of 2,000 m. Here, we report the complete genome sequence of this strain, which has a total size of 4.12 Mbp and a 56.6% G+C content.

Proposal and experimental demonstration of SDM node enabling path assignment to arbitrary wavelengths, cores, and directions.

We propose a novel simple space division multiplexing (SDM) node which is rearrangeble nonblocking, and effectively utilizes enhanced network resources through SDM. The proposed node can reduce a number of ports of wavelength selective switches (WSSs) and a number of WSS modules by modifying conventional multi-stage switches and employing integrated multiple arrayed WSSs. We experimentally actualized the newly proposed node, and demonstrate wavelength, core, and direction switching functions based on 127-Gbps Dual Polarization Quadrature Phase Shift Keying (DP-QPSK) signals. We also confirm the feasibility of the proposed SDM node through SDM transmission experiments using a 40-km multicore fiber and a multicore amplifier.

Filtering-tolerant transmission by the Walsh-Hadamard transform for super-channel beyond 100 Gb/s.

Super-channel transmission is a promising solution to increase the capacity of a channel beyond 100 Gb/s in next-generation optical networks. The performance of a super-channel comprising multiple subcarriers, however, degrades if optical filtering distortions occur in particular subcarriers. In this paper, we propose a method that improves super-channel performance by dispersing the distortions over all subcarriers. We also numerically demonstrate that the method effectively mitigates the filtering-induced penalty suffered by super-channels.

Treatment of tetracycline antibiotics by laccase in the presence of 1-hydroxybenzotriazole.

Tetracycline antibiotics are widely used in human and veterinary medicine; however, residual amounts of these antibiotics in the environment are of concern since they could contribute to selection of resistant bacteria. In this study, tetracycline (TC), chlortetracycline (CTC), doxycycline (DC) and oxytetracycline (OTC) were treated with laccase from the white rot fungus Trametes versicolor in the presence of the redox mediator 1-hydroxybenzotriazole (HBT). High performance liquid chromatography demonstrated that DC and CTC were completely eliminated after 15 min, while TC and CTC were eliminated after 1 h. This system also resulted in a complete loss of inhibition of growth of Escherichia coli and Bacillus subtilis and the green alga Pseudokirchneriella subcapitata with decreasing tetracycline antibiotic concentration. These results suggest that the laccase-HBT system is effective in eliminating tetracycline antibiotics and removing their ecotoxicity.

Statistics and performance under combined impairments induced by polarization-dependent-loss in polarization-division-multiplexing digital coherent transmission.

Two-dimensional statistics and Q-penalty performance under the combination of two major impairments induced by polarization-dependent loss, namely level imbalance and loss of orthogonality between polarization-multiplexed tributaries, for a polarization-division-multiplexing digital coherent transmission at over 100-Gb/s are presented for the first time to estimate the outage probability needed for designing the system.

Elimination of carbamazepine by repeated treatment with laccase in the presence of 1-hydroxybenzotriazole.

Carbamazepine (CBZP) is used as an antiepileptic drug and is highly persistent. In this study, CBZP was treated with laccase from white rot fungus Trametes versicolor in the presence of a redox mediator 1-hydroxybenzotriazole (HBT). A single treatment with laccase and HBT eliminated CBZP by about 22% after 24h, and repeated treatments with laccase and HBT, which were added to the reaction mixture every 8h, helped eliminate about 60% of CBZP after 48h. This suggests that repeated treatment is effective in eliminating CBZP. Mass spectrometric analyses demonstrated that two degradation products of CBZP, 10,11-dihydro-10,11-epoxycarbamazepine and 9(10H)-acridone, were formed via repeated treatment with laccase and HBT.

Elimination and detoxification of triclosan by manganese peroxidase from white rot fungus.

