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Adamczyk J, Deregowska A, Potocki L, Kuna E, Kaplan J, Pabian S, Kwiatkowska A, Lewinska A, Wnuk M. Relationships between rDNA, Nop1 and Sir complex in biotechnologically relevant distillery yeasts. Arch Microbiol 2016; 198:715-23. [PMID: 27329282 PMCID: PMC4969353 DOI: 10.1007/s00203-016-1258-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/26/2016] [Accepted: 06/09/2016] [Indexed: 11/30/2022]
Abstract
Distillery yeasts are poorly characterized physiological group among the Saccharomyces sensu stricto complex. As industrial yeasts are under constant environmental stress during fermentation processes and the nucleolus is a stress sensor, in the present study, nucleolus-related parameters were evaluated in 22 commercially available distillery yeast strains. Distillery yeasts were found to be a heterogeneous group with a variable content and length of rDNA and degree of nucleolus fragmentation. The levels of rDNA were negatively correlated with Nop1 (r = -0.59, p = 0.0038). Moreover, the protein levels of Sir transcriptional silencing complex and longevity regulators, namely Sir1, Sir2, Sir3 and Fob1, were studied and negative correlations between Sir2 and Nop1 (r = -0.45, p = 0.0332), and between Sir2 and Fob1 (r = -0.49, p = 0.0211) were revealed. In general, S. paradoxus group of distillery yeasts with higher rDNA pools and Sir2 level than S. bayanus group was found to be more tolerant to fermentation-associated stress stimuli, namely mild cold/heat stresses and KCl treatment. We postulate that rDNA state may be considered as a novel factor that may modulate a biotechnological process.
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Affiliation(s)
- Jagoda Adamczyk
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | - Anna Deregowska
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Leszek Potocki
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | - Ewelina Kuna
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | - Jakub Kaplan
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | - Sylwia Pabian
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland
| | | | - Anna Lewinska
- Department of Biochemistry and Cell Biology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
| | - Maciej Wnuk
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959, Rzeszow, Poland.
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Wnuk M, Miedziak B, Kulak K, Panek A, Golec E, Deregowska A, Adamczyk J, Lewinska A. Single-cell analysis of aneuploidy events using yeast whole chromosome painting probes (WCPPs). J Microbiol Methods 2015; 111:40-9. [PMID: 25639739 DOI: 10.1016/j.mimet.2015.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 01/27/2015] [Accepted: 01/27/2015] [Indexed: 11/18/2022]
Abstract
Aneuploidy is considered a widespread genetic variation in such cell populations as yeast strains, cell lines and cancer cells, and spontaneous changes in the chromosomal copy number may have implications for data interpretation. Thus, aneuploidy monitoring is essential during routine laboratory practice, especially while conducting biochemical and/or gene expression analyses. In the present study, we constructed a panel of whole chromosome painting probes (WCPPs) to monitor aneuploidy in a single yeast Saccharomyces cerevisiae cell. The WCPP-based system was validated using "normal" haploid and diploid cells, as well as disomic cells both with and without cell synchronisation. FISH that utilised WCPPs was combined with DNA cell cycle analysis (imaging cytometry) to provide a detailed analysis of signal variability during the cell cycle. Chromosome painting can be utilised to detect spontaneously formed disomic chromosomes and study aneuploidy-promoting conditions. For example, the frequency of disomic chromosomes was increased in cells lacking NAD(+)-dependent histone deacetylase Sir2p compared with wild-type cells (p<0.05). In conclusion, WCPPs may be considered to be a powerful molecular tool to identify individual genomic differences. Moreover, the WCPP-based system may be used at the single-cell level of analysis to supplement array-based techniques and high-throughput analyses at the population scale.
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Affiliation(s)
- Maciej Wnuk
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland.
| | - Beata Miedziak
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Klaudia Kulak
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Anita Panek
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Ewelina Golec
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Anna Deregowska
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Jagoda Adamczyk
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Anna Lewinska
- Department of Biochemistry and Cell Biology, University of Rzeszow, Poland
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Assessment of yeast chromosome XII instability: Single chromosome comet assay. Fungal Genet Biol 2014; 63:9-16. [DOI: 10.1016/j.fgb.2013.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/21/2013] [Accepted: 12/05/2013] [Indexed: 11/22/2022]
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Miyazaki T, Kobayashi T. Visualization of the dynamic behavior of ribosomal RNA gene repeats in living yeast cells. Genes Cells 2011; 16:491-502. [PMID: 21518153 DOI: 10.1111/j.1365-2443.2011.01506.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ribosomal RNA (rRNA) gene forms an extremely large repeat (rDNA) in the chromosome. In budding yeast, Saccharomyces cerevisiae, the rDNA is located on chromosome XII and occupies approximately 60% (1.5 Mb) of the chromosome and 10% of the total genome. The rDNA is composed of approximately 150 copies and produces rRNA that accounts for approximately 80% of the total RNA. Owing to its repetitive structure and high transcription activity, rDNA is recombinogenic. Thus, the repeat is a distinctive and unique region in the genome. To investigate the dynamic nature of the repeat during the cell division cycle, we developed yeast strains in which every rDNA repeat unit has lacO or tetO arrays that associate with LacI-GFP or TetR-mRFP proteins, respectively. In these strains, the entire repeat can be visualized in a living cell without the need for any special treatment. Analyses of these strains showed that the rDNA actively moved and changed shape at the boundary between the nucleolus and the nucleoplasm. At the G2/M phase, the associated sister chromatids of the rDNA formed a ring structure in the nucleolus that gave the appearance of 'rotating'. We also found that the length of the rDNA repeat affected the time taken for segregation during the M phase of cell cycle.
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Affiliation(s)
- Takaaki Miyazaki
- Division of Cytogenetics, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan
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Lewinska A, Wnuk M, Grzelak A, Bartosz G. Nucleolus as an oxidative stress sensor in the yeast Saccharomyces cerevisiae. Redox Rep 2010; 15:87-96. [PMID: 20500990 DOI: 10.1179/174329210x12650506623366] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In mammals, the nucleolus is thought to be a stress sensor; upon cellular stress conditions, a release of nucleolar proteins and down-regulation of rDNA transcription occurs. Since yeast Rrn3p is a homolog of the mammalian RNA polymerase I (Pol I)-specific transcription factor TIF-IA, we decided to investigate the role of Rrn3p in oxidant-induced nucleolar stress in yeast. We show that, after oxidant treatment, the level of Rrn3p is unaffected but Rrn3p is translocated from the nucleolus into the cytoplasm and a point mutation in the RRN3 gene leads to hypersensitivity of the yeast to oxidants. This hypersensitivity can be abolished by re-introduction of the active RRN3 gene, antioxidant supplementation and anoxic atmosphere. Additionally, we employed the PRINS technique to monitor oxidant-mediated changes in the nucleolar structure. Taken together, our results suggest the role of the yeast nucleolus in the response to oxidative stress signals.
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Affiliation(s)
- Anna Lewinska
- Department of Biochemistry and Cell Biology, University of Rzeszow, Pigonia 6, PL35-959 Rzeszow, Poland.
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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