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Lindsay RJ, Holder PJ, Hewlett M, Gudelj I. Experimental evolution of yeast shows that public-goods upregulation can evolve despite challenges from exploitative non-producers. Nat Commun 2024; 15:7810. [PMID: 39242624 PMCID: PMC11379824 DOI: 10.1038/s41467-024-52043-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 08/23/2024] [Indexed: 09/09/2024] Open
Abstract
Microbial secretions, such as metabolic enzymes, are often considered to be cooperative public goods as they are costly to produce but can be exploited by others. They create incentives for the evolution of non-producers, which can drive producer and population productivity declines. In response, producers can adjust production levels. Past studies suggest that while producers lower production to reduce costs and exploitation opportunities when under strong selection pressure from non-producers, they overproduce secretions when these pressures are weak. We challenge the universality of this trend with the production of a metabolic enzyme, invertase, by Saccharomyces cerevisiae, which catalyses sucrose hydrolysis into two hexose molecules. Contrary to past studies, overproducers evolve during evolutionary experiments even when under strong selection pressure from non-producers. Phenotypic and competition assays with a collection of synthetic strains - engineered to have modified metabolic attributes - identify two mechanisms for suppressing the benefits of invertase to those who exploit it. Invertase overproduction increases extracellular hexose concentrations that suppresses the metabolic efficiency of competitors, due to the rate-efficiency trade-off, and also enhances overproducers' hexose capture rate by inducing transporter expression. Thus, overproducers are maintained in the environment originally thought to not support public goods production.
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Affiliation(s)
- Richard J Lindsay
- Biosciences and Living Systems Institute, University of Exeter, Exeter, UK
| | - Philippa J Holder
- Biosciences and Living Systems Institute, University of Exeter, Exeter, UK
| | - Mark Hewlett
- Biosciences and Living Systems Institute, University of Exeter, Exeter, UK
| | - Ivana Gudelj
- Biosciences and Living Systems Institute, University of Exeter, Exeter, UK.
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2
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Rahnama M, Novikova O, Starnes JH, Zhang S, Chen L, Farman ML. Transposon-mediated telomere destabilization: a driver of genome evolution in the blast fungus. Nucleic Acids Res 2020; 48:7197-7217. [PMID: 32558886 PMCID: PMC7367193 DOI: 10.1093/nar/gkaa287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 04/03/2020] [Accepted: 04/14/2020] [Indexed: 01/01/2023] Open
Abstract
The fungus Magnaporthe oryzae causes devastating diseases of crops, including rice and wheat, and in various grasses. Strains from ryegrasses have highly unstable chromosome ends that undergo frequent rearrangements, and this has been associated with the presence of retrotransposons (Magnaporthe oryzae Telomeric Retrotransposons-MoTeRs) inserted in the telomeres. The objective of the present study was to determine the mechanisms by which MoTeRs promote telomere instability. Targeted cloning, mapping, and sequencing of parental and novel telomeric restriction fragments (TRFs), along with MinION sequencing of genomic DNA allowed us to document the precise molecular alterations underlying 109 newly-formed TRFs. These included truncations of subterminal rDNA sequences; acquisition of MoTeR insertions by 'plain' telomeres; insertion of the MAGGY retrotransposons into MoTeR arrays; MoTeR-independent expansion and contraction of subtelomeric tandem repeats; and a variety of rearrangements initiated through breaks in interstitial telomere tracts that are generated during MoTeR integration. Overall, we estimate that alterations occurred in approximately sixty percent of chromosomes (one in three telomeres) analyzed. Most importantly, we describe an entirely new mechanism by which transposons can promote genomic alterations at exceptionally high frequencies, and in a manner that can promote genome evolution while minimizing collateral damage to overall chromosome architecture and function.
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Affiliation(s)
- Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Olga Novikova
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - John H Starnes
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Shouan Zhang
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Li Chen
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Mark L Farman
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
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3
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Borovkova AN, Michailova YV, Naumova ES. Molecular Genetic Features of Biological Species of the Genus Saccharomyces. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720040037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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4
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Pande S, Kost C. Bacterial Unculturability and the Formation of Intercellular Metabolic Networks. Trends Microbiol 2017; 25:349-361. [DOI: 10.1016/j.tim.2017.02.015] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 11/27/2022]
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5
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Zhang CY, Lin X, Feng B, Liu XE, Bai XW, Xu J, Pi L, Xiao DG. Enhanced leavening properties of baker's yeast by reducing sucrase activity in sweet dough. Appl Microbiol Biotechnol 2016; 100:6375-6383. [PMID: 27041690 DOI: 10.1007/s00253-016-7449-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/06/2016] [Accepted: 03/08/2016] [Indexed: 11/29/2022]
Abstract
Leavening ability in sweet dough is required for the commercial applications of baker's yeast. This property depends on many factors, such as glycolytic activity, sucrase activity, and osmotolerance. This study explored the importance of sucrase level on the leavening ability of baker's yeast in sweet dough. Furthermore, the baker's yeast strains with varying sucrase activities were constructed by deleting SUC2, which encodes sucrase or replacing the SUC2 promoter with the VPS8/TEF1 promoter. The results verify that the sucrase activity negatively affects the leavening ability of baker's yeast strains under high-sucrose conditions. Based on a certain level of osmotolerance, sucrase level plays a significant role in the fermentation performance of baker's yeast, and appropriate sucrase activity is an important determinant for the leavening property of baker's yeast in sweet dough. Therefore, modification on sucrase activity is an effective method for improving the leavening properties of baker's yeast in sweet dough. This finding provides guidance for the breeding of industrial baker's yeast strains for sweet dough leavening. The transformants BS1 with deleted SUC2 genetic background provided decreased sucrase activity (a decrease of 39.3 %) and exhibited enhanced leavening property (an increase of 12.4 %). Such a strain could be useful for industrial applications.
