非常规酵母基因工程表达系统

非常规酵母系指除了酿酒酵母与粟裂殖酵母之外的酵母曹。非常规酵母可利用其自主复制序列构建载体,但整合载体是进行外源基因导入的主要方式。非常规酵母的转化有一定的宿主范围,可采用与酿酒酵母相同的方法,最常用的仍为化学法。高效表达元件可利用酿酒酵母的强启动子,也可以根据非常规酵母菌的代谢特点寻找强启动子．本文综述了近年来应用非常规酵母基因表达系统表达外源基因的一些实例。     

Detection of Helicobacter pylori-specific genes in the oral yeast

BACKGROUNDS: Until today, human stomach is the only recognized habitat of Helicobacter pylori. However, recruitment of DNA-based methods has made possible the detection of H. pylori in water and oral cavity, thus suggesting fecal-oral and oral-oral routes for transmission of H. pylori, respectively. In this study, yeast has been proposed as a common vector for transmission of H. pylori. Thus designed primers were recruited to target 16S rDNA and cagA genes in the oral yeasts by PCR. MATERIALS AND METHODS: Eighteen yeasts were examined microscopically for the presence of bacterial-like bodies. DNAs were extracted from oral yeasts using phenol-chloroform method. Amplification conditions were optimized as 33 cycles and annealing temperatures of 63 degrees C for 16S rDNA and 51 degrees C and 52 degrees C for cagA gene which was targeted in two steps. DNAs of H. pylori and Saccharomyces cerevisiae were used as controls. Polymerase chain reaction (PCR) products of two genes from one yeast and from H. pylori were cloned in pCAP and subsequently subcloned in pSK+ and were sequenced. RESULTS: Bacterial-like bodies were observed in all oral yeasts. The amplified products of 16S rDNA from all oral yeasts were homologous in size with those of H. pylori. Fifteen out of eighteen (83%) yeasts contained cagA gene, homologous to H. pylori. CagA was not amplified from three yeasts and S. cerevisiae. Analysis of the sequenced products of 16S rDNA and cagA from one oral yeast showed 98% homology with those of H. pylori. CONCLUSIONS: The presence of H. pylori inside the yeast was indicated by light microscopy and PCR. It appears that yeasts, which are abundant in nature and thrive the mucosal surfaces of human, might serve as reservoirs and vehicles of H. pylori.     

Transformation in fungi.

Transformation with exogenous deoxyribonucleic acid (DNA) now appears to be possible with all fungal species, or at least all that can be grown in culture. This field of research is at present dominated by Saccharomyces cerevisiae and two filamentous members of the class Ascomycetes, Aspergillus nidulans and Neurospora crassa, with substantial contributions also from fission yeast (Schizosaccharomyces pombe) and another filamentous member of the class Ascomycetes, Podospora anserina. However, transformation has been demonstrated, and will no doubt be extensively used, in representatives of most of the main fungal classes, including Phycomycetes, Basidiomycetes (the order Agaricales and Ustilago species), and a number of the Fungi Imperfecti. The list includes a number of plant pathogens, and transformation is likely to become important in the analysis of the molecular basis of pathogenicity. Transformation may be maintained either by using an autonomously replicating plasmid as a vehicle for the transforming DNA or through integration of the DNA into the chromosomes. In S. cerevisiae and other yeasts, a variety of autonomously replicating plasmids have been used successfully, some of them designed for use as shuttle vectors for Escherichia coli as well as for yeast transformation. Suitable plasmids are not yet available for use in filamentous fungi, in which stable transformation is dependent on chromosomal integration. In Saccharomyces cerevisiae, integration of transforming DNA is virtually always by homology; in filamentous fungi, in contrast, it occurs just as frequently at nonhomologous (ectopic) chromosomal sites. The main importance of transformation in fungi at present is in connection with gene cloning and the analysis of gene function. The most advanced work is being done with S. cerevisiae, in which the virtual restriction of stable DNA integration to homologous chromosome loci enables gene disruption and gene replacement to be carried out with greater precision and efficiency than is possible in other species that show a high proportion of DNA integration events at nonhomologous (ectopic) sites. With a little more trouble, however, the methodology pioneered for S. cerevisiae can be applied to other fungi too. Transformation of fungi with DNA constructs designed for high gene expression and efficient secretion of gene products appears to have great commercial potential.     

