Effects of bulkiness and hydrophobicity of an aliphatic amino acid in the recognition helix of the GAGA zinc finger on the stability of the hydrophobic core and DNA binding affinity

The GAGA factor of Drosophila melanogaster uses a single Cys 2His 2-type zinc finger for specific DNA binding. The conformation and DNA binding mode of the GAGA zinc finger are similar to those of other structurally characterized zinc fingers. In almost all Cys 2His 2-type zinc fingers, the fourth position of the DNA-recognizing helix is occupied by the Leu residue involved in the formation of the minimal hydrophobic core. However, no systematic study on the precise role of the Leu residue in the hydrophobic core formation and DNA binding function has been reported. In this study, the Leu residue is substituted with other aliphatic amino acids having different side chain lengths and hydrophobicities, namely, Ile, Val, Aib, and Ala. The metal binding properties were studied by UV-vis spectroscopy. The peptide conformations were examined by CD and NMR spectroscopies. Furthermore, the DNA binding ability was examined with a gel mobility shift assay. Though the Ile, Val, and Aib mutants exhibited conformations similar to those of the wild type, the DNA binding affinity decreased as the side chain length of the amino acid decreased. Interestingly, the Val mutant can bind to the cognate DNA, while Aib cannot, in spite of the similarity in their secondary structures based on the CD measurements. Variable-temperature NMR experiments clearly indicated differences in the stability of the hydrophobic core between the Val and Aib mutants. This study demonstrates that the bulkiness of the conserved aliphatic residue is important in the formation of the well-packed minimal hydrophobic core and proper ternary structure and that the hydrophobic core stabilization is apparently related to the DNA binding function of the GAGA zinc finger.     

Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides

In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of thermostable DNA polymerases used, Taq, Phusion HF, Vent(exo-), KOD Dash and KOD(exo-), the KOD Dash and KOD(exo-) DNA polymerases could smoothly read through the modified templates containing 2'-O,4'-C-methylene-linked nucleotides at intervals of a few nucleotides, even at standard enzyme concentrations for 5 min. Although the Vent(exo-) DNA polymerase also read through these modified templates, kinetic study indicates that the KOD(exo-) DNA polymerase was found to be far superior to the Vent(exo-) DNA polymerase in accurate incorporation of nucleotides. When either of the DNA polymerase was used, the presence of 2',4'-bridged nucleotides on a template strand substantially decreased the reaction rates of nucleotide incorporations. The modified templates containing sequences of seven successive 2',4'-bridged nucleotides could not be completely transcribed by any of the DNA polymerases used; yields of longer elongated products decreased in the order of steric bulkiness of the modified sugars. Successive incorporation of 2',4'-bridged nucleotides into extending strands using 2',4'-bridged nucleoside-5'-triphospates was much more difficult. These data indicate that the sugar modification would have a greater effect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template as well, as in base modification.     

Isolation of basidiomycetous anamorphic yeast-like fungus <Emphasis Type="Italic">Meira argovae</Emphasis> found on Japanese bamboo

A basidiomycetous anamorphic yeast-like fungus, isolated from new bamboo shoots collected in Japan, was assigned to Meira argovae by comparison of conidial morphology, physiological characteristics, rDNA sequences, and DNA-DNA relatedness with the ex-type strains of Meira species. This is the first record of the finding of M. argovae from other than mite cadavers and in regions other than Israel. Phylogenetic analysis based on the D1-D2 domain demonstrated that Meira species and teleomorphic Dicellomyces species, which include a bamboo leaf parasite, D. gloeosporus, formed sister clades.     

Capsule gene CAP64 is involved in the regulation of vacuole acidification in Cryptococcus neoformans

A basidiomycetous yeast Cryptococcus neoformans is stained by DBB. We found that the edges of DBB stained cells were specifically detected by using fluorescence microscopy. We also found that the only the edges of cap64Δ strain cells was not fluorescent among several acapsular mutants, although whose colonies turned to red or light pink by DBB staining. When the vacuoles were stained by FM4-64, those of the cap64Δ cells showed aberrant morphology. In addition, quinacrine treatment showed that the cap64Δ strain could not accumulate quinacrine in the vacuole. These data suggest that Cap64 was not only involved in capsule formation, but also in intracellular pH regulation.     