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Affiliation(s)
- Cui-Ying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China. .,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Xue Lin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Bing Feng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xiao-Er Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xiao-Wen Bai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Jia Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Li Pi
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Dong-Guang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China. .,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
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6
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Lindsay RJ, Kershaw MJ, Pawlowska BJ, Talbot NJ, Gudelj I. Harbouring public good mutants within a pathogen population can increase both fitness and virulence. eLife 2016; 5:e18678. [PMID: 28029337 PMCID: PMC5193496 DOI: 10.7554/elife.18678] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/14/2016] [Indexed: 01/27/2023] Open
Abstract
Existing theory, empirical, clinical and field research all predict that reducing the virulence of individuals within a pathogen population will reduce the overall virulence, rendering disease less severe. Here, we show that this seemingly successful disease management strategy can fail with devastating consequences for infected hosts. We deploy cooperation theory and a novel synthetic system involving the rice blast fungus Magnaporthe oryzae. In vivo infections of rice demonstrate that M. oryzae virulence is enhanced, quite paradoxically, when a public good mutant is present in a population of high-virulence pathogens. We reason that during infection, the fungus engages in multiple cooperative acts to exploit host resources. We establish a multi-trait cooperation model which suggests that the observed failure of the virulence reduction strategy is caused by the interference between different social traits. Multi-trait cooperative interactions are widespread, so we caution against the indiscriminant application of anti-virulence therapy as a disease-management strategy.
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Affiliation(s)
| | | | | | | | - Ivana Gudelj
- School of Biosciences, University of Exeter, Exeter, United Kingdom,
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7
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Waite AJ, Cannistra C, Shou W. Defectors Can Create Conditions That Rescue Cooperation. PLoS Comput Biol 2015; 11:e1004645. [PMID: 26690946 PMCID: PMC4687000 DOI: 10.1371/journal.pcbi.1004645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 11/05/2015] [Indexed: 11/18/2022] Open
Abstract
Cooperation based on the production of costly common goods is observed throughout nature. This is puzzling, as cooperation is vulnerable to exploitation by defectors which enjoy a fitness advantage by consuming the common good without contributing fairly. Depletion of the common good can lead to population collapse and the destruction of cooperation. However, population collapse implies small population size, which, in a structured population, is known to favor cooperation. This happens because small population size increases variability in cooperator frequency across different locations. Since individuals in cooperator-dominated locations (which are most likely cooperators) will grow more than those in defector-dominated locations (which are most likely defectors), cooperators can outgrow defectors globally despite defectors outgrowing cooperators in each location. This raises the possibility that defectors can lead to conditions that sometimes rescue cooperation from defector-induced destruction. We demonstrate multiple mechanisms through which this can occur, using an individual-based approach to model stochastic birth, death, migration, and mutation events. First, during defector-induced population collapse, defectors occasionally go extinct before cooperators by chance, which allows cooperators to grow. Second, empty locations, either preexisting or created by defector-induced population extinction, can favor cooperation because they allow cooperator but not defector migrants to grow. These factors lead to the counterintuitive result that the initial presence of defectors sometimes allows better survival of cooperation compared to when defectors are initially absent. Finally, we find that resource limitation, inducible by defectors, can select for mutations adaptive to resource limitation. When these mutations are initially present at low levels or continuously generated at a moderate rate, they can favor cooperation by further reducing local population size. We predict that in a structured population, small population sizes precipitated by defectors provide a "built-in" mechanism for the persistence of cooperation.
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Affiliation(s)
- Adam James Waite
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (AJW); (WS)
| | - Caroline Cannistra
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Wenying Shou
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (AJW); (WS)
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8
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Marques WL, Raghavendran V, Stambuk BU, Gombert AK. Sucrose and Saccharomyces cerevisiae: a relationship most sweet. FEMS Yeast Res 2015; 16:fov107. [PMID: 26658003 DOI: 10.1093/femsyr/fov107] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2015] [Indexed: 12/16/2022] Open
Abstract
Sucrose is an abundant, readily available and inexpensive substrate for industrial biotechnology processes and its use is demonstrated with much success in the production of fuel ethanol in Brazil. Saccharomyces cerevisiae, which naturally evolved to efficiently consume sugars such as sucrose, is one of the most important cell factories due to its robustness, stress tolerance, genetic accessibility, simple nutrient requirements and long history as an industrial workhorse. This minireview is focused on sucrose metabolism in S. cerevisiae, a rather unexplored subject in the scientific literature. An analysis of sucrose availability in nature and yeast sugar metabolism was performed, in order to understand the molecular background that makes S. cerevisiae consume this sugar efficiently. A historical overview on the use of sucrose and S. cerevisiae by humans is also presented considering sugarcane and sugarbeet as the main sources of this carbohydrate. Physiological aspects of sucrose consumption are compared with those concerning other economically relevant sugars. Also, metabolic engineering efforts to alter sucrose catabolism are presented in a chronological manner. In spite of its extensive use in yeast-based industries, a lot of basic and applied research on sucrose metabolism is imperative, mainly in fields such as genetics, physiology and metabolic engineering.
