Yuichiro Otsuka

Identification of Three Alcohol Dehydrogenase Genes Involved in the Stereospecific Catabolism of Arylglycerol-β-Aryl Ether by Sphingobium sp. Strain SYK-6

ABSTRACT Degradation of arylglycerol-β-aryl ether is the most important process in bacterial lignin catabolism. Sphingobium sp. strain SYK-6 degrades guaiacylglycerol-β-guaiacyl ether (GGE) to α-(2-methoxyphenoxy)-β-hydroxypropiovanillone (MPHPV), and then the ether linkage of MPHPV is cleaved to generate α-glutathionyl-β-hydroxypropiovanillone (GS-HPV) and guaiacol. We have characterized three enantioselective glutathione S-transferase genes, including two genes that are involved in the ether cleavage of two enantiomers of MPHPV and one gene that is involved in the elimination of glutathione from a GS-HPV enantiomer. However, the first step in the degradation of four different GGE stereoisomers has not been characterized. In this study, three alcohol dehydrogenase genes, ligL, ligN, and ligO, which conferred GGE transformation activity in Escherichia coli, were isolated from SYK-6 and characterized, in addition to the previously cloned ligD gene. The levels of amino acid sequence identity of the four GGE dehydrogenases, which belong to the short-chain dehydrogenase/reductase family, ranged from 32% to 39%. Each gene was expressed in E. coli, and the stereospecificities of the gene products with the four GGE stereoisomers were determined by using chiral high-performance liquid chromatography with recently synthesized authentic enantiopure GGE stereoisomers. LigD and LigO converted (αR,βS)-GGE and (αR,βR)-GGE into (βS)-MPHPV and (βR)-MPHPV, respectively, while LigL and LigN transformed (αS,βR)-GGE and (αS,βS)-GGE to (βR)-MPHPV and (βS)-MPHPV, respectively. Disruption of the genes indicated that ligD is essential for the degradation of (αR,βS)-GGE and (αR,βR)-GGE and that both ligL and ligN contribute to the degradation of the two other GGE stereoisomers.

Characterization of the Third Glutathione S-Transferase Gene Involved in Enantioselective Cleavage of the β-Aryl Ether by Sphingobium sp. Strain SYK-6

The glutathione S-transferases, LigF and LigE, of Sphingobium sp. strain SYK-6 respectively play a role in cleavage of the β-aryl ether of (+)-(βS)-α-(2-methoxyphenoxy)-β-hydroxypropiovanillone (MPHPV) and (−)-(βR)-MPHPV. The ligP gene, which showed 59% similarity to ligE at the amino acid level, was isolated from SYK-6. LigP produced in Escherichia coli revealed enantioselectivity for (−)-(βR)-MPHPV, and ligE and ligP alone contributed to the degradation of (−)-(βR)-MPHPV in SYK-6.

Burkholderia oxyphila sp. nov., a bacterium isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives.

A novel bacterium, designated strain OX-01(T), was isolated from acidic soil, taxonomically investigated and identified as an agent that catabolizes (+)-catechin into taxifolin. Strain OX-01(T) is a Gram-reaction-negative, aerobic, non-sporulating, non-motile and rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus Burkholderia and occupying a phylogenetic position closest to, but clearly distinct from, Burkholderia sacchari. Strain OX-01(T) does not have any nif genes, which are required for N(2)-fixation, in its genome, a feature that is similar to B. sacchari, which lacks nifH, but is distinct from the N(2)-fixing features of many other phylogenetically related taxa, such as Burkholderia ferrariae, B. heleia, B. mimosarum, B. nodosa, B. silvatlantica, B. tropica and B. unamae. Strain OX-01(T) has the following chemotaxonomic characteristics: the major ubiquinone is Q-8, the DNA G+C content is 64 mol% and the major fatty acids are C(16 : 0), C(17 : 0) cyclo and C(18 : 1)ω7c. It also has a unique profile of carbohydrate utilization among other species of the genus Burkholderia. The strain cannot assimilate many pentoses, hexoses and oligosaccharides, whereas it can catabolize (+)-catechin and its putative aromatic derivatives, such as 4-hydroxy-3-methoxycinnamic acid, protocatechuic acid, p-hydroxybenzoic acid, trans-p-coumaric acid and vanillic acid. Based on its morphological, physiological and chemotaxonomic characteristics, together with DNA-DNA relatedness values and 16S rRNA gene sequence comparison data, we show that strain OX-O1(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia oxyphila sp. nov. is proposed. The type strain is OX-01(T) (=NBRC 105797(T) =DSM 22550(T)).

