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Hao W. From Genome Variation to Molecular Mechanisms: What we Have Learned From Yeast Mitochondrial Genomes? Front Microbiol 2022; 13:806575. [PMID: 35126340 PMCID: PMC8811140 DOI: 10.3389/fmicb.2022.806575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/03/2022] [Indexed: 11/26/2022] Open
Abstract
Analysis of genome variation provides insights into mechanisms in genome evolution. This is increasingly appreciated with the rapid growth of genomic data. Mitochondrial genomes (mitogenomes) are well known to vary substantially in many genomic aspects, such as genome size, sequence context, nucleotide base composition and substitution rate. Such substantial variation makes mitogenomes an excellent model system to study the mechanisms dictating mitogenome variation. Recent sequencing efforts have not only covered a rich number of yeast species but also generated genomes from abundant strains within the same species. The rich yeast genomic data have enabled detailed investigation from genome variation into molecular mechanisms in genome evolution. This mini-review highlights some recent progresses in yeast mitogenome studies.
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Nespolo RF, Solano‐Iguaran JJ, Paleo‐López R, Quintero‐Galvis JF, Cubillos FA, Bozinovic F. Performance, genomic rearrangements, and signatures of adaptive evolution: Lessons from fermentative yeasts. Ecol Evol 2020; 10:5240-5250. [PMID: 32607147 PMCID: PMC7319171 DOI: 10.1002/ece3.6208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/20/2020] [Indexed: 01/27/2023] Open
Abstract
The capacity of some yeasts to extract energy from single sugars, generating CO2 and ethanol (=fermentation), even in the presence of oxygen, is known as the Crabtree effect. This phenomenon represents an important adaptation as it allowed the utilization of the ecological niche given by modern fruits, an abundant source of food that emerged in the terrestrial environment in the Cretaceous. However, identifying the evolutionary events that triggered fermentative capacity in Crabtree-positive species is challenging, as microorganisms do not leave fossil evidence. Thus, key innovations should be inferred based only on traits measured under culture conditions. Here, we reanalyzed data from a common garden experiment where several proxies of fermentative capacity were recorded in Crabtree-positive and Crabtree-negative species, representing yeast phylogenetic diversity. In particular, we applied the "lasso-OU" algorithm which detects points of adaptive shifts, using traits that are proxies of fermentative performance. We tested whether multiple events or a single event explains the actual fermentative capacity of yeasts. According to the lasso-OU procedure, evolutionary changes in the three proxies of fermentative capacity that we considered (i.e., glycerol production, ethanol yield, and respiratory quotient) are consistent with a single evolutionary episode (a whole-genomic duplication, WGD), instead of a series of small genomic rearrangements. Thus, the WGD appears as the key event behind the diversification of fermentative yeasts, which by increasing gene dosage, and maximized their capacity of energy extraction for exploiting the new ecological niche provided by single sugars.
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Affiliation(s)
- Roberto F. Nespolo
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
- Center of Applied Ecology and Sustainability (CAPES)Facultad de Ciencias BiológicasUniversidad Católica de ChileSantiagoChile
- Millennium Institute for Integrative Biology (iBio)SantiagoChile
| | | | - Rocío Paleo‐López
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | | | - Francisco A. Cubillos
- Millennium Institute for Integrative Biology (iBio)SantiagoChile
- Departamento de BiologíaFacultad de Química y BiologíaUniversidad de Santiago de 9 ChileSantiagoChile
| | - Francisco Bozinovic
- Center of Applied Ecology and Sustainability (CAPES)Facultad de Ciencias BiológicasUniversidad Católica de ChileSantiagoChile
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Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. mSystems 2019; 4:mSystems00170-18. [PMID: 30834327 PMCID: PMC6392091 DOI: 10.1128/msystems.00170-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/21/2019] [Indexed: 11/23/2022] Open
Abstract
Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism. Isozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are often retained over evolutionary time, suggesting that they contribute to fitness. We developed an unsupervised computational method for identifying environmental conditions under which isozymes are likely to make fitness contributions. This method analyzes published gene expression data to find specific experimental perturbations that induce differential isozyme expression. In yeast, we found that isozymes are strongly enriched in the pathways of central carbon metabolism and that many isozyme pairs show anticorrelated expression during the respirofermentative shift. Building on these observations, we assigned function to two minor central carbon isozymes, aconitase 2 (ACO2) and pyruvate kinase 2 (PYK2). ACO2 is expressed during fermentation and proves advantageous when glucose is limiting. PYK2 is expressed during respiration and proves advantageous for growth on three-carbon substrates. PYK2’s deletion can be rescued by expressing the major pyruvate kinase only if that enzyme carries mutations mirroring PYK2’s allosteric regulation. Thus, central carbon isozymes help to optimize allosteric metabolic regulation under a broad range of potential nutrient conditions while requiring only a small number of transcriptional states. IMPORTANCE Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism.
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Escalera-Fanjul X, Quezada H, Riego-Ruiz L, González A. Whole-Genome Duplication and Yeast’s Fruitful Way of Life. Trends Genet 2019; 35:42-54. [DOI: 10.1016/j.tig.2018.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/10/2018] [Accepted: 09/27/2018] [Indexed: 01/30/2023]
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Xu C, Liu R, Zhang Q, Chen X, Qian Y, Fang W. The Diversification of Evolutionarily Conserved MAPK Cascades Correlates with the Evolution of Fungal Species and Development of Lifestyles. Genome Biol Evol 2017; 9:311-322. [PMID: 26957028 PMCID: PMC5381651 DOI: 10.1093/gbe/evw051] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2016] [Indexed: 11/14/2022] Open
Abstract
The fungal kingdom displays an extraordinary diversity of lifestyles, developmental processes, and ecological niches. The MAPK (mitogen-activated protein kinase) cascade consists of interlinked MAPKKK, MAPKK, and MAPK, and collectively such cascades play pivotal roles in cellular regulation in fungi. However, the mechanism by which evolutionarily conserved MAPK cascades regulate diverse output responses in fungi remains unknown. Here we identified the full complement of MAPK cascade components from 231 fungal species encompassing 9 fungal phyla. Using the largest data set to date, we found that MAPK family members could have two ancestors, while MAPKK and MAPKKK family members could have only one ancestor. The current MAPK, MAPKK, and MAPKKK subfamilies resulted from duplications and subsequent subfunctionalization during the emergence of the fungal kingdom. However, the gene structure diversification and gene expansion and loss have resulted in significant diversity in fungal MAPK cascades, correlating with the evolution of fungal species and lifestyles. In particular, a distinct evolutionary trajectory of MAPK cascades was identified in single-celled fungi in the Saccharomycetes. All MAPK, MAPKK, and MAPKKK subfamilies expanded in the Saccharomycetes; genes encoding MAPK cascade components have a similar exon–intron structure in this class that differs from those in other fungi.
