Phylogenesis of fission yeasts. Contradictions surrounding the origin of a century old genus

The phylogenesis of fungi is controversial due to their simple morphology and poor fossilization. Traditional classification supported by morphological studies and physiological traits placed the fission yeasts in one group with ascomycetous yeasts. The rRNA sequence comparisions, however, revealed an enormous evolutionary gap betweenSaccharomyces andSchizosaccharomyces. As shown in this review, the protein sequences also show a large gap which is almost as large as that separatingSchizosaccharomyces from higher animals. Since the two yeasts share features (both cytological and molecular) in common which are also characteristic of ascomycetous fungi, their separation must have taken place later than the sequence differences may suggest. Possible reasons for the paradox are discussed. The sequence data also suggest a slower evolutionary rate in theSchizosaccharomyces lineage than in theSaccharomyces branch. In the fission yeast lineage two ramifications can be supposed. FirstS. japonicus (Hasegawaea japonica) branched off, thenS. octosporus (Octosporomyces octosporus) separated fromS. pombe.     

Xerotolerance in fission yeasts and the role of glycerol as compatible solute

The effect on growth of reducing the water activity (a _w) of a medium with various solutes has been investigated for 27 strains of fission yeasts (Schizosaccharomyces). The minimum-tolerated a _w (MTA) was dependent on both the nature of the solute and the species. When the strains of each species were grouped together, the lowest mean MTA values were found with glucose, fructose or glycerol as stressing solutes, being in the range 0.89–0.90 for S. pombe, S. malidevorans, S. octosporus and S. slooffiae, but in the range 0.92–0.94 for S. japonicus. With the non-metabolizable sugars sorbose and xylose and the salts NH₄Cl, KCl, and NaCl, the mean MTA values were in the range 0.96–0.985, except for (1) the single strain of S. slooffiae, which was more tolerant of NH₄Cl and KCl with values of 0.95 and 0.94, respectively, and (2) the strains of S. pombe, S. malidevorans and S. japonicus, which were less tolerant of NaCl with mean values of about 0.99. One strain of each species was examined for intracellular solutes when actively growing in the presence of near-limiting concentrations of stressing solute. With glucose, fructose or glycerol, all five strains contained substantial amounts of glycerol but no other polyol; with the other solutes no glycerol or other polyol was found, except for small amounts of glycerol in strains of S. octosporus and S. slooffiae stressed with NH₄Cl, KCl, or NaCl.Abbreviations MTA Minimum-tolerated water activity - a _w water activity - YEPG yeast extract, phosphate, glucose medium     

Insights into the ecology of Schizosaccharomyces species in natural and artificial habitats

The fission yeast genus Schizosaccharomyces contains important model organisms for biological research. In particular, S. pombe is a widely used model eukaryote. So far little is known about the natural and artificial habitats of species in this genus. Finding out where S. pombe and other fission yeast species occur and how they live in their habitats can promote better understanding of their biology. Here we investigate in which substrates S. pombe, S. octosporus, S. osmophilus and S. japonicus are present. To this end about 2100 samples consisting of soil, tree sap fluxes, fresh fruit, dried fruit, honey, cacao beans, molasses and other substrates were analyzed. Effective isolation methods that allow efficient isolation of the above mentioned species were developed. Based on the frequency of isolating different fission yeast species in various substrates and on extensive literature survey, conclusions are drawn on their ecology. The results suggest that the primary habitat of S. pombe and S. octosporus is honeybee honey. Both species were also frequently detected on certain dried fruit like raisins, mango or pineapple to which they could be brought by the honey bees during ripening or during drying. While S. pombe was regularly isolated from grape mash and from fermented raw cacao beans S. octosporus was never isolated from fresh fruit. The main habitat of S. osmophilus seems to be solitary bee beebread. It was rarely isolated from raisins. S. japonicus was mainly found in forest substrates although it occurs on fruit and in fruit fermentations, too.

