Makiko Hamamoto

Distribution and identification of red yeasts in deep-sea environments around the northwest Pacific Ocean

We isolated 99 yeast strains, including 40 red yeasts, from benthic animals and sediments collected from the deep-sea floor in various areas in the northwest Pacific Ocean. Comparing the yeast isolates from animals and sediments collected from shallow locations, the proportion of red yeasts differed considerably, comprising 81.5% and 10.6% of the isolates from animals and sediments, respectively. All of the red yeast isolates belonged to the genera Rhodotorula and Sporobolomyces. On the basis of morphological and physiological characteristics, the isolates were identified as R. aurantiaca, R. glutinis, R. minuta and R. mucilaginosa of the genus Rhodotorula, and S. salmonicolor and S. shibatanus of the genus Sporobolomyces. Only R. glutinis and R. mucilaginosa were isolated from sediments. All of the others were isolated from animal sources. Phylogenetic analyses based on internal transcribed spacer (ITS) regions and 5.8S rRNA gene sequences allowed us to establish the precise taxonomic placement of each of the isolates and thereby investigate the intraspecific relationships among the isolates. Twenty-two strains identified as members of R. glutinis, which showed a wide distribution in the deep-sea, and five isolates identified as R. minuta, which were isolated only from benthic animals, showed substantial heterogeneity within the species. The isolates phenotypically identified as Sporobolomyces species and R. mucilaginosa phylogenetically occupied the placements corresponding to these species. Some strains assigned to known species on the basis of phenotypic features should be regarded as new species as suggested by the results of molecular analysis.

Ballistosporous yeasts found on the surface of plant materials collected in New Zealand

Six new species of ballistosporous yeast, the genusSporobolomyces, were isolated from dead leaves and fruit of plants collected in New Zealand;Sp. novazealandicus, Sp. dimmenae, Sp. coprosmicola, Sp. coprosmae, Sp. dracophyllus, andSp. taupoensis. These species differ from any hitherto known species ofSporobolomyces based on chemotaxonomic characteristics.

Phylogenetic analysis of the ballistoconidium-forming yeast genus Sporobolomyces based on 18S rDNA sequences

The 18S rDNA nucleotide sequences of 25 Sporobolomyces species and five Sporidiobolus species were determined. Those of Sporobolomyces dimmenae JCM 8762T, Sporobolomyces ruber JCM 6884T, Sporobolomyces sasicola JCM 5979T and Sporobolomyces taupoensis JCM 8770T showed the presence of intron-like regions with lengths of 1586, 324, 322 and 293 nucleotides, respectively, which were presumed to be group I introns. A total of 63 18S rDNA nucleotide sequences was analysed, including 33 published reference sequences. Sporobolomyces species and the other basidiomycetes species were distributed throughout the phylogenetic tree. The resulting phylogeny indicated that Sporobolomyces is polyphyletic. Sporobolomyces species were mainly divided into four groups within the Urediniomycetes. The groups are designated as the Sporidiales, Agaricostilbum/Bensingtonia, Erythrobasidium and subbrunneus clusters. The last group, comprising four species, Sporobolomyces coprosmicola, Sporobolomyces dimmenae, Sporobolomyces linderae and Sporobolomyces subbrunneus, forms a new and distinct cluster in the phylogenetic tree in this study.

Kluyveromyces nonfermentans sp. nov., a new yeast species isolated from the deep sea.

Eleven strains of a new species of the genus Kluyveromyces, characterized as having evanescent asci and Q-6 as the major ubiquinone, were isolated from sediments, a clam and a crab collected at depths of 1000-2000 m in Suruga Bay and Sagami Bay, Japan. A phylogenetic tree based on small-subunit (18S) rRNA gene sequences placed these isolates into a cluster of Kluyveromyces. DNA complementarity and phylogenetic trees of internal transcribed spacer (ITS) regions and 5.8S rRNA genes showed that the isolates are closely related to Kluyveromyces aestuarii, but that these two species are genetically distinct. The isolates are described as Kluyveromyces nonfermentans sp. nov. Because this species lacks the fermentative ability considered to be an important criterion for the genus Kluyveromyces, the definition of the genus has been emended. The type strain of K. nonfermentans is strain SY-33T (= JCM 10232T).

Rhodotorula lamellibrachii sp. nov., a new yeast species from a tubeworm collected at the deep-sea floor in Sagami bay and its phylogenetic analysis.

A new species of the genus Rhodotorula was isolated from a tubeworm (Lamellibrachia sp.) collected at a depth of 1156 m in Sagami Bay, Japan. Strain SY-89 had physiological properties quite similar to R. aurantiaca. Two phylogenetic trees, one based on internal transcribed spacer (ITS) regions and 5.8S rDNA sequences and the other based on the D1/D2 region of the large subunit (26S) rDNA sequences, united strain SY-89 to the type strain of Sakaguchia dacryoides through a considerable evolutionary distance. Strain SY-89 was differentiated from S. dacryoides by the G+C content of the nuclear DNA and differences in the ability to utilize specific carbon and nitrogen compounds. The low complementarity of strain SY-89 DNA to that of the type strain of S. dacryoides confirmed that this strain was genetically unrelated to previously known species. The tubeworm isolates are described as R. lamellibrachii sp. nov. The type strain of R. lamellibrachii is strain SY-89 (= JCM 10907). R. lamellibrachii formed a cluster with Erythrobasidium hasegawianum, R. lactosa, S. dacryoides and Sporobolomyces elongatus on the ITS and 5.8S rDNA phylogenetic tree. These five species shared a signature sequence in 26S rDNA, although this relationship was not supported by phylogeny based on the D1/D2 region of 26S rDNA.

