101
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Yue JX, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC, Fischer G, Durbin R, Liti G. Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nat Genet 2017; 49:913-924. [PMID: 28416820 PMCID: PMC5446901 DOI: 10.1038/ng.3847] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/22/2017] [Indexed: 12/13/2022]
Abstract
Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts are likely to reflect the influence of human activities on structural genome evolution.
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Affiliation(s)
- Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Jing Li
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | - Johan Hallin
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Karl Persson
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden
| | | | | | | | - Jonas Warringer
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden
| | - Marco Cosentino Lagomarsino
- Laboratory of Computational and Quantitative Biology, Institut de Biologie Paris-Seine, UPMC University Paris 06, Sorbonne Universités, CNRS, Paris, France
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, Institut de Biologie Paris-Seine, UPMC University Paris 06, Sorbonne Universités, CNRS, Paris, France
| | | | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
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102
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Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics. Genomics 2017; 109:186-191. [PMID: 28286147 DOI: 10.1016/j.ygeno.2017.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 01/18/2023]
Abstract
Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, including detection of polymorphisms. In order to provide guidelines to the biologist for suitable selection of aligners; we have evaluated and benchmarked 5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their mapping bias based on characteristics of 5 microbial genomes. Two million simulated read pairs of various sizes (36bp, 50bp, 72bp, 100bp, 125bp, 150bp, 200bp, 250bp and 300bp) were aligned. Specific alignment features such as sensitivity of mapping, percentage of properly paired reads, alignment time and effect of tandem repeats on incorrectly mapped reads were evaluated. BWA showed faster alignment followed by Bowtie2 and Smalt. NovoAlign and Stampy were comparatively slower. Most of the aligners showed high sensitivity towards long reads (>100bp) mapping. On the other hand NovoAlign showed higher sensitivity towards both short reads (36bp, 50bp, 72bp) and long reads (>100bp) mappings; It also showed higher sensitivity towards mapping a complex genome like Plasmodium falciparum. The percentage of properly paired reads aligned by NovoAlign, BWA and Stampy were markedly higher. None of the aligners outperforms the others in the benchmark, however the aligners perform differently with genome characteristics. We expect that the results from this study will be useful for the end user to choose aligner, thus enhance the accuracy of read mapping.
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103
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Differential paralog divergence modulates genome evolution across yeast species. PLoS Genet 2017; 13:e1006585. [PMID: 28196070 PMCID: PMC5308817 DOI: 10.1371/journal.pgen.1006585] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/13/2017] [Indexed: 11/24/2022] Open
Abstract
Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. We evolved populations of S. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids between S. uvarum and S. cerevisiae for ~200–500 generations in sulfate-limited continuous culture. Wild-type S. cerevisiae cultures invariably amplify the high affinity sulfate transporter gene, SUL1. However, while amplification of the SUL1 locus was detected in S. paradoxus and S. mikatae populations, S. uvarum cultures instead selected for amplification of the paralog, SUL2. We measured the relative fitness of strains bearing deletions and amplifications of both SUL genes from different species, confirming that, converse to S. cerevisiae, S. uvarum SUL2 contributes more to fitness in sulfate limitation than S. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter of S. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfate transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive changes in genome evolution. Both comparative genomics and experimental evolution are powerful tools that can be used to make inferences about evolutionary processes. Together, these approaches provide the opportunity to observe evolutionary adaptation over millions of years where selective history is largely unknown, and over short timescales under controlled selective pressures in the laboratory. We have used comparative experimental evolution to observe the evolutionary fate of an adaptive mutation, and determined to what degree the outcome is conditional on the genetic background. We evolved several populations of different yeast species for over 200 generations in sulfate-limited conditions to determine how the differences in genomic context can alter evolutionary routes when challenged with a nutrient limitation selection pressure. We find that the gene encoding a high affinity sulfur transporter becomes amplified in most species of Saccharomyces, except in S. uvarum, in which the amplification of the paralogous sulfate transporter gene SUL2 is recovered. We attribute this change in amplification preference to mutations in the non-coding region of SUL1, likely due to reduced expression of this gene in S. uvarum. We conclude that the adaptive mutations selected for in each organism depend on the genomic context, even when faced with the same environmental condition.
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104
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Role of Ectopic Gene Conversion in the Evolution of a Candida krusei Pleiotropic Drug Resistance Transporter Family. Genetics 2017; 205:1619-1639. [PMID: 28159755 PMCID: PMC5378117 DOI: 10.1534/genetics.116.194811] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/31/2017] [Indexed: 11/18/2022] Open
Abstract
Gene duplications enable the evolution of novel gene function, but strong positive selection is required to preserve advantageous mutations in a population. This is because frequent ectopic gene conversions (EGCs) between highly similar, tandem-duplicated, sequences, can rapidly remove fate-determining mutations by replacing them with the neighboring parent gene sequences. Unfortunately, the high sequence similarities between tandem-duplicated genes severely hamper empirical studies of this important evolutionary process, because deciphering their correct sequences is challenging. In this study, we employed the eukaryotic model organism Saccharomyces cerevisiae to clone and functionally characterize all 30 alleles of an important pair of tandem-duplicated multidrug efflux pump genes, ABC1 and ABC11, from seven strains of the diploid pathogenic yeast Candida krusei Discovery and functional characterization of their closest ancestor, C. krusei ABC12, helped elucidate the evolutionary history of the entire gene family. Our data support the proposal that the pleiotropic drug resistance (PDR) transporters Abc1p and Abc11p have evolved by concerted evolution for ∼134 MY. While >90% of their sequences remained identical, very strong purifying selection protected six short DNA patches encoding just 18 core amino acid (aa) differences in particular trans membrane span (TMS) regions causing two distinct efflux pump functions. A proline-kink change at the bottom of Abc11p TMS3 was possibly fate determining. Our data also enabled the first empirical estimates for key parameters of eukaryotic gene evolution, they provided rare examples of intron loss, and PDR transporter phylogeny confirmed that C. krusei belongs to a novel, yet unnamed, third major Saccharomycotina lineage.
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105
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Mukherjee V, Radecka D, Aerts G, Verstrepen KJ, Lievens B, Thevelein JM. Phenotypic landscape of non-conventional yeast species for different stress tolerance traits desirable in bioethanol fermentation. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:216. [PMID: 28924451 PMCID: PMC5597992 DOI: 10.1186/s13068-017-0899-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/04/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND Non-conventional yeasts present a huge, yet barely exploited, resource of yeast biodiversity for industrial applications. This presents a great opportunity to explore alternative ethanol-fermenting yeasts that are more adapted to some of the stress factors present in the harsh environmental conditions in second-generation (2G) bioethanol fermentation. Extremely tolerant yeast species are interesting candidates to investigate the underlying tolerance mechanisms and to identify genes that when transferred to existing industrial strains could help to design more stress-tolerant cell factories. For this purpose, we performed a high-throughput phenotypic evaluation of a large collection of non-conventional yeast species to identify the tolerance limits of the different yeast species for desirable stress tolerance traits in 2G bioethanol production. Next, 12 multi-tolerant strains were selected and used in fermentations under different stressful conditions. Five strains out of which, showing desirable fermentation characteristics, were then evaluated in small-scale, semi-anaerobic fermentations with lignocellulose hydrolysates. RESULTS Our results revealed the phenotypic landscape of many non-conventional yeast species which have not been previously characterized for tolerance to stress conditions relevant for bioethanol production. This has identified for each stress condition evaluated several extremely tolerant non-Saccharomyces yeasts. It also revealed multi-tolerance in several yeast species, which makes those species good candidates to investigate the molecular basis of a robust general stress tolerance. The results showed that some non-conventional yeast species have similar or even better fermentation efficiency compared to S. cerevisiae in the presence of certain stressful conditions. CONCLUSION Prior to this study, our knowledge on extreme stress-tolerant phenotypes in non-conventional yeasts was limited to only few species. Our work has now revealed in a systematic way the potential of non-Saccharomyces species to emerge either as alternative host species or as a source of valuable genetic information for construction of more robust industrial S. serevisiae bioethanol production yeasts. Striking examples include yeast species like Pichia kudriavzevii and Wickerhamomyces anomalus that show very high tolerance to diverse stress factors. This large-scale phenotypic analysis has yielded a detailed database useful as a resource for future studies to understand and benefit from the molecular mechanisms underlying the extreme phenotypes of non-conventional yeast species.
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Affiliation(s)
- Vaskar Mukherjee
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, VIB Center of Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Louvain, Belgium
- Laboratory for Enzyme, Fermentation and Brewing Technology (EFBT), Department of Microbial and Molecular Systems, KU Leuven, Technology Campus Ghent, Gebroeders De Smetstraat 1, B-9000 Ghent, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium
- Present Address: Lundberg Laboratory, Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390 Göteborg, Sweden
| | - Dorota Radecka
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, VIB Center of Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Louvain, Belgium
| | - Guido Aerts
- Laboratory for Enzyme, Fermentation and Brewing Technology (EFBT), Department of Microbial and Molecular Systems, KU Leuven, Technology Campus Ghent, Gebroeders De Smetstraat 1, B-9000 Ghent, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Systems Biology, VIB Center for Microbiology, KU Leuven, Gaston Geenslaan 1, B-3001 Louvain, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, VIB Center of Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Louvain, Belgium
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106
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Shen XX, Zhou X, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data. G3 (BETHESDA, MD.) 2016; 6:3927-3939. [PMID: 27672114 PMCID: PMC5144963 DOI: 10.1534/g3.116.034744] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/21/2016] [Indexed: 01/20/2023]
Abstract
Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.