Identification of a Hydrolyzable Tannin, Oenothein B, as an Aluminum-Detoxifying Ligand in a Highly Aluminum-Resistant Tree, Eucalyptus camaldulensis

A hydrolyzable tannin isolated from roots of an aluminum-resistant eucalypt species can form nonphytotoxic complexes with aluminum ions. Eucalyptus camaldulensis is a tree species in the Myrtaceae that exhibits extremely high resistance to aluminum (Al). To explore a novel mechanism of Al resistance in plants, we examined the Al-binding ligands in roots and their role in Al resistance of E. camaldulensis. We identified a novel type of Al-binding ligand, oenothein B, which is a dimeric hydrolyzable tannin with many adjacent phenolic hydroxyl groups. Oenothein B was isolated from root extracts of E. camaldulensis by reverse-phase high-performance liquid chromatography and identified by nuclear magnetic resonance and mass spectrometry analyses. Oenothein B formed water-soluble or -insoluble complexes with Al depending on the ratio of oenothein B to Al and could bind at least four Al ions per molecule. In a bioassay using Arabidopsis (Arabidopsis thaliana), Al-induced inhibition of root elongation was completely alleviated by treatment with exogenous oenothein B, which indicated the capability of oenothein B to detoxify Al. In roots of E. camaldulensis, Al exposure enhanced the accumulation of oenothein B, especially in EDTA-extractable forms, which likely formed complexes with Al. Oenothein B was localized mostly in the root symplast, in which a considerable amount of Al accumulated. In contrast, oenothein B was not detected in three Al-sensitive species, comprising the Myrtaceae tree Melaleuca bracteata, Populus nigra, and Arabidopsis. Oenothein B content in roots of five tree species was correlated with their Al resistance. Taken together, these results suggest that internal detoxification of Al by the formation of complexes with oenothein B in roots likely contributes to the high Al resistance of E. camaldulensis.

Three-Component O-Demethylase System Essential for Catabolism of a Lignin-Derived Biphenyl Compound in Sphingobium sp. Strain SYK-6.

ABSTRACT Sphingobium sp. strain SYK-6 is able to assimilate lignin-derived biaryls, including a biphenyl compound, 5,5′-dehydrodivanillate (DDVA). Previously, ligXa (SLG_07770), which is similar to the gene encoding oxygenase components of Rieske-type nonheme iron aromatic-ring-hydroxylating oxygenases, was identified to be essential for the conversion of DDVA; however, the genes encoding electron transfer components remained unknown. Disruption of putative electron transfer component genes scattered through the SYK-6 genome indicated that SLG_08500 and SLG_21200, which showed approximately 60% amino acid sequence identities with ferredoxin and ferredoxin reductase of dicamba O-demethylase, were essential for the normal growth of SYK-6 on DDVA. LigXa and the gene products of SLG_08500 (LigXc) and SLG_21200 (LigXd) were purified and were estimated to be a trimer, a monomer, and a monomer, respectively. LigXd contains FAD as the prosthetic group and showed much higher reductase activity toward 2,6-dichlorophenolindophenol with NADH than with NADPH. A mixture of purified LigXa, LigXc, and LigXd converted DDVA into 2,2′,3-trihydroxy-3′-methoxy-5,5′-dicarboxybiphenyl in the presence of NADH, indicating that DDVA O-demethylase is a three-component monooxygenase. This enzyme requires Fe(II) for its activity and is highly specific for DDVA, with a Km value of 63.5 μM and k cat of 6.1 s−1. Genome searches in six other sphingomonads revealed genes similar to ligXc and ligXd (>58% amino acid sequence identities) with a limited number of electron transfer component genes, yet a number of diverse oxygenase component genes were found. This fact implies that these few electron transfer components are able to interact with numerous oxygenase components and the conserved LigXc and LigXd orthologs are important in sphingomonads.

Tetrahydrofolate-dependent vanillate and syringate O-demethylation links tightly to one-carbon metabolic pathway associated with amino acid synthesis and DNA methylation in the lignin metabolism of Sphingomonas paucimobilis SYK-6

Sphingomonas paucimobilis SYK-6 strain can degrade various lignin-related compounds. In the lignin metabolic pathway of this bacterium, vanillate and syringate are demethylated by the tetrahydrofolate (THF)-dependentO-demethylation system, which requires the enzymatic function of LigH. Upstream of theligH gene is the 5,10-methylene-THF reductase gene. Its gene product was essential for one-carbon metabolism involved in the amino acid synthesis and DNA methylation in all organisms. When themetF gene was inactivated in the genome of SYK-6, the resultant mutant, DLmetF, could not grow on vanillate and syringate as a sole carbon source. Furthermore, DLmetF showed significant accumulation of methyl-THF as a result of vanillate and syringateO-demethylation. We report here that THF-dependent vanillate and syringateO-demethylation links tightly to the one-carbon metabolic pathway that is associated with amino acid synthesis and DNA methylation, and the methyl group is the sole one-carbon source inS. paucimobilis SYK-6.

Beta-ketoadipic acid and muconolactone production from a lignin-related aromatic compound through the protocatechuate 3,4-metabolic pathway.

In this work, the effects of PcaJ (beta-ketoadipate:succinyl-coenzyme A transferase)- and PcaD (beta-ketoadipate enol-lactone hydrolase)-inactivation on protocatechuic acid metabolism in Pseudomonas putida KT2440 were evaluated. Beta-ketoadipic acid was produced from protocatechuic acid by the inactivation of PcaJ as expected; however, a portion of the produced beta-ketoadipic acid was converted to levulinic acid through a purification step consisting of extraction from the culture and recrystallization. On the other hand, muconolactone was purified from the culture of the PcaD-inactivated mutant of KT2440, although beta-ketoadipate enol-lactone was supposed to be produced because it is the substrate of PcaD. Under aerobic conditions, it has been reported that lignin-related aromatics are metabolized through PCA 2,3- or 3,4- or 4,5-ring cleavage pathways, and muconolactone is an intermediate observed in the metabolism of catechol, not protocatechuic acid. Our results will provide a prospective route to produce muconolactone with a high yield through the protocatechuate-3,4-metabolic pathway.