Transformation in fungi.

Transformation with exogenous deoxyribonucleic acid (DNA) now appears to be possible with all fungal species, or at least all that can be grown in culture. This field of research is at present dominated by Saccharomyces cerevisiae and two filamentous members of the class Ascomycetes, Aspergillus nidulans and Neurospora crassa, with substantial contributions also from fission yeast (Schizosaccharomyces pombe) and another filamentous member of the class Ascomycetes, Podospora anserina. However, transformation has been demonstrated, and will no doubt be extensively used, in representatives of most of the main fungal classes, including Phycomycetes, Basidiomycetes (the order Agaricales and Ustilago species), and a number of the Fungi Imperfecti. The list includes a number of plant pathogens, and transformation is likely to become important in the analysis of the molecular basis of pathogenicity. Transformation may be maintained either by using an autonomously replicating plasmid as a vehicle for the transforming DNA or through integration of the DNA into the chromosomes. In S. cerevisiae and other yeasts, a variety of autonomously replicating plasmids have been used successfully, some of them designed for use as shuttle vectors for Escherichia coli as well as for yeast transformation. Suitable plasmids are not yet available for use in filamentous fungi, in which stable transformation is dependent on chromosomal integration. In Saccharomyces cerevisiae, integration of transforming DNA is virtually always by homology; in filamentous fungi, in contrast, it occurs just as frequently at nonhomologous (ectopic) chromosomal sites. The main importance of transformation in fungi at present is in connection with gene cloning and the analysis of gene function. The most advanced work is being done with S. cerevisiae, in which the virtual restriction of stable DNA integration to homologous chromosome loci enables gene disruption and gene replacement to be carried out with greater precision and efficiency than is possible in other species that show a high proportion of DNA integration events at nonhomologous (ectopic) sites. With a little more trouble, however, the methodology pioneered for S. cerevisiae can be applied to other fungi too. Transformation of fungi with DNA constructs designed for high gene expression and efficient secretion of gene products appears to have great commercial potential.     

Yeasts acquire resistance secondary to antifungal drug treatment by adaptive mutagenesis

Acquisition of resistance secondary to treatment both by microorganisms and by tumor cells is a major public health concern. Several species of bacteria acquire resistance to various antibiotics through stress-induced responses that have an adaptive mutagenesis effect. So far, adaptive mutagenesis in yeast has only been described when the stress is nutrient deprivation. Here, we hypothesized that adaptive mutagenesis in yeast (Saccharomyces cerevisiae and Candida albicans as model organisms) would also take place in response to antifungal agents (5-fluorocytosine or flucytosine, 5-FC, and caspofungin, CSP), giving rise to resistance secondary to treatment with these agents. We have developed a clinically relevant model where both yeasts acquire resistance when exposed to these agents. Stressful lifestyle associated mutation (SLAM) experiments show that the adaptive mutation frequencies are 20 (S. cerevisiae -5-FC), 600 (C. albicans -5-FC) or 1000 (S. cerevisiae - CSP) fold higher than the spontaneous mutation frequency, the experimental data for C. albicans -5-FC being in agreement with the clinical data of acquisition of resistance secondary to treatment. The spectrum of mutations in the S. cerevisiae -5-FC model differs between spontaneous and acquired, indicating that the molecular mechanisms that generate them are different. Remarkably, in the acquired mutations, an ectopic intrachromosomal recombination with an 87% homologous gene takes place with a high frequency. In conclusion, we present here a clinically relevant adaptive mutation model that fulfils the conditions reported previously.     

Seasonal occurrence of yeasts and yeast-like organisms in the river Danube

One hundred and seventy yeast strains belonging to 14 genera and 29 species were isolated from 112 water samples of the river Danube in the area of Bratislava. The samples were collected through the year from April to March.Saccharomyces cerevisiae, Candida maltosa, Aureobasidium pullulans, Cystofilobasidium capitatum, Rhodotorula glutinis, Geotrichum candidum, and Candida krusei were the most frequent. The basidiomycetous yeasts and yeast-like organisms with oxidative metabolism were present in approximately equal numbers to those with fermentative metabolism. Saccharomyces cerevisiae was the dominant yeast and was isolated from 50% of all samples examined and represented approximately one quarter of the yeast community.Yeast densities ranged from 100 to 21,100 CFU per litre. The highest population density was observed in October. Cryptococcus albidus, Saccharomyces cerevisiae, Rhodotorula glutinis, and Aureobasidium pullulans formed the main part of the yeast population in this month.     