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Affiliation(s)
- Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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107
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Choo JH, Hong CP, Lim JY, Seo JA, Kim YS, Lee DW, Park SG, Lee GW, Carroll E, Lee YW, Kang HA. Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeast Saccharomycopsis fibuligera and its interspecies hybrid. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:246. [PMID: 27872659 PMCID: PMC5106798 DOI: 10.1186/s13068-016-0653-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/22/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Genomic studies on fungal species with hydrolytic activity have gained increased attention due to their great biotechnological potential for biomass-based biofuel production. The amylolytic yeast Saccharomycopsis fibuligera has served as a good source of enzymes and genes involved in saccharification. Despite its long history of use in food fermentation and bioethanol production, very little is known about the basic physiology and genomic features of S. fibuligera. RESULTS We performed whole-genome (WG) de novo sequencing and complete assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk in Korea. Intriguingly, the KJJ81 genome (~38 Mb) was revealed as a hybrid between the KPH12 genome (~18 Mb) and another unidentified genome sharing 88.1% nucleotide identity with the KPH12 genome. The seven chromosome pairs of KJJ81 subgenomes exhibit highly conserved synteny, indicating a very recent hybridization event. The phylogeny inferred from WG comparisons showed an early divergence of S. fibuligera before the separation of the CTG and Saccharomycetaceae clades in the subphylum Saccharomycotina. Reconstructed carbon and sulfur metabolic pathways, coupled with RNA-Seq analysis, suggested a marginal Crabtree effect under high glucose and activation of sulfur metabolism toward methionine biosynthesis under sulfur limitation in this yeast. Notably, the lack of sulfate assimilation genes in the S. fibuligera genome reflects a unique phenotype for Saccharomycopsis clades as natural sulfur auxotrophs. Extended gene families, including novel genes involved in saccharification and proteolysis, were identified. Moreover, comparative genome analysis of S. fibuligera ATCC 36309, an isolate from chalky rye bread in Germany, revealed that an interchromosomal translocation occurred in the KPH12 genome before the generation of the KJJ81 hybrid genome. CONCLUSIONS The completely sequenced S. fibuligera genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of S. fibuligera in the degradation of fermentation mash. The gene inventory facilitates the discovery of new genes applicable to the production of novel valuable enzymes and chemicals. Moreover, as the first gapless genome assembly in the genus Saccharomycopsis including members with desirable traits for bioconversion, the unique genomic features of S. fibuligera and its hybrid will provide in-depth insights into fungal genome dynamics as evolutionary adaptation.
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Affiliation(s)
- Jin Ho Choo
- Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea
| | - Chang Pyo Hong
- Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 South Korea
| | - Jeong-Ah Seo
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978 South Korea
| | - Young-Suk Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760 South Korea
| | - Dong Wook Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea
| | - Sin-Gi Park
- Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea
| | - Gir Won Lee
- Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea
| | - Emily Carroll
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978 South Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 South Korea
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea
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108
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Lu YJ, Swamy KBS, Leu JY. Experimental Evolution Reveals Interplay between Sch9 and Polyploid Stability in Yeast. PLoS Genet 2016; 12:e1006409. [PMID: 27812096 PMCID: PMC5094715 DOI: 10.1371/journal.pgen.1006409] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022] Open
Abstract
Polyploidization has crucial impacts on the evolution of different eukaryotic lineages including fungi, plants and animals. Recent genome data suggest that, for many polyploidization events, all duplicated chromosomes are maintained and genome reorganizations occur much later during evolution. However, newly-formed polyploid genomes are intrinsically unstable and often quickly degenerate into aneuploidy or diploidy. The transition between these two states remains enigmatic. In this study, laboratory evolution experiments were conducted to investigate this phenomenon. We show that robust tetraploidy is achieved in evolved yeast cells by increasing the abundance of Sch9—a protein kinase activated by the TORC1 (Target of Rapamycin Complex 1) and other signaling pathways. Overexpressing SCH9, but not TOR1, allows newly-formed tetraploids to exhibit evolved phenotypes and knocking out SCH9 diminishes the evolved phenotypes. Furthermore, when cells were challenged with conditions causing ancestral cells to evolve aneuploidy, tetraploidy was maintained in the evolved lines. Our results reveal a determinant role for Sch9 during the early stage of polyploid evolution. Polyploidy is frequently observed in eukaryotes, including in human liver cells and cancer. Evolutionary studies also suggest that polyploidy has contributed to species diversification and novel adaptation in fungi, plants and animals. However, artificially-constructed polyploids often display chromosome instability and quickly convert to aneuploids. This phenomenon conflicts with observations that many species derived from ancient genome duplications have maintained the extra number of chromosomes following polyploidization. What happened during the early stages of these polyploidy events that stabilized the duplicated genomes? We used laboratory evolution experiments to investigate this process. After being propagated in a rich medium at 23°C for 1000 generations, newly-constructed tetraploid yeast cells had evolved stable genomes. In addition, evolved cells acquired resistance to stresses specific to tetraploids and exhibited a more diploid-like transcriptome profile. Further analyses indicated that Sch9—the functional ortholog of mammalian S6 kinase involved in protein homeostasis, G1 progression, stress response and nutrient signaling—contributed to the evolved phenotypes. Evolved cells increased the protein abundance and stability of Sch9. Reconstitution experiments showed that overexpression of SCH9 enabled ancestral cells to display the evolved phenotypes and eliminating SCH9 diminished the evolved phenotypes. Finally, we show that evolved cells were able to maintain their genomes even under a condition that causes newly-formed tetraploids to evolve aneuploidy. Our results reveal that at the early stages after genome duplication, stable polyploidy can be achieved by fine-tuning a conserved key regulator coordinating multiple cellular processes.
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Affiliation(s)
- Yi-Jin Lu
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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109
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Gabaldón T, Naranjo-Ortíz MA, Marcet-Houben M. Evolutionary genomics of yeast pathogens in the Saccharomycotina. FEMS Yeast Res 2016; 16:fow064. [PMID: 27493146 PMCID: PMC5815160 DOI: 10.1093/femsyr/fow064] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/18/2016] [Accepted: 08/02/2016] [Indexed: 02/06/2023] Open
Abstract
Saccharomycotina comprises a diverse group of yeasts that includes numerous species of industrial or clinical relevance. Opportunistic pathogens within this clade are often assigned to the genus Candida but belong to phylogenetically distant lineages that also comprise non-pathogenic species. This indicates that the ability to infect humans has evolved independently several times among Saccharomycotina. Although the mechanisms of infection of the main groups of Candida pathogens are starting to be unveiled, we still lack sufficient understanding of the evolutionary paths that led to a virulent phenotype in each of the pathogenic lineages. Deciphering what genomic changes underlie the evolutionary emergence of a virulence trait will not only aid the discovery of novel virulence mechanisms but it will also provide valuable information to understand how new pathogens emerge, and what clades may pose a future danger. Here we review recent comparative genomics efforts that have revealed possible evolutionary paths to pathogenesis in different lineages, focusing on the main three agents of candidiasis worldwide: Candida albicans, C. parapsilosis and C. glabrata We will discuss what genomic traits may facilitate the emergence of virulence, and focus on two different genome evolution mechanisms able to generate drastic phenotypic changes and which have been associated to the emergence of virulence: gene family expansion and interspecies hybridization.
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Affiliation(s)
- Toni Gabaldón
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Miguel A Naranjo-Ortíz
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marina Marcet-Houben
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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110
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Prista C, Michán C, Miranda IM, Ramos J. The halotolerant Debaryomyces hansenii, the Cinderella of non-conventional yeasts. Yeast 2016; 33:523-533. [PMID: 27279567 DOI: 10.1002/yea.3177] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/10/2016] [Accepted: 05/10/2016] [Indexed: 11/10/2022] Open
Abstract
Debaryomyces hansenii is a halotolerant yeast with a high biotechnological potential, particularly in the food industry. However, research in this yeast is limited by its molecular peculiarities. In this review we summarize the state of the art of research in this microorganisms, describing both pros and cons. We discuss (i) its halotolerance, (ii) the molecular factors involved in saline and osmotic stress, (iii) its high gene density and ambiguous CUG decoding, and (iv) its biotechnological and medical interests. We trust that all the bottlenecks in its study will soon be overcome and D. hansenii will become a fundamental organism for food biotechnological processes. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Catarina Prista
- LEAF - Research Centre Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Isabel M Miranda
- Department of Microbiology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Centre for Health Technology and Services Research, Faculty of Medicine of the University of Porto, Portugal
| | - José Ramos
- Departamento de Microbiología, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain.
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Abstract
Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.
