Telomeric and dispersed repeat sequences in Candida yeasts and their use in strain identification (original) (raw)
Related papers
Isolation and characterization of a repeated sequence (RPS1) of Candida albicans
Journal of General Microbiology, 1992
A repeated sequence, named RPSl, approximately 2 kb in size, is found mainly in chromosome 6, the second most variable chromosome among the eight chromosomes of Candida albicans. Most of the RPSl units of chromosome 6 seem to be located within a single region of about 100 kb in strain FC18. In both strains FC18 and NUM812, a part of RPSl is apparently tandemly repeated. A unit of RPSl has been cloned and sequenced. It consists of 2114 bp and has a GC content of 40 mol%. The repeat unit contains smaller repeats of about 80-170 bp which are called REP1, REP2, REP3, REP4 and REPS; REP2 is duplicated. The small repeats are classified into two groups by their homology. One comprises REP1, REP2 and REPS, and the other REP3 and REP4. They are termed the REP1 and REP3 families, respectively. The two families both contain a common 29 bp sequence, called COM29. The dispersed repetitive sequence R E 1 may be involved in chromosomal rearrangements and may in part explain chromosome polymorphism in C. albicans. The origin of RPSl was not determined.
Microbiology, 1998
A novel sequence designated HOK, which is next to the RPS, a repetitive sequence specific to Candida albicans, was cloned and sequenced. HOK hybridized with all of the chromosomes on which the RPSs were located, but did not hybridize with chromosome 3, which does not harbour any RPSs. Sequence determination revealed that a portion of HOK has significant homology with the B and C1 fragments of Ca3, which is used as a molecular epidemiological probe. A homology search of the deduced amino acids of HOK against the protein database showed partial homology with an isocitrate dehydrogenase of Saccharomyces cerevisiae, although an ORF large enough to encode the enzyme was not detected. To verify the existence of other sequences homologous with HOK, a portion of the HOK sequence was amplified using PCR. Sequence determination of the 41 clones from the PCR products resulted in at least six HOK-homologous clones. Another RPS-containing clone, RB2, was isolated from the Pstl-digested chromosom...
2002
Recent studies have demonstrated that a large number of organisms carry linear mitochondrial DNA molecules possessing specialized telomeric structures at their ends. Based on this specific structural feature of linear mitochondrial genomes, we have developed an approach for identification of the opportunistic yeast pathogen Candida parapsilosis. The strategy for identification of C. parapsilosis strains is based on PCR amplification of specific DNA sequences derived from the mitochondrial telomere region. This assay is complemented by immunodetection of a protein component of mitochondrial telomeres. The results demonstrate that mitochondrial telomeres represent specific molecular markers with potential applications in yeast diagnostics and taxonomy.
Effect of the Major Repeat Sequence on Chromosome Loss in Candida albicans
Eukaryotic Cell, 2005
The major repeat sequence (MRS) is found at least once on all but one chromosome in Candida albicans , but as yet it has no known relation to the phenotype. The MRS affects karyotypic variation by serving as a hot spot for chromosome translocation and by expanding and contracting internal repeats, thereby changing chromosome length. Thus, MRSs on different chromosomes and those on chromosome homologues can differ in size. We proposed that the MRS's unique repeat structure and, more specifically, the size of the MRS could also affect karyotypic variation by altering the frequency of mitotic nondisjunction. Subsequent analysis shows that both natural and artificially induced differences in the size of the chromosome 5 MRS can affect chromosome segregation. Strains with chromosome 5 homologues that differ in the size of the naturally occurring MRSs show a preferential loss of the homologue with the larger MRS on sorbose, indicating that a larger MRS leads to a higher risk of mitoti...
Analysis of the chromosomal localization of the repetitive sequences (RPSs) in Candida albicans
Microbiology, 1995
The location and organization of repetitive sequences, members of the RPS family, which are sequences specific to Candida albicans, were determined on each chromosome of C. albicans strain FC18. Using pulsed-field gel electrophoresis, we separated seven fractions from eight chromosomes. Each chromosome was cleaved by BamHl and Xhol to excise the RPSs, which were then detected by hybridization with an RPS probe. All chromosomes except chromosome 4 carried RPSs, and these RPSs were located within a limited region on each chromosome. From the digestion of each chromosome with Sfil and probing with the RPSs, we found that these recognition sites within the RPS region were conserved among all RPS-containing chromosomes. For further characterization of the RPSs, the locations and the boundary regions of the RPSs were examined on chromosome 6 of strain FC18 as a model chromosome. Using the restriction enzymes Sfil, Smal, Xhol, BamHI, MluI and Nrul, we constructed a semi-macro physical map of the RPSs and their boundary regions on this chromosome. We also determined which part of the RPS was adjacent to each boundary by using sub-fragments of RPS as probes. The physical configuration around the RPSs and their boundary regions are presented. The results obtained should be useful for future analysis of the function of these regions.