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Affiliation(s)
- Wesley Leoricy Marques
- Department of Chemical Engineering, University of São Paulo, São Paulo-SP, 05424-970, Brazil School of Food Engineering, University of Campinas, Campinas-SP, 13083-862, Brazil
| | | | - Boris Ugarte Stambuk
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis-SC, 88040-900, Brazil
| | - Andreas Karoly Gombert
- Department of Chemical Engineering, University of São Paulo, São Paulo-SP, 05424-970, Brazil School of Food Engineering, University of Campinas, Campinas-SP, 13083-862, Brazil
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9
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Hu W, Suo F, Du LL. Bulk Segregant Analysis Reveals the Genetic Basis of a Natural Trait Variation in Fission Yeast. Genome Biol Evol 2015; 7:3496-510. [PMID: 26615217 PMCID: PMC4700965 DOI: 10.1093/gbe/evv238] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although the fission yeast Schizosaccharomyces pombe is a well-established model organism, studies of natural trait variations in this species remain limited. To assess the feasibility of segregant-pool-based mapping of phenotype-causing genes in natural strains of fission yeast, we investigated the cause of a maltose utilization defect (Mal(-)) of the S. pombe strain CBS5557 (originally known as Schizosaccharomyces malidevorans). Analyzing the genome sequence of CBS5557 revealed 955 nonconservative missense substitutions, and 61 potential loss-of-function variants including 47 frameshift indels, 13 early stop codons, and 1 splice site mutation. As a side benefit, our analysis confirmed 146 sequence errors in the reference genome and improved annotations of 27 genes. We applied bulk segregant analysis to map the causal locus of the Mal(-) phenotype. Through sequencing the segregant pools derived from a cross between CBS5557 and the laboratory strain, we located the locus to within a 2.23-Mb chromosome I inversion found in most S. pombe isolates including CBS5557. To map genes within the inversion region that occupies 18% of the genome, we created a laboratory strain containing the same inversion. Analyzing segregants from a cross between CBS5557 and the inversion-containing laboratory strain narrowed down the locus to a 200-kb interval and led us to identify agl1, which suffers a 5-bp deletion in CBS5557, as the causal gene. Interestingly, loss of agl1 through a 34-kb deletion underlies the Mal(-) phenotype of another S. pombe strain CGMCC2.1628. This work adapts and validates the bulk segregant analysis method for uncovering trait-gene relationship in natural fission yeast strains.
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Affiliation(s)
- Wen Hu
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
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10
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Black Queen evolution: the role of leakiness in structuring microbial communities. Trends Genet 2015; 31:475-82. [DOI: 10.1016/j.tig.2015.05.004] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 11/21/2022]
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11
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Naumov GI, Naumova ES. Invertase overproduction may provide for inulin fermentation by selection strains of Saccharomyces cerevisiae. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715020095] [Citation(s) in RCA: 1] [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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12
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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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13
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Naumova ES, Sadykova AZ, Martynenko NN, Naumov GI. Molecular polymorphism of β-fructosidase SUC genes in the Saccharomyces yeasts. Mol Biol 2014. [DOI: 10.1134/s0026893314040086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Abstract
The fight against cancer has drawn researchers from a wide variety of disciplines, ranging from molecular biology to physics, but the perspective of an ecological theorist has been mostly overlooked. By thinking about the cells that make up a tumour as an endangered species, cancer vulnerabilities become more apparent. Studies in conservation biology and microbial experiments indicate that extinction is a complex phenomenon, which is often driven by the interaction of ecological and evolutionary processes. Recent advances in cancer research have shown that tumours, like species striving for survival, harbour intricate population dynamics, which suggests the possibility to exploit the ecology of tumours for treatment.
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Affiliation(s)
- Kirill S Korolev
- Bioinformatics Program, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, USA
| | - Joao B Xavier
- Memorial Sloan-Kettering Cancer Center, Computational Biology Program, New York, New York, USA
| | - Jeff Gore
- Massachusetts Institute of Technology, 400 Technology Square, NE46-609 Cambridge, Massachusetts, USA
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15
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Naumova ES, Sadykova AZ, Martynenko NN, Naumov GI. Molecular genetic characteristics of Saccharomyces cerevisiae distillers’ yeasts. Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713020112] [Citation(s) in RCA: 12] [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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16
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Adaptation to a new environment allows cooperators to purge cheaters stochastically. Proc Natl Acad Sci U S A 2012; 109:19079-86. [PMID: 23091010 DOI: 10.1073/pnas.1210190109] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cooperation via production of common goods is found in diverse life forms ranging from viruses to social animals. However, natural selection predicts a "tragedy of the commons": Cheaters, benefiting from without producing costly common goods, are more fit than cooperators and should destroy cooperation. In an attempt to discover novel mechanisms of cheater control, we eliminated known ones using a yeast cooperator-cheater system engineered to supply or exploit essential nutrients. Surprisingly, although less fit than cheaters, cooperators quickly dominated a fraction of cocultures. Cooperators isolated from these cocultures were superior to the cheater isolates they had been cocultured with, even though these cheaters were superior to ancestral cooperators. Resequencing and phenotypic analyses revealed that evolved cooperators and cheaters all harbored mutations adaptive to the nutrient-limited cooperative environment, allowing growth at a much lower concentration of nutrient than their ancestors. Even after the initial round of adaptation, evolved cooperators still stochastically dominated cheaters derived from them. We propose the "adaptive race" model: If during adaptation to an environment, the fitness gain of cooperators exceeds that of cheaters by at least the fitness cost of cooperation, the tragedy of the commons can be averted. Although cooperators and cheaters sample from the same pool of adaptive mutations, this symmetry is soon broken: The best cooperators purge cheaters and continue to grow, whereas the best cheaters cause rapid self-extinction. We speculate that adaptation to changing environments may contribute to the persistence of cooperative systems before the appearance of more sophisticated mechanisms of cheater control.