A novel yeast cell-based screen identifies flavone as a tankyrase inhibitor.

The telomere-associated protein tankyrase 1 is a poly(ADP-ribose) polymerase and is considered to be a promising target for cancer therapy, especially for BRCA-associated cancers. However, an efficient assay system for inhibitor screening has not been established, mainly due to the difficulty of efficient preparation of the enzyme and its substrate. Here, we report a cell-based assay system for detecting inhibitory activity against tankyrase 1. We found that overexpression of the human tankyrase 1 gene causes a growth defect in the fission yeast Schizosaccharomyces pombe. Chemicals that restore the growth defect phenotype can be identified as potential tankyrase 1 inhibitors. We performed a high-throughput screen using this system, and identified flavone as a compound that restores the growth of yeast cells overexpressing tankyrase 1. Indeed, flavone inhibited poly(ADP-ribosyl)ation of proteins caused by overexpression of tankyrase 1 in yeast cells. This system allows rapid identification of inhibitory activity against tankyrase 1 and is amenable to high-throughput screening using robotics.

Systematic study of basidiomycetous yeasts – evaluation of the ITS regions of rDNA to delimit species of the genus Rhodosporidium

Nucleotide sequences of internal transcribed spacer (ITS) regions were determined to establish the guidelines for species identification in the genus Rhodosporidium. Forty-two strains of nine species of the genus Rhodosporidium were used for ITS (ITS1 and ITS2) analysis. Intraspecific length polymorphisms and sequence variations were observed within R. azoricum, R. diobovatum, R. paludigenum, R. sphaerocarpum and R. toruloides, while no variation was observed within R. babjevae and R. kratochvilovae. Based on comparison of the levels of intraspecific and interspecific sequence similarity, strains with identical sequences were considered to represent a single species and strains with 92% or lower similarity of ITS sequences were considered to be distinct species in the genus Rhodosporidium.

Chapter 156 – Sporobolomyces Kluyver & van Niel (1924)

Publisher Summary This chapter studies the genus Sporobolomyces. In the asexual reproduction it is seen that colonies are salmon-pink, orange-red, red, cream, or yellow-brown. Hyphae and pseudohyphae may be present. Cells are ellipsoidal, subglobose, or cylindrical. Budding is mostly polar, rarely lateral, or multilateral, with buds sessile or on short denticles, enteroblastic, and showing percurrent or sympodial proliferation. Ballistoconidia are bilaterally symmetrical, ellipsoidal, falcate, allantoid, lacrymoid, or amygdaliform. Sexual reproduction is absent. The chapter also discusses physiology/biochemistry and phylogenetic placement of the genus. The type species taken is Sporobolomyces salmonicolor. The key characters of species in the genus Sporobolomyces are presented. In the systematic discussion of the species, phylogenetic placement, growth on malt extract agar, growth in malt extract, Dalmau plate culture on corn meal agar, formation of ballistoconidia on corn meal agar, gene sequence accession numbers, type strain, origin of the strains studied, systematics, and ecology are determined.

Taxonomic Significance of Fucose in the Class Urediniomycetes: Distribution of Fucose in Cell Wall and Phylogeny of Urediniomycetous Yeasts

The carbohydrate compositions of cell wall were determined in the strains of class Urediniomycetes, mainly ballistoconidium-forming yeasts and related taxa. The major component of cell wall was mannose, and glucose was included as the second component, but xylose was not detected in any strain. Out of 41 strains examined, 39 contained galactose, 14 contained arabinose and 12 contained rhamnose. As a minor component, fucose was detected in 30 strains but not in 11 strains. A phylogenetic tree based on 18S rDNA sequences indicated that the fucose-lacking strains, Erythrobasidium hasegawianum, Rhodotolura aurantiaca, R. lactosa, R. minuta, Sakaguchia dacryoidea, Sporobolomyces coprosmae, S. elongatus, S. folicola, S. gracilis, S. kluyverinielii and S. oryzicola, constituted a distinct cluster from those strains which contained fucose. This cluster corresponded to one of the five subclusters, the Erythrobasidium cluster, in the phylogenetic tree of class Urediniomycetes. The carbohydrate composition of cell wall is believed to reflect the phylogenetic relationships among basidiomycetous fungi. The presence or absence of fucose in cell wall should be regarded as an important phenotypic characteristic in the taxonomy of basidiomycetes.

Dipodascus tetrasporeus sp. nov., an ascosporogenous yeast isolated from deep-sea sediments in the Japan Trench

Dipodascus tetrasporeus sp. nov. is described as a novel yeast species in the family Dipodascaceae to accommodate an isolate recovered from sediments collected on the deep-sea floor in the north-western Pacific Ocean. In the clade comprising the genera Dipodascus, Galactomyces and Geotrichum, this is the only species that forms asci that bear four ascospores. The ascospore is surrounded by an irregular exosporium wall, similar to what is observed in the genus Galactomyces, but they are released by rupture, which is characteristic of Dipodascus and not Galactomyces. D. tetrasporeus is remarkably divergent (>10 % difference) in its D1/D2 26S rDNA sequence from any other known species. Although maximum-likelihood analysis of combined 18S rDNA and D1/D2 26S rDNA sequences cannot elucidate a reliable position for this species, it was placed among Geotrichum carabidarum, Geotrichum cucujoidarum, Geotrichum fermentans and Geotrichum histeridarum, which also have morphological and physiological affinity with the species. The species is homothallic. The type strain of Dipodascus tetrasporeus sp. nov. is strain SY-277T (=NBRC 103136T =CBS 10071T).