Short Communication: Characterization and succession of yeast populations associated with spontaneous fermentations during the production of Brazilian sugar-cane aguardente

A succession of yeasts was observed during fermentation of aguardente with Saccharomyces cerevisiae being the predominant species. Candida sake, Kluyveromyces marxianus var. drosophilarum and apiculate yeasts were also frequent. Transient yeast species were found in variable numbers, probably due to the daily addition of sugar-cane juice. Killer yeasts were isolated and may have a role in the exclusion of some transient and contaminant species.     

Integration of an insertion-type transferred DNA vector from Agrobacterium tumefaciens into the Saccharomyces cerevisiae genome by gap repair.

Recently, it was shown that Agrobacterium tumefaciens can transfer transferred DNA (T-DNA) to Saccharomyces cerevisiae and that this T-DNA, when used as a replacement vector, is integrated via homologous recombination into the yeast genome. To test whether T-DNA can be a suitable substrate for integration via the gap repair mechanism as well, a model system developed for detection of homologous recombination events in plants was transferred to S. cerevisiae. Analysis of the yeast transformants revealed that an insertion type T-DNA vector can indeed be integrated via gap repair. Interestingly, the transformation frequency and the type of recombination events turned out to depend strongly on the orientation of the insert between the borders in such an insertion type T-DNA vector.     

Molecular identification of wine yeasts at species or strain level: a case study with strains from two vine-growing areas of Greece

The composition of wine yeast populations, present during spontaneous fermentation of musts from two wine-producing areas of Greece (Amyndeon and Santorini) and followed for two consecutive years, were studied using a range of molecular techniques. Internal Transcribed Spacer (ITS) ribotyping was convincingly applied for yeast species identification, proving its usefulness as a reliable tool for the rapid characterization of species composition in yeast population studies. Restriction Fragment Length Polymorphism (RFLP) of mitochondrial DNA (mtDNA) was shown to be a convenient criterion for the detection of intraspecies genetic diversity of both Saccharomyces and non-Saccharomyces isolate populations. Similarly, polymorphism of amplified delta interspersed element sequences provided an additional criterion for S. cerevisiae strain differentiation. Comparative analysis of S. cerevisiae genetic diversity, using mtDNA restriction patterns and delta-amplification profiles, showed a similar discriminative power of the two techniques. However, by combining these approaches it was possible to distinguish/characterize strains of the same species and draw useful conclusions about yeast diversity during alcoholic fermentation. The most significant findings in population dynamics of yeasts in the spontaneous fermentations were (i) almost complete absence of non-S.cerevisiae species from fermentations of must originating from the island Santorini, (ii) a well recorded strain polymorphism in populations of non-Saccharomyces species originating from Amyndeon and (iii) an unexpected polymorphism concerning S. cerevisiae populations, much greater than ever reported before in similar studies with wine yeasts of other geographical regions.     

Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts

In a quantitative comparative study, we elucidated the glucose metabolism in fourteen hemiascomycetous yeasts from the Genolevures project. The metabolic networks of these different species were first established by (13)C-labeling data and the inventory of the genomes. This information was subsequently used for metabolic-flux ratio analysis to quantify the intracellular carbon flux distributions in these yeast species. Firstly, we found that compartmentation of amino acid biosynthesis in most species was identical to that in Saccharomyces cerevisiae. Exceptions were the mitochondrial origin of aspartate biosynthesis in Yarrowia lipolytica and the cytosolic origin of alanine biosynthesis in S. kluyveri. Secondly, the control of flux through the TCA cycle was inversely correlated with the ethanol production rate, with S. cerevisiae being the yeast with the highest ethanol production capacity. The classification between respiratory and respiro-fermentative metabolism, however, was not qualitatively exclusive but quantitatively gradual. Thirdly, the flux through the pentose phosphate (PP) pathway was correlated to the yield of biomass, suggesting a balanced production and consumption of NADPH. Generally, this implies the lack of active transhydrogenase-like activities in hemiascomycetous yeasts under the tested growth condition, with Pichia angusta as the sole exception. In the latter case, about 40% of the NADPH was produced in the PP pathway in excess of the requirements for biomass production, which strongly suggests the operation of a yet unidentified mechanism for NADPH reoxidation in this species. In most yeasts, the PP pathway activity appears to be driven exclusively by the demand for NADPH.     

