1
|
Oliver SG. From Petri Plates to Petri Nets, a revolution in yeast biology. FEMS Yeast Res 2022; 22:6526310. [PMID: 35142857 PMCID: PMC8862034 DOI: 10.1093/femsyr/foac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| |
Collapse
|
2
|
Guo X, Pan B, Seo JE, Chen Y, Yan J, Mei N, Chen T. Whole genome sequencing analysis of small and large colony mutants from the mouse lymphoma assay. Arch Toxicol 2018; 92:3585-3595. [DOI: 10.1007/s00204-018-2318-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/19/2018] [Indexed: 11/25/2022]
|
3
|
Uršič K, Ogrizović M, Kordiš D, Natter K, Petrovič U. Tum1 is involved in the metabolism of sterol esters in Saccharomyces cerevisiae. BMC Microbiol 2017; 17:181. [PMID: 28830344 PMCID: PMC5567475 DOI: 10.1186/s12866-017-1088-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background The only hitherto known biological role of yeast Saccharomyces cerevisiae Tum1 protein is in the tRNA thiolation pathway. The mammalian homologue of the yeast TUM1 gene, the thiosulfate sulfurtransferase (a.k.a. rhodanese) Tst, has been proposed as an obesity-resistance and antidiabetic gene. To assess the role of Tum1 in cell metabolism and the putative functional connection between lipid metabolism and tRNA modification, we analysed evolutionary conservation of the rhodanese protein superfamily, investigated the role of Tum1 in lipid metabolism, and examined the phenotype of yeast strains expressing the mouse homologue of Tum1, TST. Results We analysed evolutionary relationships in the rhodanese superfamily and established that its members are widespread in bacteria, archaea and in all major eukaryotic groups. We found that the amount of sterol esters was significantly higher in the deletion strain tum1Δ than in the wild-type strain. Expression of the mouse TST protein in the deletion strain did not rescue this phenotype. Moreover, although Tum1 deficiency in the thiolation pathway was complemented by re-introducing TUM1, it was not complemented by the introduction of the mouse homologue Tst. We further showed that the tRNA thiolation pathway is not involved in the regulation of sterol ester content in S. cerevisiae, as overexpression of the tEUUC, tKUUU and tQUUG tRNAs did not rescue the lipid phenotype in the tum1Δ deletion strain, and, additionally, deletion of the key gene for the tRNA thiolation pathway, UBA4, did not affect sterol ester content. Conclusions The rhodanese superfamily of proteins is widespread in all organisms, and yeast TUM1 is a bona fide orthologue of mammalian Tst thiosulfate sulfurtransferase gene. However, the mouse TST protein cannot functionally replace yeast Tum1 protein, neither in its lipid metabolism-related function, nor in the tRNA thiolation pathway. We show here that Tum1 protein is involved in lipid metabolism by decreasing the sterol ester content in yeast cells, and that this function of Tum1 is not exerted through the tRNA thiolation pathway, but through another, currently unknown pathway.
Collapse
Affiliation(s)
- Katja Uršič
- Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Jamova cesta 39, 1000, Ljubljana, Slovenia.,Present address: Institute of Oncology Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Mojca Ogrizović
- Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Dušan Kordiš
- Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Klaus Natter
- University of Graz, Institute of Biomolecular Sciences, Humboldtstraße 50/EG, 8010, Graz, Austria
| | - Uroš Petrovič
- Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Jamova cesta 39, 1000, Ljubljana, Slovenia. .,Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia.
| |
Collapse
|
4
|
Huang CW, Walker ME, Fedrizzi B, Gardner RC, Jiranek V. Yeast genes involved in regulating cysteine uptake affect production of hydrogen sulfide from cysteine during fermentation. FEMS Yeast Res 2017; 17:3934655. [PMID: 28810701 DOI: 10.1093/femsyr/fox046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/04/2017] [Indexed: 11/13/2022] Open
Abstract
An early burst of hydrogen sulfide (H2S) produced by Saccharomyces cerevisiae during fermentation could increase varietal thiols and therefore enhance desirable tropical aromas in varieties such as Sauvignon Blanc. Here we attempted to identify genes affecting H2S formation from cysteine by screening yeast deletion libraries via a colony colour assay on media resembling grape juice. Both Δlst4 and Δlst7 formed lighter coloured colonies and produced significantly less H2S than the wild type on high concentrations of cysteine, likely because they are unable to take up cysteine efficiently. We then examined the nine known cysteine permeases and found that deletion of AGP1, GNP1 and MUP1 led to reduced production of H2S from cysteine. We further showed that deleting genes involved in the SPS-sensing pathway such as STP1 and DAL81 also reduced H2S from cysteine. Together, this study indirectly confirms that Agp1p, Gnp1p and Mup1p are the major cysteine permeases and that they are regulated by the SPS-sensing and target of rapamycin pathways under the grape juice-like, cysteine-supplemented, fermentation conditions. The findings highlight that cysteine transportation could be a limiting factor for yeast to generate H2S from cysteine, and therefore selecting wine yeasts without defects in cysteine uptake could maximise thiol production potential.
