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Buerth C, Tielker D, Ernst JF. Candida utilis and Cyberlindnera (Pichia) jadinii: yeast relatives with expanding applications. Appl Microbiol Biotechnol 2016; 100:6981-90. [DOI: 10.1007/s00253-016-7700-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 11/29/2022]
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The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms. J Biotechnol 2015; 211:20-30. [PMID: 26150016 DOI: 10.1016/j.jbiotec.2015.06.423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/18/2015] [Accepted: 06/29/2015] [Indexed: 11/22/2022]
Abstract
The yeast Cyberlindnera jadinii is a close relative of Candida utilis that is being used in the food and feed industries. Here, we present the 12.7Mb genome sequence of C. jadinii strain CBS 1600 generated by next generation sequencing. The deduced draft genome sequence consists of seven large scaffolds analogous to the seven largest chromosomes of C. utilis. An automated annotation of the C. jadinii genome identified 6147 protein-coding sequences. The level of ploidy for both genomes was analyzed by calling single nucleotide polymorphisms (SNPs) and was verified measuring nuclear DNA contents by florescence activated cell sorting (FACS). Both analyses determined the level of ploidy to diploid for C. jadinii and to triploid for C. utilis. However, SNP calling for C. jadinii also identified scaffold regions that seem to be haploid, triploid or tetraploid.
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Chang CF, Yao CH, Young SS, Limtong S, Kaewwichian R, Srisuk N, Lee CF. Candida gosingica sp. nov., an anamorphic ascomycetous yeast closely related to Scheffersomyces spartinae. Int J Syst Evol Microbiol 2010; 61:690-694. [PMID: 20382788 DOI: 10.1099/ijs.0.020511-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During surveys on yeast diversity in forest soils from Taiwan and Thailand, ten yeast strains isolated from different samples were found to have similar molecular and physiological characteristics. Sequence analysis of small subunit (SSU) rDNA, the D1/D2 domain of large subunit (LSU) rDNA and internal transcribed spacer (ITS)-5.8S rDNA demonstrated that these strains were closely related to Scheffersomyces spartinae. The novel strains could be differentiated from S. spartinae by a 0.9 % sequence divergence (5 substitutions, 0 gaps) in the D1/D2 domain of LSU rDNA, a 1.5 % divergence (8 substitutions, 0 gaps) in the ITS-5.8S rDNA and a 0.7 % divergence (12 substitutions, 2 gaps) in the SSU rDNA. The novel strains also showed specific patterns of electrophoretic karyotypes that differed from that of S. spartinae. Therefore, a novel yeast species, Candida gosingica sp. nov., is proposed to accommodate these strains. The type strain SJ7S11(T) (=BCRC 23194(T)=CBS 11433(T)) was assigned and deposited in the Bioresource Collection and Research Center (BCRC), Food Industry Development and Research Institute, Hsinchu, Taiwan, and Centraalbureau voor Schimmelcultures (CBS), Utrecht, The Netherlands.
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Affiliation(s)
- Chin-Feng Chang
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Rd, Hsinchu 30014, Taiwan
| | - Cheng-Hsu Yao
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Rd, Hsinchu 30014, Taiwan
| | - Shuh-Sen Young
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Rd, Hsinchu 30014, Taiwan
| | - Savitree Limtong
- Department of Microbiology, Kasetsart University, Bangkok 10900, Thailand
| | | | - Nantana Srisuk
- Department of Microbiology, Kasetsart University, Bangkok 10900, Thailand
| | - Ching-Fu Lee
- Department of Applied Science, National Hsinchu University of Education, 521 Nanda Rd, Hsinchu 30014, Taiwan
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Esteve-Zarzoso B, Zorman T, Belloch C, Querol A. Molecular Characterisation of the Species of the Genus Zygosaccharomyces. Syst Appl Microbiol 2003; 26:404-11. [PMID: 14529183 DOI: 10.1078/072320203322497437] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The restriction fragments polymorphisms of the mitochondrial DNA and the PCR fragment that comprised the internal transcribes spacers and the 5.8S rRNA gene, together with the electrophoretic karyotypes of 40 strains from the 10 species of the genus Zygosaccharomyces, including the new species Z. lentus were examined. The RFLP's of the ITS-5.8S region showed a specific restriction pattern for each species, including the new species Z. lentus. The only exception were the species Z. cidri and Z. fermentati that produced identical restriction profiles. The electrophoretic chromosome patterns confirmed the differences between the species of this genus, including the phylogenetic closest species Z. cidri and Z. fermentati. They present few chromosomes ranging from 3 bands (4 or 5 chromosomes) for Z. florentinus to 7 bands (8 to 10 chromosomes) for Z. cidri and Z. fermentati. The strain level resolution power of RFLP's of mtDNA of this genus enabled the characterisation of strains from the same species, even where they are isolated from the same substrate. However, in the cases of Z. bailii and Z. lentus, electrophoretic karyotyping there was considerable variation.