Polymerization of optical isomers of phenylalanine N-carboxyanhydride by poly(N-methylalanine) diethylamide

In the polymerization of phenylalanine N-carboxyanhydride (NCA) using poly(N-methyl-L -or DL -alanine) diethylamide as initiator, the polymerization rate was L -NCA ? D -NCA > DL -NCA. This is a new type of selective polymerization and indicates the incompleteness of earlier investigations to study the asymmetrically selective polymerization without D -NCA. Neither secondary structure nor optical activity of the polymeric initiator is a reason for the selectivity. Hence the cause for the selectivity was sought in the properties of the NCA's in solution. However, the selectivity was not observed in the polymerization initiated by poly(L -phenylalanine) dimethylamide. The importance of the initiator being a secondary amine type was suggested. The experimental results are discussed on the basis of these considerations.     

Cell growth on immobilized cell-growth factor; 4: Interaction of fibroblast cells with insulin immobilized on poly(methyl methacrylate) membrane.

Insulin was immobilized on the surface-hydrolyzed poly(methyl methacrylate) membrane and the growth acceleration of mouse fibroblast cells, STO, by the immobilized insulin was investigated. It was found that insulin remains immobilized on the surface of nonbiodegradable membrane and interacts specifically with receptors existing on the biological membrane of fibroblast cells. The growth acceleration by immobilized insulin was enhanced by introduction of a spacer arm between insulin and the immobilization matrix. The amount of receptor proteins present on the biological membrane of fibroblast cells after culturing with insulin, immobilized on nonbiodegradable polymer membrane, was much higher than that after culturing with free insulin, implying the suppression of down-regulation in the case of immobilized insulin.     

Production and characterization of human tumor degenerating factor (TDF)

The culture supernatant of human fibroblasts caused degenerative changes in the target cells. This tumor degenerating factor in the supernatant (TDF) appeared already on the 1st day of culture and increased gradually to the 8th day. TDF was effective on human KB, HeLa, FL and of hepatoma cells, but neither on murine L929, 3T3, SV-3T3 cells nor MDBK cells. Furthermore, TDF was not effective on human non-transformed cells, namely various human fibroblasts. Human leukocyte interferon (HuIFN-alpha) enhanced TDF production. The coculture of human fibroblasts with KB cells augmented TDF production.     

Synthesis and conformation of the cyclic octapeptides cyclo(Phe-Pro)4, cyclo(Leu-Pro)4, and cyclo[Lys(Z)-Pro]4

Cyclic octapeptides, cyclo(X-Pro)₄, where X represents Phe, Leu, or Lys(Z), were synthesized and their conformations investigated. A C₂-symmetric conformer containing two cis peptide bonds was found in all of these cyclic octapeptides. The numbers of available conformations due to the cis–trans isomerization of Pro peptide bonds depended on the nature of the solvent and X residue: they decreased in the following order: cyclo[Lys(Z)-Pro]₄ > cyclo(Leu-Pro)₄ > cyclo(Phe-Pro)₄ in CDCl₃. ¹³C spin-lattice relaxation times (T₁) of these cyclic octapeptides were measured, and the contribution of segmental mobility to T₁ was found to vary with the nature of the X residue.     

Tea tannin components modify the induction of sister-chromatid exchanges and chromosome aberrations in mutagen-treated cultured mammalian cells and mice

The modifying effects of tannin components extracted from green tea and black tea on mutagen-induced SCEs and chromosome aberrations were studied. These tannin components did not affect spontaneous SCEs and chromosome aberrations in cultured Chinese hamster cells. The frequency of SCEs and chromosome aberrations induced by mitomycin C (MMC) or UV was enhanced by the posttreatment with tea tannin components. When cells were post-treated with tea tannin components in the presence of metabolic enzymes of rat liver (S9 mix), the modifying effects on the induction of SCEs and chromosome aberrations by mutagens were complicated. MMC- and UV-induced SCEs and chromosome aberrations were suppressed by the posttreatment with tea tannin components at low concentrations (less than or equal to 6.7 micrograms/ml) with S9 mix. At a high concentration of tea tannin components (20 micrograms/ml) with S9 mix, a co-mutagenic effect was observed. The modifying effects of tea tannin components were shown to occur in the G1 phase of the cell cycle. In cells from a patient with xeroderma pigmentosum (XP) and a normal human embryo, MMC-induced SCEs were suppressed by the posttreatment with tea tannin components in the presence of S9 mix, and enhanced in the absence of S9 mix. On the other hand, tea tannin components modified SCE frequencies in UV-irradiated normal human cells but not in UV-irradiated XP cells. Our results suggested that tea tannin components themselves inhibited DNA-excision repair and resulted in a co-mutagenic effect, while in the presence of S9 mix metabolites of tea tannin components promoted DNA-excision repair activity and resulted in an antimutagenic effect. MMC-induced chromosome aberrations in mouse bone marrow cells were suppressed by the pretreatment with green tea and black tea tannin mixture.