Molecular Modeling as a Powerful Tool for the Mapping of Fibroblast Growth Factor Receptor-1 Ligand Binding Determinants

Molecular modeling has allowed us to propose that one main contact surface of the Fibroblast Growth Factor Receptor -1 (FGFR-1) to the ligand FGF-1 is formed by a 16 amino acid sequence comprised by the C-terminal region of the domain II (DII) plus the hinge linking DII and DIII domains and the N-terminal region of domain III (DIII). Therefore, this sequence was used to design the following three peptides: Ac-YQLDVVERS-NH₂ (R1); Ac-YQLDVVERSPHRPILQ-NH₂ (R2) and Ac-RSPHRPILQ-NH₂ (R3). The synthetic peptides were tested in their ability to inhibit the mitogenic activity of FGF-1 and FGF-2 in cultured Balb/c 3T3 fibroblasts. The results showed that R1 and R2 inhibited the activity of FGF-1 (ID₅₀ = 40 -50 7M) but not that of FGF-2. Molecular modeling studies of R1 and its docking to FGF-1 suggested that this peptide could assume a conformation very similar to that found in the corresponding segment of FGFR-1. All these results support our hypothesis that the C-terminal residues of the DII domain, represented by peptide R1, are part of a surface responsible for the binding of FGF-1 to FGFR-1 but not of FGF-2. Also, they indicate that peptide R1 may be useful for the development of small selective peptide inhibitors of the FGF-1 biological activities.     

Cloning and expression of subtilisin amylosacchariticus gene

The gene encoding subtilisin Amylosacchariticus from Bacillus subtilis var. amylosacchariticus was isolated and the entire nucleotide sequence of the coding sequence was determined. The deduced amino acid sequence revealed an N-terminal signal peptide and pro-peptide of 106 residues followed by the mature protein comprising 275 residues. There were discrepancies in 10 amino acids between the sequence elucidated from the nucleotide sequence and the published protein sequence (Kurihara et al. (1972) J. Biol. Chem. 247, 5619-5631). The nucleotide sequence was highly homologous to that of subtilisin E gene from B. subtilis 168, with discrepancies at 12 nucleotides out of 1,426 nucleotides we sequenced. Ten of them were found in mature subtilisin coding sequence, which resulted in two amino acid changes and another one was in the putative promoter region between two genes. The productivity of subtilisin in culture broth of B. subtilis var. amylosacchariticus was much higher than that of B. subtilis 168. The enzyme gene was inserted in a shuttle vector pHY300PLK, with which B. subtilis ISW1214 was transformed. The proteolytic activity found in the culture broth of the transformed bacterium was 20- and 4-fold higher than those of the host strain and B. subtilis var. amylosacchariticus, respectively. Subtilisin Amylosacchariticus was easily purified to a crystalline form from culture filtrate of cloned B. subtilis, after a single step of chromatography on CM-cellulose.     

Production of a Doubly Chiral Compound, (4R,6R)-4-Hydroxy-2,2,6-Trimethylcyclohexanone, by Two-Step Enzymatic Asymmetric Reduction

A practical enzymatic synthesis of a doubly chiral key compound, (4R,6R)-4-hydroxy-2,2,6-trimethylcyclohexanone, starting from the readily available 2,6,6-trimethyl-2-cyclohexen-1,4-dione is described. Chirality is first introduced at the C-6 position by a stereoselective enzymatic hydrogenation of the double bond using old yellow enzyme 2 of Saccharomyces cerevisiae, expressed in Escherichia coli, as a biocatalyst. Thereafter, the carbonyl group at the C-4 position is reduced selectively and stereospecifically by levodione reductase of Corynebacterium aquaticum M-13, expressed in E. coli, to the corresponding alcohol. Commercially available glucose dehydrogenase was also used for cofactor regeneration in both steps. Using this two-step enzymatic asymmetric reduction system, 9.5 mg of (4R,6R)-4-hydroxy-2,2,6-trimethylcyclohexanone/ml was produced almost stoichiometrically, with 94% enantiomeric excess in the presence of glucose, NAD⁺, and glucose dehydrogenase. To our knowledge, this is the first report of the application of S. cerevisiae old yellow enzyme for the production of a useful compound.     