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Affiliation(s)
- Chuan Xu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ran Liu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiangqiang Zhang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoxuan Chen
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ying Qian
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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Karademir Andersson A, Cohn M. Naumovozyma castellii: an alternative model for budding yeast molecular biology. Yeast 2016; 34:95-109. [PMID: 27794167 DOI: 10.1002/yea.3218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/18/2016] [Indexed: 11/11/2022] Open
Abstract
Naumovozyma castellii (Saccharomyces castellii) is a member of the budding yeast family Saccharomycetaceae. It has been extensively used as a model organism for telomere biology research and has gained increasing interest as a budding yeast model for functional analyses owing to its amenability to genetic modifications. Owing to the suitable phylogenetic distance to S. cerevisiae, the whole genome sequence of N. castellii has provided unique data for comparative genomic studies, and it played a key role in the establishment of the timing of the whole genome duplication and the evolutionary events that took place in the subsequent genomic evolution of the Saccharomyces lineage. Here we summarize the historical background of its establishment as a laboratory yeast species, and the development of genetic and molecular tools and strains. We review the research performed on N. castellii, focusing on areas where it has significantly contributed to the discovery of new features of molecular biology and to the advancement of our understanding of molecular evolution. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Marita Cohn
- Department of Biology, Genetics group, Lund University, Lund, Sweden
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Diversification of Paralogous α-Isopropylmalate Synthases by Modulation of Feedback Control and Hetero-Oligomerization in Saccharomyces cerevisiae. EUKARYOTIC CELL 2015; 14:564-77. [PMID: 25841022 DOI: 10.1128/ec.00033-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/01/2015] [Indexed: 11/20/2022]
Abstract
Production of α-isopropylmalate (α-IPM) is critical for leucine biosynthesis and for the global control of metabolism. The budding yeast Saccharomyces cerevisiae has two paralogous genes, LEU4 and LEU9, that encode α-IPM synthase (α-IPMS) isozymes. Little is known about the biochemical differences between these two α-IPMS isoenzymes. Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. The leu4Δ mutant, which expresses only the feedback-resistant Leu9 homodimer, grows slowly with either glucose or ethanol and accumulates elevated pools of leucine; this phenotype is alleviated by the addition of leucine. Transformation of the leu4Δ mutant with a centromeric plasmid carrying LEU4 restored the wild-type phenotype. Bimolecular fluorescent complementation analysis showed that Leu4-Leu9 heterodimeric isozymes are formed in vivo. Purification and kinetic analysis showed that the hetero-oligomeric isozyme has a distinct leucine sensitivity behavior. Determination of α-IPMS activity in ethanol-grown cultures showed that α-IPM biosynthesis and growth under these respiratory conditions depend on the feedback-sensitive Leu4 homodimer. We conclude that retention and further diversification of two yeast α-IPMSs have resulted in a specific regulatory system that controls the leucine-α-IPM biosynthetic pathway by selective feedback sensitivity of homomeric and heterodimeric isoforms.
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Blein-Nicolas M, Albertin W, Valot B, Marullo P, Sicard D, Giraud C, Huet S, Bourgais A, Dillmann C, de Vienne D, Zivy M. Yeast proteome variations reveal different adaptive responses to grape must fermentation. Mol Biol Evol 2013; 30:1368-83. [PMID: 23493259 DOI: 10.1093/molbev/mst050] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Saccharomyces cerevisiae and S. uvarum are two domesticated species of the Saccharomyces sensu stricto clade that diverged around 100 Ma after whole-genome duplication. Both have retained many duplicated genes associated with glucose fermentation and are characterized by the ability to achieve grape must fermentation. Nevertheless, these two species differ for many other traits, indicating that they underwent different evolutionary histories. To determine how the evolutionary histories of S. cerevisiae and S. uvarum are mirrored on the proteome, we analyzed the genetic variability of the proteomes of domesticated strains of these two species by quantitative mass spectrometry. Overall, 445 proteins were quantified. Massive variations of protein abundances were found, that clearly differentiated the two species. Abundance variations in specific metabolic pathways could be related to phenotypic traits known to discriminate the two species. In addition, proteins encoded by duplicated genes were shown to be differently recruited in each species. Comparing the strain differentiation based on the proteome variability to those based on the phenotypic and genetic variations further revealed that the strains of S. uvarum and some strains of S. cerevisiae displayed similar fermentative performances despite strong proteomic and genomic differences. Altogether, these results indicate that the ability of S. cerevisae and S. uvarum to complete grape must fermentation arose through different evolutionary roads, involving different metabolic pathways and duplicated genes.
