Cloning of a Sphingomonas paucimobilis SYK-6 Gene Encoding a Novel Oxygenase That Cleaves Lignin-Related Biphenyl and Characterization of the Enzyme

Sphingomonas paucimobilis SYK-6 transforms 2,2′-dihydroxy-3,3′-dimethoxy-5,5′-dicarboxybiphenyl (DDVA), a lignin-related biphenyl compound, to 5-carboxyvanillic acid via 2,2′,3-trihydroxy-3′-methoxy-5,5′-dicarboxybiphenyl (OH-DDVA) as an intermediate (15). The ring fission of OH-DDVA is an essential step in the DDVA degradative pathway. A 15-kb EcoRI fragment isolated from the cosmid library complemented the growth deficiency of a mutant on OH-DDVA. Subcloning and deletion analysis showed that a 1.4-kb DNA fragment included the gene responsible for the ring fission of OH-DDVA. An open reading frame encoding 334 amino acids was identified and designated ligZ. The deduced amino acid sequence of LigZ had 18 to 21% identity with the class III extradiol dioxygenase family, including the β subunit (LigB) of protocatechuate 4,5-dioxygenase of SYK-6 (Y. Noda, S. Nishikawa, K.-I. Shiozuka, H. Kadokura, H. Nakajima, K. Yano, Y. Katayama, N. Morohoshi, T. Haraguchi, and M. Yamasaki, J. Bacteriol. 172:2704–2709, 1990), catechol 2,3-dioxygenase I (MpcI) of Alcaligenes eutrophus JMP222 (M. Kabisch and P. Fortnagel, Nucleic Acids Res. 18:3405–3406, 1990), the catalytic subunit of the meta-cleavage enzyme (CarBb) for 2′-aminobiphenyl-2,3-diol from Pseudomonas sp. strain CA10 (S. I. Sato, N. Ouchiyama, T. Kimura, H. Nojiri, H. Yamane, and T. Omori, J. Bacteriol. 179:4841–4849, 1997), and 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB) of Escherichia coli (E. L. Spence, M. Kawamukai, J. Sanvoisin, H. Braven, and T. D. H. Bugg, J. Bacteriol. 178:5249–5256, 1996). The ring fission product formed from OH-DDVA by LigZ developed a yellow color with an absorption maximum at 455 nm, suggesting meta cleavage. Thus, LigZ was concluded to be a ring cleavage extradiol dioxygenase. LigZ activity was detected only for OH-DDVA and 2,2′,3,3′-tetrahydroxy-5,5′-dicarboxybiphenyl and was dependent on the ferrous ion.Lignin is the most common aromatic compound in the biosphere, and the degradation of lignin is a significant step in the global carbon cycle. Lignin is composed of various intermolecular linkages between phenylpropanes and guaiacyl, syringyl, p-hydroxyphenyl, and biphenyl nuclei (5, 34). Lignin breakdown therefore involves multiple biochemical reactions involving the cleavage of intermonomeric linkages, demethylations, hydroxylations, side-chain modifications, and aromatic ring fission (10, 11, 19, 40).Soil bacteria are known to display ample metabolic versatility toward aromatic substrates. Sphingomonas paucimobilis SYK-6 (formerly Pseudomonas paucimobilis SYK-6) has been isolated with 2,2′-dihydroxy-3,3′-dimethoxy-5,5′-dicarboxybiphenyl (DDVA) as a sole carbon and energy source. This strain can also grow on syringate, 3-O-methylgallic acid (3OMGA), vanillate, and other dimeric lignin compounds, including β-aryl ether, diarylpropane (β-1), and phenylcoumaran (15). Analysis of the metabolic pathway has indicated that the dimeric lignin compounds are degraded to protocatechuate or 3OMGA (15) and that these compounds are cleaved by protocatechuate 4,5-dioxygenase encoded by ligAB (30). Among the dimeric lignin compounds, the degradation of β-aryl ether and the biphenyl structure is the most important, because β-aryl ether is most abundant in lignin (50%) and the biphenyl structure is so stable that its decomposition should be rate limiting in lignin degradation. We have already characterized the β-etherase and Cα-dehydrogenase genes (23–26) (ligFE and ligD, respectively) involved in the degradation of β-aryl ether. In this study, we focused on the genes responsible for the degradation of DDVA in SYK-6.In the proposed DDVA metabolic pathway of S. paucimobilis SYK-6 illustrated in Fig. ​Fig.1A,1A, DDVA is first demethylated to produce the diol compound 2,2′,3-trihydroxy-3′-methoxy-5,5′-dicarboxybiphenyl (OH-DDVA). OH-DDVA is then degraded to 5-carboxyvanillic acid (5-CVA), and this compound is converted to 3OMGA (15). The resulting product is cleaved by protocatechuate 4,5-dioxygenase. A ring cleavage enzyme for OH-DDVA has been thought to be involved in this pathway because the production of 5-CVA from OH-DDVA resembles the formation of benzoic acid from biphenyl by 2,3-dihydroxybiphenyl through the sequential action of a meta cleavage enzyme and a meta-cleavage compound hydrolase (Fig. ​(Fig.1B)1B) (1, 9, 13, 18, 21, 28). Open in a separate windowFIG. 1(A) Proposed metabolic pathway for DDVA by S. paucimobilis SYK-6. (B) Pathway for the conversion of 2,3-dihydroxybiphenyl (2,3-DHBP) to benzoate by the polychlorinated biphenyl-degrading bacteria. The proposed DDVA metabolic pathway follows the previous one (15). Enzymes: LigZ, OH-DDVA oxygenase; LigAB, protocatechuate 4,5-dioxygenase; BphC, 2,3-dihydroxybiphenyl 1,2-dioxygenase; BphD, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid hydrolase. TCA, tricarboxylic acid.In this study, we isolated the ligZ gene encoding a ring cleavage enzyme for OH-DDVA. The nucleotide sequence of the gene was determined, and the ligZ gene product was characterized.     

