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The TOG protein Stu2 is regulated by acetylation. PLoS Genet 2022; 18:e1010358. [PMID: 36084134 PMCID: PMC9491610 DOI: 10.1371/journal.pgen.1010358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 09/21/2022] [Accepted: 07/27/2022] [Indexed: 11/27/2022] Open
Abstract
Stu2 in S. cerevisiae is a member of the XMAP215/Dis1/CKAP5/ch-TOG family of MAPs and has multiple functions in controlling microtubules, including microtubule polymerization, microtubule depolymerization, linking chromosomes to the kinetochore, and assembly of γ-TuSCs at the SPB. Whereas phosphorylation has been shown to be critical for Stu2 localization at the kinetochore, other regulatory mechanisms that control Stu2 function are still poorly understood. Here, we show that a novel form of Stu2 regulation occurs through the acetylation of three lysine residues at K252, K469, and K870, which are located in three distinct domains of Stu2. Alteration of acetylation through acetyl-mimetic and acetyl-blocking mutations did not impact the essential function of Stu2. Instead, these mutations lead to a decrease in chromosome stability, as well as changes in resistance to the microtubule depolymerization drug, benomyl. In agreement with our in silico modeling, several acetylation-mimetic mutants displayed increased interactions with γ-tubulin. Taken together, these data suggest that Stu2 acetylation can govern multiple Stu2 functions, including chromosome stability and interactions at the SPB. Microtubules are proteinaceous polymers that play several important roles in cell division and segregation of the genetic material to each daughter cell. The functions of microtubules are critically dependent upon their dynamic properties in which tubulin subunits are added or removed from the microtubule end, allowing microtubules to grow or shorten in length. These dynamic properties are controlled by several types of microtubule associated proteins. In this study using bakers yeast, we describe our discovery of a previously unappreciated way to regulate the microtubule associated protein Stu2 by a modification called acetylation. When we created mutations in the Stu2 protein that can’t be properly acetylated, the cell lost some of its chromosomes. Some of these mutations actually caused the microtubules to be resistant to drugs that normally disassemble the microtubule polymer. As similar versions of the Stu2 protein are found in diverse organisms that range from yeast and fungus, to plants, insects, mammals and humans, our work could provide unique insights into how microtubules malfunction in some human diseases. With further studies, this may provide a new understanding of chromosome loss in birth defects and/or cancer.
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Liu X, Fu L, Chun-Wei Lin J, Liu S. SRAS-net: Low-resolution chromosome image classification based on deep learning. IET Syst Biol 2022; 16:85-97. [PMID: 35373918 PMCID: PMC9290780 DOI: 10.1049/syb2.12042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 03/15/2022] [Indexed: 12/03/2022] Open
Abstract
Prenatal karyotype diagnosis is important to determine if the foetus has genetic diseases and some congenital diseases. Chromosome classification is an important part of karyotype analysis, and the task is tedious and lengthy. Chromosome classification methods based on deep learning have achieved good results, but if the quality of the chromosome image is not high, these methods cannot learn image features well, resulting in unsatisfactory classification results. Moreover, the existing methods generally have a poor effect on sex chromosome classification. Therefore, in this work, the authors propose to use a super‐resolution network, Self‐Attention Negative Feedback Network, and combine it with traditional neural networks to obtain an efficient chromosome classification method called SRAS‐net. The method first inputs the low‐resolution chromosome images into the super‐resolution network to generate high‐resolution chromosome images and then uses the traditional deep learning model to classify the chromosomes. To solve the problem of inaccurate sex chromosome classification, the authors also propose to use the SMOTE algorithm to generate a small number of sex chromosome samples to ensure a balanced number of samples while allowing the model to learn more sex chromosome features. Experimental results show that our method achieves 97.55% accuracy and is better than state‐of‐the‐art methods.
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Affiliation(s)
- Xiangbin Liu
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha, China.,College of Information Science and Engineering, Hunan Normal University, Changsha, China.,Hunan Xiangjiang Artificial Intelligence Academy, Changsha, China
| | - Lijun Fu
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha, China.,College of Information Science and Engineering, Hunan Normal University, Changsha, China.,Hunan Xiangjiang Artificial Intelligence Academy, Changsha, China
| | - Jerry Chun-Wei Lin
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Shuai Liu
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha, China.,College of Information Science and Engineering, Hunan Normal University, Changsha, China.,Hunan Xiangjiang Artificial Intelligence Academy, Changsha, China
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3
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Vítor AC, Huertas P, Legube G, de Almeida SF. Studying DNA Double-Strand Break Repair: An Ever-Growing Toolbox. Front Mol Biosci 2020; 7:24. [PMID: 32154266 PMCID: PMC7047327 DOI: 10.3389/fmolb.2020.00024] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/04/2020] [Indexed: 12/29/2022] Open
Abstract
To ward off against the catastrophic consequences of persistent DNA double-strand breaks (DSBs), eukaryotic cells have developed a set of complex signaling networks that detect these DNA lesions, orchestrate cell cycle checkpoints and ultimately lead to their repair. Collectively, these signaling networks comprise the DNA damage response (DDR). The current knowledge of the molecular determinants and mechanistic details of the DDR owes greatly to the continuous development of ground-breaking experimental tools that couple the controlled induction of DSBs at distinct genomic positions with assays and reporters to investigate DNA repair pathways, their impact on other DNA-templated processes and the specific contribution of the chromatin environment. In this review, we present these tools, discuss their pros and cons and illustrate their contribution to our current understanding of the DDR.
