Ribosomal DNA Restriction Analysis Reveals Genetic Heterogeneity in Saccharomyces cerevisiae Meyen ex Hansen

An alkaline β-glucosidase isolated from an olive brine strain of Wickerhamomyces anomalus

An efficient β-glucosidase (βG)-producing strain, Wickerhamomyces anomalus BS81, was isolated from naturally fermented olive brine and identified based on PCR/restriction fragment length polymorphism of the rDNA internal transcribed spacer and sequence analysis of the D1/D2 region of the 26S rRNA gene. The hydrolytic activity of the βG had an optimum pH of 8.5 and an optimum temperature of 35 °C. The enzyme had high substrate specificity and high catalytic efficiency (K(m) 0.99 mM, V(max) 14 U g(-1) of cells) for p-nitrophenyl-β-d-glucopyranoside. The enzyme was activated by increasing concentrations of NaCl, with maximum activity at 150 g L(-1) NaCl. Although βGs have been purified and characterized from several other sources, the W. anomalusβG is unique among βGs because its relative maximum activity occurs at alkaline pH and 35 °C. Moreover, the yeast strain has esterase activity that acts synergistically with βG to degrade oleuropein to debitter table olives and olive oil.

Genetic characterization of strains of Saccharomycescerevisiae responsible for 'refermentation' in Botrytis-affected wines

AIMS

Saccharomyces cerevisiae is responsible for alcoholic fermentation of wines. However, some strains can also spoil sweet Botrytis-affected wines. Three 'refermentation' strains were isolated during maturation. Characterization of those strains in regards to their fingerprint, rDNA sequence and resistance to SO2, which constituted the main source of stress in Botrytis-affected wines, was carried out.

METHODS AND RESULTS

Refermentation strains could be clearly discriminated by interdelta fingerprinting. However, they exhibited close relationships by karyotyping. A part of RDN1 locus sequence was examined by using PCR-RFLP and PCR-DGGE. The resistance of refermentation strains to SO2 was performed by using real time quantitative PCR focusing on SSU1 gene.

CONCLUSIONS

Results suggested that refermentation strains were heterozygote in 26S rDNA and their ITS1-5.8S rDNA-ITS2 region sequence revealed relationships with 'flor' strains. As described in the literature for flor strain, two out of three refermentation strains constitutively developed a higher level of SSU1 expression than the reference strains, improving their putative tolerance to SO2. Therefore, refermentation strains of S. cerevisiae had developed many strategies to survive during maturing sweet wines.

SIGNIFICANCE AND IMPACT OF THE STUDY

Singularities in rDNA sequence and SSU1 overexpression revealed a natural adaptation. Moreover, genomic relationship between flor and refermentation strains suggested that stress sources could induced selection of survivor strains.

Development of internal transcribed spacer regions amplification restriction fragment length polymorphism method and its application in monitoring the population of Zygosaccharomyces rouxii M2 in miso fermentation

Recently, the use of the dry yeast of Zygosaccharomyces rouxii M2 for miso (soybean paste) fermentation has been established. A molecular monitoring method was developed and validated in this study to analyze the population of Z. rouxii M2 during the fermentation. The method was based on the restriction patterns of internal transcribed spacer (ITS) regions of the rDNA using HaeIII and HhaI. Among the homologous ITS regions of Z. rouxii strains, Z. rouxii M2 produced diagnostic bands by which it can be differentiated from the other strains used. The specific restriction bands were due to the difference in nucleotide sequence of two different copies of ITS of Z. rouxii M2. Both ITS copies showed 94% sequence similarity but a 13-bp nucleotide substitution and a 19-bp deletion were found in the ITS1 region. Phylogenetic trees were constructed based on ITS and 18S rDNA sequences and it was found that the ITS sequences provide better resolution for the classification of Z. rouxii M2. Since Z. rouxii M2 is a promising strain for use in miso fermentation as a dry starter, the method developed is significant in terms of industrial application in monitoring the growth of Z. rouxii M2 in miso fermentation.