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Lashin SA, Suslov VV, Matushkin YG. Theories of biological evolution from the viewpoint of the modern systemic biology. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412030064] [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]
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Hallinan NM, Lindberg DR. Comparative analysis of chromosome counts infers three paleopolyploidies in the mollusca. Genome Biol Evol 2011; 3:1150-63. [PMID: 21859805 PMCID: PMC3194838 DOI: 10.1093/gbe/evr087] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2011] [Indexed: 01/02/2023] Open
Abstract
The study of paleopolyploidies requires the comparison of multiple whole genome sequences. If the branches of a phylogeny on which a whole-genome duplication (WGD) occurred could be identified before genome sequencing, taxa could be selected that provided a better assessment of that genome duplication. Here, we describe a likelihood model in which the number of chromosomes in a genome evolves according to a Markov process with one rate of chromosome duplication and loss that is proportional to the number of chromosomes in the genome and another stochastic rate at which every chromosome in the genome could duplicate in a single event. We compare the maximum likelihoods of a model in which the genome duplication rate varies to one in which it is fixed at zero using the Akaike information criterion, to determine if a model with WGDs is a good fit for the data. Once it has been determined that the data does fit the WGD model, we infer the phylogenetic position of paleopolyploidies by calculating the posterior probability that a WGD occurred on each branch of the taxon tree. Here, we apply this model to a molluscan tree represented by 124 taxa and infer three putative WGD events. In the Gastropoda, we identify a single branch within the Hypsogastropoda and one of two branches at the base of the Stylommatophora. We also identify one or two branches near the base of the Cephalopoda.
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Gunbin KV, Suslov VV, Turnaev II, Afonnikov DA, Kolchanov NA. Molecular evolution of cyclin proteins in animals and fungi. BMC Evol Biol 2011; 11:224. [PMID: 21798004 PMCID: PMC3162929 DOI: 10.1186/1471-2148-11-224] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 07/28/2011] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which differ considerably in primary structure from one eukaryotic organism to another. Despite these lines of evidence, the relationship between the evolution of cyclins and their function is an open issue. Here we present the results of our study on the molecular evolution of A-, B-, D-, E-type cyclin proteins in animals and fungi. RESULTS We constructed phylogenetic trees for these proteins, their ancestral sequences and analyzed patterns of amino acid replacements. The analysis of infrequently fixed atypical amino acid replacements in cyclins evidenced that accelerated evolution proceeded predominantly during paralog duplication or after it in animals and fungi and that it was related to aromorphic changes in animals. It was shown also that evolutionary flexibility of cyclin function may be provided by consequential reorganization of regions on protein surface remote from CDK binding sites in animal and fungal cyclins and by functional differentiation of paralogous cyclins formed in animal evolution. CONCLUSIONS The results suggested that changes in the number and/or nature of cyclin-binding proteins may underlie the evolutionary role of the alterations in the molecular structure of cyclins and their involvement in diverse molecular-genetic events.
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Affiliation(s)
- Konstantin V Gunbin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
| | - Valentin V Suslov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
| | - Igor I Turnaev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
- Novosibirsk state University, Pirogova, 2, Novosibirsk, Russia
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
- Novosibirsk state University, Pirogova, 2, Novosibirsk, Russia
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Capra JA, Pollard KS, Singh M. Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol 2010; 11:R127. [PMID: 21187012 PMCID: PMC3046487 DOI: 10.1186/gb-2010-11-12-r127] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 11/18/2010] [Accepted: 12/27/2010] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Genes are created by a variety of evolutionary processes, some of which generate duplicate copies of an entire gene, while others rearrange pre-existing genetic elements or co-opt previously non-coding sequence to create genes with 'novel' sequences. These novel genes are thought to contribute to distinct phenotypes that distinguish organisms. The creation, evolution, and function of duplicated genes are well-studied; however, the genesis and early evolution of novel genes are not well-characterized. We developed a computational approach to investigate these issues by integrating genome-wide comparative phylogenetic analysis with functional and interaction data derived from small-scale and high-throughput experiments. RESULTS We examine the function and evolution of new genes in the yeast Saccharomyces cerevisiae. We observed significant differences in the functional attributes and interactions of genes created at different times and by different mechanisms. Novel genes are initially less integrated into cellular networks than duplicate genes, but they appear to gain functions and interactions more quickly than duplicates. Recently created duplicated genes show evidence of adapting existing functions to environmental changes, while young novel genes do not exhibit enrichment for any particular functions. Finally, we found a significant preference for genes to interact with other genes of similar age and origin. CONCLUSIONS Our results suggest a strong relationship between how and when genes are created and the roles they play in the cell. Overall, genes tend to become more integrated into the functional networks of the cell with time, but the dynamics of this process differ significantly between duplicate and novel genes.
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Affiliation(s)
- John A Capra
- Gladstone Institutes, University of California, San Francisco, 1650 Owens St, San Francisco, CA 94158, USA.
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Chou JY, Leu JY. Speciation through cytonuclear incompatibility: Insights from yeast and implications for higher eukaryotes. Bioessays 2010; 32:401-11. [DOI: 10.1002/bies.200900162] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Fang ZA, Wang GH, Chen AL, Li YF, Liu JP, Li YY, Bolotin-Fukuhara M, Bao WG. Gene responses to oxygen availability in Kluyveromyces lactis: an insight on the evolution of the oxygen-responding system in yeast. PLoS One 2009; 4:e7561. [PMID: 19855843 PMCID: PMC2763219 DOI: 10.1371/journal.pone.0007561] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 09/16/2009] [Indexed: 11/18/2022] Open
Abstract
The whole-genome duplication (WGD) may provide a basis for the emergence of the very characteristic life style of Saccharomyces cerevisiae—its fermentation-oriented physiology and its capacity of growing in anaerobiosis. Indeed, we found an over-representation of oxygen-responding genes in the ohnologs of S. cerevisiae. Many of these duplicated genes are present as aerobic/hypoxic(anaerobic) pairs and form a specialized system responding to changing oxygen availability. HYP2/ANB1 and COX5A/COX5B are such gene pairs, and their unique orthologs in the ‘non-WGD’ Kluyveromyces lactis genome behaved like the aerobic versions of S. cerevisiae. ROX1 encodes a major oxygen-responding regulator in S. cerevisiae. The synteny, structural features and molecular function of putative KlROX1 were shown to be different from that of ROX1. The transition from the K. lactis-type ROX1 to the S. cerevisiae-type ROX1 could link up with the development of anaerobes in the yeast evolution. Bioinformatics and stochastic analyses of the Rox1p-binding site (YYYATTGTTCTC) in the upstream sequences of the S. cerevisiae Rox1p-mediated genes and of the K. lactis orthologs also indicated that K. lactis lacks the specific gene system responding to oxygen limiting environment, which is present in the ‘post-WGD’ genome of S. cerevisiae. These data suggested that the oxygen-responding system was born for the specialized physiology of S. cerevisiae.