Mobile DNA distributions refine the phylogeny of "matsutake" mushrooms, Tricholoma sect. Caligata.

Abstract“Matsutake” mushrooms are formed by several species of Tricholoma sect. Caligata distributed across the northern hemisphere. A phylogenetic analysis of matsutake based on virtually neutral mutations in DNA sequences resolved robust relationships among Tricholoma anatolicum, Tricholoma bakamatsutake, Tricholoma magnivelare, Tricholoma matsutake, and Tricholoma sp. from Mexico (=Tricholoma sp. Mex). However, relationships among these matsutake and other species, such as Tricholoma caligatum and Tricholoma fulvocastaneum, were ambiguous. We, therefore, analyzed genomic copy numbers of σmarY1, marY1, and marY2N retrotransposons by comparing them with the single-copy mobile DNA megB1 using real-time polymerase chain reaction (PCR) to clarify matsutake phylogeny. We also examined types of megB1-associated domains, composed of a number of poly (A) and poly (T) reminiscent of RNA-derived DNA elements among these species. Both datasets resolved two distinct groups, one composed of T. bakamatsutake, T. fulvocastaneum, and T. caligatum that could have diverged earlier and the other comprising T. magnivelare, Tricholoma sp. Mex, T. anatolicum, and T. matsutake that could have evolved later. In the first group, T. caligatum was the closest to the second group, followed by T. fulvocastaneum and T. bakamatsutake. Within the second group, T. magnivelare was clearly differentiated from the other species. The data suggest that matsutake underwent substantial evolution between the first group, mostly composed of Fagaceae symbionts, and the second group, comprised only of Pinaceae symbionts, but diverged little within each groups. Mobile DNA markers could be useful in resolving difficult phylogenies due to, for example, closely spaced speciation events.

Microbial conversion of glucose to a novel chemical building block, 2-pyrone-4,6-dicarboxylic acid.

2-Pyrone-4,6-dicarboxylic acid (PDC) is a catabolic intermediate in Sphingobium sp. SYK-6 (previously characterized as Sphingomonas paucimobilis SYK-6), which is a degrader of lignin-derived aromatic compounds. Recently, PDC has been also characterized as a novel starting material for several potentially useful synthetic polymers. In a previous study, we constructed a biosynthetic system in which PDC was generated efficiently from a chemically synthesized compound, protocatechuate. In order to develop an alternative system for production of PDC, we tried to generate it from glucose, which is a low-cost sugar that can be obtained from abundant cellulosic wastes and biomass crops. We designed a metabolic bypass to PDC from the shikimate pathway in recombinant Escherichia coli cells. PDC accumulated in the medium of recombinant E. coli cells that had been transformed with genes isolated from Emericella niger, E. coli, Pseudomonas putida, and Sphingobium sp. SYK-6. The yield of PDC depended on the combination of genes that we introduced into the cells and on the specific of host strain. Under optimal conditions, the yield and titer of PDC were, respectively, 17.3% and 0.35 mg/l when the concentration of glucose was 2 g/l and the culture volume was 50 ml. Our results open up the possibility of novel utilization of biomass as the source of a useful chemical building block.

A bacterial aromatic aldehyde dehydrogenase critical for the efficient catabolism of syringaldehyde

Vanillin and syringaldehyde obtained from lignin are essential intermediates for the production of basic chemicals using microbial cell factories. However, in contrast to vanillin, the microbial conversion of syringaldehyde is poorly understood. Here, we identified an aromatic aldehyde dehydrogenase (ALDH) gene responsible for syringaldehyde catabolism from 20 putative ALDH genes of Sphingobium sp. strain SYK-6. All these genes were expressed in Escherichia coli, and nine gene products, including previously characterized BzaA, BzaB, and vanillin dehydrogenase (LigV), exhibited oxidation activities for syringaldehyde to produce syringate. Among these genes, SLG_28320 (desV) and ligV were most highly and constitutively transcribed in the SYK-6 cells. Disruption of desV in SYK-6 resulted in a significant reduction in growth on syringaldehyde and in syringaldehyde oxidation activity. Furthermore, a desV ligV double mutant almost completely lost its ability to grow on syringaldehyde. Purified DesV showed similar kcat/Km values for syringaldehyde (2100 s−1·mM−1) and vanillin (1700 s−1·mM−1), whereas LigV substantially preferred vanillin (8800 s−1·mM−1) over syringaldehyde (1.4 s−1·mM−1). These results clearly demonstrate that desV plays a major role in syringaldehyde catabolism. Phylogenetic analyses showed that DesV-like ALDHs formed a distinct phylogenetic cluster separated from the vanillin dehydrogenase cluster.