Analysis of the genetic variability in the species of theSaccharomyces sensu strictocomplex

Random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis was applied to differentiate the sibling species Saccharomyces bayanus, S. cerevisiae, S. paradoxus and S. pastorianus, which constitute the most common strains of the Saccharomyces sensu stricto complex. Six decamer primers of arbitrary sequences were used to amplify the DNA of 58 strains. Species-specific (diagnostic) bands were obtained for each species. Two phylogenetic trees constructed by the neighbour-joining and maximum parsimony methods clearly showed that the delimitation of these related yeast species is possible by using RAPD analysis. Four groups of strains, corresponding to the species S. bayanus, S. cerevisiae, S. paradoxus and S. pastorianus, were obtained. Within the S. bayanus taxon, two groups of strains were observed. One includes the former type strain of S. uvarum, CECT1969(T), and closely related wine strains (S. bayanus var. uvarum), whilst the other contains S. bayanus type strain CECT1941(T) and strains CECT1991 and 10513 (S. bayanus var. bayanus). The heterogeneous S. paradoxus group was divided into three lineages, corresponding to different geographic origin, American, Japanese and European populations. In addition, due to the multilocus nature of the RAPD-PCR marker, this method is both useful and appropriate for the identification of the hybrid origin of S. pastorianus. The hybrid nature was deduced from the analysis of the fraction of bands shared by each hybrid strain and the parental species. Among the 58 strains analysed, six S. pastorianus strains were hybrids, although the fraction of genome coming from each parent varied depending on the strain.

Identification of Pichia anomala isolated from yoghurt by RFLP of the ITS region

Several packs of swollen retailed plain and flavoured yoghurt were examined. The most commonly found species was Pichia anomala, identified both by physiological tests and RFLP analysis of the rDNA internal transcribed spacer (ITS) region. The isolated strains did not ferment lactose and were positive for galactose fermentation, confirming the hypothesis that galactose-fermenting yeast could be the cause of spoilage in yoghurt.

Identification of heterotrophic nanoflagellates by restriction fragment length polymorphism analysis of small subunit ribosomal DNA

Thirty clones derived from twenty isolates of heterotrophic nanoflagellates originating from a variety of marine and freshwater environments were examined by restriction fragment length polymorphism analysis of small subunit ribosomal RNA genes amplified by the polymerase chain reaction (riboprinting). The data were compared with light and electron microscopical identification of the isolates. On morphological criteria, sixteen of the thirty clones belonged to the genus Paraphysomonas De Saedeleer, seven to the genus Spumella Cienkowski, four to the genus Pteridomonas Penard and three to the genus Cafeteria Fenchel and Patterson. Among these taxa, eleven ribotypes were detected by analysis with the restriction enzymes Hinf I, Hae III, Sau3A I, and Msp I. Differentiation of nanoflagellate taxa by the riboprinting method supported taxonomic classification based on morphology at the generic and species level. The utility of the method for discriminating the 'naked' flagellates and for confirming the identity of polymorphic forms among species of Paraphysomonas is demonstrated.

Genetic variation among European strains of Saccharomyces paradoxus: results from DNA fingerprinting

We used microsatellite fingerprinting and RAPD analysis to characterize 28 wild European strains of Saccharomyces paradoxus. In contrast to our results from a previous allozyme survey [Naumov et al. Int. J. Syst. Bacteriol. 47: 341-344 (1997a)], these methods revealed extensive genetic variation. The RAPD primers 5'AATCGGGCTG and 5'GGGTAACGCC and the microsatellite primer (GTG)5 yielded reproducible amplification patterns of sufficient clarity and variability to distinguish individual strains from the wild. UPGMA analysis tended to group the strains according to climatic and geographic origin. A comparative study of Ty1 sequence having multiple chromosomal location was also done. Each wild S. paradoxus isolate shows a unique hybridization pattern allowing discrimination to the strain level.

Molecular characterization of myxozoan parasites from Lake Sasajewun, Algonquin Park, Ontario, by riboprinting

The small subunit-rRNA genes of 18 myxozoans from Lake Sasajewun, Algonquin Park were amplified and digested with restriction endonucleases for riboprinting analysis. Identical riboprints were not found between the myxosporeans and the actinosporeans. The distinct riboprinting patterns observed among these myxozoans indicate considerable genetic diversity within this group. Identical riboprints were found between Myxobolus pendula and Myxobolus pellicides, and between triactinomyxon 'C' and Triactinomyxon ignotum. Parsimony analysis of the riboprints demonstrated that neither the myxosporeans nor the actinosporeans formed a monophyletic group. Some species of Myxobolus are more closely related to forms of triactinomyxon, echinactinomyxon or raabeia than to other Myxobolus species. These results are consistent with the two-host life cycle hypothesis of myxozoans that myxosporeans and actinosporeans are alternating stages of the same organisms.