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Affiliation(s)
- Zi-An Fang
- Université Paris Sud-11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
- Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Guang-Hui Wang
- School of Mathematics, Shandong University, Jinan, Shandong, China
- Laboratoire Mathématiques Appliquées aux Systèmes, Ecole Centrale Paris, Châtenay-Malabry, France
| | - Ai-Lian Chen
- Department of Mathematics, Fuzhou University, Fuzhou, Fujian, China
| | - You-Fang Li
- Université Paris Sud-11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
| | - Jian-Ping Liu
- Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Yang Li
- Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | | | - Wei-Guo Bao
- Université Paris Sud-11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
- * E-mail:
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Abstract
In addition to the nuclear genome, organisms have organelle genomes. Most of the DNA present in eukaryotic organisms is located in the cell nucleus. Chloroplasts have independent genomes which are inherited from the mother. Duplicated genes are common in the genomes of all organisms. It is believed that gene duplication is the most important step for the origin of genetic variation, leading to the creation of new genes and new gene functions. Despite the fact that extensive gene duplications are rare among the chloroplast genome, gene duplication in the chloroplast genome is an essential source of new genetic functions and a mechanism of neo-evolution. The events of gene transfer between the chloroplast genome and nuclear genome via duplication and subsequent recombination are important processes in evolution. The duplicated gene or genome in the nucleus has been the subject of several recent reviews. In this review, we will briefly summarize gene duplication and evolution in the chloroplast genome. Also, we will provide an overview of gene transfer events between chloroplast and nuclear genomes.
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Gordon JL, Byrne KP, Wolfe KH. Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet 2009; 5:e1000485. [PMID: 19436716 PMCID: PMC2675101 DOI: 10.1371/journal.pgen.1000485] [Citation(s) in RCA: 183] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 04/20/2009] [Indexed: 11/26/2022] Open
Abstract
Comparative genomics can be used to infer the history of genomic rearrangements that occurred during the evolution of a species. We used the principle of parsimony, applied to aligned synteny blocks from 11 yeast species, to infer the gene content and gene order that existed in the genome of an extinct ancestral yeast about 100 Mya, immediately before it underwent whole-genome duplication (WGD). The reconstructed ancestral genome contains 4,703 ordered loci on eight chromosomes. The reconstruction is complete except for the subtelomeric regions. We then inferred the series of rearrangement steps that led from this ancestor to the current Saccharomyces cerevisiae genome; relative to the ancestral genome we observe 73 inversions, 66 reciprocal translocations, and five translocations involving telomeres. Some fragile chromosomal sites were reused as evolutionary breakpoints multiple times. We identified 124 genes that have been gained by S. cerevisiae in the time since the WGD, including one that is derived from a hAT family transposon, and 88 ancestral loci at which S. cerevisiae did not retain either of the gene copies that were formed by WGD. Sites of gene gain and evolutionary breakpoints both tend to be associated with tRNA genes and, to a lesser extent, with origins of replication. Many of the gained genes in S. cerevisiae have functions associated with ethanol production, growth in hypoxic environments, or the uptake of alternative nutrient sources.
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Affiliation(s)
- Jonathan L. Gordon
- Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
- Department of Plant Systems Biology, VIB, Ghent, Belgium
| | - Kevin P. Byrne
- Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
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Chen H, Xu L, Gu Z. Regulation dynamics of WGD genes during yeast metabolic oscillation. Mol Biol Evol 2008; 25:2513-6. [PMID: 18815125 DOI: 10.1093/molbev/msn212] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Saccharomyces cerevisiae and its close relatives are characterized by their propensity to ferment even in the presence of oxygen. It was hypothesized that whole-genome duplication (WGD) led to the development of this efficient fermentative lifestyle (WGD-fermentation hypothesis, Piskur 2001. In this study, we found that a significantly higher proportion of WGD genes than non-WGD genes are dynamically regulated during metabolic oscillation in response to oxygen change. The same data set also shows that the WGD genes, as compared with the smaller scale duplicate genes, are enriched with pairs where both copies have cyclic expression during the metabolic oscillation (either with the same or different phases). These results provide new evidences for the WGD-fermentation hypothesis and new insights into the relationship between the genome duplication and the evolution of new lifestyles in eukaryotic organisms.
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Jiang H, Guan W, Pinney D, Wang W, Gu Z. Relaxation of yeast mitochondrial functions after whole-genome duplication. Genes Dev 2008; 18:1466-71. [PMID: 18669479 PMCID: PMC2527710 DOI: 10.1101/gr.074674.107] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 05/14/2008] [Indexed: 12/20/2022]
Abstract
Mitochondria are essential for cellular energy production in most eukaryotic organisms. However, when glucose is abundant, yeast species that underwent whole-genome duplication (WGD) mostly conduct fermentation even under aerobic conditions, and most can survive without a functional mitochondrial genome. In this study, we show that the rate of evolution for the nuclear-encoded mitochondrial genes was greater in post-WGD species than pre-WGD species. Furthermore, codon usage bias was relaxed for these genes in post-WGD yeast species. The codon usage pattern and the distribution of a particular transcription regulatory element suggest that the change to an efficient aerobic fermentation lifestyle in this lineage might have emerged after WGD between the divergence of Kluyveromyces polysporus and Saccharomyces castellii from their common ancestor. This new energy production strategy could have led to the relaxation of mitochondrial function in the relevant yeast species.