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17
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Starnes JH, Thornbury DW, Novikova OS, Rehmeyer CJ, Farman ML. Telomere-targeted retrotransposons in the rice blast fungus Magnaporthe oryzae: agents of telomere instability. Genetics 2012; 191:389-406. [PMID: 22446319 PMCID: PMC3374306 DOI: 10.1534/genetics.111.137950] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 03/11/2012] [Indexed: 02/07/2023] Open
Abstract
The fungus Magnaporthe oryzae is a serious pathogen of rice and other grasses. Telomeric restriction fragments in Magnaporthe isolates that infect perennial ryegrass (prg) are hotspots for genomic rearrangement and undergo frequent, spontaneous alterations during fungal culture. The telomeres of rice-infecting isolates are very stable by comparison. Sequencing of chromosome ends from a number of prg-infecting isolates revealed two related non-LTR retrotransposons (M. oryzae Telomeric Retrotransposons or MoTeRs) inserted in the telomere repeats. This contrasts with rice pathogen telomeres that are uninterrupted by other sequences. Genetic evidence indicates that the MoTeR elements are responsible for the observed instability. MoTeRs represent a new family of telomere-targeted transposons whose members are found exclusively in fungi.
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Affiliation(s)
| | - David W. Thornbury
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | - Olga S. Novikova
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | | | - Mark L. Farman
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
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18
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Social interaction in synthetic and natural microbial communities. Mol Syst Biol 2011; 7:483. [PMID: 21487402 PMCID: PMC3101950 DOI: 10.1038/msb.2011.16] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/08/2011] [Indexed: 12/13/2022] Open
Abstract
How do molecular networks at the single-cell level define collective cell behavior? This Review discusses recent studies on synthetic and natural microbial communities that dissect the molecular and dynamical mechanisms underlying microbial social evolution. Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual- and population-level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same ‘social interaction motifs' may be general to many cell populations.
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19
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Naumov GI. Are melibiose-fermenting intestinal and alpechin strains of Saccharomyces cerevisiae a novel type of yeast probiotics? DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2011; 439:262-263. [PMID: 21953238 DOI: 10.1134/s0012496611040223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Indexed: 05/31/2023]
Affiliation(s)
- G I Naumov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, Pervyi Dorozhnyi pr. 1, Moscow 117545, Russia
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20
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Naumov GI, Naumova ES. Comparative genetics of yeast Saccharomyces cerevisiae. Chromosomal translocations carrying the SUC2 marker. RUSS J GENET+ 2011. [DOI: 10.1134/s102279541011102x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Schuster S, Kreft JU, Brenner N, Wessely F, Theissen G, Ruppin E, Schroeter A. Cooperation and cheating in microbial exoenzyme production--theoretical analysis for biotechnological applications. Biotechnol J 2010; 5:751-8. [PMID: 20540107 DOI: 10.1002/biot.200900303] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The engineering of microorganisms to produce a variety of extracellular enzymes (exoenzymes), for example for producing renewable fuels and in biodegradation of xenobiotics, has recently attracted increasing interest. Productivity is often reduced by "cheater" mutants, which are deficient in exoenzyme production and benefit from the product provided by the "cooperating" cells. We present a game-theoretical model to analyze population structure and exoenzyme productivity in terms of biotechnologically relevant parameters. For any given population density, three distinct regimes are predicted: when the metabolic effort for exoenzyme production and secretion is low, all cells cooperate; at intermediate metabolic costs, cooperators and cheaters coexist; while at high costs, all cells use the cheating strategy. These regimes correspond to the harmony game, snowdrift game, and Prisoner's Dilemma, respectively. Thus, our results indicate that microbial strains engineered for exoenzyme production will not, under appropriate conditions, be outcompeted by cheater mutants. We also analyze the dependence of the population structure on cell density. At low costs, the fraction of cooperating cells increases with decreasing cell density and reaches unity at a critical threshold. Our model provides an estimate of the cell density maximizing exoenzyme production.
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Affiliation(s)
- Stefan Schuster
- Department of Bioinformatics, School of Biology and Pharmaceutics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, Jena, Germany
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22
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A mixture of "cheats" and "co-operators" can enable maximal group benefit. PLoS Biol 2010; 8. [PMID: 20856906 PMCID: PMC2939026 DOI: 10.1371/journal.pbio.1000486] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 08/04/2010] [Indexed: 11/19/2022] Open
Abstract
Is a group best off if everyone co-operates? Theory often considers this to be so (e.g. the "conspiracy of doves"), this understanding underpinning social and economic policy. We observe, however, that after competition between "cheat" and "co-operator" strains of yeast, population fitness is maximized under co-existence. To address whether this might just be a peculiarity of our experimental system or a result with broader applicability, we assemble, benchmark, dissect, and test a systems model. This reveals the conditions necessary to recover the unexpected result. These are 3-fold: (a) that resources are used inefficiently when they are abundant, (b) that the amount of co-operation needed cannot be accurately assessed, and (c) the population is structured, such that co-operators receive more of the resource than the cheats. Relaxing any of the assumptions can lead to population fitness being maximized when cheats are absent, which we experimentally demonstrate. These three conditions will often be relevant, and hence in order to understand the trajectory of social interactions, understanding the dynamics of the efficiency of resource utilization and accuracy of information will be necessary.
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Arvas M, Haiminen N, Smit B, Rautio J, Vitikainen M, Wiebe M, Martinez D, Chee C, Kunkel J, Sanchez C, Nelson MA, Pakula T, Saloheimo M, Penttilä M, Kivioja T. Detecting novel genes with sparse arrays. Gene 2010; 467:41-51. [PMID: 20691772 DOI: 10.1016/j.gene.2010.07.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/30/2010] [Accepted: 07/15/2010] [Indexed: 11/19/2022]
Abstract
Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods and tiling arrays can be used to find genes without prior information and they have demonstrated that novel genes can still be found from extensively studied model organisms. Unfortunately, these methods are expensive and thus are not easily applicable, e.g., to finding genes that are expressed only in very specific conditions. We demonstrate a method for finding novel genes with sparse arrays, applying it on the 33.9 Mb genome of the filamentous fungus Trichoderma reesei. Our computational method does not require normalisations between arrays and it takes into account the multiple-testing problem typical for analysis of microarray data. In contrast to tiling arrays, that use overlapping probes, only one 25 mer microarray oligonucleotide probe was used for every 100b. Thus, only relatively little space on a microarray slide was required to cover the intergenic regions of a genome. The analysis was done as a by-product of a conventional microarray experiment with no additional costs. We found at least 23 good candidates for novel transcripts that could code for proteins and all of which were expressed at high levels. Candidate genes were found to neighbour ire1 and cre1 and many other regulatory genes. Our simple, low-cost method can easily be applied to finding novel species-specific genes without prior knowledge of their sequence properties.