     

Archiascomycetes: detection of a major new lineage within the Ascomycota

For phylogenetic analysis of the higher fungi, we sequenced the nuclear small subunit rRNA (18S rRNA) gene fromTaphrina populina, the type species of the genusTaphrina, andProtomyces lactucae-debilis. The molecular phylogeny inferred from these 2 sequences and 75 sequences from the DNA data bank divided the Ascomycota into three major lineages: the hemiascomycetes, the euascomycetes, and the archiascomycetes, newly described herein. The former two lineages are monophyletic, whereas the archiascomycetes, which originated first and are comprised ofTaphrina, Protomyces, Saitoella, Schizosaccharomyces, andPneumocystis, may not be monophyletic. Among the archiascomycetes, theTaphrina/Protomyces branch is monophyletic. Confirmation of the archiascomycetes as a monophyletic taxonomic class will require comparison of additional genetically defined characters.This work was supported in part by grants 05454030 from the Ministry of Education, Science, and Culture of Japan (to J. S.) and 4369 from the Japan Society for the Promotion of Science Fellowship Programs (to H. N.).     

Actinomycin D inactivating enzymes fromActinoplanes missouriensis and several other members of theActinoplanaceae family

Summary The enzymes for inactivating actinomycin D appear to be widely distributed amongst species belonging to the familyActinoplanaceae. Actinomycin D was completely or partially inactivated by cell-free extracts fromActinoplanes missouriensis, Streptosporangium viridogriseum, S. violaceocbromogenes, S. roseum, S. brasiliense, S. albidum, Spirillospora sp.,Sp. albida, Kitasatoa kauaiensis, Planobispora longispora, P. rosea, Dactylosporangium aurantiacum, andD. thailandense. No inactivation was obtained with extracts fromAmorphosphorangium auranticolor, Ampullariella lobata, Planomonospora parontospora, andP. venezuelensis. Actinomycin lactonase was partially purified by ultracentrifugation, ultrafiltration, and isoelectric focusing from noninduced cells ofActinoplanes missouriensis. The enzyme has a molecular weight of greater than 200,000 daltons and an isoelectric point of 4.3 to 4.4.     

Electrophoretic mobilities of superoxide dismutases from species ofPhotobacterium,beneckea, vibrio,and selected terrestrial enterobacteria

Cell-free extracts of 93 strains from 23 species and biotypes ofPhotobacterium, Beneckea, andVibrio were electrophoresed on polyacrylamide gels and then stained for superoxide dismutase (SOD) activity. All strains exhibited a single activity band with the exception ofPhotobacterium leiognathi, which had one major and two minor bands. Strains representative of all three genera were found to have SOD activities that were sensitive to treatment with H₂O₂, suggesting that they were iron-containing enzymes. Examination of the effect of gel concentration on relative mobility (Rm) suggested that all the iron-containing SODs had very similar molecular weight. Most species could be distinguished on the basis of differences in the Rm values of their SODs.Vibrio was readily separable fromBeneckea andPhotobacterium. A limited electrophoretic analysis of the SODs fromAeromonas, Serratia, Proteus, Erwinia, and other species of terrestrial enterobacteria indicated groupings that were in agreement with previous studies.     

Interspecific protoplast fusion in fission yeasts

Protoplasts of auxotrophic mutants isolated fromSchizosaccharomyces pombe andSchizosaccharomyces octosporus were fused. The fusion products were capable of complementation and growth on minimal medium, but the morphological observations suggested a disturbed physiological balance, which was reflected in low viability, osmotic sensitivity, and the formation of incomplete cell wall. Their asymmetric segregation indicated thatSchizosaccharomyces octosporus might be dominant in the fused cells.     