Collapse
Affiliation(s)
- Chien-Wei Huang
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| | - Michelle E Walker
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| | - Bruno Fedrizzi
- Wine Science Programme, School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Richard C Gardner
- Wine Science Programme, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| |
Collapse
|
5
|
Laiba E, Glikaite I, Levy Y, Pasternak Z, Fridman E. Genome scan for nonadditive heterotic trait loci reveals mainly underdominant effects in Saccharomyces cerevisiae. Genome 2016; 59:231-42. [PMID: 26967146 DOI: 10.1139/gen-2015-0127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The overdominant model of heterosis explains the superior phenotype of hybrids by synergistic allelic interaction within heterozygous loci. To map such genetic variation in yeast, we used a population doubling time dataset of Saccharomyces cerevisiae 16 × 16 diallel and searched for major contributing heterotic trait loci (HTL). Heterosis was observed for the majority of hybrids, as they surpassed their best parent growth rate. However, most of the local heterozygous loci identified by genome scan were surprisingly underdominant, i.e., reduced growth. We speculated that in these loci adverse effects on growth resulted from incompatible allelic interactions. To test this assumption, we eliminated these allelic interactions by creating hybrids with local hemizygosity for the underdominant HTLs, as well as for control random loci. Growth of hybrids was indeed elevated for most hemizygous to HTL genes but not for control genes, hence validating the results of our genome scan. Assessing the consequences of local heterozygosity by reciprocal hemizygosity and allele replacement assays revealed the influence of genetic background on the underdominant effects of HTLs. Overall, this genome-wide study on a multi-parental hybrid population provides a strong argument against single gene overdominance as a major contributor to heterosis, and favors the dominance complementation model.
Collapse
Affiliation(s)
- Efrat Laiba
- b Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet-Dagan, P.O. Box 6, 50250, Israel
| | - Ilana Glikaite
- a The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Yael Levy
- b Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet-Dagan, P.O. Box 6, 50250, Israel
| | - Zohar Pasternak
- c Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Eyal Fridman
- b Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet-Dagan, P.O. Box 6, 50250, Israel
| |
Collapse
|
6
|
Kaboli S, Miyamoto T, Sunada K, Sasano Y, Sugiyama M, Harashima S. Improved stress resistance and ethanol production by segmental haploidization of the diploid genome in Saccharomyces cerevisiae. J Biosci Bioeng 2015; 121:638-644. [PMID: 26690924 DOI: 10.1016/j.jbiosc.2015.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/25/2015] [Accepted: 10/27/2015] [Indexed: 12/21/2022]
Abstract
Saccharomyces cerevisiae strains from industrial and natural geographical environments are reported to show great variation in copy number of chromosomal regions. Such variation contributes to the mechanisms underlying adaptation to different environments. Here, we created and phenotypically analyzed segmentally haploidized strains, each harboring a deletion of one copy of approximately 100-300 kb of the left or right terminal region of 16 chromosomes in a diploid strain by using a PCR-mediated chromosomal deletion method. No haploidized strain of the 158-kb deleted right terminal region of chromosome III or the 172-kb deleted right terminal region of chromosome VI was produced; however, segmentally haploidized strains of the remaining 30 terminal regions were obtained. Among these 30 strains, two exhibited higher lactic acid resistance and two displayed higher thermo-tolerance at 41°C versus the host diploid strain. By contrast, four and two segmentally haploidized strains showed sensitivity to 6% lactic acid and low temperature at 13°C, respectively. The effect of the decreased copy number of the chromosomal terminal regions on ethanol production was analyzed. As compared with the host diploid strain, a 3.8% and 4.3% improvement in ethanol production in 10% glucose medium was observed for two strains in which one of two copies of the 197-kb left terminal region of chromosome V and one of two copies of the 195-kb left terminal region of chromosome X was deleted, respectively. These results indicate that artificial segmental haploidization might contribute to improvement of industrially important phenotypes and provide a new approach to breeding superior yeast strains.