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Affiliation(s)
- Alexandra C Vítor
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Pablo Huertas
- Department of Genetics, University of Seville, Seville, Spain.,Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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Hart RS, Jolly NP, Ndimba BK. Characterisation of hybrid yeasts for the production of varietal Sauvignon blanc wine – A review. J Microbiol Methods 2019; 165:105699. [DOI: 10.1016/j.mimet.2019.105699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/15/2019] [Accepted: 08/21/2019] [Indexed: 10/26/2022]
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5
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Perpetuini G, Tittarelli F, Mattarelli P, Modesto M, Cilli E, Suzzi G, Tofalo R. Intraspecies polymorphisms of Kluyveromyces marxianus strains from Yaghnob valley. FEMS Microbiol Lett 2019; 365:4834011. [PMID: 29401260 DOI: 10.1093/femsle/fny028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/31/2018] [Indexed: 02/07/2023] Open
Abstract
In this study, 29 strains of Kluyveromyces marxianus with peculiar genetic and phenotypic traits previously isolated from a fermented goat milk of Yaghnob valley were investigated for chromosome length polymorphism (CLP) by PFGE, adhesion properties and carbon usage by Biolog analysis. Obtained data showed that strains differed in terms of number and size of chromosome bands. The number of bands ranged from 5 to 7, suggesting a probable genome size from 1.4 to 2.6 Mb. Strains showed a certain level of cell surface hydrophobicity ranging from 32% to 77.7%. Strains were also tested for their ability to form a biofilm on polystyrene plates: planktonic cells ranged from 6.3 cfu/mL to 7.95 cfu/mL, while sessile from 7.11 cfu/mL to 8.6 cfu/mL. The strains able to adhere to polystyrene plates were also able to form a mature MAT. Biolog analysis revealed that almost all strains were able to use putrescine, malic acid, α-D lactose, phenylethylamine, β-methyl D-gucoside and xylose; 5 strains were able to grow on cellobiose and 3 were able to catabolise α-ketobutyric. The obtained data highlighted a number of interesting features underlying the peculiar capacities of these strains for industrial applications.
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Affiliation(s)
- Giorgia Perpetuini
- Department of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, Teramo 64100, Italy.,Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, I-40127 Bologna, Italy
| | - Fabrizia Tittarelli
- Department of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, Teramo 64100, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, I-40127 Bologna, Italy
| | - Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, I-40127 Bologna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, I-48121 Ravenna, Italy
| | | | - Rosanna Tofalo
- Department of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, Teramo 64100, Italy
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Lopez-Canovas L, Martinez Benitez MB, Herrera Isidron JA, Flores Soto E. Pulsed Field Gel Electrophoresis: Past, present, and future. Anal Biochem 2019; 573:17-29. [PMID: 30826351 DOI: 10.1016/j.ab.2019.02.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/27/2022]
Abstract
Pulsed Field Gel Electrophoresis (PFGE) has been considered for many years the 'gold-standard' for characterizing many pathogenic organisms as well as for subtyping bacterial species causing infection outbreaks. This article reviews the basic principles of PFGE and it includes the main advantages and limitations of the different electrode configurations that have been used in PFGE equipment and their influence on the DNA electrophoretic separation. Remarkably, we summarize here the most relevant theoretical and practical aspects that we have learned for more than 20 years developing and using the miniaturized PFGE systems. We also discussed the theoretical aspects related to DNA migration in PFGE agarose gels. It served as the basis for simulating the DNA electrophoretic patterns in CHEF mini gels and mini-chambers during experimental design and optimization. A critical comparison between standard and miniaturized PFGE systems, as well as the enzymatic and non-enzymatic methods for intact immobilized DNA preparation, is provided throughout the review. The PFGE current applications, advantages, limitations and future challenges of the methodology are also discussed.
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Affiliation(s)
- Lilia Lopez-Canovas
- Postgraduate Program in Genomic Sciences, School of Science and Technology (CCyT), Autonomous University of Mexico City (UACM), Mexico City, Mexico.
| | - Maximo B Martinez Benitez
- Postgraduate Program in Genomic Sciences, School of Science and Technology (CCyT), Autonomous University of Mexico City (UACM), Mexico City, Mexico.
| | | | - Eduardo Flores Soto
- Academy of Biology, School of Sciences and Humanities, UACM, Mexico City, Mexico.