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Affiliation(s)
- Huifeng Jiang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, People’s Republic of China
- Graduate School of Chinese Academy Sciences, Beijing 100039, People’s Republic of China
| | - Wenjun Guan
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
- Zhejiang University, College of Life Sciences, Hangzhou 310058, People’s Republic of China
| | - David Pinney
- Department of Mathematics, Cornell University, Ithaca, New York 14853, USA
| | - Wen Wang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, People’s Republic of China
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
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20
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Quezada H, Aranda C, DeLuna A, Hernández H, Calcagno ML, Marín-Hernández Á, González A. Specialization of the paralogue LYS21 determines lysine biosynthesis under respiratory metabolism in Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2008; 154:1656-1667. [PMID: 18524920 DOI: 10.1099/mic.0.2008/017103-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the first committed step of the lysine biosynthetic pathway is catalysed by two homocitrate synthases encoded by LYS20 and LYS21. We undertook a study of the duplicate homocitrate synthases to analyse whether their retention and presumable specialization have affected the efficiency of lysine biosynthesis in yeast. Our results show that during growth on ethanol, homocitrate is mainly synthesized through Lys21p, while under fermentative metabolism, Lys20p and Lys21p play redundant roles. Furthermore, results presented in this paper indicate that, in contrast to that which had been found for Lys20p, lysine is a strong allosteric inhibitor of Lys21p (K(i) 0.053 mM), which, in addition, induces positive co-operativity for alpha-ketoglutarate (alpha-KG) binding. Differential lysine inhibition and modulation by alpha-KG of the two isozymes, and the regulation of the intracellular amount of the two isoforms, give rise to an exquisite regulatory system, which balances the rate at which alpha-KG is diverted to lysine biosynthesis or to other metabolic pathways. It can thus be concluded that retention and further biochemical specialization of the LYS20- and LYS21-encoded enzymes with partially overlapping roles contributed to the acquisition of facultative metabolism.
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Affiliation(s)
- Héctor Quezada
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
| | - Cristina Aranda
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
| | - Alexander DeLuna
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
| | - Hugo Hernández
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
| | - Mario L Calcagno
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México DF 04510, México
| | - Álvaro Marín-Hernández
- Instituto Nacional de Cardiología, Departamento de Bioquímica, Tlalpan, México DF, México
| | - Alicia González
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
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21
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Martin N, Ruedi EA, LeDuc R, Sun FJ, Caetano-Anollés G. Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event? Biol Direct 2007; 2:23. [PMID: 17894859 PMCID: PMC2134927 DOI: 10.1186/1745-6150-2-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 09/25/2007] [Indexed: 11/24/2022] Open
Abstract
Background Recent comparative genomic studies claim local syntenic gene-interleaving relationships in Ashbya gossypii and Kluyveromyces waltii are compelling evidence for an ancient whole-genome duplication event in Saccharomyces cerevisiae. We here test, using Hannenhalli-Pevzner rearrangement algorithms that address the multiple genome rearrangement problem, whether syntenic patterns are proof of paleopolyploidization. Results We focus on (1) pairwise comparison of gene arrangement sequences in A. gossypii and S. cerevisiae, (2) reconstruction of gene arrangements ancestral to A. gossypii, S. cerevisiae, and K. waltii, (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets. The existence of syntenic patterns between ancestral gene sets and A. gossypii, S. cerevisiae, and K. waltii, and other evidence, suggests that gene-interleaving relationships are the natural consequence of topological rearrangements in chromosomes and that a more gradual scenario of genome evolution involving segmental duplication and recombination constitutes a more parsimonious explanation. Furthermore, phylogenetic trees reconstructed under alternative hypotheses placed the putative whole-genome duplication event after the divergence of the S. cerevisiae and K. waltii lineages, but in the lineage leading to K. waltii. This is clearly incompatible with an ancient genome duplication event in S. cerevisiae. Conclusion Because the presence of syntenic patterns appears to be a condition that is necessary, but not sufficient, to support the existence of the whole-genome duplication event, our results prompt careful re-evaluation of paleopolyploidization in the yeast lineage and the evolutionary meaning of syntenic patterns. Reviewers This article was reviewed by Kenneth H. Wolfe (nominated by Nicolas Galtier), Austin L. Hughes (nominated by Eugene Koonin), Mikhail S. Gelfand, and Mark Gerstein.
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Affiliation(s)
- Nicolas Martin
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
| | - Elizabeth A Ruedi
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
| | - Richard LeDuc
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
| | - Feng-Jie Sun
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
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22
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Abstract
With almost 20 genomes sequenced from unicellular ascomycetes (Saccharomycotina), and the prospect of many more in the pipeline, we review the patterns and processes of yeast genome evolution. A central core of about 4000 genes is shared by all the sequenced yeast genomes. Gains of genes by horizontal gene transfer seem to be very rare. Gene losses are more frequent, and losses of whole sets of genes in some pathways in some species can be understood in terms of species-specific differences in biology. The wholesale loss of redundant copies of duplicated genes after whole-genome duplication in the ancestor of one clade of yeasts is likely to have caused the emergence of many reproductively isolated lineages of yeasts at that time, but other processes are responsible for species barriers that arose more recently among close relatives of Saccharomyces cerevisiae.
