Identification of Open Reading Frames in Schizosaccharomyces pombe cDNAs

A total of 214 non-overlapping cDNA clones from Schizosaccharomycespombe were selected and completely sequenced. The clones notpreviously reported were divided into the following three groups:1) homologous to Saccharomyces cerevisiae genes (139 clones);2) homologous to genes from other organisms but not to thosefrom Sac. cerevisiae (4 clones); and 3) no similar sequences(40 clones). Among the 31 sequences identical to those in thepublic databases, 4 genes have regions corresponding to introns.Protein sequences which had homologs both in budding yeast andmammals were compared with those from Sac. cerevisiae and mammals.The search revealed that the evolutionary distances among thesespecies are similar at least with genes of this category.     

Studies on Independent Synthesis of Cytoplasmic Ribonucleic Acids in Acetabularia mediterranea

1. The RNA content of anucleate and nucleate fragments of Acetabularia has been measured. It was found that there is a net synthesis of RNA in nucleate fragments. On the other hand, the RNA content of anucleate fragments did not change significantly after enucleation. 2. Anucleate fragments, however, can readily incorporate ¹⁴C-labeled adenine, orotic acid, and carbon dioxide into their cytoplasmic RNA. 3. The results of experiments on ¹⁴CO₂ incorporation into the RNA of anucleate and nucleate fragments suggest that there is a mechanism for de novo synthesis of RNA in anucleate cytoplasm. 4. In Acetabularia, 81 per cent of the cytoplasmic RNA is bound to a large granule fraction, consisting mainly of chloroplasts. Even after removal of the nucleus, RNA is synthesized in this "chloroplast" fraction. The chloroplasts are thus a major site of RNA synthesis in the cytoplasm of these algae. Synthesis of "chloroplastic" RNA, in anucleate fragments, possibly occurs at the expense of the RNA present in other fractions (microsomes and supernatant). 5. 8-Azaguanine stimulates regeneration and cap formation in anucleate fragments and does not inhibit RNA synthesis in these fragments.     

Transfer ribonucleic acids from radish seedlings germinated with 4-thiouridine

Transfer RNAs containing 4-thiouridine residues were prepared from etiolated cotyledons or isolated chloroplasts of radish seedlings germinated with the analog. They possess a higher melting temperature and tend to have a reduced hyperchromicity. Incorporation of 4-thiouridine into tRNA reduces the ability to accept a mixture of 14 amino acids or phenylalanine alone. After desulphurization of 4-thiouridine to uridine in the tRNA, aminoacylation was restored almost completely to the level of control tRNA prepared from untreated seedlings. These results indicate that a tRNA containing 4-thiouridine in the anticodon and/or in another part of molecule has low or no ability to accept amino acids.     

Development of a protein–ligand-binding site prediction method based on interaction energy and sequence conservation

We present a new method for predicting protein–ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure database, LigASite. Ligand-bound structure prediction (bound prediction) indicated that 74.0 % of predicted ligand-binding sites overlapped with real ligand-binding sites by over 25 % of their volume. Ligand-unbound structure prediction (unbound prediction) indicated that 73.9 % of predicted ligand-binding residues overlapped with real ligand-binding residues. The amino acid conservation score improved the average prediction accuracy by 17.0 and 17.6 points for the bound and unbound predictions, respectively. These results demonstrate the effectiveness of the combined use of the interaction energy and amino acid conservation in the ligand-binding site prediction.     

Lack of the evidence for the enzymatic catabolism of Man1GlcNAc2 in Saccharomyces cerevisiae

In the cytosol of Saccharomyces cerevisiae, most of the free N-glycans (FNGs) are generated from misfolded glycoproteins by the action of the cytoplasmic peptide: N-glycanase (Png1). A cytosol/vacuole α-mannosidase, Ams1, then trims the FNGs to eventually form a trisaccharide composed of Manβ1,4GlcNAc β1,4GlcNAc (Man₁GlcNAc₂). Whether or not the resulting Man₁GlcNAc₂ is enzymatically degraded further, however, is currently unknown. The objective of this study was to unveil the fate of Man₁GlcNAc₂ in S. cerevisiae. Quantitative analyses of the FNGs revealed a steady increase in the amount of Man₁GlcNAc₂ produced in the post-diauxic and stationary phases, suggesting that this trisaccharide is not catabolized during this period. Inoculation of the stationary phase cells into fresh medium resulted in a reduction in the levels of Man₁GlcNAc₂. However, this reduction was caused by its dilution due to cell division in the fresh medium. Our results thus indicate that Man₁GlcNAc₂ is not enzymatically catabolized in S. cerevisiae.     