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MESH Headings
- Chromosomes, Fungal
- DNA, Fungal/analysis
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/genetics
- DNA, Ribosomal Spacer/analysis
- DNA, Ribosomal Spacer/genetics
- Genes, rRNA
- Karyotyping/methods
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 5.8S/analysis
- Zygosaccharomyces/classification
- Zygosaccharomyces/genetics
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Affiliation(s)
- Braulio Esteve-Zarzoso
- Departamento de Biotecnologia, Instituto de Agroquimica y Tecnologia de Alimentos (CSIC), Burjassot, Valincia, Spain
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Abstract
An elderly male was seen at an outpatient urology clinic over a period of 3 years with repeat urine specimens containing 10(4) to 10(5) CFU of a "Candida species, not C. albicans." The urine specimens were described as infected due to the presence of pyuria, but no antifungal therapy was administered. On two occasions, the patient presented to the emergency room and urine specimens were sent to the clinical microbiology laboratory. On both occasions, a yeast was isolated at concentrations of >10(5) CFU/ml. The organism was identified as the anamorphic yeast Candida utilis (teleomorph: Pichia jadinii) by conventional methods. Molecular methods, including karyotyping and restriction enzyme analysis, confirmed that the isolates were identical and were C. utilis. The patient developed benign prostatic hypertrophy and chronic obstructive pulmonary disease during the 3-year course. This report is the first demonstration of the isolation of the industrially important yeast C. utilis from a urinary tract infection. In the present case, the organism was associated with chronic, symptomatic disease. The significance of this unusual, low-virulence isolate from a case of urinary tract infection is discussed.
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Affiliation(s)
- K C Hazen
- Division of Clinical Microbiology, Department of Pathology, University of Virginia Medical Center, Charlottesville, Virginia 22908, USA.
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Abstract
The analysis of the electrophoretic chromosome patterns of the species of the genus Kluyveromyces, reveals a high polymorphism in size, number and intensity of bands. Different sets of electrophoresis running conditions were used to establish species-specific patterns and also to detect intraspecific variation. According to their karyotypes, the species of this genus can be divided into two major groups. The first group includes the species K. africanus, K. bacillisporus, K. delphensis, K. lodderae, K. phaffi, K. polysporus and K. yarrowii, composing the so-called 'Saccharomyces cerevisiae-like' group, because their karyotypes resemble that of the species S. cerevisiae. The second group comprises the species K. aestuarii, K. blattae, K. dobzhanskii, K. lactis, K. marxianus, K. thermotolerans, K. waltii and K. wickerhamii, whose chromosomal patterns exhibit common characteristics very different to those of the species included in the 'S. cerevisiae-like' group. This division is concordant with the position of these species in previous phylogenetic reconstructions. Additionally, the intraspecific analysis of the chromosome patterns show a rich polymorphism in the heterogeneous species K. dobzhanskii, K. lactis, and K. marxianus, which is in concordance with the variability observed with other phenotypic or genetic markers. On the contrary, K. thermotolerans exhibits a homogeneous karyotype indicative of a very low level of chromosomal polymorphism, which is congruent with the reduced variability found in this species with other molecular markers.