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Affiliation(s)
- Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, PO Box FI-1000, 02044 VTT, Espoo, Finland.
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Lin Z, Li WH. Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts. Mol Biol Evol 2010; 28:131-42. [PMID: 20660490 DOI: 10.1093/molbev/msq184] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The genetic basis of organisms' adaptation to different environments is a central issue of molecular evolution. The budding yeast Saccharomyces cerevisiae and its relatives predominantly ferment glucose into ethanol even in the presence of oxygen. This was suggested to be an adaptation to glucose-rich habitats, but the underlying genetic basis of the evolution of aerobic fermentation remains unclear. In S. cerevisiae, the first step of glucose metabolism is transporting glucose across the plasma membrane, which is carried out by hexose transporter proteins. Although several studies have recognized that the rate of glucose uptake can affect how glucose is metabolized, the role of HXT genes in the evolution of aerobic fermentation has not been fully explored. In this study, we identified all members of the HXT gene family in 23 fully sequenced fungal genomes, reconstructed their evolutionary history to pinpoint gene gain and loss events, and evaluated their adaptive significance in the evolution of aerobic fermentation. We found that the HXT genes have been extensively amplified in the two fungal lineages that have independently evolved aerobic fermentation. In contrast, reduction of the number of HXT genes has occurred in aerobic respiratory species. Our study reveals a strong positive correlation between the copy number of HXT genes and the strength of aerobic fermentation, suggesting that HXT gene expansion has facilitated the evolution of aerobic fermentation.
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Affiliation(s)
- Zhenguo Lin
- Department of Ecology and Evolution, University of Chicago, USA
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25
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Hauser NC, Fellenberg K, Gil R, Bastuck S, Hoheisel JD, Pérez-Ortín JE. Whole genome analysis of a wine yeast strain. Comp Funct Genomics 2010; 2:69-79. [PMID: 18628902 PMCID: PMC2447197 DOI: 10.1002/cfg.73] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2000] [Accepted: 02/21/2001] [Indexed: 11/28/2022] Open
Abstract
Saccharomyces cerevisiae strains frequently exhibit rather specific phenotypic features
needed for adaptation to a special environment. Wine yeast strains are able to ferment
musts, for example, while other industrial or laboratory strains fail to do so. The genetic
differences that characterize wine yeast strains are poorly understood, however. As a first
search of genetic differences between wine and laboratory strains, we performed DNA-array
analyses on the typical wine yeast strain T73 and the standard laboratory
background in S288c. Our analysis shows that even under normal conditions, logarithmic
growth in YPD medium, the two strains have expression patterns that differ significantly in
more than 40 genes. Subsequent studies indicated that these differences correlate with
small changes in promoter regions or variations in gene copy number. Blotting copy
numbers vs. transcript levels produced patterns, which were specific for the individual
strains and could be used for a characterization of unknown samples.
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Affiliation(s)
- N C Hauser
- Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, Heidelberg D-69120, Germany
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26
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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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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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Gore J, Youk H, van Oudenaarden A. Snowdrift game dynamics and facultative cheating in yeast. Nature 2009; 459:253-6. [PMID: 19349960 PMCID: PMC2888597 DOI: 10.1038/nature07921] [Citation(s) in RCA: 413] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2008] [Accepted: 02/11/2009] [Indexed: 12/04/2022]
Abstract
The origin of cooperation is a central challenge to our understanding of evolution1–3. Microbial interactions can be manipulated in ways that animal interactions cannot, thus leading to growing interest in microbial models of cooperation4–10 and competition11,12. In order for the budding yeast S. cerevisiae to grow on sucrose, the disaccharide must first be hydrolyzed by the enzyme invertase13,14. This hydrolysis reaction is performed outside of the cytoplasm in the periplasmic space between the plasma membrane and the cell wall. Here we demonstrate that the vast majority (~99%) of the monosaccharides created by sucrose hydrolysis diffuse away before they can be imported into the cell, thus making invertase production and secretion a cooperative behavior15,16. A mutant cheater strain that does not produce invertase is able to take advantage of and invade a population of wildtype cooperator cells. However, over a wide range of conditions, the wildtype cooperator can also invade a population of cheater cells. Therefore, we observe coexistence between the two strains in well-mixed culture at steady state resulting from the fact that rare strategies outperform common strategies—the defining features of what game theorists call the snowdrift game17. A model of the cooperative interaction incorporating nonlinear benefits explains the origin of this coexistence. We are able to alter the outcome of the competition by varying either the cost of cooperation or the glucose concentration in the media. Finally, we note that glucose repression of invertase expression in wildtype cells produces a strategy which is optimal for the snowdrift game—wildtype cells cooperate only when competing against cheater cells.