Characteristics and Efficiency of Glutamine Production by Coupling of a Bacterial Glutamine Synthetase Reaction with the Alcoholic Fermentation System of Baker’s Yeast

Glutamine production with bacterial glutamine synthetase (GS) and the sugar-fermenting system of baker’s yeast for ATP regeneration was investigated by determining the product yield obtained with the energy source for ATP regeneration (i.e., glucose) for yeast fermentation. Fructose 1,6-bisphosphate was accumulated temporarily prior to the formation of glutamine in mixtures which consisted of dried yeast cells, GS, their substrate (glucose and glutamate and ammonia), inorganic phosphate, and cofactors. By an increase in the amounts of GS and inorganic phosphate, the amounts of glutamine formed increased to 19 to 54 g/liter, with a yield increase of 69 to 72% based on the energy source (glucose) for ATP regeneration. The analyses of sugar fermentation of the yeast in the glutamine-producing mixtures suggested that the apparent hydrolysis of ATP by a futile cycle(s) at the early stage of glycolysis in the yeast cells reduces the efficiency of ATP utilization. Inorganic phosphate inhibits phosphatase(s) and thus improves glutamine yield. However, the analyses of GS activity in the glutamine-producing mixtures suggested that the higher concentration of inorganic phosphate as well as the limited amount of ATP-ADP caused the low reactivity of GS in the glutamine-producing mixtures. A result suggestive of improved glutamine yield under the conditions with lower concentrations of inorganic phosphate was obtained by using a yeast mutant strain that had low assimilating ability for glycerol and ethanol. In the mutant, the activity of the enzymes involved in gluconeogenesis, especially fructose 1,6-bisphosphatase, was lower than that in the wild-type strain.Glutamine is one of the most important compounds in nitrogen metabolism; it is not only a constituent of proteins but is also a donor of the amino (amido) moiety in the biosynthesis of other amino acids, purines, pyrimidines, pyridine coenzymes, and complex carbohydrates. Glutamine is also used in the treatment of gastric ulcers and has been produced commercially by direct fermentation with certain bacteria (6–10).In recent years, enzymatic synthesis has come to rival direct fermentation as a means of producing amino acids. In the case of glutamine, however, the need for a stoichiometric supply of ATP for the endoergonic reaction of glutamine synthetase (GS) precludes the development of an economically valuable method, unless ATP can be regenerated and recycled.Processes for the production of various substances using dried yeast cells as an enzyme source were established by Tochikura and colleagues (2, 4, 16, 18–20). The processes are driven by the chemical energy of ATP released by the alcoholic fermentation by the yeast, which has been wasted in alcoholic brewing (17). Tochikura and colleagues also designed a process in which the yeast fermentation of sugar is combined with an endoergonic reaction catalyzed by an enzyme from a different microorganism (3). The results suggest that the process offers the possibility of producing many compounds at a high yield by using various biosynthetic reactions and high concentrations of substrates. Tochikura et al. introduced the general idea of coupled fermentation with energy transfer for the process; its principle is indicated in Fig. ​Fig.1,1, with glutamine production as an example. Open in a separate windowFIG. 