Protein A-Mouse Acidic Mammalian Chitinase-V5-His Expressed in Periplasmic Space of Escherichia coli Possesses Chitinase Functions Comparable to CHO-Expressed Protein

Acidic mammalian chitinase (AMCase) has been shown to be associated with asthma in mouse models, allergic inflammation and food processing. Here, we describe an E. coli-expression system that allows for the periplasmic production of active AMCase fused to Protein A at the N-terminus and V5 epitope and (His)₆ tag (V5-His) at the C-terminus (Protein A-AMCase-V5-His) in E. coli. The mouse AMCase cDNA was cloned into the vector pEZZ18, which is an expression vector containing the Staphylococcus Protein A promoter, with the signal sequence and truncated form of Protein A for extracellular expression in E. coli. Most of the Protein A-AMCase-V5-His was present in the periplasmic space with chitinolytic activity, which was measured using a chromogenic substrate, 4-nitrophenyl N,N′-diacetyl-β-D-chitobioside. The Protein A-AMCase-V5-His was purified from periplasmic fractions using an IgG Sepharose column followed by a Ni Sepharose chromatography. The recombinant protein showed a robust peak of activity with a maximum observed activity at pH 2.0, where an optimal temperature was 54°C. When this protein was preincubated between pH 1.0 and pH 11.0 on ice for 1 h, full chitinolytic activity was retained. This protein was also heat-stable till 54°C, both at pH 2.0 and 7.0. The chitinolytic activity of the recombinant AMCase against 4-nitrophenyl N,N′-diacetyl-β-D-chitobioside was comparable to the CHO-expressed AMCase. Furthermore, the recombinant AMCase bound to chitin beads, cleaved colloidal chitin and released mainly N,N′-diacetylchitobiose fragments. Thus, the E. coli-expressed Protein A-mouse AMCase-V5-His fusion protein possesses chitinase functions comparable to the CHO-expressed AMCase. This recombinant protein can be used to elucidate detailed biomedical functions of the mouse AMCase.     

Determination of absolute configuration of photo-degraded catechinopyranocyanidin A by modified Mosher's method

Catechinopyranocyanidins A and B (cpcA and cpcB) are two purple pigments present in the seed-coat of red adzuki bean, Vigna angularis, of which cpcA is the major pigment, containing two chiral carbons in the catechin part. Their absolute configurations were determined by comparison of their experimental and quantum chemical calculated electronic circular dichroisms (ECDs). These purple pigments are labile on light irradiation and easily decompose to photo-degraded catechinopyranocyanidins A and B (pdcpcA and pdcpcB), while retaining the stereostructure of the catechin residue. We applied modified Mosher's method for determining the chirality of the secondary alcohol in pdcpcA. Hexamethylation of pdcpcA by diazomethane followed by esterification using (S)- and (R)-MTPACl gave (R)- and (S)-MTPA esters, respectively. By analysis of the NMR spectra of (R)- and (S)-MTPA esters of tetramethylated (+)-catechin, the chirality of pdcpcA was determined to be 2R, 3S, same as the absolute configuration of cpcA.     

Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population

Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, that is, dysfunctional interactions between proteins encoded in the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we de novo sequenced the 747‐Mb genome of the coastal goby, Chaenogobius annularis, and investigated its integrative genomic phylogeographics using RNA‐sequencing, RAD‐sequencing, genome resequencing, whole mitogenome sequencing, amplicon sequencing, and small RNA‐sequencing. Chaenogobius annularis populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO‐lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage‐specific selection on mitochondria‐related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.     

Effects of double rice cropping with irrigation on the diversity of herbaceous plants and their utilization as a food source in paddy fields of southern Lao People’s Democratic Republic

Herbaceous plant diversity including rare aquatic species has been lost in many countries by agricultural intensification and abandonment. In paddy fields of the Lao People’s Democratic Republic (Lao PDR), irrigation facilities have been constructed rapidly since 1997. The aim of this study was to clarify the impacts of double rice cropping accompanied by the introduction of irrigation systems on herbaceous plant diversity and utilization in paddy fields of southern Lao PDR. Ground vegetation surveys and interviews were conducted in Kok Deau and Lak 30 villages in Champasak Province, and propagule bank survey was conducted in Kok Deau village. The species richness and species diversity, measured by the Shannon’s diversity index, were not significantly different between the irrigated and rainfed paddies (p?>?0.05), when compared in both the wet and dry seasons. However, double rice cropping with irrigation systems affected herbaceous plant species composition in paddy fields. Increased use of chemical fertilizers in irrigated paddies resulted in predominance of tall undesirable species, such as Fimbristylis miliacea (L.) Vahl and Echinochloa colona (L.) Link. Small and frequently submerged species were dominant in the ground vegetation and propagule banks of the rainfed paddies. Since small submerged species are often sensitive to environmental changes, increase of irrigated paddy area may lead to a decrease in the variety of aquatic herbaceous plants in Lao PDR. While a total of 9 herbaceous plant species were utilized as foods in the villages, no change was recognized by farmers in species composition and frequency of utilization of paddy plants as food before and after the development of the irrigation systems.

     

Flavonoids isolated from the leaves of Melicope triphylla and their extracellular-superoxide dismutase-inducing activity

Two novel flavonoids, named meliflavones A (1) and B (2), were isolated from the leaves of Melicope triphylla (Lam.) Merr., along with thirteen known compounds (3–15). Four of the polymethoxyflavonoids bearing a prenyloxy (3-methylbut-2-enyloxy) function (1, 3–5) induced the expression of extracellular-superoxide dismutase (EC-SOD) in a human leukemic U937 cell-based assay.