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Affiliation(s)
- Jeff Gore
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Craig Maclean R, Brandon C. Stable public goods cooperation and dynamic social interactions in yeast. J Evol Biol 2008; 21:1836-43. [PMID: 18643862 DOI: 10.1111/j.1420-9101.2008.01579.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite long-standing theoretical interest in the evolution of cooperation, empirical data on the evolutionary dynamics of cooperative traits remain limited. Here, we investigate the evolutionary dynamics of a simple public goods cooperative trait, invertase secretion, using a long-term selection experiment in Saccharomyces cerevisiae. We show that average investment in cooperation remains essentially constant over a period of hundreds of generations in viscous populations with high relatedness. Average cooperation remains constant despite transient local selection for high and low levels of cooperation that generate dynamic social interactions. Natural populations of yeast show similar variation in social strategies, which is consistent with the existence of similar selective pressures on public goods cooperation in nature.
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Affiliation(s)
- R Craig Maclean
- NERC Centre for Population Biology, Imperial College London, Silwood Park, Ascot, UK.
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30
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Badotti F, Dário MG, Alves SL, Cordioli MLA, Miletti LC, de Araujo PS, Stambuk BU. Switching the mode of sucrose utilization by Saccharomyces cerevisiae. Microb Cell Fact 2008; 7:4. [PMID: 18304329 PMCID: PMC2268662 DOI: 10.1186/1475-2859-7-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Accepted: 02/27/2008] [Indexed: 11/17/2022] Open
Abstract
Background Overflow metabolism is an undesirable characteristic of aerobic cultures of Saccharomyces cerevisiae during biomass-directed processes. It results from elevated sugar consumption rates that cause a high substrate conversion to ethanol and other bi-products, severely affecting cell physiology, bioprocess performance, and biomass yields. Fed-batch culture, where sucrose consumption rates are controlled by the external addition of sugar aiming at its low concentrations in the fermentor, is the classical bioprocessing alternative to prevent sugar fermentation by yeasts. However, fed-batch fermentations present drawbacks that could be overcome by simpler batch cultures at relatively high (e.g. 20 g/L) initial sugar concentrations. In this study, a S. cerevisiae strain lacking invertase activity was engineered to transport sucrose into the cells through a low-affinity and low-capacity sucrose-H+ symport activity, and the growth kinetics and biomass yields on sucrose analyzed using simple batch cultures. Results We have deleted from the genome of a S. cerevisiae strain lacking invertase the high-affinity sucrose-H+ symporter encoded by the AGT1 gene. This strain could still grow efficiently on sucrose due to a low-affinity and low-capacity sucrose-H+ symport activity mediated by the MALx1 maltose permeases, and its further intracellular hydrolysis by cytoplasmic maltases. Although sucrose consumption by this engineered yeast strain was slower than with the parental yeast strain, the cells grew efficiently on sucrose due to an increased respiration of the carbon source. Consequently, this engineered yeast strain produced less ethanol and 1.5 to 2 times more biomass when cultivated in simple batch mode using 20 g/L sucrose as the carbon source. Conclusion Higher cell densities during batch cultures on 20 g/L sucrose were achieved by using a S. cerevisiae strain engineered in the sucrose uptake system. Such result was accomplished by effectively reducing sucrose uptake by the yeast cells, avoiding overflow metabolism, with the concomitant reduction in ethanol production. The use of this modified yeast strain in simpler batch culture mode can be a viable option to more complicated traditional sucrose-limited fed-batch cultures for biomass-directed processes of S. cerevisiae.
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Affiliation(s)
- Fernanda Badotti
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil.
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Arvas M, Kivioja T, Mitchell A, Saloheimo M, Ussery D, Penttila M, Oliver S. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. BMC Genomics 2007; 8:325. [PMID: 17868481 PMCID: PMC2045113 DOI: 10.1186/1471-2164-8-325] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 09/17/2007] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Several dozen fungi encompassing traditional model organisms, industrial production organisms and human and plant pathogens have been sequenced recently and their particular genomic features analysed in detail. In addition comparative genomics has been used to analyse specific sub groups of fungi. Notably, analysis of the phylum Saccharomycotina has revealed major events of evolution such as the recent genome duplication and subsequent gene loss. However, little has been done to gain a comprehensive comparative view to the fungal kingdom. We have carried out a computational genome wide comparison of protein coding gene content of Saccharomycotina and Pezizomycotina, which include industrially important yeasts and filamentous fungi, respectively. RESULTS Our analysis shows that based on genome redundancy, the traditional model organisms Saccharomyces cerevisiae and Neurospora crassa are exceptional among fungi. This can be explained by the recent genome duplication in S. cerevisiae and the repeat induced point mutation mechanism in N. crassa. Interestingly in Pezizomycotina a subset of protein families related to plant biomass degradation and secondary metabolism are the only ones showing signs of recent expansion. In addition, Pezizomycotina have a wealth of phylum specific poorly characterised genes with a wide variety of predicted functions. These genes are well conserved in Pezizomycotina, but show no signs of recent expansion. The genes found in all fungi except Saccharomycotina are slightly better characterised and predicted to encode mainly enzymes. The genes specific to Saccharomycotina are enriched in transcription and mitochondrion related functions. Especially mitochondrial ribosomal proteins seem to have diverged from those of Pezizomycotina. In addition, we highlight several individual gene families with interesting phylogenetic distributions. CONCLUSION Our analysis predicts that all Pezizomycotina unlike Saccharomycotina can potentially produce a wide variety of secondary metabolites and secreted enzymes and that the responsible gene families are likely to evolve fast. Both types of fungal products can be of commercial value, or on the other hand cause harm to humans. In addition, a great number of novel predicted and known enzymes are found from all fungi except Saccharomycotina. Therefore further studies and exploitation of fungal metabolism appears very promising.