Collapse
Affiliation(s)
- Saeed Kaboli
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Miyamoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Sunada
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yu Sasano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Minetaka Sugiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Harashima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
7
|
Ferroni L, Della Puppa A, D'Avella D, Isola M, Scienza R, Gardin C, Zavan B. Tissue Engineering Strategies as Tools for Personalized Meningioma Treatment. Artif Organs 2015; 39:E114-26. [DOI: 10.1111/aor.12483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Letizia Ferroni
- Department of Biomedical Sciences; University of Padova; Padova Italy
| | | | | | - Maurizio Isola
- Department of Animal Medicine, Production and Health (MAPS); University of Padova; Padova Italy
| | - Renato Scienza
- Department of Neurosciences; University of Padova; Padova Italy
| | - Chiara Gardin
- Department of Biomedical Sciences; University of Padova; Padova Italy
| | - Barbara Zavan
- Department of Biomedical Sciences; University of Padova; Padova Italy
| |
Collapse
|
8
|
Michel S, Keller MA, Wamelink MMC, Ralser M. A haploproficient interaction of the transaldolase paralogue NQM1 with the transcription factor VHR1 affects stationary phase survival and oxidative stress resistance. BMC Genet 2015; 16:13. [PMID: 25887987 PMCID: PMC4331311 DOI: 10.1186/s12863-015-0171-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/21/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Studying the survival of yeast in stationary phase, known as chronological lifespan, led to the identification of molecular ageing factors conserved from yeast to higher organisms. To identify functional interactions among yeast chronological ageing genes, we conducted a haploproficiency screen on the basis of previously identified long-living mutants. For this, we created a library of heterozygous Saccharomyces cerevisiae double deletion strains and aged them in a competitive manner. RESULTS Stationary phase survival was prolonged in a double heterozygous mutant of the metabolic enzyme non-quiescent mutant 1 (NQM1), a paralogue to the pentose phosphate pathway enzyme transaldolase (TAL1), and the transcription factor vitamin H response transcription factor 1 (VHR1). We find that cells deleted for the two genes possess increased clonogenicity at late stages of stationary phase survival, but find no indication that the mutations delay initial mortality upon reaching stationary phase, canonically defined as an extension of chronological lifespan. We show that both genes influence the concentration of metabolites of glycolysis and the pentose phosphate pathway, central metabolic players in the ageing process, and affect osmolality of growth media in stationary phase cultures. Moreover, NQM1 is glucose repressed and induced in a VHR1 dependent manner upon caloric restriction, on non-fermentable carbon sources, as well as under osmotic and oxidative stress. Finally, deletion of NQM1 is shown to confer resistance to oxidizing substances. CONCLUSIONS The transaldolase paralogue NQM1 and the transcription factor VHR1 interact haploproficiently and affect yeast stationary phase survival. The glucose repressed NQM1 gene is induced under various stress conditions, affects stress resistance and this process is dependent on VHR1. While NQM1 appears not to function in the pentose phosphate pathway, the interplay of NQM1 with VHR1 influences the yeast metabolic homeostasis and stress tolerance during stationary phase, processes associated with yeast ageing.
Collapse
Affiliation(s)
- Steve Michel
- Max Planck Institute for Molecular Genetics, Ihnestr 73, Berlin, 14195, Germany.
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
| | - Mirjam M C Wamelink
- Metabolic Unit, Department of Clinical Chemistry, VU University Medical Centre Amsterdam, Amsterdam, The Netherlands.
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK.
| |
Collapse
|
9
|
Ford SA, Blanck G. Signal persistence and amplification in cancer development and possible, related opportunities for novel therapies. Biochim Biophys Acta Rev Cancer 2015; 1855:18-23. [DOI: 10.1016/j.bbcan.2014.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/23/2014] [Accepted: 11/04/2014] [Indexed: 12/28/2022]
|
10
|
Copy number loss or silencing of apoptosis-effector genes in cancer. Gene 2014; 554:50-7. [PMID: 25307873 DOI: 10.1016/j.gene.2014.10.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/09/2014] [Indexed: 11/22/2022]
Abstract
Cancer cells undergo a variety of DNA copy number gains and losses (CNV), raising two important questions related to cancer development: (i) Which genes are affected? (ii) And how do CNVs, that do not represent complete deletions but do represent gene-dosage alterations, impact cancer cell functions? Recent studies have indicated that CNVs in cancer can impact genes for regulatory proteins long known to be associated with cancer development, but less is understood about CNVs affecting effector genes. Also, we have recently indicated the likely importance of transcription factor binding site (TFBS) copies in effector genes, in regulating the transition from a proliferative to an apoptotic state. Here we report data-mining analyses that indicate that copies of apoptosis-effector genes are commonly lost in cancer development, in comparison to proliferation-effector genes, and when not, apoptosis effector genes have silenced chromatin structures.
