Sporobolomyces diospyroris sp. nov., Sporobolomyces lophatheri sp. nov. and Sporobolomyces pyrrosiae sp. nov., three new species of ballistoconidium-forming yeasts in the Agaricostilbum lineage isolated from plants in Taiwan

Three strains of xylose-lacking and ubiquinone-10-having ballistoconidium-forming yeasts isolated from plant leaves collected in Taiwan were found to represent respective new species. In phylogenetic trees constructed based on the nucleotide sequences of 18S rDNA and D1/D2 domain of 26S rDNA, they were located in the Agaricostilbum lineage (Agaricostilbum/Bensingtonia cluster). Since the taxonomic properties of these species coincide with those of the genus Sporobolomyces, they are described as Sporobolomyces diospyroris sp. nov., Sporobolomyces lophatheri sp. nov. and Sporobolomyces pyrrosiae sp. nov., respectively.     

Can the low-resolution structures of photointermediates of bacteriorhodopsin explain their crystal structures?

To understand the molecular mechanism of light-driven proton pumps, the structures of the photointermediates of bacteriorhodopsin have been intensively investigated. Low-resolution diffraction techniques have demonstrated substantial conformational changes at the helix level in the M and N intermediates, between which there are noticeable differences. The intermediate structures at atomic resolution have also been solved by x-ray crystallography. Although the crystal structures have demonstrated local structural changes, such as hydrogen bond network rearrangements including water molecules, the large conformational changes at the helix level are not necessarily observed. Furthermore, the two reported crystal structures of an intermediate accumulated using a common method were distinct. To reconcile these apparent discrepancies, low-resolution projection maps were calculated from the crystal structures and compared to the low-resolution intermediate structures obtained using native membranes. The crystal structures can be categorized into three groups, which qualitatively correspond to the low-resolution structures of the M1-type, M2-type, and N-type determined in the native membrane. Based on these results, we conclude that at least three types of intermediate structures play a role during the photocycle.     

Phosphorylation of STEF/Tiam2 by protein kinase A is critical for Rac1 activation and neurite outgrowth in dibutyryl cAMP-treated PC12D cells

The second messenger cAMP plays a pivotal role in neurite/axon growth and guidance, but its downstream pathways leading to the regulation of Rho GTPases, centrally implicated in neuronal morphogenesis, remain elusive. We examined spatiotemporal changes in Rac1 and Cdc42 activity and phosphatidylinositol 3,4,5-triphosphate (PIP₃) concentration in dibutyryl cAMP (dbcAMP)-treated PC12D cells using Förster resonance energy transfer–based biosensors. During a 30-min incubation with dbcAMP, Rac1 activity gradually increased throughout the cells and remained at its maximal level. There was no change in PIP₃ concentration. After a 5-h incubation with dbcAMP, Rac1 and Cdc42 were activated at the protruding tips of neurites without PIP₃ accumulation. dbcAMP-induced Rac1 activation was principally mediated by protein kinase A (PKA) and Sif- and Tiam1-like exchange factor (STEF)/Tiam2. STEF depletion drastically reduced dbcAMP-induced neurite outgrowth. PKA phosphorylates STEF at three residues (Thr-749, Ser-782, Ser-1562); Thr-749 phosphorylation was critical for dbcAMP-induced Rac1 activation and neurite extension. During dbcAMP-induced neurite outgrowth, PKA activation at the plasma membrane became localized to neurite tips; this localization may contribute to local Rac1 activation at the same neurite tips. Considering the critical role of Rac1 in neuronal morphogenesis, the PKA—STEF–Rac1 pathway may play a crucial role in cytoskeletal regulation during neurite/axon outgrowth and guidance, which depend on cAMP signals.     

Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice

Summary The entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice (Oryza sativa cv. Nipponbare) was identified using clone banks that cover the chloroplast and mitochondrial genomes. The mitochondrial fragments that were homologous to chloroplast DNA were mapped and sequenced. The nucleotide sequences around the termini of integrated chloroplast sequences in the rice mtDNA revealed no common sequences or structures that might enhance the transfer of DNA. Sixteen chloroplast sequences, ranging from 32 bases to 6.8 kb in length, were found to be dispersed throughout the rice mitochondrial genome. The total length of these sequences is equal to approximately 6% (22 kb) of the rice mitochondrial genome and to 19% of the chloroplast genome. The transfer of segments of chloroplast DNA seems to have occurred at different times, both before and after the divergence of rice and maize. The mitochondrial genome appears to have been rearranged after the transfer of chloroplast sequences as a result of recombination at these sequences. The rice mitochondrial DNA contains nine intact tRNA genes and three tRNA pseudogenes derived from the chloroplast genome.     

Determination of NAD Malic Enzyme in Leaves of C(4) Plants : EFFECTS OF MALATE DEHYDROGENASE AND OTHER FACTORS

Malate dehydrogenase may interfere with the assay of NAD malic enzyme, as NADH is formed during the conversion of malate to oxaloacetate. During the present study, two additional effects of malate dehydrogenase were investigated; they are evident only if the malate dehydrogenase reaction is allowed to reach equilibrium prior to initiating the malic enzyme reaction. One of these (Outlaw, Manchester 1980 Plant Physiol 65: 1136-1138) might cause an underestimation of NAD reduction by malic enzyme due to the oxidation of NADH during reversal of the malate dehydrogenase reaction. A second effect may result in overestimation of malic enzyme activity, as Mn²⁺-catalyzed oxaloacetate decarboxylation causes continuing net NADH formation via malate dehydrogenase. These effects were studied by assaying the activity of a partially purified preparation of Amaranthus retroflexus NAD malic enzyme in the presence or absence of purified NAD malate dehydrogenase.     