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Affiliation(s)
- Mikko Arvas
- VTT, Tietotie 2, Espoo, P.O. Box 1500, 02044 VTT, Finland
| | - Teemu Kivioja
- Biomedicum, P.O. Box 63 (Haartmaninkatu 8), FI-00014 University of Helsinki, Finland
| | - Alex Mitchell
- EMBL Outstation – Hinxton, European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - David Ussery
- Center for Biological Sequence Analysis BioCentrum-DTU The Technical University of Denmark DK-2800 Kgs. Lyngby, Denmark
| | - Merja Penttila
- VTT, Tietotie 2, Espoo, P.O. Box 1500, 02044 VTT, Finland
| | - Stephen Oliver
- University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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Rehmeyer C, Li W, Kusaba M, Kim YS, Brown D, Staben C, Dean R, Farman M. Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucleic Acids Res 2006; 34:4685-701. [PMID: 16963777 PMCID: PMC1635262 DOI: 10.1093/nar/gkl588] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Eukaryotic pathogens of humans often evade the immune system by switching the expression of surface proteins encoded by subtelomeric gene families. To determine if plant pathogenic fungi use a similar mechanism to avoid host defenses, we sequenced the 14 chromosome ends of the rice blast pathogen, Magnaporthe oryzae. One telomere is directly joined to ribosomal RNA-encoding genes, at the end of the ∼2 Mb rDNA array. Two are attached to chromosome-unique sequences, and the remainder adjoin a distinct subtelomere region, consisting of a telomere-linked RecQ-helicase (TLH) gene flanked by several blocks of tandem repeats. Unlike other microbes, M.oryzae exhibits very little gene amplification in the subtelomere regions—out of 261 predicted genes found within 100 kb of the telomeres, only four were present at more than one chromosome end. Therefore, it seems unlikely that M.oryzae uses switching mechanisms to evade host defenses. Instead, the M.oryzae telomeres have undergone frequent terminal truncation, and there is evidence of extensive ectopic recombination among transposons in these regions. We propose that the M.oryzae chromosome termini play more subtle roles in host adaptation by promoting the loss of terminally-positioned genes that tend to trigger host defenses.
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Affiliation(s)
- Cathryn Rehmeyer
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
| | - Weixi Li
- Department of Biology, University of KentuckyLexington, KY 40546 USA
| | - Motoaki Kusaba
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
| | - Yun-Sik Kim
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
| | - Doug Brown
- Center for Integrated Fungal Research, North Carolina State UniversityRaleigh, NC 27695 USA
| | - Chuck Staben
- Department of Biology, University of KentuckyLexington, KY 40546 USA
| | - Ralph Dean
- Center for Integrated Fungal Research, North Carolina State UniversityRaleigh, NC 27695 USA
| | - Mark Farman
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
- To whom correspondence should be addressed. Tel: 859 257 7445, ext. 80728; Fax: 859 323 1961;
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Korshunova IV, Naumova ES, Naumov GI. Comparative Molecular Genetic Analysis of β-Fructosidases of Yeasts Saccharomyces. Mol Biol 2005. [DOI: 10.1007/s11008-005-0051-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Fabre E, Muller H, Therizols P, Lafontaine I, Dujon B, Fairhead C. Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres. Mol Biol Evol 2004; 22:856-73. [PMID: 15616141 DOI: 10.1093/molbev/msi070] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The recent release of sequences of several unexplored yeast species that cover an evolutionary range comparable to the entire phylum of chordates offers us a unique opportunity to investigate how genes involved in adaptation have been shaped by evolution. We have examined how three different sets of genes, all related to adaptative processes at the genomic level, have evolved in hemiascomycetes: (1) the mating-type genes that govern sexuality, (2) the silencing genes that are connected to regulation of mating-type cassettes and to telomere position effect, and (3) the gene families found repeated in subtelomeric regions. We report new combinations of mating-type genes and cassettes in hemiascomycetous species; we show that silencing proteins diverge rapidly. We have also found that in all species studied, subtelomeric gene families exist and are specific to each species.
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Affiliation(s)
- Emmanuelle Fabre
- Unité de Génétique Moléculaire des Levures, URA2171 CNRS, UFR Université Pierre et Marie Curie, Département Structure et Dynamique des Génomes, Institut Pasteur, 75724 Cedex Paris, France.
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Abstract
The SUC multigene family of the single-celled yeast Saccharomyces cerevisiae is polymorphic, with genes varying both in number and activity. All of the genes encode invertase, an enzyme that is secreted to digest sucrose outside of the cell. This communal endeavour creates the potential for individual cells to defect (cheat) by stealing the sugar digested by their neighbours without contributing the enzyme themselves. We measured the fitness of a defector, with a deleted suc2 gene, relative to an otherwise isogenic cooperator, with a functional SUC2 gene. We manipulated the level of social interaction within the community by varying the population density and found that the defector is less fit than the cooperator at low levels of sociality but more fit in dense communities. We propose that selection for antisocial cheating causes SUC polymorphism in nature. The infamous Prisoner's Dilemma game shows that social behaviour is generally unstable, and the success of both cooperation and defection can vary continuously in time and space. The variation in SUC genes reflects constant adaptation to an ever-changing biotic environment that is a consequence of the instability of cooperation. It is interesting that social interactions can have a direct effect on molecular evolution, even in an organism as simple as yeast.
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Affiliation(s)
- Duncan Greig
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.