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Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei. G3-GENES GENOMES GENETICS 2018; 8:2967-2977. [PMID: 30097472 PMCID: PMC6118302 DOI: 10.1534/g3.118.200476] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Saccharomyces sensu stricto complex consist of yeast species, which are not only important in the fermentation industry but are also model systems for genomic and ecological analysis. Here, we present the complete genome assemblies of Saccharomyces jurei, a newly discovered Saccharomyces sensu stricto species from high altitude oaks. Phylogenetic and phenotypic analysis revealed that S. jurei is more closely related to S. mikatae, than S. cerevisiae, and S. paradoxus. The karyotype of S. jurei presents two reciprocal chromosomal translocations between chromosome VI/VII and I/XIII when compared to the S. cerevisiae genome. Interestingly, while the rearrangement I/XIII is unique to S. jurei, the other is in common with S. mikatae strain IFO1815, suggesting shared evolutionary history of this species after the split between S. cerevisiae and S. mikatae. The number of Ty elements differed in the new species, with a higher number of Ty elements present in S. jurei than in S. cerevisiae. Phenotypically, the S. jurei strain NCYC 3962 has relatively higher fitness than the other strain NCYC 3947T under most of the environmental stress conditions tested and showed remarkably increased fitness in higher concentration of acetic acid compared to the other sensu stricto species. Both strains were found to be better adapted to lower temperatures compared to S. cerevisiae.
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Treich I, Carles C, Riva M, Sentenac A. RPC10 encodes a new mini subunit shared by yeast nuclear RNA polymerases. Gene Expr 2018; 2:31-7. [PMID: 1617300 PMCID: PMC6057363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Yeast RNA polymerases A, B, and C share five small subunits, two of which, ABC10 alpha and ABC10 beta, comigrate on SDS polyacrylamide gels. The gene encoding ABC10 alpha, RPC10, was isolated based on microsequence data. RPC10 is a single copy gene localized on chromosome VIII. It codes for a very basic protein of only 70 amino acids, which contains a zinc binding domain of the form CX2CX13CX2C. Deletion of its gene indicated that, despite its very small size, the ABC10 alpha subunit is essential for yeast cell viability. ABC10 alpha and ABC10 beta have little sequence similarity.
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Affiliation(s)
- I Treich
- DBCM, Section of Biochemistry and Molecular Genetics, Saclay Research Center, Gif-sur-Yvette, France
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Hicks L, van der Graaf CM, Childress J, Cook E, Schmidt K, Rosenzweig F, Kroll E. Streamlined preparation of genomic DNA in agarose plugs for pulsed-field gel electrophoresis. J Biol Methods 2018; 5:e86. [PMID: 31453239 PMCID: PMC6706164 DOI: 10.14440/jbm.2018.218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 11/23/2022] Open
Abstract
Genome analysis using pulsed-field gel electrophoresis (PFGE) has been used in applications ranging from typing bacterial strains to radiobiology to cancer research. While methods for running PFGE have been significantly improved since its invention, the method for preparing chromosomal DNA itself has remained essentially unchanged. This limits the applicability of PFGE, especially when analyses require many samples. We have streamlined sample preparation for routine applications of PFGE through the use of deep-well 48-well plates. Besides saving time, our protocol has the added advantage of reducing the volume of expensive reagents. Our improved protocol enables us to reduce throughput time and simplify the procedure, facilitating wider application of PFGE-based analyses in the laboratory.
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Affiliation(s)
- Linda Hicks
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | - Jacob Childress
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Emily Cook
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Karen Schmidt
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Frank Rosenzweig
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Eugene Kroll
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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Pedersen MB. Molecular Analyses of Yeast DNA—Tools for Pure Yeast Maintenance in the Brewery. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-52-0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Mogens Bohl Pedersen
- Carlsberg Research Laboratory, Gamle Carlsberg Vej 10, DK2500 Copenhagen Valby, Denmark
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11
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Takata Y, Watari J, Nishikawa N, Kamada K. Electrophoretic Banding Patterns of Chromosomal DNA from Yeasts. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-47-0109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yoshihiro Takata
- Research & Development Laboratories, Sapporo Breweries Ltd., Okatohme 10, Yaizu-shi, Shizuoka, 425 Japan
| | - Junji Watari
- Research & Development Laboratories, Sapporo Breweries Ltd., Okatohme 10, Yaizu-shi, Shizuoka, 425 Japan
| | - Norio Nishikawa
- Research & Development Laboratories, Sapporo Breweries Ltd., Okatohme 10, Yaizu-shi, Shizuoka, 425 Japan
| | - Kôzô Kamada
- Research & Development Laboratories, Sapporo Breweries Ltd., Okatohme 10, Yaizu-shi, Shizuoka, 425 Japan
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Casey GP, Pringle AT, Erdmann PA. Evaluation of Recent Techniques Used to Identify Individual Strains ofSaccharomycesYeasts. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-48-0100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Gregory P. Casey
- Anheuser-Busch Companies, Corporate R&D, One Busch Place, St. Louis, MO 63118
| | - A. T. Pringle
- Anheuser-Busch Companies, Corporate R&D, One Busch Place, St. Louis, MO 63118
| | - P. A. Erdmann
- Anheuser-Busch Companies, Corporate R&D, One Busch Place, St. Louis, MO 63118
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13
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Casey GP, Xiao W, Rank GH. Construction of α-Galactosidase-Positive Strains of Industrial Baker's (Saccharomyces Cerevisiae)Yeasts. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-46-0067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Gregory P. Casey
- Department of Applied Microbiology and Food Science (Food Biotechnology Group), University of Saskatchewan, Saskatoon, Canada S7N 0W0
| | - Wei Xiao
- Department of Biology, University of Saskatchewan, Saskatoon, Canada S7N 0W0
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Jood I, Hoff JW, Setati ME. Evaluating fermentation characteristics of Kazachstania spp. and their potential influence on wine quality. World J Microbiol Biotechnol 2017; 33:129. [PMID: 28585169 DOI: 10.1007/s11274-017-2299-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
Abstract
The current study is the first one to demonstrate the wine fermentation potential of members of several species of the genus Kazachstania including strains derived from grape must. The fermentation characteristics were evaluated in synthetic grape juice medium and in Sauvignon blanc. Our data show that none of the species evaluated could ferment to dryness in monoculture fermentations. However, at least 75% of the sugar was consumed before the fermentations got stuck. In mixed-culture fermentations with Saccharomyces cerevisiae diverse aroma profiles were evident especially in Sauvignon blanc fermentations. Four distinct potential aroma associations were identified: (i) Kazachstania solicola-vinegar and solvent-like, (ii) Kazachstania hellenica-spirituous, cheesy, (iii) Kazachstania aerobia CBS-fruity, floral (iv) K. aerobia IWBT, Kazachstania unispora and Kazachstania servazii-rancid, harsh. Furthermore, strain variation was apparent as the two K. aerobia strains displayed distinct karyotypes and aroma potential. Our data show that although members of the genus Kazachstania are typically encountered at low frequency in grape must, some of the species have positive aroma attributes that should be explored further.