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112
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Non-Saccharomyces Yeasts and Their Importance in the Brewing Industry Part I -Brettanomyces (Dekkera). KVASNY PRUMYSL 2016. [DOI: 10.18832/kp2016024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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113
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Boundy-Mills KL, Glantschnig E, Roberts IN, Yurkov A, Casaregola S, Daniel HM, Groenewald M, Turchetti B. Yeast culture collections in the twenty-first century: new opportunities and challenges. Yeast 2016; 33:243-60. [PMID: 27144478 DOI: 10.1002/yea.3171] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 11/06/2022] Open
Abstract
The twenty-first century has brought new opportunities and challenges to yeast culture collections, whether they are long-standing or recently established. Basic functions such as archiving, characterizing and distributing yeasts continue, but with expanded responsibilities and emerging opportunities. In addition to a number of well-known, large public repositories, there are dozens of smaller public collections that differ in the range of species and strains preserved, field of emphasis and services offered. Several collections have converted their catalogues to comprehensive databases and synchronize them continuously through public services, making it easier for users worldwide to locate a suitable source for specific yeast strains and the data associated with these yeasts. In-house research such as yeast taxonomy continues to be important at culture collections. Because yeast culture collections preserve a broad diversity of species and strains within a species, they are able to make discoveries in many other areas as well, such as biotechnology, functional, comparative and evolution genomics, bioprocesses and novel products. Due to the implementation of the Convention of Biological Diversity (CBD) and the Nagoya Protocol (NP), there are new requirements for both depositors and users to ensure that yeasts were collected following proper procedures and to guarantee that the country of origin will be considered if benefits arise from a yeast's utilization. Intellectual property rights (IPRs) are extremely relevant to the current access and benefit-sharing (ABS) mechanisms; most research and development involving genetic resources and associated traditional knowledge will be subject to this topic. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Kyria L Boundy-Mills
- Phaff Yeast Culture Collection. Food Science and Technology, University of California, Davis, Davis, CA, USA
| | | | - Ian N Roberts
- National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Andrey Yurkov
- Leibniz Institute DSMZ - German Collection of Micro-organisms and Cell Cultures, Braunschweig, Germany
| | - Serge Casaregola
- Micalis Institute INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, Thiverval-Grignon, France
| | - Heide-Marie Daniel
- Mycothéque de l'Université Catholique de Louvain (BCCM/MUCL), Earth and Life Institute, Applied Microbiology, Laboratory of Mycology, Louvain-la-Neuve, Belgium
| | | | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Science, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
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114
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Weissenbach J. The rise of genomics. C R Biol 2016; 339:231-9. [PMID: 27263360 DOI: 10.1016/j.crvi.2016.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/19/2016] [Accepted: 04/19/2016] [Indexed: 11/17/2022]
Abstract
A brief history of the development of genomics is provided. Complete sequencing of genomes of uni- and multicellular organisms is based on important progress in sequencing and bioinformatics. Evolution of these methods is ongoing and has triggered an explosion in data production and analysis. Initial analyses focused on the inventory of genes encoding proteins. Completeness and quality of gene prediction remains crucial. Genome analyses profoundly modified our views on evolution, biodiversity and contributed to the detection of new functions, yet to be fully elucidated, such as those fulfilled by non-coding RNAs. Genomics has become the basis for the study of biology and provides the molecular support for a bunch of large-scale studies, the omics.
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Affiliation(s)
- Jean Weissenbach
- Commissariat à l'énergie atomique et aux énergies alternatives, Institut de génomique, Genoscope, 2, rue Gaston-Crémieux, 91000 Évry, France; CNRS, Unité de génomique métabolique UMR8030, 2, rue Gaston-Crémieux, 91000 Évry, France; Université d'Évry, Unité de génomique métabolique UMR8030, 2, rue Gaston-Crémieux, 91000 Évry, France.
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115
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Abstract
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent-due to events such as incomplete lineage sorting or horizontal gene transfer-it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such "process-agnostic" approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward's method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta We release treeCl, a new program to cluster genes of common evolutionary history (http://git.io/treeCl).
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Affiliation(s)
- Kevin Gori
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Campus, Hinxton, United Kingdom
| | - Tomasz Suchan
- Department of Ecology and Evolution, Biophore Building, UNIL-Sorge, University of Lausanne, Lausanne, Switzerland
| | - Nadir Alvarez
- Department of Ecology and Evolution, Biophore Building, UNIL-Sorge, University of Lausanne, Lausanne, Switzerland
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Campus, Hinxton, United Kingdom
| | - Christophe Dessimoz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Campus, Hinxton, United Kingdom Department of Ecology and Evolution, Biophore Building, UNIL-Sorge, University of Lausanne, Lausanne, Switzerland Department of Genetics, Evolution & Environment, University College London, London, United Kingdom Department of Computer Science, University College London, London, United Kingdom Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Biophore, Lausanne, Switzerland
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116
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Staneva D, Georgieva M, Miloshev G. Kluyveromyces lactis genome harbours a functional linker histone encoding gene. FEMS Yeast Res 2016; 16:fow034. [PMID: 27189369 DOI: 10.1093/femsyr/fow034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2016] [Indexed: 11/14/2022] Open
Abstract
Linker histones are essential components of chromatin in eukaryotes. Through interactions with linker DNA and nucleosomes they facilitate folding and maintenance of higher-order chromatin structures and thus delicately modulate gene activity. The necessity of linker histones in lower eukaryotes appears controversial and dubious. Genomic data have shown that Schizosaccharomyces pombe does not possess genes encoding linker histones while Kluyveromyces lactis has been reported to have a pseudogene. Regarding this controversy, we have provided the first direct experimental evidence for the existence of a functional linker histone gene, KlLH1, in K. lactis genome. Sequencing of KlLH1 from both genomic DNA and copy DNA confirmed the presence of an intact open reading frame. Transcription and splicing of the KlLH1 sequence as well as translation of its mRNA have been studied. In silico analysis revealed homology of KlLH1p to the histone H1/H5 protein family with predicted three domain structure characteristic for the linker histones of higher eukaryotes. This strongly proves that the yeast K. lactis does indeed possess a functional linker histone gene thus entailing the evolutionary preservation and significance of linker histones. The nucleotide sequences of KlLH1 are deposited in the GenBank under accession numbers KT826576, KT826577 and KT826578.
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Affiliation(s)
- Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
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117
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Booth GT, Wang IX, Cheung VG, Lis JT. Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast. Genome Res 2016; 26:799-811. [PMID: 27197211 PMCID: PMC4889974 DOI: 10.1101/gr.204578.116] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/19/2016] [Indexed: 12/29/2022]
Abstract
Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites genome-wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation, specific to S. pombe, that requires the conserved elongation factor subunit Spt4 and resembles promoter-proximal pausing in metazoans. PRO-seq profiles in strains lacking Spt4 reveal globally elevated levels of transcribing RNA Polymerase II (Pol II) within genes in both species. Messenger RNA abundance, however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.
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Affiliation(s)
- Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA
| | - Isabel X Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA
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118
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Paleo-López R, Quintero-Galvis JF, Solano-Iguaran JJ, Sanchez-Salazar AM, Gaitan-Espitia JD, Nespolo RF. A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts. Ecol Evol 2016; 6:3851-61. [PMID: 27516851 PMCID: PMC4972215 DOI: 10.1002/ece3.2097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 02/06/2023] Open
Abstract
When novel sources of ecological opportunity are available, physiological innovations can trigger adaptive radiations. This could be the case of yeasts (Saccharomycotina), in which an evolutionary novelty is represented by the capacity to exploit simple sugars from fruits (fermentation). During adaptive radiations, diversification and morphological evolution are predicted to slow‐down after early bursts of diversification. Here, we performed the first comparative phylogenetic analysis in yeasts, testing the “early burst” prediction on species diversification and also on traits of putative ecological relevance (cell‐size and fermentation versatility). We found that speciation rates are constant during the time‐range we considered (ca., 150 millions of years). Phylogenetic signal of both traits was significant (but lower for cell‐size), suggesting that lineages resemble each other in trait‐values. Disparity analysis suggested accelerated evolution (diversification in trait values above Brownian Motion expectations) in cell‐size. We also found a significant phylogenetic regression between cell‐size and fermentation versatility (R2 = 0.10), which suggests correlated evolution between both traits. Overall, our results do not support the early burst prediction both in species and traits, but suggest a number of interesting evolutionary patterns, that warrant further exploration. For instance, we show that the Whole Genomic Duplication that affected a whole clade of yeasts, does not seems to have a statistically detectable phenotypic effect at our level of analysis. In this regard, further studies of fermentation under common‐garden conditions combined with comparative analyses are warranted.
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Affiliation(s)
- Rocío Paleo-López
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile
| | - Julian F Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile
| | - Jaiber J Solano-Iguaran
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile
| | - Angela M Sanchez-Salazar
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile
| | - Juan D Gaitan-Espitia
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile; CSIRO Oceans & Atmosphere GPO Box 1538 Hobart 7001 Tasmania Australia
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile; Center of Applied Ecology and Sustainability (CAPES) Facultad de Ciencias Biológicas Universidad Católica de Chile Santiago 6513677 Chile
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119
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Chavez-Dozal AA, Bernardo SM, Lee SA. The exocyst in Candida albicans polarized secretion and filamentation. Curr Genet 2016; 62:343-6. [PMID: 26762634 PMCID: PMC4978426 DOI: 10.1007/s00294-015-0553-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 12/08/2015] [Indexed: 11/30/2022]
Abstract
The exocyst is an octameric complex that orchestrates the docking and tethering of vesicles to the plasma membrane during exocytosis and is fundamental for key biological processes including growth and establishment of cell polarity. Although components of the exocyst are well conserved among fungi, the specific functions of each component of the exocyst complex unique to Candida albicans biology and pathogenesis are not fully understood. This commentary describes recent findings regarding the role of exocyst subunits Sec6 and Sec15 in C. albicans filamentation and virulence.
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Affiliation(s)
- Alba A. Chavez-Dozal
- Section of Infectious Diseases, New Mexico VA Healthcare System, 1501 San Pedro SE, Mail Code 111-J, Albuquerque, NM 87108, USA
- Division of Infectious Diseases, University of New Mexico Health Science Center, Albuquerque, NM 87131, USA
| | - Stella M. Bernardo
- Section of Infectious Diseases, New Mexico VA Healthcare System, 1501 San Pedro SE, Mail Code 111-J, Albuquerque, NM 87108, USA
- Division of Infectious Diseases, University of New Mexico Health Science Center, Albuquerque, NM 87131, USA
| | - Samuel A. Lee
- Section of Infectious Diseases, New Mexico VA Healthcare System, 1501 San Pedro SE, Mail Code 111-J, Albuquerque, NM 87108, USA
- Division of Infectious Diseases, University of New Mexico Health Science Center, Albuquerque, NM 87131, USA
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120
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Kobert K, Salichos L, Rokas A, Stamatakis A. Computing the Internode Certainty and Related Measures from Partial Gene Trees. Mol Biol Evol 2016; 33:1606-17. [PMID: 26915959 PMCID: PMC4868120 DOI: 10.1093/molbev/msw040] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We present, implement, and evaluate an approach to calculate the internode certainty (IC) and tree certainty (TC) on a given reference tree from a collection of partial gene trees. Previously, the calculation of these values was only possible from a collection of gene trees with exactly the same taxon set as the reference tree. An application to sets of partial gene trees requires mathematical corrections in the IC and TC calculations. We implement our methods in RAxML and test them on empirical datasets. These tests imply that the inclusion of partial trees does matter. However, in order to provide meaningful measurements, any dataset should also include trees containing the full species set.