Complete Genome Sequence of an Aerobic Hyper-thermophilic Crenarchaeon, Aeropyrum pernix K1

The complete sequence of the genome of an aerobic hyper-thermophiliccrenarchaeon, Aeropyrum pernix K1, which optimally grows at95°C, has been determined by the whole genome shotgun methodwith some modifications. The entire length of the genome was1,669,695 bp. The authenticity of the entire sequence was supportedby restriction analysis of long PCR products, which were directlyamplified from the genomic DNA. As the potential protein-codingregions, a total of 2,694 open reading frames (ORFs) were assigned.By similarity search against public databases, 633 (23.5%) ofthe ORFs were related to genes with putative function and 523(19.4%) to the sequences registered but with unknown function.All the genes in the TCA cycle except for that of alpha-ketoglutaratedehydrogenase were included, and instead of the alpha-ketoglutaratedehydrogenase gene, the genes coding for the two subunits of2-oxoacid:ferredoxin oxidoreductase were identified. The remaining1,538 ORFs (57.1%) did not show any significant similarity tothe sequences in the databases. Sequence comparison among theassigned ORFs suggested that a considerable member of ORFs weregenerated by sequence duplication. The RNA genes identifiedwere a single 16S–23S rRNA operon, two 5S rRNA genes and47 tRNA genes including 14 genes with intron structures. Allthe assigned ORFs and RNA coding regions occupied 89.12% ofthe whole genome. The data presented in this paper are availableon the internet homepage (http://www.mild.nite.go.jp).     

Macrolide Resistance in Staphylococcus aureus

A heat-inducible mutant, resistant to macrolide antibiotics (Mac), was isolated from Staphylococcus aureus MS537 in which Mac-resistance was induced by subinhibitory concentrations of erythromycin (EM). After induction at 42 C, this mutant acquired a high resistance to both Mac and lincomycin (LMC). Transduction and biochemical studies revealed that spiramycin (SP)-resistance in this mutant was induced by exposure to a high temperature (42 C) or by treatment with EM in broth but not in phosphate buffer. Induction did not take place when chloramphenicol (CM) was added to the induction mixture. Ribosomes from the mutant cultured at 42 C decreased their affinity for SP and consequently polypeptide synthesis on such ribosomes was not inhibited by SP, when compared with those cultured at 30 C. From these results, it was concluded that alteration of ribosomes took place after induction by exposure at high temperatures or by EM-treatment and that the mechanism of SP-resistance after induction was accounted for by a decrease in SP-binding to ribosomes.     

Macrolide Resistance in Staphylococcus aureus

It was demonstrated that spiramycin (SP)-resistance could be related to the decrease in binding of ribosomes to SP and that the SP-binding to ribosomes was related with inhibition of polypeptide synthesis by SP in a cell-free system in staphylococcal strains. These facts were also observed in Mac (macrolide)-inducible strains, in which resistance to Mac antibiotics is enhanced by prior treatment with subinhibitory concentrations of erythromycin. From these results, it was concluded that the mechanism of resistance to Mac antibiotics is accounted for by alteration of ribosomes in staphylococcal strains and that this alteration of ribosomes is caused not only by mutation but also by induction.     

Geographic Assessment of Present Protected Areas in Japan for Representativeness of Forest Communities

Most assessments of present protected areas have focused on which features are or are not represented and to what extent, but they have not considered the environmental gradients and the geographic context within each biodiversity feature under a conservation network. We examined how protected areas are distributed with respect to the distribution of six forest community types. Three analyses were applied to the dataset in the Red Data Book of Plant Communities in Japan and the related survey: (1) recursive partitioning was used to contrast environmental factors of conserved communities with nonconserved communities; (2) point pattern analysis, based on Ripley's K function, was used to describe the spatial pattern of conserved communities; and (3) the spatial scan statistic was used to detect spatial representation gaps. Overall, environmental bias was greatest in relation to soil and topography. However, the results of point pattern analysis showed that the spatial pattern of conserved communities did not depend entirely on the distribution of environmental factors. Four types of gaps in spatial representation were detected by the spatial scan statistic, irrespective of environmental bias. These results showed that although a community type might be well protected in total or along the environmental gradients, conserved communities might not capture the full range of geographic context. To ensure appropriate representation or protection, it is important that conservation planning for protected areas take into account both the environmental gradients and the geographic context within each biodiversity feature.     

Cyclic AMP binding proteins in early embryos of Drosophila melanogaster.

A variety of effects of cyclic AMP on cellular and subcellular phenomena suggest that there may be other modes of action of cyclic AMP then activation of protein kinase. It is also known that developing embryos contain cyclic AMP and its related enzymes. In order to explore the role of cyclic AMP in embryogenesis, a survey of proteins capable of binding cyclic AMP in the embryonic supernatant of Drosophila melanogaster was carried out. As the result, two cyclic AMP-binding proteins were found and characterized. The one (L) is, as expected, associated with protein kinase and has a dissociation constant of about 10(-9) M. Its molecular weight of 21 000 daltons is extremely small when compared with similar proteins in other organisms. The other (H), whose function is yet to be found, has a molecular weight of about 200 000 daltons and has a dissociation constant of about 10-7 M. Some laxity in binding specificity of the latter protein among adenosine nucleotides was observed, but cyclic AMP is the strongest ligand among them.