A New Synthetic Route to N-Benzyl Carboxamides through the Reverse Reaction of N-Substituted Formamide Deformylase

Previously, we isolated a new enzyme, N-substituted formamide deformylase, that catalyzes the hydrolysis of N-substituted formamide to the corresponding amine and formate (H. Fukatsu, Y. Hashimoto, M. Goda, H. Higashibata, and M. Kobayashi, Proc. Natl. Acad. Sci. U. S. A. 101:13726–13731, 2004, doi:10.1073/pnas.0405082101). Here, we discovered that this enzyme catalyzed the reverse reaction, synthesizing N-benzylformamide (NBFA) from benzylamine and formate. The reverse reaction proceeded only in the presence of high substrate concentrations. The effects of pH and inhibitors on the reverse reaction were almost the same as those on the forward reaction, suggesting that the forward and reverse reactions are both catalyzed at the same catalytic site. Bisubstrate kinetic analysis using formate and benzylamine and dead-end inhibition studies using a benzylamine analogue, aniline, revealed that the reverse reaction of this enzyme proceeds via an ordered two-substrate, two-product (bi-bi) mechanism in which formate binds first to the enzyme active site, followed by benzylamine binding and the subsequent release of NBFA. To our knowledge, this is the first report of the reverse reaction of an amine-forming deformylase. Surprisingly, analysis of the substrate specificity for acids demonstrated that not only formate, but also acetate and propionate (namely, acids with numbers of carbon atoms ranging from C₁ to C₃), were active as acid substrates for the reverse reaction. Through this reaction, N-substituted carboxamides, such as NBFA, N-benzylacetamide, and N-benzylpropionamide, were synthesized from benzylamine and the corresponding acid substrates.     

Species diversity estimation of ambrosia and bark beetles in temperate mixed forests in Japan based on host phylogeny and specificity

Understandings of the effect of host plant phylogeny on the structure of herbivore assemblage is useful for estimating global species richness of herbivores. Here we test the relationship between host plant phylogeny and two assemblages including ambrosia beetle assemblage that have been considered to be the lowest host specificity among plant-dependent guilds. These results of local scale were used for estimating regional species richness by extrapolating to the number of plant order and species in Japan. The estimated numbers were compared with the numbers of described species in Japan. Tree trunks of 17 plant species representing 17 orders of all major lineages of Japanese tree flora were exposed for collecting wood boring beetle species. A total of 12 ambrosia and four bark beetle species were collected. Similarity of both ambrosia and bark beetle assemblages showed a significant negative trend with phylogenetic distance between focal host plant species. The regression model for this relationship was well fit by a linear model whereas previous studies used a semi-log model, which suggests a difference in mechanism of host utilization with host taxonomic levels. Our results showed a broader host range of ambrosia beetle assemblage in temperate forest than to a comparable study in tropical rainforests. Species richness estimated is lower than the described species in Japan, suggesting the need for more samples along the altitudinal gradients for accurate estimation for the Japanese fauna.     

Functional analysis of three novel cell lines derived from human papillary thyroid carcinomas with three different clinical courses

Papillary thyroid carcinoma (PTC) is the most frequent thyroid carcinoma. PTC cell lines have been of considerable value in studying aspects of thyroid cancer, such as gene expression, cell proliferation, and differentiation. Here we report three novel PTC lines established from three patients with different backgrounds. Case 1 was a 38-year-old woman with PTC in the right thyroid lobe, with no metastasis. The cell line was established from the resection sample and named D-PTC. The cell line consisted of epithelial cells with few lysosomes and showed a pavement structure and follicular formation at confluency. There was a little pilling up. The secretion of free thyroxin (fT4) and thyroglobulin (Tg) was increased by TSH, or GH and IGF-I treatment. Case 2 was a 22-year-old woman with PTC initially in the right thyroid lobe, but 4 years after the right lobe resection, PTC metastasis was observed in left lobe. The cell line was established from a sample of the second resection and named UD-PTC. This cell line consisted of small epithelial cells with evident lysosomes and exhibited floating cell clusters. The secretion of fT4 and Tg was slightly increased by TSH, or GH and IGF-I treatment. Case 3 was an 85-year-old man with PTC and with acromegaly. Metastasis was observed at cervical lymph nodes. The cell line was derived from the metastasis region and named A-PTC. This cell line consisted of small epithelial cells and many lysosomes. The cells frequently showed pilling up. The secretion of fT4 and Tg was significantly increased by GH and IGF-I treatment. We have established three PTC cell lines with substantial variation in their phenotype. The cell lines may be useful for thyroid cancer research.     