A polyphasic study on the taxonomic position of industrial sour dough yeasts

The sour dough bread making process is extensively used to produce wholesome palatable rye bread. The process is traditionally done using a back-slopping procedure. Traditional sour doughs in Finland comprise of lactic acid bacteria and yeasts. The yeasts present in these doughs have been enriched in the doughs due to their metabolic activities, e.g. acid tolerance. We characterized the yeasts in five major sour bread bakeries in Finland. We found that most of the commercial sour doughs contained yeasts which were similar to Candida milleri on the basis of 18S rDNA and EF-3 PCR-RFLP patterns and metabolic activities. Some of the bakery yeasts exhibited extensive karyotype polymorphism. The minimum growth temperature was 8 degrees C for C. milleri and also for most of sour dough yeasts.

A phylogenetic analysis of Saccharomyces species by the sequence of 18S-28S rRNA spacer regions

Sequences of two internally transcribed spacer regions between 18S and 28S rRNA genes were determined to assess the phylogenetic relationship in the strains belonging to the genus Saccharomyces. The sequences of S. bayanus and S. pastorianus were quite similar, but not identical. Two phylogenetic trees constructed by the neighbor-joining method showed that all the species examined were distinguished from one another. The Saccharomyces sensu stricto species: S. cerevisiae, S. bayanus, S. paradoxus and S. pastorianus, were closely related and far from the Saccharomyces sensu lato species including S. barnetti, S. castellii, S. dairensis, S. exiguus, S. servazzii, S. spencerorum and S. unisporus, and an outlying species, S. kluyveri.

Riboprinting: a tool for the study of genetic diversity in microorganisms

Classical morphology-based methods of taxonomic and phylogenetic analysis are inadequate in many groups of structurally simple eukaryotes. Molecular methods can generate data independently of the complexity of the organisms' morphology. Riboprinting is one such technique, and involves restriction enzyme analysis of polymerase chain reaction amplified small subunit ribosomal RNA genes. The utility of the method is illustrated with examples from several genera of intestinal and bloodstream parasites. Among the applications of riboprinting are the detection of cryptic genetic variation within species, organism misidentifications and culture mix-ups, independent verification of DNA sequences, and the rapid generation of data useful in phylogenetic analyses.

Application of DNA typing methods and genetic analysis to epidemiology and taxonomy of Saccharomyces isolates

We have previously described differences in phenotype and virulence among clinical and nonclinical isolates of Saccharomyces. To further characterize these isolates, a comparison of restriction fragment length polymorphism (RFLP) patterns and genetic analysis were done. The cellular DNA of each of 49 clinical and 11 nonclinical isolates of Saccharomyces was digested with the endonuclease EcoRI, and the resultant fragments were separated by electrophoresis. Sixty isolates were grouped on the basis of the presence (group B) or absence (group A) of a 3-kb band. Group A contained 43 isolates (35 clinical and 8 nonclinical isolates) in 31 discernible subgroups, and group B had 17 isolates (14 clinical and 3 nonclinical isolates) in 10 subgroups. Interestingly, six of eight known vaginal isolates were group B, with four of those six being identical. Virulence of isolates was associated with membership in group A (P = 0.03). Comparison of known members of sibling species within the genus Saccharomyces, which cannot be distinguished by standard biochemical tests, showed that S. paradoxus, S. bayanus, and S. cerevisiae could be differentiated by RFLP analysis. Genetic analysis of the isolates forming viable spores showed that most group A isolates were diploid and members of the species S. cerevisiae. Those group A and B isolates unable to form viable spores may be diploid hybrids between Saccharomyces species. The group B isolates that formed viable spores were tetraploid and may also be interspecific hybrids. Overall, clinical isolates of Saccharomyces were very heterogeneous and exhibited little clonality. RFLP pattern analysis could be a useful method of demonstrating transmission in patients with infection or between environmental sources and patients.

Rapid characterization of wild and collection strains of the genus Zygosaccharomyces according to mitochondrial DNA patterns

Several wild and collection strains of the genus Zygosaccharomyces were characterized using a rapid and simple method of restriction analysis of mitochondrial DNA. Patterns obtained with three endonucleases (HaeIII, HinfI and RsaI) made it possible to differentiate each species and to identify the wild strains, isolated from the same spoiled concentrated must, as belonging to the species Z. rouxii. The HinfI restriction enzyme produced a strain-specific pattern which allowed us to recognize that the seven wild isolates belonged to only three strains.