Gene expression and biochemical analysis of cheese-ripening yeasts: focus on catabolism of L-methionine, lactate, and lactose

DNA microarrays of 86 genes from the yeasts Debaryomyces hansenii, Kluyveromyces marxianus, and Yarrowia lipolytica were developed to determine which genes were expressed in a medium mimicking a cheese-ripening environment. These genes were selected for potential involvement in lactose/lactate catabolism and the biosynthesis of sulfur-flavored compounds. Hybridization conditions to follow specifically the expression of homologous genes belonging to different species were set up. The microarray was first validated on pure cultures of each yeast; no interspecies cross-hybridization was observed. Expression patterns of targeted genes were studied in pure cultures of each yeast, as well as in coculture, and compared to biochemical data. As expected, a high expression of the LAC genes of K. marxianus was observed. This is a yeast that efficiently degrades lactose. Several lactate dehydrogenase-encoding genes were also expressed essentially in D. hansenii and K. marxianus, which are two efficient deacidifying yeasts in cheese ripening. A set of genes possibly involved in l-methionine catabolism was also used on the array. Y. lipolytica, which efficiently assimilates l-methionine, also exhibited a high expression of the Saccharomyces cerevisiae orthologs BAT2 and ARO8, which are involved in the l-methionine degradation pathway. Our data provide the first evidence that the use of a multispecies microarray could be a powerful tool to investigate targeted metabolism and possible metabolic interactions between species within microbial cocultures.     

Molecular mechanisms of insertional mutagenesis in yeasts and mycelium fungi

Random insertional mutagenesis is an efficient tool for studying molecular mechanisms of many genetically determined processes. An improved variant of this method is REMI (Restriction Enzyme Mediated Integration) mutagenesis. In this method, the insertion cassette is introduced into the recipient cell together with restriction endonuclease. As a result, the REMI cassette insertion occurs in sites recognized by the restriction enzyme. The use of restriction endonucleases enhances transformation rate and provides cassette insertion in virtually any locus. A mutation is tagged by the insertion cassette, which can be identified by isolating the REMI cassette together with the flanking genomic DNA regions. The review describes general requirements to REMI. The mechanisms of REMI mutagenesis are surveyed with special reference to yeast Saccharomyces cerevisiae. Special attention is given to the development and use of REMI for other lower eukaryotes (yeasts and mould fungi). Drawbacks of the method and perspectives of its use are discussed.     

Yeast orthologues associated with glycerol transport and metabolism

Glycerol is a key compound in the regulation of several metabolic pathways in Saccharomyces cerevisiae. From this yeast most of the genes involved in glycerol consumption, production and transport are now available. Some of the mechanisms involving glycerol metabolism and transport are common to other yeasts. This work presents a search for GPD1/2, GUT1, GUP1/2 and FPS1 orthologues in a series of hemiascomycetous yeasts. All the genes cloned were able to complement S. cerevisiae mutant phenotypes and presented a high degree of similarity to the corresponding genes in this yeast. A phylogenetic analysis is presented. The allocation of GUP genes in the membrane bound O-acyl transferases (MBOAT) family is suggested as more consistent than their inclusion in the TC-DB/glycerol uptake family.     

Chimeric types of chromosome X in bottom-fermenting yeasts

Aim:  To determine the structure of the chimeric chromosome X of bottom-fermenting yeasts.
Methods and Results:  Eight cosmid clones carrying DNA from chromosome X of bottom-fermenting yeasts were selected by end-sequencing. Four of the cosmid clones had Saccharomyces cerevisiae (SC)-type and Saccharomyces bayanus (SB)-type chimeric ends, two had SC-type ends and two had SB-type ends. Sequencing revealed that the bottom-fermenting yeast strains in this study had four types of chromosome X: SC–SC, SC–SB, SB–SC and SB–SB. The translocation site in the chimeric chromosome is conserved among bottom-fermenting yeast strains, and was created by homologous recombination within a region of high sequence identity between the SC-type sequence and the SB-type sequence.
Conclusions:  Existing bottom-fermenting yeast strains share a common ancestor in which the chimeric chromosome X was generated.
Significance and Impact of the Study:  The knowledge gained in this study sheds light on the evolution of bottom-fermenting yeasts.     