Simultaneous estimation of mixing rates and genetic drift under successive sampling of genetic markers with application to the mud crab (Scylla paramamosain) in Japan

In stock enhancement programs, it is important to assess mixing rates of released individuals in stocks. For this purpose, genetic stock identification has been applied. The allele frequencies in a composite population are expressed as a mixture of the allele frequencies in the natural and released populations. The estimation of mixing rates is possible, under successive sampling from the composite population, on the basis of temporal changes in allele frequencies. The allele frequencies in the natural population may be estimated from those of the composite population in the preceding year. However, it should be noted that these frequencies can vary between generations due to genetic drift. In this article, we develop a new method for simultaneous estimation of mixing rates and genetic drift in a stock enhancement program. Numerical simulation shows that our procedure estimates the mixing rate with little bias. Although the genetic drift is underestimated when the amount of information is small, reduction of the bias is possible by analyzing multiple unlinked loci. The method was applied to real data on mud crab stocking, and the result showed a yearly variation in the mixing rate.     

Caveolar endocytosis and microdomain association of a glycosphingolipid analog is dependent on its sphingosine stereochemistry

We have previously shown that glycosphingolipid analogs are internalized primarily via caveolae in various cell types. This selective internalization was not dependent on particular carbohydrate headgroups or sphingosine chain length. Here, we examine the role of sphingosine structure in the endocytosis of BODIPYtrade mark-tagged lactosylceramide (LacCer) analogs via caveolae. We found that whereas the LacCer analog with the natural (D-erythro) sphingosine stereochemistry is internalized mainly via caveolae, the non-natural (L-threo) LacCer analog is taken up via clathrin-, RhoA-, and Cdc42-dependent mechanisms and largely excluded from uptake via caveolae. Unlike the D-erythro-LacCer analog, the L-threo analog did not cluster in membrane microdomains when added at higher concentrations (5-20 microm). In vitro studies using small unilamellar vesicles and giant unilamellar vesicles demonstrated that L-threo-LacCer did not undergo a concentration-dependent excimer shift in fluorescence emission such as that seen with BODIPYtrade mark-sphingolipids with natural stereochemistry. Molecular modeling studies suggest that in d-erythro-LacCer, the disaccharide moiety extends above and in the same plane as the sphingosine hydrocarbon chain, while in L-threo-LacCer the carbohydrate group is nearly perpendicular to the hydrocarbon chain. Together, these results suggest that the altered stereochemistry of the sphingosine group in L-threo-LacCer results in a perturbed structure, which is unable to pack closely with natural membrane lipids, leading to a reduced inclusion in plasma membrane microdomains and decreased uptake by caveolar endocytosis. These findings demonstrate the importance of the sphingolipid stereochemistry in the formation of membrane microdomains.     

Phylogenetic constraints to soil properties determine elevational diversity gradients of forest understory vegetation

Elevational diversity gradients (EDGs) of vegetation are shaped by the evolutionary histories of plants as well as by ecological factors. However, few studies of EDGs have focused on the roles of phylogenetic constraints and the effects of complicated interactions among environmental factors. Here, we examine the direct and indirect effects of environmental factors in forming EDGs of forest understory vegetation. The study plots were selected along elevational gradients in cool-temperate and sub-alpine forests in the University of Tokyo Chichibu Forest of central Japan. Tree seedlings and herbs were identified, and environmental factors (elevation, soil temperature, soil pH, soil CN ratio, forest type, basal area, canopy openness, and slope) were measured in these plots. Structural equation modeling (SEM) including taxonomic and phylogenetic diversity was used to consider the causal relationships between environmental conditions and the diversity of understory vegetation. In addition, phylogenetic signals in habitat requirements were tested. The taxonomic and phylogenetic diversities of tree seedlings increased monotonically with elevation, and the same pattern was found for the taxonomic diversity of herbs. The SEM indicated that both the taxonomic and phylogenetic diversity of tree seedlings were most affected by soil properties, although the phylogenetic diversity of herbs was determined by light conditions. These results highlight the importance of environmental filtering by soil properties in shaping EDGs of tree seedlings. This study implies that phylogenetic constraints in the adaptation to soil properties should be considered when predicting changes in EDGs under environmental fluctuations.     

Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges.