Identification and Functional Analysis of the erh1 + Gene Encoding Enhancer of Rudimentary Homolog from the Fission Yeast Schizosaccharomyces pombe

The ERH gene encodes a highly conserved small nuclear protein with a unique amino acid sequence and three-dimensional structure but unknown function. The gene is present in animals, plants, and protists but to date has only been found in few fungi. Here we report that ERH homologs are also present in all four species from the genus Schizosaccharomyces, S. pombe, S. octosporus, S. cryophilus, and S. japonicus, which, however, are an exception in this respect among Ascomycota and Basidiomycota. The ERH protein sequence is moderately conserved within the genus (58% identity between S. pombe and S. japonicus), but the intron-rich genes have almost identical intron-exon organizations in all four species. In S. pombe, erh1⁺ is expressed at a roughly constant level during vegetative growth and adaptation to unfavorable conditions such as nutrient limitation and hyperosmotic stress caused by sorbitol. Erh1p localizes preferentially to the nucleus with the exception of the nucleolus, but is also present in the cytoplasm. Cells lacking erh1⁺ have an aberrant cell morphology and a comma-like shape when cultured to the stationary phase, and exhibit a delayed recovery from this phase followed by slower growth. Loss of erh1⁺ in an auxotrophic background results in enhanced arrest in the G1 phase following nutritional stress, and also leads to hypersensitivity to agents inducing hyperosmotic stress (sorbitol), inhibiting DNA replication (hydroxyurea), and destabilizing the plasma membrane (SDS); this hypersensitivity can be abolished by expression of S. pombe erh1⁺ and, to a lesser extent, S. japonicus erh1⁺ or human ERH. Erh1p fails to interact with the human Ciz1 and PDIP46/SKAR proteins, known molecular partners of human ERH. Our data suggest that in Schizosaccharomyces sp. erh1⁺ is non-essential for normal growth and Erh1p could play a role in response to adverse environmental conditions and in cell cycle regulation.     

Formation of aerial hyphae and conidia under orthophosphate-limited conditions inNeurospora crassa: Role of repressible cyclic phosphodiesterase

A wild type strain ofNeurospora crassa produced aerial hyphae and luxuriant conidia in standing culture in low phosphate liquid media.nuc-1 andnuc-2, which have no ability to derepress repressible cyclic phosphodiesterase (cPDase) (3′; 5′-cyclic AMP 5′-nucleotidohydrolase, EC 3.1.4.17) and several other repressible enzymes, did not form them. Heterocaryon between them restored the abilities not only to produce aerial hyphae and conidia but also to produce cPDase. Revertants fromnuc-1 and a mutant in alkaline phosphatase,pho-2, produced aerial hyphae and conidia in low phosphate condition, whereas a mutant in cPDase,pho-3, produced only a limited amount of them. In media containing low levels of 2′, 3′-cAMP, the wild type, the revertants fromnuc-1, pho-2 andpho-3 produced aerial hyphae and conidia in abundance, whereas in media containing 3′, 5′-cAMP these strains produced no or only limited amounts of them. In low phosphate medianuc-1, nuc-2 andpho-3 showed higher levels of 3′, 5′-cAMP as compared with those strains which have the ability to derepress cPDase. The cPDase activities in crude mycelial extracts fromnuc-1 andpho-3 grown in low phosphate media were 5.6 and 17.5% of that ofpho-2 when assayed for 3′,5′-cAMP at an intracellular level of 2 μM.     

Phylogenetic relationships inSecale (Poaceae): An isozymatic study

The genetic frequencies of 9 isozyme loci have been estimated in 23 samples of 4 species ofSecale by means of starch gel electrophoresis. The populations ofS. silvestre andS. vavilovii were monomorphic and uniform within each species, those ofS. montanum andS. cereale were polymorphic for most of the isozyme loci. On the basis of isozyme patterns as well as allelic and genotypic frequencies of isozyme loci,S. silvestre can be distinguished fromS. vavilovii, and both fromS. cereale andS. montanum; but there is no clear differentiation between the two latter species. Clusters constructed from genetic distances separateS. silvestre andS. vavilovii, whereasS. cereale andS. montanum were grouped together. The isozymatic data presented here, along with cytogenetic and life habit data, agree with the generally admitted existence of 4 species inSecale, and support the relationships suggested byKhush & Stebbins (1961).     