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Affiliation(s)
- C Belloch
- Colección Española de Cultivos Tipo, Universitat de València, Spain
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Kondo K, Saito T, Kajiwara S, Takagi M, Misawa N. A transformation system for the yeast Candida utilis: use of a modified endogenous ribosomal protein gene as a drug-resistant marker and ribosomal DNA as an integration target for vector DNA. J Bacteriol 1995; 177:7171-7. [PMID: 8522525 PMCID: PMC177597 DOI: 10.1128/jb.177.24.7171-7177.1995] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have developed a transformation system for the yeast Candida utilis. A novel strategy was applied to construct the transformation system, since auxotrophic mutants which could be used as hosts for transformation are not available. A gene encoding the ribosomal protein L41 was cloned from C. utilis, which is sensitive to cycloheximide, and used as a marker gene conferring cycloheximide resistance after modification of its amino acid sequence. The marker gene was constructed by substitution of the proline codon at position 56 with the glutamine codon by in vitro mutagenesis, as it had been reported previously that the 56th amino acid residue of L41 is responsible for the cycloheximide sensitivity of various organisms (S. Kawai, S. Murao, M. Mochizuki, I. Shibuya, K. Yano, and M. Takagi, J. Bacteriol. 174:254-262 1992). The ribosomal DNA (i.e., DNA coding for rRNA) of C. utilis was also cloned and used as a multiple-copy target for the integration of vector DNA into the genome, which resulted in a high transformation efficiency. Transformants were obtained by electroporation with a maximum efficiency of approximately 1,400 transformants per 1 microgram of linearized DNA carrying the gene for cycloheximide resistance and part of the ribosomal DNA. No transformants were obtained with intact plasmids. Multiple copies of the linearized plasmid were integrated into the host chromosome by homologous recombination. Southern analysis of the transformants in which vector DNA was integrated at the L41 gene locus indicated that there are two copies of gene for the L41 protein per cell, suggesting that C. utilis is diploid. Transformants were obtained from a variety of C. utilis strains, indicating that this method is applicable to the transformation of other C. utilis strains, even though there is significant heterogeneity in chromosomal karyotypes among these strains.
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Affiliation(s)
- K Kondo
- Central Laboratories for Key Technology, Kirin Brewery Co., Ltd., Kanagawa, Japan
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Filipp D, Filipp P, Nosek J, Hladká M. Electrophoretic karyotype of Dipodascus (Endomyces) magnusii: two main intraspecific chromosomal polymorphisms associated with the difference in total genome size. Curr Genet 1995; 29:81-7. [PMID: 8595662 DOI: 10.1007/bf00313197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This study describes the karyotype of strain 270 of the yeast-like fungus Endomyces magnusii. It consists of 13 chromosomal DNA molecules, the size of which range between 1.2 and 5.7Mb producing a genome size of approximately 38Mb. By comparing the karyotype of six strains of E. magnusii, we revealed two main chromosome length polymorphisms (CLPs) associated with a pronounced difference in the total genome size (roughly 50%). Karyotype heterogeneity between two main CLPs was demonstrated by Southern analysis with three heterologous probes. The same species affiliation of six E. magnusii strains was confirmed by morphological and cytological studies, protein fingerprint comparisons, as well as restriction analysis of mitochondrial DNA and genomic Southern analysis.
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Affiliation(s)
- D Filipp
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B1, 842 15 Bratislava, Slovakia
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Abstract
The examination of fungal chromosomes by pulsed-field gel electrophoresis has revealed that length polymorphism is widespread in both sexual and asexual species. This review summarizes characteristics of fungal chromosome-length polymorphism and possible mitotic and meiotic mechanisms of chromosome length change. Most fungal chromosome-length polymorphisms are currently uncharacterized with respect to content and origin. However, it is clear that long tandem repeats, such as tracts of rRNA genes, are frequently variable in length and that other chromosomal rearrangements are suppressed during normal mitotic growth. Dispensable chromosomes and dispensable chromosome regions, which have been well documented for some fungi, also contribute to the variability of the fungal karyotype. For sexual species, meiotic recombination increases the overall karyotypic variability in a population while suppressing genetic translocations. The range of karyotypes observed in fungi indicates that many karyotypic changes may be genetically neutral, at least under some conditions. In addition, new linkage combinations of genes may also be advantageous in allowing adaptation of fungi to new environments.
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Affiliation(s)
- M E Zolan
- Department of Biology, Indiana University, Bloomington 47405, USA
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Versavaud A, Hallet JN. Pulsed-field Gel Electrophoresis Combined with Rare-cutting Endonucleases for Strain Differentiation of Candida famata, Kloeckera apiculata and Schizosaccharomyces pombe with Chromosome Number and Size Estimation of the Two Former. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80401-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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