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Affiliation(s)
- Kassian Kobert
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Leonidas Salichos
- Department of Molecular Biophysics and Biochemistry, Yale University Department of Biological Sciences, Vanderbilt University
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University Department of Biomedical Informatics, Vanderbilt University Medical Center
| | - Alexandros Stamatakis
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Postfach 6980, Karlsruhe, 76128, Germany
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121
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Tekaia F. Inferring Orthologs: Open Questions and Perspectives. GENOMICS INSIGHTS 2016; 9:17-28. [PMID: 26966373 PMCID: PMC4778853 DOI: 10.4137/gei.s37925] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/30/2015] [Accepted: 01/02/2016] [Indexed: 01/25/2023]
Abstract
With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species. Yet, the dynamic remodeling of genome content through gain, loss, transfer of genes, and segmental and whole-genome duplication hinders reliable orthology detection. Moreover, the lack of direct functional evidence and the questionable quality of some available genome sequences and annotations present additional difficulties to assess orthology. This article reviews the existing computational methods and their potential accuracy in the high-throughput era of genome sequencing and anticipates open questions in terms of methodology, reliability, and computation. Appropriate taxon sampling together with combination of methods based on similarity, phylogeny, synteny, and evolutionary knowledge that may help detecting speciation events appears to be the most accurate strategy. This review also raises perspectives on the potential determination of orthology throughout the whole species phylogeny.
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Affiliation(s)
- Fredj Tekaia
- Institut Pasteur, Unit of Structural Microbiology, CNRS URA 3528 and University Paris Diderot, Sorbonne Paris Cité, Paris, France
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122
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Zhou Y, Yuikawa N, Nakatsuka H, Maekawa H, Harashima S, Nakanishi Y, Kaneko Y. Core regulatory components of the PHO pathway are conserved in the methylotrophic yeast Hansenula polymorpha. Curr Genet 2016; 62:595-605. [PMID: 26794724 PMCID: PMC4929164 DOI: 10.1007/s00294-016-0565-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 12/26/2022]
Abstract
To gain better understanding of the diversity and evolution of the gene regulation system in eukaryotes, the phosphate signal transduction (PHO) pathway in non-conventional yeasts has been studied in recent years. Here we characterized the PHO pathway of Hansenula polymorpha, which is genetically tractable and distantly related to Saccharomyces cerevisiae and Schizosaccharomyces pombe, in order to get more information for the diversity and evolution of the PHO pathway in yeasts. We generated several pho gene-deficient mutants based on the annotated draft genome of H. polymorpha BY4329. Except for the Hppho2-deficient mutant, these mutants exhibited the same phenotype of repressible acid phosphatase (APase) production as their S. cerevisiae counterparts. Subsequently, Hppho80 and Hppho85 mutants were isolated as suppressors of the Hppho81 mutation and Hppho4 was isolated from Hppho80 and Hppho85 mutants as the sole suppressor of the Hppho80 and Hppho85 mutations. To gain more complete delineation of the PHO pathway in H. polymorpha, we screened for UV-irradiated mutants that expressed APase constitutively. As a result, three classes of recessive constitutive mutations and one dominant constitutive mutation were isolated. Genetic analysis showed that one group of recessive constitutive mutations was allelic to HpPHO80 and that the dominant mutation occurred in the HpPHO81 gene. Epistasis analysis between Hppho81 and the other two classes of recessive constitutive mutations suggested that the corresponding new genes, named PHO51 and PHO53, function upstream of HpPHO81 in the PHO pathway. Taking these findings together, we conclude that the main components of the PHO pathway identified in S. cerevisiae are conserved in the methylotrophic yeast H. polymorpha, even though these organisms separated from each other before duplication of the whole genome. This finding is useful information for the study of evolution of the PHO regulatory system in yeasts.
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Affiliation(s)
- Ying Zhou
- Yeast Genetic Resources Laboratory, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan
| | - Naoya Yuikawa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan
| | - Hiroki Nakatsuka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan
| | - Hiromi Maekawa
- Yeast Genetic Resources Laboratory, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan
| | - Satoshi Harashima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan.,Division of Applied Microbial Technology, Graduate School of Engineering, Sojo University, Kumamoto, 860-0082, Japan
| | - Yoichi Nakanishi
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshinobu Kaneko
- Yeast Genetic Resources Laboratory, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan.
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123
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Becker-Kettern J, Paczia N, Conrotte JF, Kay DP, Guignard C, Jung PP, Linster CL. Saccharomyces cerevisiae Forms D-2-Hydroxyglutarate and Couples Its Degradation to D-Lactate Formation via a Cytosolic Transhydrogenase. J Biol Chem 2016; 291:6036-58. [PMID: 26774271 DOI: 10.1074/jbc.m115.704494] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 12/23/2022] Open
Abstract
The D or L form of 2-hydroxyglutarate (2HG) accumulates in certain rare neurometabolic disorders, and high D-2-hydroxyglutarate (D-2HG) levels are also found in several types of cancer. Although 2HG has been detected in Saccharomyces cerevisiae, its metabolism in yeast has remained largely unexplored. Here, we show that S. cerevisiae actively forms the D enantiomer of 2HG. Accordingly, the S. cerevisiae genome encodes two homologs of the human D-2HG dehydrogenase: Dld2, which, as its human homolog, is a mitochondrial protein, and the cytosolic protein Dld3. Intriguingly, we found that a dld3Δ knock-out strain accumulates millimolar levels of D-2HG, whereas a dld2Δ knock-out strain displayed only very moderate increases in D-2HG. Recombinant Dld2 and Dld3, both currently annotated as D-lactate dehydrogenases, efficiently oxidized D-2HG to α-ketoglutarate. Depletion of D-lactate levels in the dld3Δ, but not in the dld2Δ mutant, led to the discovery of a new type of enzymatic activity, carried by Dld3, to convert D-2HG to α-ketoglutarate, namely an FAD-dependent transhydrogenase activity using pyruvate as a hydrogen acceptor. We also provide evidence that Ser3 and Ser33, which are primarily known for oxidizing 3-phosphoglycerate in the main serine biosynthesis pathway, in addition reduce α-ketoglutarate to D-2HG using NADH and represent major intracellular sources of D-2HG in yeast. Based on our observations, we propose that D-2HG is mainly formed and degraded in the cytosol of S. cerevisiae cells in a process that couples D-2HG metabolism to the shuttling of reducing equivalents from cytosolic NADH to the mitochondrial respiratory chain via the D-lactate dehydrogenase Dld1.
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Affiliation(s)
- Julia Becker-Kettern
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Nicole Paczia
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Jean-François Conrotte
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Daniel P Kay
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Cédric Guignard
- the Luxembourg Institute of Science and Technology, 41 Rue du Brill, L-4422 Belvaux, Luxembourg
| | - Paul P Jung
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Carole L Linster
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
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124
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Freel KC, Friedrich A, Sarilar V, Devillers H, Neuvéglise C, Schacherer J. Whole-Genome Sequencing and Intraspecific Analysis of the Yeast Species Lachancea quebecensis. Genome Biol Evol 2016; 8:733-41. [PMID: 26733577 PMCID: PMC4823976 DOI: 10.1093/gbe/evv262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The gold standard in yeast population genomics has been the model organism Saccharomyces cerevisiae. However, the exploration of yeast species outside the Saccharomyces genus is essential to broaden the understanding of genome evolution. Here, we report the analyses of whole-genome sequences of nineisolates from the recently described yeast species Lachancea quebecensis. The genome of one isolate was assembled and annotated, and the intraspecific variability within L. quebecensis was surveyed by comparing the sequences from the eight other isolates to this reference sequence. Our study revealed that these strains harbor genomes with an average nucleotide diversity of π = 2 × 10−3 which is slightly lower, although on the same order of magnitude, as that previously determined for S. cerevisiae (π = 4 × 10−3). Our results show that even though these isolates were all obtained from a relatively isolated geographic location, the same ecological source, and represent a smaller sample size than is available for S. cerevisiae, the levels of divergence are similar to those observed in this model species. This divergence is essentially linked to the presence of two distinct clusters delineated according to geographic location. However, even with relatively similar ranges of genome divergence, L. quebecensis has an extremely low global phenotypic variance of 0.062 compared with 0.59 previously determined in S. cerevisiae.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Véronique Sarilar
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Hugo Devillers
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
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125
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Sabir F, Prista C, Madeira A, Moura T, Loureiro-Dias MC, Soveral G. Water Transport in Yeasts. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:107-124. [PMID: 26721272 DOI: 10.1007/978-3-319-25304-6_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Water moves across membranes through the lipid bilayer and through aquaporins, in this case in a regulated manner. Aquaporins belong to the MIP superfamily and two subfamilies are represented in yeasts: orthodox aquaporins considered to be specific water channels and aquaglyceroporins (heterodox aquaporins). In Saccharomyces cerevisiae genome, four aquaporin isoforms were identified, two of which are genetically close to orthodox aquaporins (ScAqy1 and ScAqy2) and the other two are more closely related to the aquaglyceroporins (ScFps1 and ScAqy3). Advances in the establishment of water channels structure are reviewed in this chapter in relation with the mechanisms of selectivity, conductance and gating. Aquaporins are important for key aspects of yeast physiology. They have been shown to be involved in sporulation, rapid freeze-thaw tolerance, osmo-sensitivity, and modulation of cell surface properties and colony morphology, although the underlying exact mechanisms are still unknown.