Reproductive ecology of three ocypodid crabs II. Incubation sites and egg mortality

Mortality of eggs during incubation was estimated for three ocypodid crabs,Scopimera globosa, Ilyoplax pusillus andMacrophthalmus japonicus, and the influence of incubation sites was discussed. These crabs all lived in isolated burrows and fed on sediments during day time low tide.S. globosa andI. pusillus inhabited the upper intertidal sandflats, whereasM. japonicus inhabited the lower intertidal mudflats. Females of bothS. globosa andI. pusillus remained in their plugged burrows without feeding throughout incubation and the mortality of eggs was low despite large broods relative to body size. On the other hand, females ofM. japonicus fed actively on surface mud during incubation and the mortality of eggs was high despiite small broods relative to body size. InS. globosa andI. pusillus, the ovaries of ovigerous females were small until egg-hatching, whereas inM. japonicus, the ovaries grew rapidly during incubation and females were able to produce consecutive broods. I conclude that incubation of eggs in burrows may be advantageous in species which inhabit the upper interidal sandflats, even though the crabs cannot forage during incubation, since otherwise their eggs would be exposed to strong heat stress and desication during the summer. Furthermore, such species may produce few large broods because of less frequent interruption of feeding than that associated with production of many small broods.     

Aflatoxin: A metabolic product of several fungi

Summary Culture extracts produced by 107 fungi isolated from corn grains were assayed by thin layer chromatography for aflatoxin. Certain isolates ofAspergillus flavus, A. niger, A. parasiticus, A. ruber, A. wentii, Penicillium citrinum, andP. variabile produced aflatoxin.Penicillium frequentans andP. puberulum elaborated this toxin only in trace amounts. Bioassays of extracts from 4 of these fungi showed that only the extract fromA. parasiticus was highly toxic.     

Phage specificity and lipopolysaccarides of stem- and root-nodulating bacteria (Azorhizobium caulinodans, Sinorhizobium spp., and Rhizobium spp.) of Sesbania spp

Phage susceptibility pattern and its correlation with lipopolysaccharide (LPS) and plasmid profiles may help in understanding the phenotypic and genotypic diversity among highly promiscuous group of rhizobia nodulating Sesbania spp.; 43 phages were from two stem-nodulating bacteria of S. rostrata and 16 phages were from root-nodulating bacteria of S. sesban, S. aegyptica and S. rostrata. Phage susceptibility pattern of 38 Sesbania nodulating bacteria was correlated with their LPS rather than plasmid profiles. Different species of bacteria (A. caulinodans- ORS571, SRS1-3 and Sinorhizobium saheli- SRR907, SRR912) showing distinct LPS subtypes were susceptible to different group of phages. Phages could also discriminate the strains of Si. saheli (SSR312, SAR610) possessing distinct LPS subtypes. Phages of Si. meliloti (SSR302) were strain-specific. All the strains of R. huautlense having incomplete LPS (insignificant O-chain) were phage-resistant. In in vitro assay, 100% of the phages were adsorbed to LPS of indicator bacterium or its closely related strain(s) only. These observations suggest the significance of LPS in phage specificity of Sesbania nodulating rhizobia. Highly specific phages may serve as biological marker for monitoring the susceptible bacterial strains in culture collections and environment.     

Delayed fermentation of sucrose by certain haploid species ofSaccharomyces

Summary Several haploid species ofSaccharomyces andSchiz. octosporus were shown to ferment sucrose in Durham tubes after a delay of 3 to 4 weeks. Detailed studies were done with a strain ofS. rouxii. The delayed fermentation of sucrose was not caused by mutationselection or by inducible enzyme formation, since young glucose grown cells after drying, freezing, aging or autolysis contained an active sucrase. Cells pretreated by drying or freezing fermented sucrose nearly as fast as glucose. After autolysis, the sucrase ofS. rouxii is only present in the cell debris and not in the autolysate. The use of a heavy inoculum in the van Iterson-Kluyver fermentometer resulted in a slow, but non-delayed fermentation. Variation in the pH or sucrose concentration had little effect on the delayed fermentation. It is suggested that after sufficient aging of the cells, the cell wall permeability undergoes a rather abrupt change, allowing the sucrose to come in contact with the sucrase of the cells.     