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Affiliation(s)
- Illse Jood
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, P/Bag X1, Matieland, 7602, South Africa
| | - Justin Wallace Hoff
- Agricultural Research Council Infruitec-Nietvoorbij, P/Bag X5026, Stellenbosch, 7599, South Africa
| | - Mathabatha Evodia Setati
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, P/Bag X1, Matieland, 7602, South Africa.
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Hart R, Jolly N, Mohamed G, Booyse M, Ndimba B. Characterisation of Saccharomyces cerevisiae hybrids selected for low volatile acidity formation and the production of aromatic Sauvignon blanc wine. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajb2016.15388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Fasoli G, Tofalo R, Lanciotti R, Schirone M, Patrignani F, Perpetuini G, Grazia L, Corsetti A, Suzzi G. Chromosome arrangement, differentiation of growth kinetics and volatile molecule profiles in Kluyveromyces marxianus strains from Italian cheeses. Int J Food Microbiol 2015; 214:151-158. [DOI: 10.1016/j.ijfoodmicro.2015.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/29/2015] [Accepted: 08/06/2015] [Indexed: 11/16/2022]
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17
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Dujon B. Basic principles of yeast genomics, a personal recollection: Graphical Abstract Figure. FEMS Yeast Res 2015; 15:fov047. [DOI: 10.1093/femsyr/fov047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2015] [Indexed: 12/12/2022] Open
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18
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Bozdag GO, Greig D. The genetics of a putative social trait in natural populations of yeast. Mol Ecol 2014; 23:5061-71. [PMID: 25169714 PMCID: PMC4285311 DOI: 10.1111/mec.12904] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 08/21/2014] [Accepted: 08/25/2014] [Indexed: 11/29/2022]
Abstract
The sharing of secreted invertase by yeast cells is a well-established laboratory model for cooperation, but the only evidence that such cooperation occurs in nature is that the SUC loci, which encode invertase, vary in number and functionality. Genotypes that do not produce invertase can act as ‘cheats’ in laboratory experiments, growing on the glucose that is released when invertase producers, or ‘cooperators’, digest sucrose. However, genetic variation for invertase production might instead be explained by adaptation of different populations to different local availabilities of sucrose, the substrate for invertase. Here we find that 110 wild yeast strains isolated from natural habitats, and all contained a single SUC locus and produced invertase; none were ‘cheats’. The only genetic variants we found were three strains isolated instead from sucrose-rich nectar, which produced higher levels of invertase from three additional SUC loci at their subtelomeres. We argue that the pattern of SUC gene variation is better explained by local adaptation than by social conflict.
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Affiliation(s)
- G O Bozdag
- Max Planck Institute for Evolutionary Biology, August Thienemann Strasse 2, Plön, 24306, Germany
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Comparative genomic analysis of Saccharomyces cerevisiae yeasts isolated from fermentations of traditional beverages unveils different adaptive strategies. Int J Food Microbiol 2014; 171:129-35. [DOI: 10.1016/j.ijfoodmicro.2013.10.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/11/2013] [Accepted: 10/27/2013] [Indexed: 11/17/2022]
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Abstract
One of the top things on a geneticist's wish list has to be a set of mutants for every gene in their particular organism. Such a set was produced for the yeast, Saccharomyces cerevisiae near the end of the 20th century by a consortium of yeast geneticists. However, the functional genomic analysis of one chromosome, its smallest, had already begun more than 25 years earlier as a project that was designed to define most or all of that chromosome's essential genes by temperature-sensitive lethal mutations. When far fewer than expected genes were uncovered, the relatively new field of molecular cloning enabled us and indeed, the entire community of yeast researchers to approach this problem more definitively. These studies ultimately led to cloning, genomic sequencing, and the production and phenotypic analysis of the entire set of knockout mutations for this model organism as well as a better concept of what defines an essential function, a wish fulfilled that enables this model eukaryote to continue at the forefront of research in modern biology.