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Affiliation(s)
- Farzana Sabir
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal. .,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal.
| | - Catarina Prista
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Ana Madeira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal
| | - Teresa Moura
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal
| | - Maria C Loureiro-Dias
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Graça Soveral
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal
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126
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Genomics and the making of yeast biodiversity. Curr Opin Genet Dev 2015; 35:100-9. [PMID: 26649756 DOI: 10.1016/j.gde.2015.10.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 12/22/2022]
Abstract
Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies.
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127
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Olsen RA, Bunikis I, Tiukova I, Holmberg K, Lötstedt B, Pettersson OV, Passoth V, Käller M, Vezzi F. De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping. Gigascience 2015; 4:56. [PMID: 26617983 PMCID: PMC4661999 DOI: 10.1186/s13742-015-0094-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND It remains a challenge to perform de novo assembly using next-generation sequencing (NGS). Despite the availability of multiple sequencing technologies and tools (e.g., assemblers) it is still difficult to assemble new genomes at chromosome resolution (i.e., one sequence per chromosome). Obtaining high quality draft assemblies is extremely important in the case of yeast genomes to better characterise major events in their evolutionary history. The aim of this work is two-fold: on the one hand we want to show how combining different and somewhat complementary technologies is key to improving assembly quality and correctness, and on the other hand we present a de novo assembly pipeline we believe to be beneficial to core facility bioinformaticians. To demonstrate both the effectiveness of combining technologies and the simplicity of the pipeline, here we present the results obtained using the Dekkera bruxellensis genome. METHODS In this work we used short-read Illumina data and long-read PacBio data combined with the extreme long-range information from OpGen optical maps in the task of de novo genome assembly and finishing. Moreover, we developed NouGAT, a semi-automated pipeline for read-preprocessing, de novo assembly and assembly evaluation, which was instrumental for this work. RESULTS We obtained a high quality draft assembly of a yeast genome, resolved on a chromosomal level. Furthermore, this assembly was corrected for mis-assembly errors as demonstrated by resolving a large collapsed repeat and by receiving higher scores by assembly evaluation tools. With the inclusion of PacBio data we were able to fill about 5 % of the optical mapped genome not covered by the Illumina data.
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Affiliation(s)
- Remi-Andre Olsen
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, NGI/SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, SE-752 37 Uppsala, Sweden
| | - Ievgeniia Tiukova
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-75007 Uppsala, Sweden
| | - Kicki Holmberg
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
| | - Britta Lötstedt
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
| | - Olga Vinnere Pettersson
- Uppsala Genome Center, NGI/SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, SE-752 37 Uppsala, Sweden
| | - Volkmar Passoth
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-75007 Uppsala, Sweden
| | - Max Käller
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
| | - Francesco Vezzi
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
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128
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Martínez-Lumbreras S, Taverniti V, Zorrilla S, Séraphin B, Pérez-Cañadillas JM. Gbp2 interacts with THO/TREX through a novel type of RRM domain. Nucleic Acids Res 2015; 44:437-48. [PMID: 26602689 PMCID: PMC4705658 DOI: 10.1093/nar/gkv1303] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 11/07/2015] [Indexed: 12/11/2022] Open
Abstract
Metazoan SR and SR-like proteins are important regulatory factors in RNA splicing, export, translation and RNA decay. We determined the NMR structures and nucleic acid interaction modes of Gbp2 and Hrb1, two paralogous budding yeast proteins with similarities to mammalian SR proteins. Gbp2 RRM1 and RRM2 recognise preferentially RNAs containing the core motif GGUG. Sequence selectivity resides in a non-canonical interface in RRM2 that is highly related to the SRSF1 pseudoRRM. The atypical Gbp2/Hrb1 C-terminal RRM domains (RRM3) do not interact with RNA/DNA, likely because of their novel N-terminal extensions that block the canonical RNA binding interface. Instead, we discovered that RRM3 is crucial for interaction with the THO/TREX complex and identified key residues essential for this interaction. Moreover, Gbp2 interacts genetically with Tho2 as the double deletion shows a synthetic phenotype and preventing Gbp2 interaction with the THO/TREX complex partly supresses gene expression defect associated with inactivation of the latter complex. These findings provide structural and functional insights into the contribution of SR-like proteins in the post-transcriptional control of gene expression.
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Affiliation(s)
- Santiago Martínez-Lumbreras
- Department of Biological Physical Chemistry, Instituto de Química-Física 'Rocasolano', CSIC, Serrano-119, 28006 Madrid, Spain
| | - Valerio Taverniti
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGMBC), Centre National de Recherche Scientifique (CNRS) UMR 7104/Institut National de Santé et de Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France
| | - Silvia Zorrilla
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Bertrand Séraphin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGMBC), Centre National de Recherche Scientifique (CNRS) UMR 7104/Institut National de Santé et de Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France
| | - José Manuel Pérez-Cañadillas
- Department of Biological Physical Chemistry, Instituto de Química-Física 'Rocasolano', CSIC, Serrano-119, 28006 Madrid, Spain
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Knight SJ, Goddard MR. Sporulation in soil as an overwinter survival strategy in Saccharomyces cerevisiae. FEMS Yeast Res 2015; 16:fov102. [PMID: 26568201 PMCID: PMC5815064 DOI: 10.1093/femsyr/fov102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2015] [Indexed: 01/12/2023] Open
Abstract
Due to its commercial value and status as a research model there is an extensive body of knowledge concerning Saccharomyces cerevisiae's cell biology and genetics. Investigations into S. cerevisiae's ecology are comparatively lacking, and are mostly focused on the behaviour of this species in high sugar, fruit-based environments; however, fruit is ephemeral, and presumably, S. cerevisiae has evolved a strategy to survive when this niche is not available. Among other places, S. cerevisiae has been isolated from soil which, in contrast to fruit, is a permanent habitat. We hypothesize that S. cerevisiae employs a life history strategy targeted at self-preservation rather than growth outside of the fruit niche, and resides in forest niches, such as soil, in a dormant and resistant sporulated state, returning to fruit via vectors such as insects. One crucial aspect of this hypothesis is that S. cerevisiae must be able to sporulate in the ‘forest’ environment. Here, we provide the first evidence for a natural environment (soil) where S. cerevisiae sporulates. While there are further aspects of this hypothesis that require experimental verification, this is the first step towards an inclusive understanding of the more cryptic aspects of S. cerevisiae's ecology. The ability of Saccharomyces cerevisiae to sporulate in soil supports a ‘fruit forest-reservoir’ life-cycle.
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Affiliation(s)
- Sarah J Knight
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand;
| | - Matthew R Goddard
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand; School of Life Sciences, University of Lincoln, Lincoln, LN6 7DL, UK
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130
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Kolondra A, Labedzka-Dmoch K, Wenda JM, Drzewicka K, Golik P. The transcriptome of Candida albicans mitochondria and the evolution of organellar transcription units in yeasts. BMC Genomics 2015; 16:827. [PMID: 26487099 PMCID: PMC4618339 DOI: 10.1186/s12864-015-2078-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/13/2015] [Indexed: 02/06/2023] Open
Abstract
Background Yeasts show remarkable variation in the organization of their mitochondrial genomes, yet there is little experimental data on organellar gene expression outside few model species. Candida albicans is interesting as a human pathogen, and as a representative of a clade that is distant from the model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Unlike them, it encodes seven Complex I subunits in its mtDNA. No experimental data regarding organellar expression were available prior to this study. Methods We used high-throughput RNA sequencing and traditional RNA biology techniques to study the mitochondrial transcriptome of C. albicans strains BWP17 and SN148. Results The 14 protein-coding genes, two ribosomal RNA genes, and 24 tRNA genes are expressed as eight primary polycistronic transcription units. We also found transcriptional activity in the noncoding regions, and antisense transcripts that could be a part of a regulatory mechanism. The promoter sequence is a variant of the nonanucleotide identified in other yeast mtDNAs, but some of the active promoters show significant departures from the consensus. The primary transcripts are processed by a tRNA punctuation mechanism into the monocistronic and bicistronic mature RNAs. The steady state levels of various mature transcripts exhibit large differences that are a result of posttranscriptional regulation. Transcriptome analysis allowed to precisely annotate the positions of introns in the RNL (2), COB (2) and COX1 (4) genes, as well as to refine the annotation of tRNAs and rRNAs. Comparative study of the mitochondrial genome organization in various Candida species indicates that they undergo shuffling in blocks usually containing 2–3 genes, and that their arrangement in primary transcripts is not conserved. tRNA genes with their associated promoters, as well as GC-rich sequence elements play an important role in these evolutionary events. Conclusions The main evolutionary force shaping the mitochondrial genomes of yeasts is the frequent recombination, constantly breaking apart and joining genes into novel primary transcription units. The mitochondrial transcription units are constantly rearranged in evolution shaping the features of gene expression, such as the presence of secondary promoter sites that are inactive, or act as “booster” promoters, simplified transcriptional regulation and reliance on posttranscriptional mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2078-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Karolina Labedzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Joanna M Wenda
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Katarzyna Drzewicka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Pawel Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland. .,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
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131
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Lin Q, Qi H, Wu Y, Yuan Y. Robust orthogonal recombination system for versatile genomic elements rearrangement in yeast Saccharomyces cerevisiae. Sci Rep 2015; 5:15249. [PMID: 26477943 PMCID: PMC4609996 DOI: 10.1038/srep15249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/26/2015] [Indexed: 11/25/2022] Open
Abstract
Rearrangement of genomic DNA elements in a dynamic controlled fashion is a fundamental challenge. Site-specific DNA recombinases have been tamed as a powerful tool in genome editing. Here, we reported a DNA element rearrangement on the basis of a pairwise orthogonal recombination system which is comprised of two site-specific recombinases of Vika/vox and Cre/loxp in yeast Saccharomyces Creevisiae. Taking the advantage of the robust pairwise orthogonality, we showed that multi gene elements could be organized in a programmed way, in which rationally designed pattern of loxP and vox determined the final genotype after expressing corresponding recombinases. Finally, it was demonstrated that the pairwise orthogonal recombination system could be utilized to refine synthetic chromosome rearrangement and modification by loxP-mediated evolution, SCRaMbLE, in yeast cell carrying a completely synthesized chromosome III.