Growth requirements of some fungi causing maduromycosis

Three strains ofMadurella mycetomi, two ofM. grisea, and two ofRhinocladiella mansonii have been studied for possible differences in growth requirements which might be used for distinguishing these species. Under the experimental conditions, an incubation temperature of 37C suitedM. mycetomi about as well as 30C.R. mansonii grew less well at 37C than at 30C, andM. grisea did not grow at the higher temperature. M. grisea andR. mansonii further differed fromM. mycetomi in that they required thiamine for growth. The pH tolerance of all the strains was very wide. Asparagine and potassium nitrate were readily utilized by all the strains, but ammonium salts were not. Urea was poorly used byM. mycetomi; the other species did not use it. A possible relationship ofM. grisea andR. mansonii is discussed.     

Arthropod cell lines in the isolation and propagation of tickborne spiroplasmas

The ability of several continuous tick cell culture lines to support growth of tickborne spiroplasmas (helical, wall-less prokaryotes in the classMollicutes) was assessed. Seven triturates, prepared from pools ofIxodes pacificus ticks naturally infected with theSpiroplasma sp. (group VI) organism, were retrieved from frozen (–70°C) storage and passaged in three distinct tick cell lines, in antibiotic-free tick cell culture medium alone, or in spiroplasma culture medium (SP-4 formulation). Six spiroplasma strains were recovered in the RML-19 cell line fromDermacentor variabilis, and five isolations were made in another cell line (RML-15) from this tick species. None was recovered in aRhipicephalus sanguineus cell line (RML-23), in tick cell culture medium, or in SP-4 broth medium. One of the spiroplasma isolates (Y43) was maintained through four consecutive weekly refeedings of theD. variabilis cell line and for three feedings ofR. sanguineus cells, where numbers of spiroplasmas in cell supernatants reached levels comparable to those obtained in the SP-4 medium.A laboratory-adapted strain (SMCA) ofSpiroplasma mirum, a second helical mollicute of tick origin (the suckling mouse cataract agent), grew in three tick cell lines (RML-15, RML-23, and RML-16 cells fromD. parumapertus), in three mosquito cell lines (fromAedes albopictus, Ae. aegypti, andCulex quinquefasciatus), and in both cell culture medium alone and in SP-4 medium. The organisms survived for 1–2 weeks, but failed to multiply, in cell lines fromC. tritaeniorhynchus, Antheraea eucalypti, orXenopus laevis. Some evidence of cytopathic effect ofS. mirum on tick cell lines was seen, although growth of the organism in mosquito cell cultures was not associated with cell toxicity. The use of arthropod cell lines appears to have value in the primary isolation of arthropod- or insect-derived mollicutes and for the study of cytopathogenicity of these wall-less prokaryotes.     

Amylostereum laevigatum associated with the Japanese horntail,Urocerus japonicus

The fungus associated with the Japanese horntail,Urocerus japonicus, in Kochi, Kagawa and Ehime Prefectures was studied. Cultures isolated from the mycangia of 113 adult females of the horntail showed the same cultural characteristics. Four of basidiocarps found on felled logs ofCryptomeria japonica were identifieds asAmylostereum laevigatum based on morphological characteristics. This was the first record ofA. laevigatum from Japan. The cultures isolated from the basidiocarps had the same cultural characteristics as those from the mycangia ofU. japonicus. One mycangial isolate produced basidiocarps on artificially inoculated stem segments ofCr. japonica after a 6-mo incubation and was identified asA. laevigatum. One isolate from the basidiocarps ofA. laevigatum and one from the mycangium ofU. japonicus were artificially inoculated into five trees each ofChamaecyparis obtusa andCr. japonica. The wood of all inoculated trees showed discoloration, with no difference in shape and pattern of discoloration between the two isolates. The inoculated fungi were reisolated from the areas of discoloration in the inoculated trees.     