The crystal structure of a quinohemoprotein amine dehydrogenase from Pseudomonas putida has been determined at 1.9-A resolution. The enzyme comprises three non-identical subunits: a four-domain alpha-subunit that harbors a di-heme cytochrome c, a seven-bladed beta-propeller beta-subunit that provides part of the active site, and a small gamma-subunit that contains a novel cross-linked, proteinous quinone cofactor, cysteine tryptophylquinone. More surprisingly, the catalytic gamma-subunit contains three additional chemical cross-links that encage the cysteine tryptophylquinone cofactor, involving a cysteine side chain bridged to either an Asp or Glu residue all in a hitherto unknown thioether bonding with a methylene carbon atom of acidic amino acid side chains. Thus, the structure of the 79-residue gamma-subunit is quite unusual, containing four internal cross-links in such a short polypeptide chain that would otherwise be difficult to fold into a globular structure.     

Proteomic analysis of laser-microdissected paraffin-embedded tissues: (1) Stage-related protein candidates upon non-metastatic lung adenocarcinoma

We used formalin-fixed paraffin-embedded (FFPE) materials for biomarker discovery in cases of lung cancer using proteomic analysis. We conducted a retrospective global proteomic study in order to characterize protein expression reflecting clinical stages of individual patients with stage I lung adenocarcinoma without lymph node involvement (n = 7). In addition, we studied more advanced stage IIIA with spread to lymph nodes (n = 6), because the degree of lymph node involvement is the most important factor for staging. FFPE sections of cancerous lesions resected surgically from patients with well-characterized clinical history were subjected to laser microdissection (LMD) followed by Liquid Tissue? solubilization and digestion trypsin. Spectral counting was used to measure the amounts of proteins identified by shotgun liquid chromatography (LC)/tandem mass spectrometry (MS/MS). More than 500 proteins were identified from IA and IIIA cases, and non-parametric statistics showed that 81 proteins correlated significantly with stage IA or IIIA. A subset of those proteins were verified by multiple-reaction monitoring mass spectrometric quantitation (MRM assay), described in other paper in this issue. These results demonstrated the technical feasibility of a global proteomic study using clinically well documented FFPE sections, and its possible utility for detailed retrospective disease analyses in order to improve therapeutic strategy.     

Human ZG16p recognizes pathogenic fungi through non-self polyvalent mannose in the digestive system

Human zymogen granule protein 16 (ZG16p) contains a Jacalin-like lectin domain, although its glycan-binding properties are not fully understood. Here, we screened the glycan-binding specificity of ZG16p by recently developed glycoconjugate microarray. ZG16p appeared to exhibit selective binding to α- and β-linked mannose-polyacrylamide-biotin probes. In more quantitative analysis using frontal affinity chromatography, dissociation constants to two types of polyvalent mannose, i.e. high-density mannose and yeast mannan, were determined to be 1.3 and 1.7?μM, respectively. Mutation of the evolutionarily conserved amino acid Asp151, which is involved in sugar binding among the Jacalin-related lectins (JRLs), abolished binding activity to mannose. By immunohistochemical staining, ZG16p was specifically detected in mucus-secreting cells of the digestive system such as serosanguineous acinar cells of the parotid gland, acinar cells of the pancreas and goblet cells of the intestine. Finally, we showed that ZG16p recognizes pathogenic Candida and Malassezia species in a polyvalent mannose-dependent manner. We propose that ZG16p is a novel member of mannose-specific JRLs, which recognizes pathogenic fungi through non-self polyvalent mannose in the digestive system.     

Increase of histidine decarboxylase activity in murine myelomonocytic leukemia cells (WEHI-3B) in parallel to their differentiation into macrophages

When cells of mouse myelomonocytyc leukemia cell line, WEHI-3B, were cultured in the presence of actinomycin D plus the serum which was obtained from mice injected with bacterial endotoxin, i.e., lipopolysaccharide, their histidine decarboxylase (l-histidine carboxy-lyase, EC 4.1.1.22) (HDC) activity increased about 100-fold with a peak at 48 h. According to the increase in HDC activity, the expression of surface antigens associated with macrophages, such as Mac II, Mac III and Ia, increased markedly on WEHI-3B cells as well as their morphological changes to macrophages. Histamine levels in the culture medium increased concomitantly with the increase in the HDC activity in WEHI-3B cells, whereas the histamine contents inside the cells did not increase remarkably. Furthermore, the addition of lipopolysaccharide to the culture medium caused an additional 2-fold increase in the HDC activity of WEHI-3B cells. These results indicate that the increase in HDC activity in WEHI-3B cells may represent an event in the process of the differentiation to macrophages.