Collapse
|
11
|
Zhang H, Singh KK. Global genetic determinants of mitochondrial DNA copy number. PLoS One 2014; 9:e105242. [PMID: 25170845 PMCID: PMC4149433 DOI: 10.1371/journal.pone.0105242] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/19/2014] [Indexed: 11/18/2022] Open
Abstract
Many human diseases including development of cancer is associated with depletion of mitochondrial DNA (mtDNA) content. These diseases are collectively described as mitochondrial DNA depletion syndrome (MDS). High similarity between yeast and human mitochondria allows genomic study of the budding yeast to be used to identify human disease genes. In this study, we systematically screened the pre-existing respiratory-deficient Saccharomyces cerevisiae yeast strains using fluorescent microscopy and identified 102 nuclear genes whose deletions result in a complete mtDNA loss, of which 52 are not reported previously. Strikingly, these genes mainly encode protein products involved in mitochondrial protein biosynthesis process (54.9%). The rest of these genes either encode protein products associated with nucleic acid metabolism (14.7%), oxidative phosphorylation (3.9%), or other protein products (13.7%) responsible for bud-site selection, mitochondrial intermembrane space protein import, assembly of cytochrome-c oxidase, vacuolar protein sorting, protein-nucleus import, calcium-mediated signaling, heme biosynthesis and iron homeostasis. Thirteen (12.7%) of the genes encode proteins of unknown function. We identified human orthologs of these genes, conducted the interaction between the gene products and linked them to human mitochondrial disorders and other pathologies. In addition, we screened for genes whose defects affect the nuclear genome integrity. Our data provide a systematic view of the nuclear genes involved in maintenance of mitochondrial DNA. Together, our studies i) provide a global view of the genes regulating mtDNA content; ii) provide compelling new evidence toward understanding novel mechanism involved in mitochondrial genome maintenance and iii) provide useful clues in understanding human diseases in which mitochondrial defect and in particular depletion of mitochondrial genome plays a critical role.
Collapse
Affiliation(s)
- Hengshan Zhang
- Hengshan Zhang, Department of Central Laboratory, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Keshav K. Singh
- Departments of Genetics, Pathology, Environmental Health, Center for Free Radical Biology, Center for Aging and UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, and Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, United States of America
- * E-mail:
| |
Collapse
|
12
|
Bisschops MMM, Zwartjens P, Keuter SGF, Pronk JT, Daran-Lapujade P. To divide or not to divide: a key role of Rim15 in calorie-restricted yeast cultures. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1020-30. [PMID: 24487068 DOI: 10.1016/j.bbamcr.2014.01.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 01/20/2014] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
Abstract
The PAS kinase Rim15 is proposed to integrate signals from different nutrient-sensing pathways and to control transcriptional reprogramming of Saccharomyces cerevisiae upon nutrient depletion. Despite this proposed role, previous transcriptome analyses of rim15 mutants solely focused on growing cultures. In the present work, retentostat cultivation enabled analysis of the role of Rim15 under severely calorie-restricted, virtually non-growing conditions. Under these conditions, deletion of RIM15 affected transcription of over 10-fold more genes than in growing cultures. Transcriptional responses, metabolic rates and cellular morphology indicated a key role of Rim15 in controlled cell-cycle arrest upon nutrient depletion. Moreover, deletion of rim15 reduced heat-shock tolerance in non-growing, but not in growing cultures. The failure of rim15 cells to adapt to calorie restriction by entering a robust post-mitotic state resembles cancer cell physiology and shows that retentostat cultivation of yeast strains can provide relevant models for healthy post-mitotic and transformed human cells.
Collapse
Affiliation(s)
- Markus M M Bisschops
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, PO Box 5057, 2600 GA Delft, The Netherlands
| | - Priscilla Zwartjens
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, PO Box 5057, 2600 GA Delft, The Netherlands
| | - Sebastiaan G F Keuter
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, PO Box 5057, 2600 GA Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, PO Box 5057, 2600 GA Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, PO Box 5057, 2600 GA Delft, The Netherlands.
| |
Collapse
|
13
|
Dunham MJ, Fowler DM. Contemporary, yeast-based approaches to understanding human genetic variation. Curr Opin Genet Dev 2013; 23:658-64. [PMID: 24252429 DOI: 10.1016/j.gde.2013.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 01/11/2023]
Abstract
Determining how genetic variation contributes to human health and disease is a critical challenge. As one of the most genetically tractable model organisms, yeast has played a central role in meeting this challenge. The advent of new technologies, including high-throughput DNA sequencing and synthesis, proteomics, and computational methods, has vastly increased the power of yeast-based approaches to determine the consequences of human genetic variation. Recent successes include systematic exploration of the effects of gene dosage, large-scale analysis of the effect of coding variation on gene function, and the use of humanized yeast to model disease. By virtue of its manipulability, small genome size, and genetic tractability, yeast is poised to help us understand human genetic variation.