1Scheme of glutamine production by the coupled fermentation with energy transfer method. ∗1, glycolytic pathway is abridged. ∗2, inorganic phosphate (P_i) is recycled.In the process of coupled fermentation with energy transfer, a catalytic amount of ATP is regenerated with the energy of sugar fermented by yeast, in the form of baker’s yeast (4, 16, 18, 19, 23). The energy-utilizing system for the synthesis can involve the enzyme(s) of yeast itself or those of other organisms. It should be noted that, from another point of view, the use of the energy-utilizing system results in ADP regeneration to complete the fermentation of glucose, and that, if there is no ADP regeneration, the yeast fermentation of sugar can proceed only as follows, in the presence of inorganic phosphate (the Harden-Young effect of inorganic phosphate [1]), 2 · glucose + 2 · inorganic phosphate → fructose 1,6-bisphosphate (FBP) + 2 · C₂H₅OH + 2 · CO₂ (Harden-Young equation), where ADP regeneration for the fermentation of 1 mol of glucose is carried out by the phosphorylation of another mole of glucose to FBP.We previously reported glutamine production, obtained by employing a combination of baker’s yeast cells and GS from Gluconobacter suboxydans, as the first application of the coupled fermentation with energy transfer method for the production of a nonphosphorylated compound (12, 13). In addition, we achieved high-yield glutamine production by using the Corynebacterium glutamicum (Micrococcus glutamicus) enzyme and larger amounts of the substrates (15). The maximum amounts of glutamine formed (23 to 25 g/liter) and the yield based on glutamate (50 to 100%) were to some extent satisfactory, but the yield based on the energy source (glucose) for ATP regeneration was not satisfactory (about 40% of the theoretical value; 2 mol of glutamine can be formed when 1 mol of glucose is consumed).In the present study, we examined the characteristics of glutamine production regarding product yield based on the energy source for ATP regeneration and regarding the reactivity of GS during glutamine production, which is closely related to the product yield. The results of preliminary attempts to improve glutamine production are also described. In these experiments, a yeast mutant which has a low assimilating ability for glycerol and/or ethanol was used.     

Cytosolic r{beta}-Cyanoalanine Synthase Activity Attributed to Cysteine Synthases in Cocklebur Seeds. Purification and Characterization of Cytosolic Cysteine Synthases

The activity of rß-cyanoalanine synthase (CAS, EC4.4.1.9 [EC] ) in cotyledons of cocklebur seeds (Xanthium penn-sylvanicumWallr.) was detected both in the soluble and particulate fractions.The CAS activity of the soluble fraction (cytosolic CAS activity)was 10 times higher than that of the particulate fraction. TheCAS activity of the particulate fraction was confirmed to belocalized in the mitochondria. Both enzymatic activities wereclearly separated by non-denaturing PAGE. The enzyme with cytosolicCAS activity has been extensively purified and separated intothree different forms designated as cyt-1, cyt-2, and cyt-3.According to the SDS-PAGE analysis, the three enzymes are estimatedto be a homodimer composed of 35-kDa sub-units. The purifiedenzymes showed CS activity. Partial amino acid sequences ofcyt-1 were determined and had a high homology with cysteinesynthases (CS, EC 4.2.99.8 [EC] ) from other plant sources. The catalyticaction of the purified CSs in converting cyanide and cysteineinto H₂S and rß-cyanoalanine was confirmed by thedetection of significant ¹⁴CN incorporation into rß-cyanoalanine.These results indicated that cytosolic CAS activity is due tocytosolic CS and suggested that the CAS activity of CS is likelyto be involved in cyanide metabolism in plant tissues. (Received January 7, 1998; Accepted March 16, 1998)     