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León K, Riverón AM, Arencibia O, Santamaría Y, López-Cánovas L. Two-Dimensional Pulsed Field Minigel Electrophoresis with High Throughput Sample Format. J Food Saf 2013. [DOI: 10.1111/jfs.12042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Karen León
- Molecular Biology Department; Cuban Neurosciences Center; Ave. 25 y 158 No. 15202, Cubanacan, Playa Havana 11600 Cuba
| | - Ana María Riverón
- Molecular Biology Department; Cuban Neurosciences Center; Ave. 25 y 158 No. 15202, Cubanacan, Playa Havana 11600 Cuba
| | - Oscar Arencibia
- Molecular Biology Department; Cuban Neurosciences Center; Ave. 25 y 158 No. 15202, Cubanacan, Playa Havana 11600 Cuba
| | - Yenis Santamaría
- Molecular Biology Department; Cuban Neurosciences Center; Ave. 25 y 158 No. 15202, Cubanacan, Playa Havana 11600 Cuba
| | - Lilia López-Cánovas
- Molecular Biology Department; Cuban Neurosciences Center; Ave. 25 y 158 No. 15202, Cubanacan, Playa Havana 11600 Cuba
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22
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Naumov GI, Naumova ES, Martynenko NN, Korhola M. Reidentification of chromosomal CUP1 translocations in the wine yeasts Saccharomyces cerevisiae. Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713010104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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23
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Panchal CJ, Bast L, Dowiianick T, Stewart GG. A RAPID, SIMPLE AND RELIABLE METHOD OF DIFFERENTIATING BREWING YEAST STRAINS BASED ON DNA RESTRICTION PATTERNS. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1987.tb04512.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Casey GP, Xiao W, Rank GH. APPLICATION OF PULSED FIELD CHROMOSOME ELECTROPHORESIS IN THE STUDY OF CHROMOSOMEXIIIAND THE ELECTROPHORETIC KARYOTYPE OF INDUSTRIAL STRAINS OFSACCHAROMYCESYEASTS. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1988.tb04579.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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The Anti-Corrosion Handbook and Directory. Compiled and edited by J. E. Bean. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1988.tb04576.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Dunn B, Paulish T, Stanbery A, Piotrowski J, Koniges G, Kroll E, Louis EJ, Liti G, Sherlock G, Rosenzweig F. Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression. PLoS Genet 2013; 9:e1003366. [PMID: 23555283 PMCID: PMC3605161 DOI: 10.1371/journal.pgen.1003366] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 01/20/2013] [Indexed: 12/17/2022] Open
Abstract
Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow ~1-kb region of chromosome 14, and all producing an "interspecific fusion junction" within the MEP2 gene coding sequence, such that the 5' portion derives from S. cerevisiae and the 3' portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the homeologous S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome; these events result in the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that, when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unavailable evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in numerous eukaryotic phyla, that does not require repeated backcrossing to one of the parental species.
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Affiliation(s)
- Barbara Dunn
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Terry Paulish
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Alison Stanbery
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Jeff Piotrowski
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Chemical Genomics Research Group, RIKEN Advance Science Institute, Wako, Japan
| | - Gregory Koniges
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Evgueny Kroll
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Edward J. Louis
- Center of Genetics and Genomics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Gianni Liti
- Center of Genetics and Genomics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (GS); (FR)
| | - Frank Rosenzweig
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- * E-mail: (GS); (FR)
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van Breda V, Jolly N, van Wyk J. Characterisation of commercial and natural Torulaspora delbrueckii wine yeast strains. Int J Food Microbiol 2013; 163:80-8. [PMID: 23558190 DOI: 10.1016/j.ijfoodmicro.2013.02.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 02/19/2013] [Accepted: 02/24/2013] [Indexed: 11/17/2022]
Abstract
Forty-three South African Torulaspora delbrueckii yeast isolates from the ARC Infruitec-Nietvoorbij yeast culture collection, the T. delbrueckii type strain (CBS 1146), one reference T. delbrueckii strain (CBS 4663), two T. delbrueckii strains isolated from commercial yeast blends (Viniflora® Harmony.nsac and Viniflora® Melody.nsac), and a commercial Saccharomyces cerevisiae yeast (VIN 13) had their identities confirmed and were characterised using conventional and molecular microbiological techniques. These included a selection of growth media as well as CHEF electrophoretic karyotyping and PCR-RFLP analyses. Based on the biochemical and physiological results the strains were divided into 13 groups. The performances of the yeasts were also monitored by means of laboratory-scale fermentations in grape must at 15 °C and 22 °C. The fermentation kinetic data showed that at 22 °C, the yeasts were divided into two distinct groups, a faster and a slower fermenting group. The fermentation curves of the laboratory-scale study at 15 °C showed that, at this lower temperature, the yeasts also fermented at different speeds, but the fermentation curves showed greater separation. The biochemical and physiological grouping did not coincide with the fermentation abilities and good fermenters could be found in more than one group. Chemical analyses of the resultant wines (alcohol, volatile acidity, glycerol, total SO2, residual sugar) were used in Principle Component Analyses. The yeasts that grouped close to the S. cerevisiae reference strain (VIN 13) showed more acceptable wine chemical profiles, while those further away displayed less acceptable profiles. Three locally isolated strains and one commercial T. delbrueckii yeast strain, Viniflora® Harmony.nsac. produced wines with acceptable chemical profiles at both temperatures. These strains also had comparable fermentation kinetics to the S. cerevisiae reference. Therefore, depending on the fermentation temperature, different T. delbrueckii strains will be suitable for specific wine styles and some may even be considered for single inoculations without S. cerevisiae in industrial fermentations.