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Affiliation(s)
- Qiuhui Lin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Hao Qi
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Yi Wu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
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132
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Roy S, Thompson D. Evolution of regulatory networks in Candida glabrata: learning to live with the human host. FEMS Yeast Res 2015; 15:fov087. [PMID: 26449820 DOI: 10.1093/femsyr/fov087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2015] [Indexed: 12/12/2022] Open
Abstract
The opportunistic human fungal pathogen Candida glabrata is second only to C. albicans as the cause of Candida infections and yet is more closely related to Saccharomyces cerevisiae. Recent advances in functional genomics technologies and computational approaches to decipher regulatory networks, and the comparison of these networks among these and other Ascomycete species, have revealed both unique and shared strategies in adaptation to a human commensal/opportunistic pathogen lifestyle and antifungal drug resistance in C. glabrata. Recently, several C. glabrata sister species in the Nakeseomyces clade representing both human associated (commensal) and environmental isolates have had their genomes sequenced and analyzed. This has paved the way for comparative functional genomics studies to characterize the regulatory networks in these species to identify informative patterns of conservation and divergence linked to phenotypic evolution in the Nakaseomyces lineage.
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Affiliation(s)
- Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison, Madison, WI 53715, USA Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Dawn Thompson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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133
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Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nat Rev Genet 2015; 16:567-82. [PMID: 26347030 DOI: 10.1038/nrg3937] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolve and resequence (E&R) experiments use experimental evolution to adapt populations to a novel environment, then next-generation sequencing to analyse genetic changes. They enable molecular evolution to be monitored in real time on a genome-wide scale. Here, we review the field of E&R experiments across diverse systems, ranging from simple non-living RNA to bacteria, yeast and the complex multicellular organism Drosophila melanogaster. We explore how different evolutionary outcomes in these systems are largely consistent with common population genetics principles. Differences in outcomes across systems are largely explained by different starting population sizes, levels of pre-existing genetic variation, recombination rates and adaptive landscapes. We highlight emerging themes and inconsistencies that future experiments must address.
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134
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Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF. Genome-wide replication landscape of Candida glabrata. BMC Biol 2015; 13:69. [PMID: 26329162 PMCID: PMC4556013 DOI: 10.1186/s12915-015-0177-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/05/2015] [Indexed: 11/25/2022] Open
Abstract
Background The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments. Results We identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus. Conclusions Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0177-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stéphane Descorps-Declère
- Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), F-75015, Paris, France.
| | - Cyril Saguez
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, F-75015, Paris, France. .,CNRS, UMR3525, F-75015, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75252, Paris, Cedex 05, France.
| | - Axel Cournac
- CNRS, UMR3525, F-75015, Paris, France. .,Institut Pasteur, Groupe Régulation Spatiale des Génomes, Département Génomes & Génétique, F-75015, Paris, France.
| | - Martial Marbouty
- CNRS, UMR3525, F-75015, Paris, France. .,Institut Pasteur, Groupe Régulation Spatiale des Génomes, Département Génomes & Génétique, F-75015, Paris, France.
| | - Thomas Rolland
- Present address: Institut Pasteur, Unité de Génétique Humaine et Fonctions Cognitives, Département des Neurosciences, F-75015, Paris, France.
| | - Laurence Ma
- Institut Pasteur, Plate-forme Génomique, Département Génomes & Génétique, F-75015, Paris, France.
| | - Christiane Bouchier
- Institut Pasteur, Plate-forme Génomique, Département Génomes & Génétique, F-75015, Paris, France.
| | - Ivan Moszer
- Present address: Plate-forme Bio-informatique/Biostatistique, Institut de Neurosciences Translationnelles IHU-A-ICM, Hôpital Pitié-Salpêtrière, 47-83 bd de l'Hôpital, 75561, Paris, Cedex 13, France.
| | - Bernard Dujon
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, F-75015, Paris, France. .,CNRS, UMR3525, F-75015, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75252, Paris, Cedex 05, France.
| | - Romain Koszul
- CNRS, UMR3525, F-75015, Paris, France. .,Institut Pasteur, Groupe Régulation Spatiale des Génomes, Département Génomes & Génétique, F-75015, Paris, France.
| | - Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, F-75015, Paris, France. .,CNRS, UMR3525, F-75015, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75252, Paris, Cedex 05, France.
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135
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Natesuntorn W, Iwami K, Matsubara Y, Sasano Y, Sugiyama M, Kaneko Y, Harashima S. Genome-wide construction of a series of designed segmental aneuploids in Saccharomyces cerevisiae. Sci Rep 2015. [PMID: 26224198 PMCID: PMC4519793 DOI: 10.1038/srep12510] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Segmental aneuploidy can play an important role in environmental adaptation. However, study of segmental aneuploids is severely hampered by the difficulty of creating them in a designed fashion. Here, we describe a PCR-mediated chromosome duplication (PCDup) technology that enables the generation of segmental aneuploidy at any desired chromosomal region in Saccharomyces cerevisiae. We constructed multiple strains harboring 100 kb to 200 kb segmental duplications covering the whole of the S. cerevisiae genome. Interestingly, some segmental aneuploidies confer stress tolerance, such as to high temperature, ethanol and strong acids, while others induce cell lethality and stress sensitivity, presumably as result of the simultaneous increases in dosages of multiple genes. We suggest that our PCDup technology will accelerate studies into the phenotypic changes resulting from alteration of gene dosage balance of multiple genes and will provide new insights into the adaptive molecular mechanisms in the genome in segmental aneuploidy-derived human diseases.
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Affiliation(s)
- Waranya Natesuntorn
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kotaro Iwami
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuki Matsubara
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yu Sasano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Minetaka Sugiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshinobu Kaneko
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Satoshi Harashima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Abstract
Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains. This review summarizes current knowledge and recent advances on the diversity and evolutionary history of Saccharomyces cerevisiae wine yeasts, focusing on the domestication fingerprints identified in these strains.
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Affiliation(s)
- Souhir Marsit
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Sylvie Dequin
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
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137
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Kobayashi N, Suzuki Y, Schoenfeld LW, Müller CA, Nieduszynski C, Wolfe KH, Tanaka TU. Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres. Curr Biol 2015; 25:2026-33. [PMID: 26166782 PMCID: PMC4533239 DOI: 10.1016/j.cub.2015.06.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/26/2015] [Accepted: 06/10/2015] [Indexed: 11/30/2022]
Abstract
Centromeres are the chromosomal regions promoting kinetochore assembly for chromosome segregation. In many eukaryotes, the centromere consists of up to mega base pairs of DNA. On such “regional centromeres,” kinetochore assembly is mainly defined by epigenetic regulation [1]. By contrast, a clade of budding yeasts (Saccharomycetaceae) has a “point centromere” of 120–200 base pairs of DNA, on which kinetochore assembly is defined by the consensus DNA sequence [2, 3]. During evolution, budding yeasts acquired point centromeres, which replaced ancestral, regional centromeres [4]. All known point centromeres among different yeast species share common consensus DNA elements (CDEs) [5, 6], implying that they evolved only once and stayed essentially unchanged throughout evolution. Here, we identify a yeast centromere that challenges this view: that of the budding yeast Naumovozyma castellii is the first unconventional point centromere with unique CDEs. The N. castellii centromere CDEs are essential for centromere function but have different DNA sequences from CDEs in other point centromeres. Gene order analyses around N. castellii centromeres indicate their unique, and separate, evolutionary origin. Nevertheless, they are still bound by the ortholog of the CBF3 complex, which recognizes CDEs in other point centromeres. The new type of point centromere originated prior to the divergence between N. castellii and its close relative Naumovozyma dairenensis and disseminated to all N. castellii chromosomes through extensive genome rearrangement. Thus, contrary to the conventional view, point centromeres can undergo rapid evolutionary changes. These findings give new insights into the evolution of point centromeres. A new type of point centromere has been identified in budding yeast N. castellii Its DNA sequence and evolutionary origin are different from other point centromeres N. castellii centromeres are bound by CBF3 that recognizes other point centromeres Contrary to the conventional view, point centromeres can change rapidly in evolution
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Affiliation(s)
- Norihiko Kobayashi
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Yutaka Suzuki
- Department of Computational Biology, School of Frontier Medicine, University of Tokyo, Chiba 277-8562, Japan
| | - Lori W Schoenfeld
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carolin A Müller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Conrad Nieduszynski
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kenneth H Wolfe
- UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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138
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Heiss S, Puxbaum V, Gruber C, Altmann F, Gasser B, Mattanovich D. Multistep processing of the secretion leader of the extracellular protein Epx1 in Pichia pastoris and implications for protein localization. Microbiology (Reading) 2015; 161:1356-68. [DOI: 10.1099/mic.0.000105] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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139
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Radecka D, Mukherjee V, Mateo RQ, Stojiljkovic M, Foulquié-Moreno MR, Thevelein JM. Looking beyond Saccharomyces: the potential of non-conventional yeast species for desirable traits in bioethanol fermentation. FEMS Yeast Res 2015; 15:fov053. [PMID: 26126524 DOI: 10.1093/femsyr/fov053] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2015] [Indexed: 01/18/2023] Open
Abstract
Saccharomyces cerevisiae has been used for millennia in the production of food and beverages and is by far the most studied yeast species. Currently, it is also the most used microorganism in the production of first-generation bioethanol from sugar or starch crops. Second-generation bioethanol, on the other hand, is produced from lignocellulosic feedstocks that are pretreated and hydrolyzed to obtain monomeric sugars, mainly D-glucose, D-xylose and L-arabinose. Recently, S. cerevisiae recombinant strains capable of fermenting pentose sugars have been generated. However, the pretreatment of the biomass results in hydrolysates with high osmolarity and high concentrations of inhibitors. These compounds negatively influence the fermentation process. Therefore, robust strains with high stress tolerance are required. Up to now, more than 2000 yeast species have been described and some of these could provide a solution to these limitations because of their high tolerance to the most predominant stress conditions present in a second-generation bioethanol reactor. In this review, we will summarize what is known about the non-conventional yeast species showing unusual tolerance to these stresses, namely Zygosaccharomyces rouxii (osmotolerance), Kluyveromyces marxianus and Ogataea (Hansenula) polymorpha (thermotolerance), Dekkera bruxellensis (ethanol tolerance), Pichia kudriavzevii (furan derivatives tolerance) and Z. bailii (acetic acid tolerance).