Chloroplast Development in 4-Thiouridine-Cultured Radish Seedlings XI. Inhibition of RNA Synthesis by 4-Thiouridine Nucleotides during Germination of Radish Seeds

The effects of 4-thiouridine and its metabolites on RNA synthesisin radish (Raphanus sativus) cotyledons were investigated. The4-thiouridine nucleotides, 4-thioUTP and 4-thioUDP, were foundto inhibit DNA-dependent RNA polymerase activities of isolatednuclei and of chloroplasts from radish cotyledons. These inhibitorsappeared to compete with UTP for its binding to RNA polymerase.Neither 4-thiouridine nor 4-thioUMP inhibited RNA polymeraseactivities. Reduced RNA accumulation accompanied by the inhibition of protochlorophyllideaccumulation was observed in cotyledons of dark-grown radishseedlings germinated and grown with 4-thiouridine. On the otherhand, 4-thiouridine had no effect on chloroplast developmentin the control seedlings germinated and grown without 4-thiouridine.These results suggest that the inhibition of chloroplast developmentby 4-thiouridine may in part be due to the inhibition of RNAsynthesis by 4-thiouridine nucleotide during germination, resultingin inhibition of etioplast development. (Received December 9, 1985; Accepted June 26, 1986)     

Expression of Na+, K+-ATPase α-Subunit in Animalized and Vegetalized Embryos of the Sea Urchin, Hemicentrotus pulcherrimus.

A marked increase in the Na⁺, K⁺-ATPase activity of sea urchin embryos occurred following an elevation of its mRNA level, revealed by Northern blotting analysis, in developmental period between the swimming blastula and the late gastrula stage. cDNA clone of Na⁺, K⁺-ATPase α-subunit, obtained from γgt10 cDNA library of sea urchin gastrulae, was digested with EcoRl ad Hindlll. The obtained 268 bp cDNA fragment, hybridized to a 4.6 Kb RNA, was used as probe for Northern blotting analysis. The level of Na⁺, K⁺-ATPase mRNA was higher in embryo-wall cell fraction isolated from late gastrulae (ectoderm cells) than the level in the bag fraction, containing mesenchyme cells (mesoderm cells) and archenteron (endoderm cells). The activity of Na⁺, K⁺-ATPase and the level of its mRNA were higher in animalized embryos obtained by pulse treatment with A23187 for 3 hr, starting at the 8–16 cell stage and were considerably lower in vegetalized embryos induced by 3 hr treatment with Li⁺ than that in normal embryos at the post gastrula corresponidng stage. Augmentation of Na⁺, K⁺-ATPase gene expression can be regarded as a marker for ectoderm cell differentiation at the post gastrula stage, which results from determination of cell fate in prehatching period.     

The distribution of diploids and polyploids of theScilla scilloides complex in the northeastern district of China

A cytological analysis was made of 1504 individuals ofScilla scilloides Druce from the northeastern district of China. In terms of genome combination four cytotypes were found: AA (90.95%), AAAA (0.07%), AABB (8.92%) and AABB+2 (0.07%). In the cytotypes A and B denote genome A (x=8) and genome B (x=9), respectively. Most of 18 natural populations examined consist of one cytotype: indeed, all individuals examined of 15 of the populations are AA diploids, those of one population AABB allotetraploids, and individuals examined of two other populations have two cytotypes each, AA and AAAA, and AABB and AABB+2. In karyotype the genome A of the AA and AAAA was different from that of the AABB, and a direction of morphological change of chromosomes in the genome A is discussed in light of results of hybridization experiments reported elsewhere. Taken together with information available for the distribution of different cytotypes in China, Korea and Japan, the results of the present study support the view of Maekawa thatScilla scilloides was native to mainland China and lately introduced to Japan.     

The mode of recognition of tumor antigens by noncytolytic-type antitumor T cells: Role of antigen-presenting cells and their surface class I and class II H-2 molecules

Summary The present study investigated the role of antigen-presenting cells (APC) in the activation of noncytolytic T cells against tumor antigens. The noncytolytic-type T cells exerted their antitumor effect by producing -interferon (IFN-) and by activating macrophages as the ultimate effectors. The production of IFN- by these noncytolytic T cells following the stimulation with tumor cells required the participation of Ia⁺ APC, since the depletion of APC from cultures of tumor-immunized spleen cells resulted in almost complete inhibition of the IFN- production. Both L3T4⁺ and Lyt-2⁺ subsets of T cells were capable of producing IFN-, and the requirement of APC for the production of IFN- was the case irrespective of whether noncytolytic T cells were of L3T4⁺ or Lyt-2⁺ phenotype. More importantly, it was demonstrated that the production of IFN- by L3T4⁺ and Lyt-2⁺ T cells was inhibited by addition of the respective anti-class II and anti-class I H-2 antibody to cultures. These results indicate that antitumor L3T4⁺ or Lyt-2⁺ noncytolytic T cells are activated for the IFN- production by recognizing tumor antigens in the context of self-class II or -class I H-2 molecules on APC.This work was supported by a Grant-in-Aid for the Special Project Cancer-Bioscience from the Ministry of Education, Science and Culture, Japan