The antimicrobial and preservative agent triclosan (TCS) is an emerging and persistent pollutant with a ubiquitous presence in the aquatic environment. Thus, TCS was treated with manganese peroxidase (MnP), laccase and the laccase-mediator system with 1-hydroxybenzotriazole. MnP was most effective in eliminating TCS among the three enzymatic treatments, with TCS concentration being reduced by about 94% after 30 min following treatment with 0.5 nkat mL(-1) MnP and being almost completely eliminated after 60 min. Furthermore, MnP (0.5 nkat mL(-1)) caused the complete loss of bacterial growth inhibition by TCS after 30 min and reduced the algal growth inhibition of TCS by 75% and 90% after 30 and 60 min, respectively. These results strongly suggest that MnP is effective in removing the ecotoxicity of TCS.

Removal of diclofenac and mefenamic acid by the white rot fungus Phanerochaete sordida YK-624 and identification of their metabolites after fungal transformation.

The non-steroidal anti-inflammatory drugs diclofenac (DCF) and mefenamic acid (MFA) were treated with the white rot fungus Phanerochaete sordida YK-624. DCF completely disappeared and MFA decreased by about 90% after 6 days of treatment. It was also confirmed that the fungus almost completely removed the acute lethal toxicity of DCF and MFA towards the freshwater crustacean Thamnocephalus platyurus after 6 days of treatment. Mass spectrometric and (1)H nuclear magnetic resonance analyses demonstrated that two mono-hydroxylated DCFs (4'-hydroxydiclofenac and 5-hydroxydiclofenac) and one di-hydroxylated DCF (4',5-dihydroxydiclofenac) were formed via fungal transformation. The four metabolites of MFA were identified as 3'-hydroxymethylmefenamic acid (mono-hydroxylated MFA), 3'-hydroxymethyl-5-hydroxymefenamic acid (di-hydroxylated MFA), 3'-hydroxymethyl-6'-hydroxymefenamic acid (di-hydroxylated MFA) and 3'-carboxymefenamic acid. These results suggest that hydroxylation catalyzed by cytochrome P450 (CYP) in P. sordida YK-624 may be involved in the elimination and detoxification of DCF and MFA. This notion was further supported by the fact that smaller decreases in DCF and MFA were observed in cultures of P. sordida YK-624 incubated with 1-aminobenzotriazole, a known inhibitor of CYP.

Removal of estrogenic activity of iso-butylparaben and n-butylparaben by laccase in the presence of 1-hydroxybenzotriazole.

In the presence of a redox mediator, 1-hydroxybenzotriazole (HBT), iso-butylparaben (iso-BP) and n-butylparaben (n-BP) were treated with laccase from white rot fungus Trametes versicolor. HPLC analysis demonstrated that iso-BP and n-BP almost completely disappeared from the reaction mixture after 4 h of treatment with the laccase-HBT system. Using the yeast two-hybrid assay system, it was also confirmed that the laccase-HBT system substantially removed the estrogenic activity of iso-BP and n-BP after 4 h of treatment. Furthermore, there was a linear relationship between the removal of estrogenic activity of both parabens and the decrease in their concentrations. These results demonstrate that the laccase-HBT system is effective in eliminating iso-BP and n-BP, and removing the estrogenic activity of both parabens.

Removal of estrogenic activity of 4-tert-octylphenol by ligninolytic enzymes from white rot fungi.

4-tert-Octylphenol (4-t-OP) was treated with the white rot fungus Phanerochaete sordida YK-624 under ligninolytic condition with low-nitrogen and high-carbon culture medium. 4-t-OP completely disappeared after 5 days of treatment and the activities of ligninolytic enzymes, laccase and manganese peroxidase (MnP), were detected during this period, thus suggesting that the disappearance of 4-t-OP is related to these extracellular enzymes. Therefore, 4-t-OP was treated with laccase and MnP prepared from white rot fungi cultures. HPLC analysis demonstrated that 4-t-OP completely disappeared in the reaction mixture after 1 h of treatment with either laccase or MnP. Using the yeast two-hybrid assay system, it was also confirmed that laccase and MnP substantially removed the estrogenic activity of 4-t-OP after 1 and 2 h of treatment, respectively. These results strongly demonstrate that ligninolytic enzymes are effective in removing the estrogenic activity of 4-t-OP.