Biodiversity and conservation of yeasts

In the framework of initiatives, aiming at a better definition of biodiversity in microorganisms and of its role in ecosystem function, the biology of yeasts is revisited with particular emphasis on their ecology and classification. The limited number of different species isolated from, as well as the exceedingly low yeast cell counts in, most natural environments are discussed and possible explanations presented. The impact of the use of molecular taxonomic techniques of classification on the extent of biodiversity within yeasts is also debated, as well as the possible repercussions of more aggressive pre-isolation treatments of samples.     

The expanding realm of ballistosporous yeasts

The recent progress in the systematics of ballistosporous yeasts is discussed. The extensive isolation studies carried out in the last decade resulted in a marked increase in the number of ballistosporous yeast species which now number nearly fifty. The increased number of species has expanded the complexity of taxonomic properties in the following ways: expansion of the range of mol% G+C of nuclear DNA to 39–68.5, thus overlapping that of all basidiomycetous yeasts; increased complexity of conidiogenesis with the finding of the generaBallistosporomyces andKockovaella. Based on partial sequencing of 18S ribosomal RNA (positions 1451–1618 inSaccharomyces cerevisiae), it is suggested that mode of conidiogenesis has little value for defining genera. Consequently, ballistosporous yeasts merely represent the ballistosporous stage of various taxa which cover the whole evolutionary spectrum of basidiomycetous yeasts. The importance of continuing isolation of ballistosporous yeasts is stressed, which together with molecular studies, will aid further progress in the systematics of basidiomycetous yeasts.     

The intron of the mitochondrial 21S rRNA gene: distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae

We have screened numerous different yeast species for the presence of sequences homologous to the intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae (intron r1) and found them in all Kluyveromyces species, some of the Saccharomyces species and none of the other yeasts tested. We have determined the nucleotide sequence of the r1-intron in K. thermotolerans and compared it with that of S. cerevisiae. The two introns are inserted at the same position within the 21S rRNA gene. They contain homologous internal open reading frames (ORFs) initiated at the same AUG codon which can be aligned over their entire length. Several silent multi-substitutions indicate that these intronic ORFs represent selectively conserved functional genes. Other intron segments, on the contrary, reveal short blocks of extensive homology separated by non-homologous stretches and/or additions-deletions. Comparison of our two yeast r1-introns with equivalent introns of N. crassa and A. nidulans mitochondria reveals that introns with very similar RNA secondary structures can accommodate different types of ORFs.     

Massive isolation of anamorphous ascomycete yeasts <Emphasis Type="Italic">Candida oleophila</Emphasis> from plant phyllosphere

Many years of research has confirmed a wide distribution of anamorphous ascomycete yeasts in the phyllosphere of diverse plants of Moscow and the Moscow oblast. Based on the standard morphological and physiological criteria, on the results of restriction analysis of the 5.8S-ITS rDNA region, and on the sequencing of the D1D2 region of 26S rDNA, these yeasts were identified as Candida oleophila Montrocher. Previous isolation of this species has been rare, possibly due to its incorrect identification. This species, together with phytobiotic basidiomycete yeasts, was shown to be dominant in the yeast epiphytic communities on the surface parts of plants. The relative abundance of C. oleophila is highest on plant fruits and increases significantly by the end of the vegetation period. Wide occurrence of this yeast species on fruits and in the phyllosphere may be related to its ability to compete with rapidly growing phytopathogenic fungi.     

Competition for glucose between the yeasts Saccharomyces cerevisiae and Candida utilis.

The competition between the yeasts Saccharomyces cerevisiae CBS 8066 and Candida utilis CBS 621 for glucose was studied in sugar-limited chemostat cultures. Under aerobic conditions, C. utilis always successfully completed against S. cerevisiae. Only under anaerobic conditions did S. cerevisiae become the dominant species. The rationale behind these observations probably is that under aerobic glucose-limited conditions, high-affinity glucose/proton symporters are present in C. utilis, whereas in S. cerevisiae, glucose transport occurs via facilitated diffusion with low-affinity carriers. Our results explain the frequent occurrence of infections by Crabtree-negative yeasts during bakers' yeast production.