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Affiliation(s)
- Devin R Scannell
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
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23
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Lai LC, Kosorukoff AL, Burke PV, Kwast KE. Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. EUKARYOTIC CELL 2006; 5:1468-89. [PMID: 16963631 PMCID: PMC1563586 DOI: 10.1128/ec.00107-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We conducted a comprehensive genomic analysis of the temporal response of yeast to anaerobiosis (six generations) and subsequent aerobic recovery ( approximately 2 generations) to reveal metabolic-state (galactose versus glucose)-dependent differences in gene network activity and function. Analysis of variance showed that far fewer genes responded (raw P value of <or=10(-8)) to the O(2) shifts in glucose (1,603 genes) than in galactose (2,388 genes). Gene network analysis reveals that this difference is due largely to the failure of "stress"-activated networks controlled by Msn2/4, Fhl1, MCB, SCB, PAC, and RRPE to transiently respond to the shift to anaerobiosis in glucose as they did in galactose. After approximately 1 generation of anaerobiosis, the response was similar in both media, beginning with the deactivation of Hap1 and Hap2/3/4/5 networks involved in mitochondrial functions and the concomitant derepression of Rox1-regulated networks for carbohydrate catabolism and redox regulation and ending (>or=2 generations) with the activation of Upc2- and Mot3-regulated networks involved in sterol and cell wall homeostasis. The response to reoxygenation was rapid (<5 min) and similar in both media, dominated by Yap1 networks involved in oxidative stress/redox regulation and the concomitant activation of heme-regulated ones. Our analyses revealed extensive networks of genes subject to combinatorial regulation by both heme-dependent (e.g., Hap1, Hap2/3/4/5, Rox1, Mot3, and Upc2) and heme-independent (e.g., Yap1, Skn7, and Puf3) factors under these conditions. We also uncover novel functions for several cis-regulatory sites and trans-acting factors and define functional regulons involved in the physiological acclimatization to changes in oxygen availability.
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Affiliation(s)
- Liang-Chuan Lai
- Department of Molecular and Integrative Physiology, University of Illinois, 524 Burrill Hall, 407 S. Goodwin Ave., Urbana, 61801, USA
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24
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Abstract
Yeasts provide a powerful model system for comparative genomics research. The availability of multiple complete genome sequences from different fungal groups--currently 18 hemiascomycetes, 8 euascomycetes and 4 basidiomycetes--enables us to gain a broad perspective on genome evolution. The sequenced genomes span a continuum of divergence levels ranging from multiple individuals within a species to species pairs with low levels of protein sequence identity and no conservation of gene order. One of the most interesting emerging areas is the growing number of events such as gene losses, gene displacements and gene relocations that can be attributed to the action of natural selection.
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Affiliation(s)
- Kenneth H Wolfe
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland.
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25
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Cliften PF, Fulton RS, Wilson RK, Johnston M. After the duplication: gene loss and adaptation in Saccharomyces genomes. Genetics 2006; 172:863-72. [PMID: 16322519 PMCID: PMC1456250 DOI: 10.1534/genetics.105.048900] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Accepted: 11/08/2005] [Indexed: 11/18/2022] Open
Abstract
The ancient duplication of the Saccharomyces cerevisiae genome and subsequent massive loss of duplicated genes is apparent when it is compared to the genomes of related species that diverged before the duplication event. To learn more about the evolutionary effects of the duplication event, we compared the S. cerevisiae genome to other Saccharomyces genomes. We demonstrate that the whole genome duplication occurred before S. castellii diverged from S. cerevisiae. In addition to more accurately dating the duplication event, this finding allowed us to study the effects of the duplication on two separate lineages. Analyses of the duplication regions of the genomes indicate that most of the duplicated genes (approximately 85%) were lost before the speciation. Only a small amount of paralogous gene loss (4-6%) occurred after speciation. On the other hand, S. castellii appears to have lost several hundred genes that were not retained as duplicated paralogs. These losses could be related to genomic rearrangements that reduced the number of chromosomes from 16 to 9. In addition to S. castellii, other Saccharomyces sensu lato species likely diverged from S. cerevisiae after the duplication. A thorough analysis of these species will likely reveal other important outcomes of the whole genome duplication.
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Affiliation(s)
- Paul F Cliften
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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26
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Abstract
Recent sequencing efforts and experiments have advanced our understanding of genome evolution in yeasts, particularly the Saccharomyces yeasts. The ancestral genome of the Saccharomyces sensu stricto complex has been subject to both whole-genome duplication, followed by massive sequence loss and divergence, and segmental duplication. In addition the subtelomeric regions are subject to further duplications and rearrangements via ectopic exchanges. Translocations and other gross chromosomal rearrangements that break down syntenic relationships occur; however, they do not appear to be a driving force of speciation. Analysis of single genomes has been fruitful for hypothesis generation such as the whole-genome duplication, but comparative genomics between close and more distant species has proven to be a powerful tool in testing these hypotheses as well as elucidating evolutionary processes acting on the genome. Future work on population genomics and experimental evolution will keep yeast at the forefront of studies in genome evolution.
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Affiliation(s)
- Gianni Liti
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom.
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27
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Avendaño A, Riego L, DeLuna A, Aranda C, Romero G, Ishida C, Vázquez-Acevedo M, Rodarte B, Recillas-Targa F, Valenzuela L, Zonszein S, González A. Swi/SNF-GCN5-dependent chromatin remodelling determines induced expression of GDH3, one of the paralogous genes responsible for ammonium assimilation and glutamate biosynthesis in Saccharomyces cerevisiae. Mol Microbiol 2005; 57:291-305. [PMID: 15948967 DOI: 10.1111/j.1365-2958.2005.04689.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
It is accepted that Saccharomyces cerevisiae genome arose from complete duplication of eight ancestral chromosomes; functionally normal ploidy was recovered because of the massive loss of 90% of duplicated genes. There is evidence that indicates that part of this selective conservation of gene pairs is compelling to yeast facultative metabolism. As an example, the duplicated NADP-glutamate dehydrogenase pathway has been maintained because of the differential expression of the paralogous GDH1 and GDH3 genes, and the biochemical specialization of the enzymes they encode. The present work has been aimed to the understanding of the regulatory mechanisms that modulate GDH3 transcriptional activation. Our results show that GDH3 expression is repressed in glucose-grown cultures, as opposed to what has been observed for GDH1, and induced under respiratory conditions, or under stationary phase. Although GDH3 pertains to the nitrogen metabolic network, and its expression is Gln3p-regulated, complete derepression is ultimately determined by the carbon source through the action of the SAGA and SWI/SNF chromatin remodelling complexes. GDH3 carbon-mediated regulation is over-imposed to that exerted by the nitrogen source, highlighting the fact that operation of facultative metabolism requires strict control of enzymes, like Gdh3p, involved in biosynthetic pathways that use tricarboxylic acid cycle intermediates.