Genomic reorganization between two sibling yeast species, Saccharomyces bayanus and Saccharomyces cerevisiae

Genomic comparison of two sibling yeast species, Saccharomyces bayanus and Saccharomyces cerevisiae, was performed by Southern blot analysis with various S. cerevisiae gene probes following electrophoretic karyotyping. Fifteen genes on chromosome IV of S. cerevisiae were examined and classified into two groups. Gene probes of CEN4 and TRP1, as well as six other genes located on the left arm of the chromosome hybridized to a 1100-kb chromosome of S. bayanus that is smaller than chromosome IV of S. cerevisiae. On the other hand, probes of seven genes located on the right arm of chromosome IV hybridized to a 1350-kb chromosome that is homeologous to chromosome IV, judging from its size. Two genes located on the left arm of chromosome II hybridized to the 1350-kb chromosome, while four genes on the right arm hybridized to the 1100-kb chromosome. These pieces of evidence indicate that chromosomes II and IV of S. cerevisiae are rearranged into 1350-kb and 1100-kb chromosomes in S. bayanus. Furthermore, it is suggested that chromosome XV is rearranged into two chromosomes (800 and 850 kb in size) in S. bayanus. The translocation points of chromosomes II and IV were delimited using S. cerevisiae prime clone membranes. The results indicated that the translocation points are located close to the FUR4 locus on chromosome II and close to the RAD57 locus on chromosome IV.

Molecular characterization and identification of Saprolegnia by restriction analysis of genes coding for ribosomal RNA

Restriction fragment length polymorphisms (RFLPs) in two regions of the ribosomal DNA (rDNA) repeat unit were examined in 33 strains representing 18 species of Saprolegnia. The Polymerase Chain Reaction (PCR) was used to separately amplify the 18S rDNA and the region spanning the two internal transcribed spacers (ITS) and the 5.8S ribosomal RNA gene. Amplified products were subjected to a battery of restriction endonucleases to generate various fingerprints. The internal transcribed spacer region exhibited more variability than the 18S rDNA and yielded distinctive profiles for most of the species examined. Most of the species showing 100% similarity for the 18S rDNA could be distinguished by 5.8S + ITS restriction polymorphisms except for S. hypogyna, S. delica, S. lapponica, and S. mixta. The rDNA data indicate that S. lapponica and S. lapponica and S. mixta are conspecific with S. ferax, whereas there is no support for the proposed synonymies of S. diclina with S. delica and of S. mixta with S. monoica. Results from cluster analysis of the two data sets were very consistent and tree topologies were the same, regardless of the clustering method used. A further examination of multiple strains in the S. diclina-S. parasitica complex showed that restriction profiles are conserved across different strains of S. parasitica originating from the U.K. and Japan. HhaI and BsaI restriction polymorphisms were observed in isolates from the U.S. and India. The endonuclease BstUI was diagnostic for S. parasitica, generating identical fingerprints for all stains regardless of host and geographic origin. Except for the atypical strain ATCC 36144, restriction patterns were also largely conserved in S. diclina. Correlation of the rDNA data with morphological and ultrastructural features showed that S. diclina and S. parasitica are not conspecific. Restriction polymorphisms in PCR-amplified rDNA provide a molecular basis for the classification of Saprolegnia and will be useful for the identification of strains that fail to produce antheridia and oogonia.

PCR-ribotyping of type isolates of currently accepted Exophiala and Phaeococcomyces species

Portion of the ribosomal repeat of the type strains of the genera Exophiala and Phaeococcomyces were subjected to RFLP analysis. The amplicon length of the small subunit rRNA, the fragment NS1-NS24, was found to vary between 1800 to 3200 nucleotides. In contrast, the length of the fragment ITS1-ITS4 comprising the internal transcribed spacers (ITS1 and ITS2) was found to be constant at 600 nucleotides. Analysis of restriction profiles confirmed the synonymy of Exophiala dermatitidis and Mycotorula schawaii. Torula bergeri and Sporotrichum gougerotii were found to be identical to Phaeoannellomyces elegans, but different from their alleged synonym E. castellanii. A phenogram is presented.