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Affiliation(s)
- Valmary van Breda
- Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
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29
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Kumar S, Burgers PM. Lagging strand maturation factor Dna2 is a component of the replication checkpoint initiation machinery. Genes Dev 2013; 27:313-21. [PMID: 23355394 DOI: 10.1101/gad.204750.112] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Initiation of the DNA replication checkpoint in yeast is mainly mediated by Mec1 protein kinase, the ortholog of human ATR, while its homolog Tel1, the ortholog of human ATM, has a minor replication checkpoint function. Checkpoint initiation requires stimulation of Mec1 kinase activity by specific activators. Saccharomyces cerevisiae Dna2, a nuclease-helicase that is essential for Okazaki fragment maturation, is employed specifically during S phase to stimulate Mec1 kinase and initiate the replication checkpoint. Mutations (W128A and Y130A) in the unstructured N terminus of Dna2 abrogate its checkpoint function in vitro and in vivo. Dna2 shows partial redundancy for the replication checkpoint with checkpoint initiators 9-1-1 (S. cerevisiae Ddc1-Mec3-Rad17 and human Rad9-Rad1-Hus1) and Dpb11, the ortholog of human TopBP1. A triple mutant that eliminates the checkpoint functions of all three initiators abrogates the Mec1-dependent checkpoint.
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Affiliation(s)
- Sandeep Kumar
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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30
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Meaden P. DNA FINGERPRINTING OF BREWERS' YEAST: CURRENT PERSPECTIVES. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1990.tb01027.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Vezinhet F, Barre P, Laurent M, Valade M. INTRODUCTION OF FLOCCULATION INTO AN INDUSTRIAL YEAST STRAIN BY TRANSFER OF A SINGLE CHROMOSOME. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1992.tb01114.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Zhou H, Cheng JS, Wang BL, Fink GR, Stephanopoulos G. Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae. Metab Eng 2012; 14:611-22. [PMID: 22921355 DOI: 10.1016/j.ymben.2012.07.011] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 07/10/2012] [Accepted: 07/21/2012] [Indexed: 11/28/2022]
Abstract
Xylose is the main pentose and second most abundant sugar in lignocellulosic feedstocks. To improve xylose utilization, necessary for the cost-effective bioconversion of lignocellulose, several metabolic engineering approaches have been employed in the yeast Saccharomyces cerevisiae. In this study, we describe the rational metabolic engineering of a S. cerevisiae strain, including overexpression of the Piromyces xylose isomerase gene (XYLA), Pichia stipitis xylulose kinase (XYL3) and genes of the non-oxidative pentose phosphate pathway (PPP). This engineered strain (H131-A3) was used to initialize a three-stage process of evolutionary engineering, through first aerobic and anaerobic sequential batch cultivation followed by growth in a xylose-limited chemostat. The evolved strain H131-A3-AL(CS) displayed significantly increased anaerobic growth rate (0.203±0.006 h⁻¹) and xylose consumption rate (1.866 g g⁻¹ h⁻¹) along with high ethanol conversion yield (0.41 g/g). These figures exceed by a significant margin any other performance metrics on xylose utilization and ethanol production by S. cerevisiae reported to-date. Further inverse metabolic engineering based on functional complementation suggested that efficient xylose assimilation is attributed, in part, to the elevated expression level of xylose isomerase, which was accomplished through the multiple-copy integration of XYLA in the chromosome of the evolved strain.