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Affiliation(s)
- Amaranta Avendaño
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico City, México
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28
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Flores CL, Gancedo C. Yarrowia lipolytica mutants devoid of pyruvate carboxylase activity show an unusual growth phenotype. EUKARYOTIC CELL 2005; 4:356-64. [PMID: 15701798 PMCID: PMC549329 DOI: 10.1128/ec.4.2.356-364.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2004] [Accepted: 12/02/2004] [Indexed: 11/20/2022]
Abstract
We have cloned and characterized the gene PYC1, encoding the unique pyruvate carboxylase in the dimorphic yeast Yarrowia lipolytica. The protein putatively encoded by the cDNA has a length of 1,192 amino acids and shows around 70% identity with pyruvate carboxylases from other organisms. The corresponding genomic DNA possesses an intron of 269 bp located 133 bp downstream of the starting ATG. In the branch motif of the intron, the sequence CCCTAAC, not previously found at this place in spliceosomal introns of Y. lipolytica, was uncovered. Disruption of the PYC1 gene from Y. lipolytica did not abolish growth in glucose-ammonium medium, as is the case in other eukaryotic microorganisms. This unusual growth phenotype was due to an incomplete glucose repression of the function of the glyoxylate cycle, as shown by the lack of growth in that medium of double pyc1 icl1 mutants lacking both pyruvate carboxylase and isocitrate lyase activity. These mutants grew when glutamate, aspartate, or Casamino Acids were added to the glucose-ammonium medium. The cDNA from the Y. lipolytica PYC1 gene complemented the growth defect of a Saccharomyces cerevisiae pyc1 pyc2 mutant, but introduction of either the S. cerevisiae PYC1 or PYC2 gene into Y. lipolytica did not result in detectable pyruvate carboxylase activity or in growth on glucose-ammonium of a Y. lipolytica pyc1 icl1 double mutant.
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Affiliation(s)
- Carmen-Lisset Flores
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-Universidad Autónoma de Madrid, Madrid, Spain.
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29
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Abstract
Two new genome sequences confirm that a whole genome duplication occurred in an ancestor of Saccharomyces cerevisiae. This left a legacy of about 500 pairs of duplicated genes, many of which contribute to this yeast's ability to ferment glucose anaerobically; a few have been evolving so quickly they retain almost no sequence similarity to each other.
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Affiliation(s)
- Ken Wolfe
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland.
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30
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Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 2004; 428:617-24. [PMID: 15004568 DOI: 10.1038/nature02424] [Citation(s) in RCA: 1011] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Accepted: 01/19/2004] [Indexed: 11/09/2022]
Abstract
Whole-genome duplication followed by massive gene loss and specialization has long been postulated as a powerful mechanism of evolutionary innovation. Recently, it has become possible to test this notion by searching complete genome sequence for signs of ancient duplication. Here, we show that the yeast Saccharomyces cerevisiae arose from ancient whole-genome duplication, by sequencing and analysing Kluyveromyces waltii, a related yeast species that diverged before the duplication. The two genomes are related by a 1:2 mapping, with each region of K. waltii corresponding to two regions of S. cerevisiae, as expected for whole-genome duplication. This resolves the long-standing controversy on the ancestry of the yeast genome, and makes it possible to study the fate of duplicated genes directly. Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions.
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Affiliation(s)
- Manolis Kellis
- The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02138, USA.
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31
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Spírek M, Yang J, Groth C, Petersen RF, Langkjaer RB, Naumova ES, Sulo P, Naumov GI, Piskur J. High-rate evolution of Saccharomyces sensu lato chromosomes. FEMS Yeast Res 2003; 3:363-73. [PMID: 12748049 DOI: 10.1016/s1567-1356(02)00204-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Forty isolates belonging to the Saccharomyces sensu lato complex were analyzed for one nuclear and two mitochondrial sequences, and for their karyotypes. These data are useful for description and definition of yeast species based on the phylogenetic species concept. The deduced phylogenetic relationships among isolates based on the nuclear and mitochondrial sequences were usually similar, suggesting that horizontal transfer/introgression has not been frequent. The highest degree of polymorphism was observed at the chromosome level. Even isolates which had identical nuclear and mitochondrial sequences often exhibited variation in the number and size of their chromosomes. Apparently, yeast chromosomes have been frequently reshaped and therefore also the position of genes has been dynamic during the evolutionary history of yeasts.
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Affiliation(s)
- Mário Spírek
- Eukaryote Molecular Biology Group, BioCentrum-DTU, Technical University of Denmark, Building 301, 2800, Lyngby, Denmark
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32
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Langkjaer RB, Cliften PF, Johnston M, Piskur J. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 2003; 421:848-52. [PMID: 12594514 DOI: 10.1038/nature01419] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2002] [Accepted: 01/03/2003] [Indexed: 11/09/2022]
Abstract
Gene redundancy has been observed in yeast, plant and human genomes, and is thought to be a consequence of whole-genome duplications. Baker's yeast, Saccharomyces cerevisiae, contains several hundred duplicated genes. Duplication(s) could have occurred before or after a given speciation. To understand the evolution of the yeast genome, we analysed orthologues of some of these genes in several related yeast species. On the basis of the inferred phylogeny of each set of genes, we were able to deduce whether the gene duplicated and/or specialized before or after the divergence of two yeast lineages. Here we show that the gene duplications might have occurred as a single event, and that it probably took place before the Saccharomyces and Kluyveromyces lineages diverged from each other. Further evolution of each duplicated gene pair-such as specialization or differentiation of the two copies, or deletion of a single copy--has taken place independently throughout the evolution of these species.