Role of 1-hydroxybenzotriazole in oxidation by laccase from Trametes versicolor. Kinetic analysis of the laccase-1-hydroxybenzotriazole couple.

In the current studies, we used Lineweaver-Burke analysis to examine the role of 1-hydroxybenzotriazole (HBT) in the oxidation of various compounds by laccase from Trametes versicolor. At low concentrations, HBT was a competitive inhibitor of the oxidation, but at high concentrations, it was a noncompetitive inhibitor. Analysis of the oxidation of ferrocytochrome c by the laccase-HBT couple showed that increasing the concentration of ferrocytochrome c did not affect the V(max) but reduced the apparent K(m). In addition, in the manganese peroxidase-Mn(II) reaction, which is a typical oxidation system by mediator, the apparent K(m) and V(max) increased as the concentration of the substrate 2,6-dimethoxyphenol was increased. These results indicate that HBT is involved in the binding of laccase and substrates that laccase cannot oxidize alone.

Removal of estrogenic activity of natural steroidal hormone estrone by ligninolytic enzymes from white rot fungi.

Natural steroidal hormone estrone (E1) was treated with the white rot fungus Phanerochaete sordida YK-624 under ligninolytic condition with low-nitrogen and high-carbon culture medium. E1 decreased by 98% after 5 d of treatment and the activities of ligninolytic enzymes, manganese peroxidase (MnP) and laccase, were detected during treatment, which suggested that the disappearance of E1 is related to ligninolytic enzymes produced extracellularly by white rot fungus. Therefore, E1 was treated with MnP and laccase prepared from the culture of white rot fungi. HPLC analysis demonstrated that E1 disappeared completely in the reaction mixture after 1 h of treatment with either MnP or laccase. Using the yeast two-hybrid assay system, it was also confirmed that both enzymatic treatments completely removed the estrogenic activity of E1 after 2 h. These results strongly suggest that ligninolytic enzymes are effective in removing the estrogenic activity of E1.

Characteristics of novel lignin peroxidases produced by white-rot fungus Phanerochaete sordida YK-624.

We characterized a lignin peroxidase (YK-LiP2) isolated from shaking culture inoculated with the white-rot fungus Phanerochaete sordida YK-624. The YK-LiP2 enzyme was identified and purified to homogeneity by anion-exchange chromatography and gel permeation chromatography. The molecular weight of YK-LiP2 was approximately 45 kDa, and its absorption spectrum was almost the same as that of the LiP (Pc-LiP) from P. chrysosporium. Steady-state kinetics of veratryl alcohol (VA) oxidation by YK-LiP2 revealed an ordered bi-bi ping-pong mechanism, although the Pc-LiP oxidation of ferrocytochrome c obeys peroxidase ping-pong kinetics rather than ordered bi-bi ping-pong kinetics. Degradation of dimeric lignin model compounds by YK-LiP2 was more effective than that by Pc-LiP. Moreover, YK-LiP2 and YK-LiP1, which was previously isolated from static culture inoculated with P. sordida YK-624, oxidized VA under a higher concentration of hydrogen peroxide (>2.5 mM) although Pc-LiP could not oxidize VA in the presence of 2.5 mM hydrogen peroxide.

Removal of estrogenic activity of endocrine-disrupting genistein by ligninolytic enzymes from white rot fungi.

Endocrine-disrupting genistein was treated with the white rot fungus Phanerochaete sordida YK-624 under ligninolytic condition with low-nitrogen and high-carbon culture medium. Genistein decreased by 93% after 4 days of treatment and the activities of ligninolytic enzymes, manganese peroxidase (MnP) and laccase, were detected during treatment, thus suggesting that the disappearance of genistein is related to ligninolytic enzymes produced extracellularly by white rot fungi. Therefore, genistein was treated with MnP, laccase, and the laccase-mediator system with 1-hydroxybenzotriazole (HBT) as a mediator. HPLC analysis demonstrated that genistein disappeared almost completely in the reaction mixture after 4 h of treatment with either MnP, laccase, or the laccase-HBT system. Using the yeast two-hybrid assay system, it was also confirmed that three enzymatic treatments completely removed the estrogenic activity of genistein after 4h. These results strongly suggest that ligninolytic enzymes are effective in removing the estrogenic activity of genistein.