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Affiliation(s)
- Hang Zhou
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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33
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Fu R, Ding L, Zhu J, Li P, Zheng AP. Morphological structure of propagules and electrophoretic karyotype analysis of false smut Villosiclava virens in rice. J Microbiol 2012; 50:263-9. [DOI: 10.1007/s12275-012-1456-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/08/2011] [Indexed: 11/30/2022]
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Piotrowski JS, Nagarajan S, Kroll E, Stanbery A, Chiotti KE, Kruckeberg AL, Dunn B, Sherlock G, Rosenzweig F. Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve. BMC Evol Biol 2012; 12:46. [PMID: 22471618 PMCID: PMC3372441 DOI: 10.1186/1471-2148-12-46] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 04/02/2012] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Interspecific hybridization occurs in every eukaryotic kingdom. While hybrid progeny are frequently at a selective disadvantage, in some instances their increased genome size and complexity may result in greater stress resistance than their ancestors, which can be adaptively advantageous at the edges of their ancestors' ranges. While this phenomenon has been repeatedly documented in the field, the response of hybrid populations to long-term selection has not often been explored in the lab. To fill this knowledge gap we crossed the two most distantly related members of the Saccharomyces sensu stricto group, S. cerevisiae and S. uvarum, and established a mixed population of homoploid and aneuploid hybrids to study how different types of selection impact hybrid genome structure. RESULTS As temperature was raised incrementally from 31°C to 46.5°C over 500 generations of continuous culture, selection favored loss of the S. uvarum genome, although the kinetics of genome loss differed among independent replicates. Temperature-selected isolates exhibited greater inherent and induced thermal tolerance than parental species and founding hybrids, and also exhibited ethanol resistance. In contrast, as exogenous ethanol was increased from 0% to 14% over 500 generations of continuous culture, selection favored euploid S. cerevisiae x S. uvarum hybrids. Ethanol-selected isolates were more ethanol tolerant than S. uvarum and one of the founding hybrids, but did not exhibit resistance to temperature stress. Relative to parental and founding hybrids, temperature-selected strains showed heritable differences in cell wall structure in the forms of increased resistance to zymolyase digestion and Micafungin, which targets cell wall biosynthesis. CONCLUSIONS This is the first study to show experimentally that the genomic fate of newly-formed interspecific hybrids depends on the type of selection they encounter during the course of evolution, underscoring the importance of the ecological theatre in determining the outcome of the evolutionary play.
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Affiliation(s)
- Jeff S Piotrowski
- Chemical Genomics Research Group, RIKEN Advance Science Institute, Wako, Wako, Japan
- Division of Biological Sciences, The University of Montana, Missoula MT 59812, USA
| | - Saisubramanian Nagarajan
- School of Chemical and Biotechnology, SASTRA University, Tirumalaisamudram Thanjavur- 613401, Tamil Nadu, India
- Division of Biological Sciences, The University of Montana, Missoula MT 59812, USA
| | - Evgueny Kroll
- Division of Biological Sciences, The University of Montana, Missoula MT 59812, USA
| | - Alison Stanbery
- Division of Biological Sciences, The University of Montana, Missoula MT 59812, USA
| | - Kami E Chiotti
- Division of Biological Sciences, The University of Montana, Missoula MT 59812, USA
| | | | - Barbara Dunn
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
| | - Frank Rosenzweig
- Division of Biological Sciences, The University of Montana, Missoula MT 59812, USA
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Franco-Duarte R, Mendes I, Gomes AC, Santos MAS, de Sousa B, Schuller D. Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics. Electrophoresis 2011; 32:1447-55. [DOI: 10.1002/elps.201000640] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 01/24/2011] [Accepted: 02/22/2011] [Indexed: 11/06/2022]
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In vivo virulence of commercial Saccharomyces cerevisiae strains with pathogenicity-associated phenotypical traits. Int J Food Microbiol 2010; 144:393-9. [PMID: 21081253 DOI: 10.1016/j.ijfoodmicro.2010.10.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 10/14/2010] [Accepted: 10/21/2010] [Indexed: 01/01/2023]
Abstract
Two commercial Saccharomyces cerevisiae strains, a baker's strain and the bio-therapeutic agent Ultralevure, have been proposed as a possible exogenous source of human colonization (de Llanos et al., 2004, 2006a). Moreover, these strains express phenotypical traits associated to pathogenicity (de Llanos et al., 2006b). Taking into account that both commercial preparations represent an important source of living S. cerevisiae cells we have performed an in vivo study to evaluate whether there is a potential safety risk to humans. Their virulence was compared with that of other commercial strains with less virulent traits, and with clinical isolates, using two murine models (BALB/c and DBA/2N mice). Burden determination in the brain and kidneys showed that the ability to disseminate, colonize and persist was manifested not only by clinical isolates but also by commercial strains. Among these, the baker's strain and Ultralevure were able to cause the death of BALB/c mice at rates similar to those shown by two of the clinical isolates. These results highlight the pathogenic potential of these strains and show that four-week-old BALB/c mice are an appropriate murine model to study the virulence of yeasts with low or moderate pathogenicity. Furthermore, we have shown the positive effect of an immunosuppressive therapy with cyclophosphamide in the virulence of the baker's strains and Ultralevure but not in the rest of the commercial strains under study. The data suggest that although S. cerevisiae has always been considered a GRAS microorganism, commercial preparations should include only those strains shown to be safe in order to minimize complications in risk groups.