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Daran-Lapujade P, Daran JM, Kötter P, Petit T, Piper MDW, Pronk JT. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res 2004; 4:259-69. [PMID: 14654430 DOI: 10.1016/s1567-1356(03)00156-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
To analyse the reliability and accuracy of genotype analysis with high-density oligonucleotide microarrays, this method and other experimental approaches were used to analyse genomic DNA of two popular Saccharomyces cerevisiae laboratory strains. S288C was used for systematic sequencing of 'the' S. cerevisiae genome; CEN.PK113-7D is a popular strain for physiological studies and functional genomics. Random amplified polymorphic DNA, electrophoretic karyotyping and microarray analysis all indicated a high level of sequence similarity between the two strains. In the microarray analysis, as few as 288 (4.5%) of the ca. 6300 represented yeast genes were identified that yielded significantly different hybridisation intensities between the two strains. These could be classified as amplified, absent, or with sequence polymorphism in CEN.PK113-7D compared to S288C. A detailed analysis focused on the subset of 25 genes called absent in CEN.PK113-7D. Among these absent genes, 17 were clustered together on five chromosomes, mainly in subtelomeric regions. Thorough analysis of these regions by polymerase chain reaction (PCR) and restriction fragment length polymorphism confirmed the absence of these genes in CEN.PK113-7D. Surprisingly, three of these regions were not smaller in CEN.PK113-7D chromosomes, indicating that they may harbour unidentified and potentially new sequences. In addition, eight genes called absent by the microarrays were scattered over the chromosomes. Using diagnostic PCR most of these genes were actually found to be present in CEN.PK113-7D, but after sequencing were found to differ significantly at the DNA level from S288C, explaining the poor hybridisation to the arrays. Our results indicate that DNA microarrays are a powerful tool for determining genotypic similarity between different yeast strains. However, to obtain meaningful information at the individual gene level, this method should be backed up by additional techniques.
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Affiliation(s)
- Pascale Daran-Lapujade
- Kluyver Laboratory of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands.
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Naumova ES, Korshunova IV, Jespersen L, Naumov GI. Molecular genetic identification of Saccharomyces sensu stricto strains from African sorghum beer. FEMS Yeast Res 2003; 3:177-84. [PMID: 12702450 DOI: 10.1016/s1567-1356(02)00191-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Genetic relationships of 24 phenotypically different strains isolated from sorghum beer in West Africa and the type cultures of the Saccharomyces sensu stricto species were investigated by universally primed polymerase chain reaction (PCR) analysis, microsatellite fingerprinting and PCR-restriction fragment length polymorphism (RFLP) of the ribosomal internal transcribed spacers. The results demonstrate that internal transcribed spacer (ITS) PCR-RFLP analysis with the endonucleases HaeIII, HpaII, ScrFI and TaqI is useful for discriminating S. cerevisiae, S. kudriavzevii, S. mikatae from one another and from the S. bayanus/S. pastorianus and S. cariocanus/S. paradoxus pairs. The sorghum beer strains exhibited the same restriction patterns as the type culture of S. cerevisiae CBS 1171. PCR profiles generated with the microsatellite primer (GTG)(5) and the universal primer N21 were almost identical for all isolates and strain CBS 1171. Despite phenotypic peculiarities, the strains involved in sorghum beer production in Ghana and Burkina Faso belong to S. cerevisiae. However, based on sequencing of the rDNA ITS1 region and Southern hybridisation analysis, these strains represent a divergent population of S. cerevisiae.
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MESH Headings
- Base Sequence
- Beer/microbiology
- Blotting, Southern
- Burkina Faso
- DNA Fingerprinting
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Electrophoresis, Gel, Pulsed-Field
- Genetic Variation
- Ghana
- Microsatellite Repeats/genetics
- Molecular Sequence Data
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- Saccharomyces/classification
- Saccharomyces/genetics
- Saccharomyces/metabolism
- Sequence Alignment
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Affiliation(s)
- Elena S Naumova
- State Institute for Genetics and Selection of Industrial Microorganisms, I-Dorozhnyi 1, Moscow 117545, Russia
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Genetic diversity of yeasts in wine production. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1874-5334(02)80005-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Rincón AM, Codón AC, Castrejón F, Benítez T. Improved properties of baker's yeast mutants resistant to 2-deoxy-D-glucose. Appl Environ Microbiol 2001; 67:4279-85. [PMID: 11526034 PMCID: PMC93158 DOI: 10.1128/aem.67.9.4279-4285.2001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2001] [Accepted: 05/27/2001] [Indexed: 11/20/2022] Open
Abstract
We isolated spontaneous mutants from Saccharomyces cerevisiae (baker's yeast V1) that were resistant to 2-deoxy-D-glucose and had improved fermentative capacity on sweet doughs. Three mutants could grow at the same rate as the wild type in minimal SD medium (0.17% Difco yeast nitrogen base without amino acids and ammonium sulfate, 0.5% ammonium sulfate, 2% glucose) and had stable elevated levels of maltase and/or invertase under repression conditions but lower levels in maltose-supplemented media. Two of the mutants also had high levels of phosphatase active on 2-deoxy-D-glucose-6-phosphate. Dough fermentation (CO2 liberation) by two of the mutants was faster and/or produced higher final volumes than that by the wild type, both under laboratory and industrial conditions, when the doughs were supplemented with glucose or sucrose. However, the three mutants were slower when fermenting plain doughs. Fermented sweet bakery products obtained with these mutants were of better quality than those produced by the wild type, with regard to their texture and their organoleptic properties.
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Affiliation(s)
- A M Rincón
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41080 Sevilla, Spain
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Abstract
The recent characterisation of subtelomeric regions from a variety of organisms from yeast to man has led to the realisation that all chromosome ends are similar in structure although maintenance of the terminus varies. The mosaic of repeats and proteins associated with telomeres has an architectural role which divides the genome into two domains, allowing for the adaptive use of the region as well as the evolution of non-telomerase-mediated telomere maintenance.
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Affiliation(s)
- F E Pryde
- Institut of Molecular Medicine, John Radcliffe Hospital, Oxford UK
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Naumov G. Genetic identification of biological species in theSaccharomyces sensu stricto complex. J Ind Microbiol Biotechnol 1996. [DOI: 10.1007/bf01574704] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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