Phylogenetic relationships among anuran trypanosomes as revealed by riboprinting

Twenty trypanosome isolates from Anura (frogs and toads) assigned to several species were characterized by riboprinting-restriction enzyme digestion of polymerase chain reaction amplified small subunit ribosomal RNA genes. Restriction site polymorphisms allowed distinction of all the recognized species and no intraspecific variation in riboprint patterns was detected. Phylogenetic reconstruction using parsimony and distance estimates based on restriction fragment comigration showed Trypanosoma chattoni to be only distantly related to the other species, while T. ranarum and T. fallisi appear to be sister taxa despite showing non-overlapping host specificities.

Saccharomyces species assignment by long range ribotyping

Type strains of 10 genotypically distinct Saccharomyces species are differentiated by ribosomal DNA restriction fragment analysis (ribotyping). The full length of the chromosomal ribosomal repeat was amplified in two parts, the 18SrDNA including both ITS region (2600 bp) and the 25SrDNA (3300 bp). Restriction fragments generated by 9 enzymes from these two products yield characteristic patterns, by which unknown Saccharomyces isolates are assigned to the type strains. For convenient separation and detection only fragments longer than 200 bp were monitored. In contrast to molecular differentiation methods of highest resolution as RAPD-PCR or fingerprinting, the results from ribotyping are absolutely reproducible and thereby suitable for databases. The phylogeny computed from the discrete character matrix for presence/absence of fragments by the PHYLIP program package is in complete accordance to the phylogeny derived from ribosomal RNA sequence analysis. By this the field of application of the long range ribotyping can be regarded basically as equal to DNA sequence analysis of the same locus. Because distant relationships are recognized, misidentified genera were detected upon the species assignment. This cannot be done by methods of higher resolution like RAPD-PCR or fingerprinting.

Physical constitution of ribosomal genes in common strains of Saccharomyces cerevisiae

Several recent investigations, employing restriction endonucleases that do not cleave within rDNA units, revealed that a number of laboratory strains of Saccharomyces cerevisiae apparently contains a single tandem array of approximately 50 to 200 rDNA units on each chromosome XII homolog. The number of these rDNA units varies from strain to strain, among subclones of the same strain, and after different conditions of growth. In contrast, the commonly-used strain S288C and its derivatives contain two clusters on each chromosome XII homolog. Although the two clusters are stably maintained, the number of rDNA units within each cluster can vary as in strains with single clusters.

Use of electrophoretic karyotyping and DNA-DNA hybridization in yeast identification

Contour-clamped homogeneous electric field (CHEF) gel electrophoresis was used to separate intact, chromosome-size DNA of different species of Saccharomyces and Zygosaccharomyces. Strains of the same Saccharomyces species had similar electrophoretic karyotypes. However, reproducible differences between individual bands indicated that strain-specific chromosome length polymorphism (CLP) is widely spread in these organisms. Strains of Zygosaccharomyces spp. showed karyotype differences beyond chromosome length polymorphism. A new, DNA-DNA hybridization technique was developed to test conspecificity, using individual chromosomes as templates to prepare randomly primed, radioactive probes. Under our conditions of stringency, species and chromosome-specific hybridization reactions were achieved with these probes. Using isolated chromosomes of Sacch. cerevisiae, Sacch. bayanus, and Zygosacch. rouxii as templates for probe preparation, conspecificity of strains was established, and closely related yeast species were distinguished with high reproducibility. This method is an efficient tool for studying genetic diversity of a given yeast species. Also, it can assist in yeast species identification and taxonomy.

Restriction polymorphisms in the internal transcribed spacers and 5.8S rDNA ofSaccharomyces

Polymorphisms in enzymatically amplified ribosomal DNA (rDNA) were examined in 18 strains of Saccharomyces. Restriction patterns generated from the region spanning the internal transcribed spacers (ITS) and the 5.8S rDNA produced two clusters corresponding to S. bayanus and S. cerevisiae. The type culture of S. carlsbergensis (ATCC 76529), which could not be separated from the S. cerevisiae group by small subunit (SSU) rDNA patterns, showed a ScrfI profile that was distinct from all the other strains. The type culture of S. intermedius var. turicensis (ATCC 76519) is assigned to S. bayanus on the basis of the combined results of SSU and ITS restriction analyses. S. kluyveri occurred at a separate branch of the distance tree and is unrelated to any of the strains. Results were in general agreement with reported DNA homologies and are discussed in relation to other molecular and genetic data.