Collapse
Affiliation(s)
- Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Foege Building, Box 355065, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
| | | |
Collapse
|
14
|
Alcasabas AA, de Clare M, Pir P, Oliver SG. Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids. BMC Genomics 2013; 14:744. [PMID: 24176122 PMCID: PMC3826841 DOI: 10.1186/1471-2164-14-744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/18/2013] [Indexed: 11/29/2022] Open
Abstract
Background In the model eukaryote, Saccharomyces cerevisiae, previous experiments have identified those genes that exert the most significant control over cell growth rate. These genes are termed HFC for high flux control. Such genes are overrepresented within pathways controlling the mitotic cell cycle. Results We postulated that the increase/decrease in growth rate is due to a change in the rate of progression through specific cell cycle steps. We extended and further developed an existing logical model of the yeast cell cycle in order elucidate how the HFC genes modulated progress through the cycle. This model can simulate gene dosage-variation and calculate the cycle time, determine the order and relative speed at which events occur, and predict arrests and failures to correctly execute a step. To experimentally test our model’s predictions, we constructed a tetraploid series of deletion mutants for a set of eight genes that control the G2/M transition. This system allowed us to vary gene copy number through more intermediate levels than previous studies and examine the impact of copy-number variation on growth, cell-cycle phenotype, and response to different cellular stresses. Conclusions For the majority of strains, the predictions agreed with experimental observations, validating our model and its use for further predictions. Where simulation and experiment diverged, we uncovered both novel tetraploid-specific phenotypes and a switch in the determinative execution point of a key cell-cycle regulator, the Cdc28 kinase, from the G1/S to the S/G2 boundaries.
Collapse
Affiliation(s)
| | | | | | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
| |
Collapse
|
15
|
Choy JS, O'Toole E, Schuster BM, Crisp MJ, Karpova TS, McNally JG, Winey M, Gardner MK, Basrai MA. Genome-wide haploinsufficiency screen reveals a novel role for γ-TuSC in spindle organization and genome stability. Mol Biol Cell 2013; 24:2753-63. [PMID: 23825022 PMCID: PMC3756926 DOI: 10.1091/mbc.e12-12-0902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 06/19/2013] [Accepted: 06/24/2013] [Indexed: 02/02/2023] Open
Abstract
How subunit dosage contributes to the assembly and function of multimeric complexes is an important question with implications in understanding biochemical, evolutionary, and disease mechanisms. Toward identifying pathways that are susceptible to decreased gene dosage, we performed a genome-wide screen for haploinsufficient (HI) genes that guard against genome instability in Saccharomyces cerevisiae. This led to the identification of all three genes (SPC97, SPC98, and TUB4) encoding the evolutionarily conserved γ-tubulin small complex (γ-TuSC), which nucleates microtubule assembly. We found that hemizygous γ-TuSC mutants exhibit higher rates of chromosome loss and increases in anaphase spindle length and elongation velocities. Fluorescence microscopy, fluorescence recovery after photobleaching, electron tomography, and model convolution simulation of spc98/+ mutants revealed improper regulation of interpolar (iMT) and kinetochore (kMT) microtubules in anaphase. The underlying cause is likely due to reduced levels of Tub4, as overexpression of TUB4 suppressed the spindle and chromosome segregation defects in spc98/+ mutants. We propose that γ-TuSC is crucial for balanced assembly between iMTs and kMTs for spindle organization and accurate chromosome segregation. Taken together, the results show how gene dosage studies provide critical insights into the assembly and function of multisubunit complexes that may not be revealed by using traditional studies with haploid gene deletion or conditional alleles.
Collapse
Affiliation(s)
- John S. Choy
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Eileen O'Toole
- Department of Cellular and Developmental Biology, University of Colorado–Boulder, Boulder, CO 80309
| | - Breanna M. Schuster
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
| | - Matthew J. Crisp
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Tatiana S. Karpova
- Fluorescent Imaging Facility, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - James G. McNally
- Fluorescent Imaging Facility, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Mark Winey
- Department of Cellular and Developmental Biology, University of Colorado–Boulder, Boulder, CO 80309
| | - Melissa K. Gardner
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
| | - Munira A. Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| |
Collapse
|