Rhododendrol biosynthesis and metabolism in Acer nikoense callus

Cell suspensions derived from Acer nikoense callus, not containing (S)-rhododendrol, converted 4-(p-hydroxyphenyl)-2- butanone into (R)-, (S)-rhododendrol and their glycosides. (R)- and (S)-rhododendrol formed was only detected in the culture medium and their glycosides only in the cells. The former compound disappeared within a short time and the latter one also tended to decrease during prolonged culture. Quantitative analysis of rhododendrol glycosides in the callus showed that most of them were (S)-rhododendrol 2-O--D-glucopyranoside and its content was much lower than that of the original plants. © Rapid Science Ltd. 1998     

The flowering-time geneFT and regulation of flowering inArabidopsis

Transition from vegetative to reproductive development (flowering) is one of the most important decisions during the post-embryonic development of flowering plants. More than twenty loci are known to regulate this process inArabidopsis. Some of these flowering-time genes may act at the shoot apical meristem to regulate its competence to respond to floral inductive signals and floral evocation. Genetic and phenotypic analyses of mutants suggest that the late-flowering geneFT may be a good candidate for such genes. To test this, we have cloned theFT gene using aFT-deficiency line associated with a T-DNA insertion. Cloned genes and loss-of-function mutants in hand, it is now possible to analyse the role ofFT and other genes in flowering at the biochemical and cellular levels as well as at the genetic level. The deduced FT protein has homology with TFL1 and CEN proteins believed to be involved in regulation of inflorescence meristem identity. Phylogenetic analysis suggests that theFT group and theTFL1/CEN group of genes diverged before the diversification of major angiosperm clades. This raises the interesting question of the evolutionary relationship between the regulation of vegetative/reproductive switching in the shoot apical meristem and the regulation of inflorescence architecture in angiosperms. The extended abstract of a paper presented at the 13th International Symposium in Conjugation with Award of the International Prize for Biology “Fronitier of Plant Biology”     

MAPKKK-Related protein kinase NPK1: Regulation of the M phase of plant cell cycle

The tobaccoNPK1 gene encodes a homolog of mitogenactivated protein kinase kinase kinases. We have recently identified tobacco kinesin-like proteins (NACK1/2) as activators for NPK1. Immunochemical analyses of NPK1 and NACK1 proteins suggest that NPK1 is involved in the regulation of some process in the M phase of the plant cell cycle. The extended abstract of a paper presented at the 13th International Symposium in Conjugation with Award of the International Prize for Biology “Frontier of Plant Biology”     

Correlation between genetic and cytogenetic maps of the rat

To correlate rat genetic linkage maps with cytogenetic maps, we localized 25 new cosmid-derived simple sequence length polymorphism (SSLP) markers and 14 existing genetic markers on cytogenetic bands of chromosomes, using fluorescence in situ hybridization (FISH). Next, a total of 58 anchor loci, consisting of the 39 new and 19 previously reported ones, were integrated into the genetic linkage maps. Since most of the new anchor loci were developed to be localized near the terminals of the genetic or cytogenetic maps for each chromosome, the orientation and coverage of the whole genetic linkage maps were determined or confirmed with respect to the cytogenetic maps. Thus, we provide here a new base for rat genetic maps. Received: 9 September 1997 / Accepted: 11 November 1997     

Isolation of 48 genetic markers appropriate for high throughput genotyping of inbred rat strains by B1 repetitive sequence-representational difference analysis

Mapping of genetic suppressors, modifiers, and quantitative trait loci (QTLs) requires genetic markers that can be efficiently and inexpensively genotyped for a large number of individuals. To isolate rat genetic markers suitable for this purpose, representational difference analysis (RDA) was performed with amplicons prepared by PCR with the B1 repetitive sequence used as the primer (B1-amplicons). In total, 48 polymorphic DNA fragments were isolated by five series of RDA, subtracting the B1-amplicons prepared from an ACI/N (ACI) rat from those prepared from BUF/Nac (BUF), and vice versa. All the polymorphic fragments detected ``presence-or-absence' polymorphisms with B1-amplicons prepared from ACI, BUF, and their F₂ progeny, and each fragment was linkage mapped. Dot-blotting amplicons onto filters at a high density and hybridization of the filters with these B1-RDA markers made it possible to genotype a large number of rats simultaneously for multiple loci. These B1-RDA markers were polymorphic between two given inbred strains of rat at frequencies between 30% and 70%. This is the first report on the isolation of B1-RDA markers among inbred strains of rats. Received: 15 July 1998 / Accepted: 18 August 1998