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Affiliation(s)
- Rikke B Langkjaer
- BioCentrum-DTU, Technical University of Denmark, Building 301, DK-2800 Lyngby, Denmark
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33
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Thomas JW, Schueler MG, Summers TJ, Blakesley RW, McDowell JC, Thomas PJ, Idol JR, Maduro VVB, Lee-Lin SQ, Touchman JW, Bouffard GG, Beckstrom-Sternberg SM, Green ED. Pericentromeric duplications in the laboratory mouse. Genome Res 2003; 13:55-63. [PMID: 12529306 PMCID: PMC430956 DOI: 10.1101/gr.791403] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of duplications can be inferred. By comparative mapping in human, mouse, and rat, we previously found evidence for a recent chromosome-fission event that occurred in the mouse lineage. Cytogenetic mapping revealed that the genomic segments flanking the fission site appeared to be duplicated, with copies residing near the centromere of multiple mouse chromosomes. Here we report the mapping and sequencing of the regions of mouse chromosomes 5 and 6 involved in this chromosome-fission event as well as the results of comparative sequence analysis with the orthologous human and rat genomic regions. Our data indicate that the duplications associated with mouse chromosomes 5 and 6 are recent and that the resulting duplicated segments share significant sequence similarity with a series of regions near the centromeres of the mouse chromosomes previously identified by cytogenetic mapping. We also identified pericentromeric duplicated segments shared between mouse chromosomes 5 and 1. Finally, novel mouse satellite sequences as well as putative chimeric transcripts were found to be associated with the duplicated segments. Together, these findings demonstrate that pericentromeric duplications are not restricted to primates and may be a common mechanism for genome evolution in mammals.
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Affiliation(s)
- James W Thomas
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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34
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Abstract
In this review, we give a summary of recent examples of hybridisation in fungi. Reports on hybridisation between pathogenic fungi infecting plants have increased during the last decade. Hybrids of plant pathogens may create devastating new diseases on both cultivated and wild plants; at the same time, hybridisation is one of the natural processes in the course of evolution of new taxa.
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Affiliation(s)
- Ake Olson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden.
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35
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Kwast KE, Lai LC, Menda N, James DT, Aref S, Burke PV. Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response. J Bacteriol 2002; 184:250-65. [PMID: 11741867 PMCID: PMC134782 DOI: 10.1128/jb.184.1.250-265.2002] [Citation(s) in RCA: 193] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA arrays were used to investigate the functional role of Rox1 in mediating acclimatization to anaerobic conditions in Saccharomyces cerevisiae. Multiple growth conditions for wild-type and rox1 null strains were used to identify open reading frames with a statistically robust response to this repressor. These results were compared to those obtained for a wild-type strain in response to oxygen availability. Transcripts of nearly one-sixth of the genome were differentially expressed (P < 0.05) with respect to oxygen availability, the majority (>65%) being down-regulated under anoxia. Of the anaerobically induced genes, about one-third (106) contain putative Rox1-binding sites in their promoters and were significantly (P < 0.05) up-regulated in the rox1 null strains under aerobiosis. Additional promoter searches revealed that nearly one-third of the anaerobically induced genes contain an AR1 site(s) for the Upc2 transcription factor, suggesting that Upc2 and Rox1 regulate the majority of anaerobically induced genes in S. cerevisiae. Functional analyses indicate that a large fraction of the anaerobically induced genes are involved in cell stress (approximately 1/3), cell wall maintenance (approximately 1/8), carbohydrate metabolism (approximately 1/10), and lipid metabolism (approximately 1/12), with both Rox1 and Upc2 predominating in the regulation of this latter group and Upc2 predominating in cell wall maintenance. Mapping the changes in expression of functional regulons onto metabolic pathways has provided novel insight into the role of Rox1 and other trans-acting factors in mediating the physiological response of S. cerevisiae to anaerobic conditions.
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Affiliation(s)
- Kurt E Kwast
- Department of Molecular & Integrative Physiology, University of Illinois, Urbana, Illinois 61801, USA.
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36
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DeLuna A, Avendano A, Riego L, Gonzalez A. NADP-glutamate dehydrogenase isoenzymes of Saccharomyces cerevisiae. Purification, kinetic properties, and physiological roles. J Biol Chem 2001; 276:43775-83. [PMID: 11562373 DOI: 10.1074/jbc.m107986200] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, two NADP(+)-dependent glutamate dehydrogenases (NADP-GDHs) encoded by GDH1 and GDH3 catalyze the synthesis of glutamate from ammonium and alpha-ketoglutarate. The GDH2-encoded NAD(+)-dependent glutamate dehydrogenase degrades glutamate producing ammonium and alpha-ketoglutarate. Until very recently, it was considered that only one biosynthetic NADP-GDH was present in S. cerevisiae. This fact hindered understanding the physiological role of each isoenzyme and the mechanisms involved in alpha-ketoglutarate channeling for glutamate biosynthesis. In this study, we purified and characterized the GDH1- and GDH3-encoded NADP-GDHs; they showed different allosteric properties and rates of alpha-ketoglutarate utilization. Analysis of the relative levels of these proteins revealed that the expression of GDH1 and GDH3 is differentially regulated and depends on the nature of the carbon source. Moreover, the physiological study of mutants lacking or overexpressing GDH1 or GDH3 suggested that these genes play nonredundant physiological roles. Our results indicate that the coordinated regulation of GDH1-, GDH3-, and GDH2-encoded enzymes results in glutamate biosynthesis and balanced utilization of alpha-ketoglutarate under fermentative and respiratory conditions. The possible relevance of the duplicated NADP-GDH pathway in the adaptation to facultative metabolism is discussed.
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Affiliation(s)
- A DeLuna
- Departamento de Genética Molecular, Instituto de Fisiologia Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, México
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