A comparison of three fission yeast mitochondrial genomes

The fission yeasts are members of the fungal order Schizosaccharomycetales, a candidate deep-diverging group within Ascomycota. Although a great deal of molecular information is available from Schizosaccharomyces pombe, a model eukaryote, very little is available from other members of this group. In order to better characterize mitochondrial genome evolution in this fungal lineage, the mitochondrial DNA (mtDNA) of two additional fission yeasts, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus var. japonicus, was sequenced. Whereas the mtDNA of S.pombe is only 19 431 bp, the mtDNA of S.octosporus is 44 227 bp, and that of S.japonicus var. japonicus is over 80 kb. The size variation of these mtDNAs is due largely to non-coding regions. The gene content in the latter two mtDNAs is almost identical to that of the completely sequenced S.pombe mtDNA, which encodes 25 tRNA species, the large and small mitochondrial ribosomal RNAs (rnl and rns), the RNA component of mitochondrial RNaseP (rnpB), mitochondrial small subunit ribosomal protein 3 (rps3), cytochrome oxidase subunits 1, 2 and 3 (cox1, cox2 and cox3) and ATP-synthase subunits 6, 8 and 9 (atp6, atp8 and atp9). However, trnI2(cau) (C modified to lysidine) is absent in the S.octosporus mtDNA, as are corresponding ATA codons in its protein-coding genes, and rps3 and rnpB are not found in the mtDNA of S.japonicus var. japonicus. The mtDNA of S.octosporus contains five double hairpin elements, the first report of these elements in an ascomycete. This study provides further evidence in favor of the mobility of these elements, and supports their role in mitochondrial genome rearrangement. The results of our phylogenetic analysis support the monophyly of the Schizosaccharomycetales, but question their grouping within the Archiascomycota.     

Molecular relationships between closely related strains and species of nematodes

Summary Electrophoretic comparisons have been made for 24 enzymes in theBergerac andBristol strains ofCaenorhabditis elegans and the related species,Caenorhabditis briggsae. No variation was detected between the two strains ofC. elegans. In contrast, the two species,C. elegans andC. briggsae exhibited electrophoretic differences in 22 of 24 enzymes. A consensus 5S rRNA sequence was determined forC. elegans and found to be identical to that fromC. briggsae. By analogy with other species with relatively well established fossil records it can be inferred that the time of divergence between the two nematode species is probably in the tens of millions of years.The limited anatomical evolution during a time period in which proteins undergo extensive changes supports the hypothesis that anatomical evolution is not dependent on overall protein changes.     

Relationships betweenOryza species (Poaceae) based on 5S DNA sequences

Relationships between 9Oryza species, covering 6 different genomes, have been studied using hybridization and nucleotide sequence information from the5S Dna locus. Four to five units of the major size class of 5S DNA in each species, 55 units in all, were cloned and sequenced. Both hybridization and sequence data confirmed the basic differences between the A and B, C, D genome species suggested by morphological and cytological data. The 5S DNA units of the A genome species were very similar, as were the ones from the B, C, and D genome-containing species. The 5S DNA ofO. australiensis (E genome) grouped with the B, C, D cluster, while the units ofO. brachyantha (F genome) were quite different and grouped away from all other species. 5S DNA units fromO. minuta, O. latifolia, O. australiensis, andO. brachyantha hybridized strongly, and preferentially, to the genomic DNA from which the units were isolated and hence could be useful as species/genome specific probes. The 5S DNA units fromO. sativa, O. nivara, andO. rufipogon provided A genome-specific probes as they hybridized preferentially to A genome DNA. The units fromO. punctata andO. officinalis displayed weaker preferential hybridization toO. punctata DNA, possibly reflecting their shared genome (C genome).