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Affiliation(s)
- Dorota Radecka
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Vaskar Mukherjee
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium Laboratory for Process Microbial Ecology and Bioinspirational Management, Cluster for Bioengineering Technology (CBeT), Department of Microbial and Molecular Systems (M2S), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Flanders, Belgium
| | - Raquel Quintilla Mateo
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Marija Stojiljkovic
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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140
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Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, Souciet JL, Gabaldón T, Tinsley CR, Casaregola S. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci Rep 2015; 5:11571. [PMID: 26108467 PMCID: PMC4479816 DOI: 10.1038/srep11571] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/29/2015] [Indexed: 12/13/2022] Open
Abstract
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
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Affiliation(s)
- Guillaume Morel
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Lieven Sterck
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Dominique Swennen
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Djamila Onesime
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Anthony Levasseur
- INRA UMR1163, Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Noémie Jacques
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Sandrine Mallet
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Arnaux Couloux
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Karine Labadie
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Joëlle Amselem
- INRA UR1164, Unité de Recherche Génomique – Info, 78000 Versailles, France
| | - Jean-Marie Beckerich
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | | | - Yves Van de Peer
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
- Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
| | - Patrick Wincker
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
- CNRS UMR 8030, 2 Rue Gaston Crémieux, Évry, 91000, France
- Université d’Evry, Bd François Mitterand, Evry,91025, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, Strasbourg, 67000, France
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Colin R. Tinsley
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Serge Casaregola
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
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141
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Dujon B. Basic principles of yeast genomics, a personal recollection: Graphical Abstract Figure. FEMS Yeast Res 2015; 15:fov047. [DOI: 10.1093/femsyr/fov047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2015] [Indexed: 12/12/2022] Open
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142
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Wolfe KH, Armisén D, Proux-Wera E, ÓhÉigeartaigh SS, Azam H, Gordon JL, Byrne KP. Clade- and species-specific features of genome evolution in the Saccharomycetaceae. FEMS Yeast Res 2015; 15:fov035. [PMID: 26066552 PMCID: PMC4629796 DOI: 10.1093/femsyr/fov035] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2015] [Indexed: 12/12/2022] Open
Abstract
Many aspects of the genomes of yeast species in the family Saccharomycetaceae have been well conserved during evolution. They have similar genome sizes, genome contents, and extensive collinearity of gene order along chromosomes. Gene functions can often be inferred reliably by using information from Saccharomyces cerevisiae. Beyond this conservative picture however, there are many instances where a species or a clade diverges substantially from the S. cerevisiae paradigm—for example, by the amplification of a gene family, or by the absence of a biochemical pathway or a protein complex. Here, we review clade-specific features, focusing on genomes sequenced in our laboratory from the post-WGD genera Naumovozyma, Kazachstania and Tetrapisispora, and from the non-WGD species Torulaspora delbrueckii. Examples include the loss of the pathway for histidine synthesis in the cockroach-associated species Tetrapisispora blattae; the presence of a large telomeric GAL gene cluster in To. delbrueckii; losses of the dynein and dynactin complexes in several independent yeast lineages; fragmentation of the MAT locus and loss of the HO gene in Kazachstania africana; and the patchy phylogenetic distribution of RNAi pathway components. The authors review species-specific evolutionary attributes of yeast genomes.
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Affiliation(s)
- Kenneth H Wolfe
- UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - David Armisén
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon - CNRS UMR 5242 - INRA USC 1370, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Estelle Proux-Wera
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Science for Life Laboratory, Dept. of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Seán S ÓhÉigeartaigh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Centre for the Study of Existential Risk, University of Cambridge, CRASSH, Alison Richard Building, 7 West Road, Cambridge, CB3 9DT, UK
| | - Haleema Azam
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jonathan L Gordon
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland CIRAD, UMR CMAEE, Site de Duclos, Prise d'eau, F-97170, Petit-Bourg, Guadeloupe, France
| | - Kevin P Byrne
- UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
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143
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Lipids containing medium-chain fatty acids are specific to post-whole genome duplication Saccharomycotina yeasts. BMC Evol Biol 2015; 15:97. [PMID: 26018144 PMCID: PMC4446107 DOI: 10.1186/s12862-015-0369-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 04/29/2015] [Indexed: 12/04/2022] Open
Abstract
Background Yeasts belonging to the subphylum Saccharomycotina have been used for centuries in food processing and, more recently, biotechnology. Over the past few decades, these yeasts have also been studied in the interest of their potential to produce oil to replace fossil resources. Developing yeasts for massive oil production requires increasing yield and modifying the profiles of the fatty acids contained in the oil to satisfy specific technical requirements. For example, derivatives of medium-chain fatty acids (MCFAs, containing 6–14 carbons) are used for the production of biodiesels, cleaning products, lubricants and cosmetics. Few studies are available in the literature on the production of MCFAs in yeasts. Results We analyzed the MCFA content in Saccharomyces cerevisiae grown in various conditions. The results revealed that MCFAs preferentially accumulated when cells were grown on synthetic media with a high C/N ratio at low temperature (23 °C). Upon screening deletion mutant strains for genes encoding lipid droplet-associated proteins, we found two genes, LOA1 and TGL3, involved in MCFA homeostasis. A phylogenetic analysis on 16 Saccharomycotina species showed that fatty acid profiles differed drastically among yeasts. Interestingly, MCFAs are only present in post-whole genome duplication yeast species. Conclusions In this study, we produced original data on fatty acid diversity in yeasts. We demonstrated that yeasts are amenable to genetic and metabolic engineering to increase their MCFA production. Furthermore, we revealed that yeast lipid biodiversity has not been fully explored, but that yeasts likely harbor as-yet-undiscovered strains or enzymes that can contribute to the production of high-value fatty acids for green chemistry. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0369-2) contains supplementary material, which is available to authorized users.
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144
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Freel KC, Friedrich A, Schacherer J. Mitochondrial genome evolution in yeasts: an all-encompassing view. FEMS Yeast Res 2015; 15:fov023. [PMID: 25969454 DOI: 10.1093/femsyr/fov023] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2015] [Indexed: 12/26/2022] Open
Abstract
Mitochondria are important organelles that harbor their own genomes encoding a key set of proteins that ensure respiration and provide the eukaryotic cell with energy. Recent advances in high-throughput sequencing technologies present a unique opportunity to explore mitochondrial (mt) genome evolution. The Saccharomycotina yeasts have proven to be the leading organisms for mt comparative and population genomics. In fact, the explosion of complete yeast mt genome sequences has allowed for a broader view of the mt diversity across this incredibly diverse subphylum, both within and between closely related species. Here, we summarize the present state of yeast mitogenomics, including the currently available data and what it reveals concerning the diversity of content, organization, structure and evolution of mt genomes.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156 Strasbourg 67083, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156 Strasbourg 67083, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156 Strasbourg 67083, France
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145
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Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Res 2015; 43:5331-9. [PMID: 25940625 PMCID: PMC4477656 DOI: 10.1093/nar/gkv424] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/17/2015] [Indexed: 11/16/2022] Open
Abstract
Centromeres are essential for proper chromosome segregation. Despite extensive research, centromere locations in yeast genomes remain difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation capture assay, Hi-C, has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single genome from Hi-C data by exploiting the centromeres’ tendency to cluster in three-dimensional space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use Centurion to infer centromere locations in 14 yeast species. Across all microbes that we consider, Centurion predicts 89% of centromeres within 5 kb of their known locations. We also demonstrate the robustness of the approach in datasets with low sequencing depth. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results show that Centurion can be used for centromere identification for diverse species of yeast and possibly other microorganisms.
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Affiliation(s)
- Nelle Varoquaux
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 35 rue St Honoré 77300 Fontainebleau, France Institut Curie, Paris, F-75248, France U900, INSERM, Paris, F-75248, France
| | - Ivan Liachko
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Joshua N Burton
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Jean-Philippe Vert
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 35 rue St Honoré 77300 Fontainebleau, France Institut Curie, Paris, F-75248, France U900, INSERM, Paris, F-75248, France
| | - William S Noble
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA Department of Computer Science and Engineering, University of Washington, 185 Stevens Way, Seattle, WA 98195, USA
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146
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Dee JM, Mollicone M, Longcore JE, Roberson RW, Berbee ML. Cytology and molecular phylogenetics of Monoblepharidomycetes provide evidence for multiple independent origins of the hyphal habit in the Fungi. Mycologia 2015; 107:710-28. [PMID: 25911696 DOI: 10.3852/14-275] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 04/08/2015] [Indexed: 12/20/2022]
Abstract
The evolution of filamentous hyphae underlies an astounding diversity of fungal form and function. We studied the cellular structure and evolutionary origins of the filamentous form in the Monoblepharidomycetes (Chytridiomycota), an early-diverging fungal lineage that displays an exceptional range of body types, from crescent-shaped single cells to sprawling hyphae. To do so, we combined light and transmission electron microscopic analyses of hyphal cytoplasm with molecular phylogenetic reconstructions. Hyphae of Monoblepharidomycetes lack a complex aggregation of secretory vesicles at the hyphal apex (i.e. Spitzenkörper), have centrosomes as primary microtubule organizing centers and have stacked Golgi cisternae instead of tubular/fenestrated Golgi equivalents. The cytoplasmic distribution of actin in Monoblepharidomycetes is comparable to the arrangement observed previously in other filamentous fungi. To discern the origins of Monoblepharidomycetes hyphae, we inferred a phylogeny of the fungi based on 18S and 28S ribosomal DNA sequence data with maximum likelihood and Bayesian inference methods. We focused sampling on Monoblepharidomycetes to infer intergeneric relationships within the class and determined 78 new sequences. Analyses showed class Monoblepharidomycetes to be monophyletic and nested within Chytridiomycota. Hyphal Monoblepharidomycetes formed a clade sister to the genera without hyphae, Harpochytrium and Oedogoniomyces. A likelihood ancestral state reconstruction indicated that hyphae arose independently within the Monoblepharidomycetes lineage and in at least two other lineages. Cytological differences among monoblepharidalean and other fungal hyphae are consistent with these convergent origins.