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NEKRASOVA IRINAV, PRZYBOŚ EWA, RAUTIAN MARIAS, POTEKHIN ALEXEYA. Electrophoretic Karyotype Polymorphism of Sibling Species of the Paramecium aurelia Complex. J Eukaryot Microbiol 2010; 57:494-507. [DOI: 10.1111/j.1550-7408.2010.00507.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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38
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Naumov GI, Naumova ES. Polygenic control for fermentation of β-fructosides in the yeast Saccharomyces cerevisiae: New genes SUC9 and SUC10. Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710020050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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39
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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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Rodríguez M, Infante J, Molina M, Domínguez M, Rebordinos L, Cantoral J. Genomic characterization and selection of wine yeast to conduct industrial fermentations of a white wine produced in a SW Spain winery. J Appl Microbiol 2010; 108:1292-302. [DOI: 10.1111/j.1365-2672.2009.04524.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Naumov GI, Naumova ES. Comparative genetics of yeasts: A novel β-fructosidase gene SUC8 in Saccharomyces cerevisiae. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410030099] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lopes CA, Barrio E, Querol A. Natural hybrids of S. cerevisiae×S. kudriavzevii share alleles with European wild populations of Saccharomyces kudriavzevii. FEMS Yeast Res 2010; 10:412-21. [PMID: 20337723 DOI: 10.1111/j.1567-1364.2010.00614.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Christian A Lopes
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
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Matsunaga S, Endo T, Yagita K, Hirukawa Y, Tomino S, Matsugo S, Tsuruhara T. Chromosome size polymorphisms in the genus acanthamoeba electrokaryotype by pulsed-field gel electrophoresis. Protist 2009. [PMID: 23194715 DOI: 10.1016/s1434-4610(98)70039-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Twenty-eight strains from 12 species from the genus Acanthamoeba, including five isolates from amoebic keratitis patients, were subjected to molecular karyotyping by pulsed-field gel electrophoresis. 9 to 21 chromosome-sized DNA bands ranging from 200 kb to 3 Mb in size were detected. Molecular karyotypes also showed a wide multifariousness, i.e. there existed inter- and intraspecific heterogeneity. The five isolates from amoebic keratitis patients did not exhibit characteristic molecular karyotypes distinguishable from environmental isolates. Although karyotypic heterogeneity was observed within group I amoeba, they are distinguishable from those of group II and III. Strains having identical restriction fragment length polymorphism profiles of mtDNA did not have an identical molecular karyotype, i.e. weak correlation was found between molecular karyotypes and mtDNA restriction fragment length polymorphism profiles.
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Affiliation(s)
- S Matsunaga
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo 184-8501, Japan
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Anthony RM, Howell SA, Lloyd DH, Pinter L. Application of DNA Typing Methods to the Study of the Epidemiology of Malassezia pachydermatis. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2009. [DOI: 10.3109/08910609409141346] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- R. M. Anthony
- Department of Microbial Diseases, St John's Institute of Dermatology, UMDS St Thomas' Hospital, London, SE1 4TH, UK
| | - S. A. Howell
- Department of Microbial Diseases, St John's Institute of Dermatology, UMDS St Thomas' Hospital, London, SE1 4TH, UK
| | - D. H. Lloyd
- Dermatology Unit, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, AL9 7TA, UK
| | - L. Pinter
- Microbiology Department, Veterinary Faculty Zagreb, Heinzelova 55, 41000, Zagreb, Croatia
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Lee CF, Yao CH, Liu YR, Hsieh CW, Young SS. Lachancea dasiensis sp. nov., an ascosporogenous yeast isolated from soil and leaves in Taiwan. Int J Syst Evol Microbiol 2009; 59:1818-22. [DOI: 10.1099/ijs.0.008789-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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46
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Lee CF, Yao CH, Liu YR, Young SS, Chang KS. Kazachstania wufongensis sp. nov., an ascosporogenous yeast isolated from soil in Taiwan. Antonie van Leeuwenhoek 2009; 95:335-41. [DOI: 10.1007/s10482-009-9319-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 02/10/2009] [Indexed: 12/01/2022]
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47
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Molecular methods as ways of dealing with terminological difficulties in fungal ecology. ECOLOGICAL QUESTIONS 2009. [DOI: 10.2478/v10090-009-0016-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Nassonova ES. Pulsed field gel electrophoresis: Theory, instruments and application. ACTA ACUST UNITED AC 2008. [DOI: 10.1134/s1990519x08060011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Genome size and ploidy level: new insights for elucidating relationships in Zygosaccharomyces species. Fungal Genet Biol 2008; 45:1582-90. [PMID: 18952188 DOI: 10.1016/j.fgb.2008.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 09/15/2008] [Accepted: 10/02/2008] [Indexed: 10/21/2022]
Abstract
Ploidy is a fundamental genetic trait with important physiological and genomic implications. We applied complementary molecular tools to highlight differences in genome size and ploidy between Zygosaccharomyces rouxii strain CBS 732T and other related wild strains (ATCC 42981, ABT 301, and ABT 601). The cell cycle analysis by flow cytometry revealed a genome size of 12.7+/-0.2 Mb for strain CBS 732T, 21.9+/-0.2 Mb for ATCC 42981, 28.1+/-1.3 Mb for ABT 301, and 39.00+/-0.3 Mb for ABT 601. Moreover, karyotyping analysis showed a high variability, with wild strains having a higher number of chromosomal bands than CBS 732T. The ploidy level was assessed comparing genome size from flow cytometry with the average haploid size from electrophoretic karyotyping. Strain CBS 732T showed an haploid DNA content, whereas the wild strains a diploid DNA content. In addition gene probe-chromosome hybridization targeted to ZSOD genes showed that wild strains with a diploid DNA content have two ZSOD copies located on different chromosomes.
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Yashchenko VV, Potekhin AA, Migunova AV, Kvitko KV, Rautian MS. Identification of Chlorella viruses in Paramecium bursaria clones by pulse-field electrophoresis. Microbiology (Reading) 2008. [DOI: 10.1134/s0026261708050135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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