NMR analysis of lignins in CAD-deficient plants. Part 1. Incorporation of hydroxycinnamaldehydes and hydroxybenzaldehydes into lignins.

Peroxidase/H2O2-mediated radical coupling of 4-hydroxycinnamaldehydes produces 8-O-4-, 8-5-, and 8-8-coupled dehydrodimers as has been documented earlier, as well as the 5-5-coupled dehydrodimer. The 8-5-dehydrodimer is however produced kinetically in its cyclic phenylcoumaran form at neutral pH. Synthetic polymers produced from mixtures of hydroxycinnamaldehydes and normal monolignols provide the next level of complexity. Spectral data from dimers, oligomers, and synthetic polymers have allowed a more substantive assignment of aldehyde components in lignins isolated from a CAD-deficient pine mutant and an antisense-CAD-downregulated transgenic tobacco. CAD-deficient pine lignin shows enhanced levels of the typical benzaldehyde and cinnamaldehyde end-groups, along with evidence for two types of 8-O-4-coupled coniferaldehyde units. The CAD-downregulated tobacco also has higher levels of hydroxycinnamaldehyde and hydroxybenzaldehyde (mainly syringaldehyde) incorporation, but the analogous two types of 8-O-4-coupled products are the dominant features. 8-8-Coupled units are also clearly evident. There is clear evidence for coupling of hydroxycinnamaldehydes to each other and then incorporation into the lignin, as well as for the incorporation of hydroxycinnamaldehyde monomers into the growing lignin polymer. Coniferaldehyde and sinapaldehyde (as well as vanillin and syringaldehyde) co-polymerize with the traditional monolignols into lignins and do so at enhanced levels when CAD-deficiency has an impact on the normal monolignol production. The implication is that, particularly in angiosperms, the aldehydes behave like the traditional monolignols and should probably be regarded as authentic lignin monomers in normal and CAD-deficient plants.

Substrate specificity of the alpha-L-arabinofuranosidase from Rhizomucor pusillus HHT-1.

The alpha-L-arabinofuranosidase (AF) from the fungus Rhizomucor pusillus HHT-1 released arabinose at appreciable rates from (1-->5)-alpha-L-arabinofuranooligosaccharides, sugar beet arabinan and debranched arabinan. This enzyme preferentially hydrolyzed the terminal arabinofuranosyl residue [alpha-(1-->5)-linked] of the arabinan backbone rather than the arabinosyl side chain [alpha-(1-->3)-linked residues]. The enzyme-hydrolyzed arabinan reacted at and debranched the arabinan almost at the same rate, and the degree of conversion for both cases was 65%. Methylation analysis of arabinan showed that the arabinosyl-linkage proportions were 2:2:2:1, respectively, for (1-->5)-Araf, T-Araf, (1-->3, 5)-Araf and (1-->3)-Araf, while the ratios for the AF-digested arabinan shifted to 3:1:2:1. Enzyme digestion resulted in an increase in the proportion of (1-->5)-linked arabinose and a decrease in the proportion of terminal arabinose indicated this AF cleaved the terminal arabinosyl residue of the arabinan back bone [alpha-(1-->5)-linked residues]. Peak assignments in the 13C NMR spectra also confirmed this linkage composition of four kinds of arabinose residues. Both 1H and 13C NMR spectra are dominated by signals of the alpha-anomeric configuration of the arabinofuranosyl moieties. No signals were recorded for arabinopyranosyl moieties in the NMR spectra. Methylation and NMR analysis of native and AF-digested arabinan revealed that this alpha-L-arabinofuranosidase can only hydrolyse alpha-L-arabinofuranosyl residues of arabinan.