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Affiliation(s)
- Jaclyn M Dee
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T-1Z4 Canada
| | - Marilyn Mollicone
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - Joyce E Longcore
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - Robert W Roberson
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Mary L Berbee
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T-1Z4 Canada
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147
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Steensels J, Daenen L, Malcorps P, Derdelinckx G, Verachtert H, Verstrepen KJ. Brettanomyces yeasts--From spoilage organisms to valuable contributors to industrial fermentations. Int J Food Microbiol 2015; 206:24-38. [PMID: 25916511 DOI: 10.1016/j.ijfoodmicro.2015.04.005] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/23/2015] [Accepted: 04/03/2015] [Indexed: 12/13/2022]
Abstract
Ever since the introduction of controlled fermentation processes, alcoholic fermentations and Saccharomyces cerevisiae starter cultures proved to be a match made in heaven. The ability of S. cerevisiae to produce and withstand high ethanol concentrations, its pleasant flavour profile and the absence of health-threatening toxin production are only a few of the features that make it the ideal alcoholic fermentation organism. However, in certain conditions or for certain specific fermentation processes, the physiological boundaries of this species limit its applicability. Therefore, there is currently a strong interest in non-Saccharomyces (or non-conventional) yeasts with peculiar features able to replace or accompany S. cerevisiae in specific industrial fermentations. Brettanomyces (teleomorph: Dekkera), with Brettanomyces bruxellensis as the most commonly encountered representative, is such a yeast. Whilst currently mainly considered a spoilage organism responsible for off-flavour production in wine, cider or dairy products, an increasing number of authors report that in some cases, these yeasts can add beneficial (or at least interesting) aromas that increase the flavour complexity of fermented beverages, such as specialty beers. Moreover, its intriguing physiology, with its exceptional stress tolerance and peculiar carbon- and nitrogen metabolism, holds great potential for the production of bioethanol in continuous fermentors. This review summarizes the most notable metabolic features of Brettanomyces, briefly highlights recent insights in its genetic and genomic characteristics and discusses its applications in industrial fermentation processes, such as the production of beer, wine and bioethanol.
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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Department of Microbial and Molecular Systems (M(2)S), Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Luk Daenen
- AB-InBev SA/NV, Brouwerijplein 1, B-3000 Leuven, Belgium
| | | | - Guy Derdelinckx
- Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems (M(2)S), LFoRCe, KU Leuven, Kasteelpark Arenberg 33, 3001 Leuven, Belgium
| | - Hubert Verachtert
- Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems (M(2)S), LFoRCe, KU Leuven, Kasteelpark Arenberg 33, 3001 Leuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Department of Microbial and Molecular Systems (M(2)S), Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium.
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148
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McMullan M, Gardiner A, Bailey K, Kemen E, Ward BJ, Cevik V, Robert-Seilaniantz A, Schultz-Larsen T, Balmuth A, Holub E, van Oosterhout C, Jones JDG. Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite. eLife 2015; 4. [PMID: 25723966 PMCID: PMC4384639 DOI: 10.7554/elife.04550] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 02/26/2015] [Indexed: 12/13/2022] Open
Abstract
How generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies of five isolates, we show they represent three races that are genetically diverged by ∼1%. Despite this divergence, their genomes are mosaic-like, with ∼25% being introgressed from other races. Sequential infection experiments show that infection by adapted races enables subsequent infection of hosts by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin's finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment.
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Affiliation(s)
| | | | - Kate Bailey
- The Sainsbury Laboratory, Norwich, United Kingdom
| | - Eric Kemen
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ben J Ward
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Volkan Cevik
- The Sainsbury Laboratory, Norwich, United Kingdom
| | | | - Torsten Schultz-Larsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Eric Holub
- Warwick Crop Centre, University of Warwick, School of Life Sciences, Warwick, United Kingdom
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
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149
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Thierry A, Khanna V, Créno S, Lafontaine I, Ma L, Bouchier C, Dujon B. Macrotene chromosomes provide insights to a new mechanism of high-order gene amplification in eukaryotes. Nat Commun 2015; 6:6154. [PMID: 25635677 PMCID: PMC4317496 DOI: 10.1038/ncomms7154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/15/2014] [Indexed: 12/30/2022] Open
Abstract
Copy number variation of chromosomal segments is now recognized as a major source of genetic polymorphism within natural populations of eukaryotes, as well as a possible cause of genetic diseases in humans, including cancer, but its molecular bases remain incompletely understood. In the baker's yeast Saccharomyces cerevisiae, a variety of low-order amplifications (segmental duplications) were observed after adaptation to limiting environmental conditions or recovery from gene dosage imbalance, and interpreted in terms of replication-based mechanisms associated or not with homologous recombination. Here we show the emergence of novel high-order amplification structures, with corresponding overexpression of embedded genes, during evolution under favourable growth conditions of severely unfit yeast cells bearing genetically disabled genomes. Such events form massively extended chromosomes, which we propose to call macrotene, whose characteristics suggest the products of intrachromosomal rolling-circle type of replication structures, probably initiated by increased accidental template switches under important cellular stress conditions.
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Affiliation(s)
- Agnès Thierry
- Institut Pasteur, Unité de Génétique moléculaire des levures, CNRS UMR3525, Sorbonne Universités, UPMC, Univ. Paris 06 UFR927, 25, rue du Docteur Roux, F-75724 Paris, France
| | - Varun Khanna
- Institut Pasteur, Unité de Génétique moléculaire des levures, CNRS UMR3525, Sorbonne Universités, UPMC, Univ. Paris 06 UFR927, 25, rue du Docteur Roux, F-75724 Paris, France
| | - Sophie Créno
- Institut Pasteur, Genomic platform, 28, rue du Docteur Roux, F-75724 Paris, France
| | - Ingrid Lafontaine
- Institut Pasteur, Unité de Génétique moléculaire des levures, CNRS UMR3525, Sorbonne Universités, UPMC, Univ. Paris 06 UFR927, 25, rue du Docteur Roux, F-75724 Paris, France
| | - Laurence Ma
- Institut Pasteur, Genomic platform, 28, rue du Docteur Roux, F-75724 Paris, France
| | - Christiane Bouchier
- Institut Pasteur, Genomic platform, 28, rue du Docteur Roux, F-75724 Paris, France
| | - Bernard Dujon
- Institut Pasteur, Unité de Génétique moléculaire des levures, CNRS UMR3525, Sorbonne Universités, UPMC, Univ. Paris 06 UFR927, 25, rue du Docteur Roux, F-75724 Paris, France
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150
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Hagman A, Piškur J. A study on the fundamental mechanism and the evolutionary driving forces behind aerobic fermentation in yeast. PLoS One 2015; 10:e0116942. [PMID: 25617754 PMCID: PMC4305316 DOI: 10.1371/journal.pone.0116942] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/16/2014] [Indexed: 02/03/2023] Open
Abstract
Baker’s yeast Saccharomyces cerevisiae rapidly converts sugars to ethanol and carbon dioxide at both anaerobic and aerobic conditions. The later phenomenon is called Crabtree effect and has been described in two forms, long-term and short-term effect. We have previously studied under fully controlled aerobic conditions forty yeast species for their central carbon metabolism and the presence of long-term Crabtree effect. We have also studied ten steady-state yeast cultures, pulsed them with glucose, and followed the central carbon metabolism and the appearance of ethanol at dynamic conditions. In this paper we analyzed those wet laboratory data to elucidate possible mechanisms that determine the fate of glucose in different yeast species that cover approximately 250 million years of evolutionary history. We determine overflow metabolism to be the fundamental mechanism behind both long- and short-term Crabtree effect, which originated approximately 125–150 million years ago in the Saccharomyces lineage. The “invention” of overflow metabolism was the first step in the evolution of aerobic fermentation in yeast. It provides a general strategy to increase energy production rates, which we show is positively correlated to growth. The “invention” of overflow has also simultaneously enabled rapid glucose consumption in yeast, which is a trait that could have been selected for, to “starve” competitors in nature. We also show that glucose repression of respiration is confined mainly among S. cerevisiae and closely related species that diverged after the whole genome duplication event, less than 100 million years ago. Thus, glucose repression of respiration was apparently “invented” as a second step to further increase overflow and ethanol production, to inhibit growth of other microbes. The driving force behind the initial evolutionary steps was most likely competition with other microbes to faster consume and convert sugar into biomass, in niches that were semi-anaerobic.
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Affiliation(s)
- Arne Hagman
- Department of Biology, Lund University, Lund, Sweden
- * E-mail:
| | - Jure Piškur
- Department of Biology, Lund University, Lund, Sweden
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