Yeast-specific DNA probes and their application for the detection of Candida albicans
Journal of Medical Microbiology, 1992
Two DNA fragments cloned from the genome of Candida albicans ATCC 10261 may be useful in the rapid diagnosis of disseminated candidosis. One sequence (probe EOB1) was specific for C. albicans (positive hybridisation with 45 strains tested). The second sequence (probe EOB2) detected C. albicans, as well as five other pathogenic Candida spp. and Saccharomyces cerevisiae, but did not react with human or bacterial DNA. Both probes were repetitive sequences in the genome of C. albicans. Probe EOBl was used to detect, without DNA amplification, 500 C. albicans yeast cells in 1 ml of human blood.
Journal of Bacteriology, 1987
Restriction fragment length polymorphisms in the ribosomal DNA (rDNA) have been shown to be a useful criterion for distinguishing among various isolates of Candida albicans. In a sample of 12 clinical isolates, we found six different classes based on variations in the fragments produced from genomic DNA by EcoRI and visualized after Southern transfer by being probed with a plasmid containing Saccharomyces cerevisiae rDNA. Some of the classes appeared to be heterozygous at the rDNA locus. Similar digestion of other Candida species showed that each could be identified on the basis of its restriction patterns. Since these are highly reiterated genes, the differences were apparent on ethidium bromide-stained gels; Southern transfers were not necessary. EcoRI restriction maps of the rDNA of C. albicans, C. stellatoidea, C. tropicalis, and C. guilliermondii were determined.
Japanese journal of infectious diseases, 2009
The nucleotide sequences of the inner repeats of the repetitive sequence (RPS), termed ALTs, of Candida albicans and its related species C. albicans var. stellatoidea and C. dubliniensis, were analyzed. ALT sequences were grouped into 4 types for C. albicans (Aa, Ab, Ac and Ad) and C. albicans var. stellatoidea (Sa1, Sa2, Sb, Sc and Sd), and 3 types for C. dubliniensis (Da, Db and Dc). In addition to the primer set P-II (specific to RPS), 2 primer sets (AS-I and AiR-I) specific to the nucleotide sequences of C. albicans ALT were designed and tested for their potential for RPS-based identification/genotyping of C. albicans. PCRs using AS-I and AiR-I clearly distinguished C. albicans from both C. albicans var. stellatoidea and C. dubliniensis. Furthermore, the strains of C. albicans that showed similar electrophoretic patterns in the PCR using P-II were discriminated at the subtype level. These results indicate that the PCRs using RPS- and ALT-specific primer sets are useful as simple...
Centromeric DNA sequences in the pathogenic yeast Candida albicans are all different and unique
Proceedings of The National Academy of Sciences, 2004
In an approach to clone and characterize centromeric DNA sequences of Candida albicans by chromatin immunoprecipitation, we have used antibodies directed against an evolutionarily conserved histone H3-like protein, CaCse4p (CENP-A homolog). Sequence analysis of clones obtained by this procedure reveals that only eight relatively small regions (Ϸ3 kb each) of the Can. albicans genome are selectively enriched. These CaCse4-bound sequences are located within 4-to 18-kb regions lacking ORFs and occur once in each of the eight chromosomes of Can. albicans. Binding of another evolutionarily conserved kinetochore protein, CaMif2p (CENP-C homolog), colocalizes with CaCse4p. Deletion of the CaCse4p-binding region of chromosome 7 results in a high rate of loss of the altered chromosome, confirming that CaCse4p, a centromeric histone in the CENP-A family, indeed identifies the functional centromeric DNA of Can. albicans. The CaCse4p-rich regions not only lack conserved DNA motifs of point (<400 bp) centromeres and repeated elements of regional (>40 kb) centromeres, but also each chromosome of Can. albicans contains a different and unique CaCse4p-rich centromeric DNA sequence, a centromeric property previously unobserved in other organisms.
Journal of Bacteriology, 1994
In a previous study, a repeated sequence, RPS1, was cloned from the genomic DNA of Candida albicans. It was 2.1 kb in length and was tandemly repeated in a limited region of almost all of the chromosomes. In this study, we examined and characterized the diversity of the repeating structure of the RPS units were of 2.1, 2.3, 2.5, and 2.9 kbp in length after digestion of the genomic DNA with SmaI and 2.1 and 2.3 kbp after digestion with PstI, with the differences being multiples of approximately 0.2 kbp. Moreover, one or two types of RPS unit were present specifically on each chromosome. We cloned 14 RPS units from the mixed DNA of chromosomes 1 and 2 and 59 RPS units from chromosome 6. These RPS units were classified into four types by their SfiI digestion profiles and chromosomal origins. Sequence comparisons revealed a tandem arrangement of internal, small repeating units of 172 bp. This unit of repetition was designated alt (C. albicans tandem repeating unit). The size of RPS unit...