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Kito K, Ito H, Nohara T, Ohnishi M, Ishibashi Y, Takeda D. Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication. Mol Cell Proteomics 2015; 15:218-35. [PMID: 26560065 DOI: 10.1074/mcp.m115.051854] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 11/06/2022] Open
Abstract
Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history.
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Affiliation(s)
- Keiji Kito
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Haruka Ito
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Takehiro Nohara
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Mihoko Ohnishi
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Yuko Ishibashi
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Daisuke Takeda
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
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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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Romagnoli G, Verhoeven MD, Mans R, Fleury Rey Y, Bel-Rhlid R, van den Broek M, Seifar RM, Ten Pierick A, Thompson M, Müller V, Wahl SA, Pronk JT, Daran JM. An alternative, arginase-independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme. Mol Microbiol 2014; 93:369-89. [PMID: 24912400 PMCID: PMC4149782 DOI: 10.1111/mmi.12666] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2014] [Indexed: 11/26/2022]
Abstract
Most available knowledge on fungal arginine metabolism is derived from studies on Saccharomyces cerevisiae, in which arginine catabolism is initiated by releasing urea via the arginase reaction. Orthologues of the S. cerevisiae genes encoding the first three enzymes in the arginase pathway were cloned from Kluyveromyces lactis and shown to functionally complement the corresponding deletion in S. cerevisiae. Surprisingly, deletion of the single K. lactis arginase gene KlCAR1 did not completely abolish growth on arginine as nitrogen source. Growth rate of the deletion mutant strongly increased during serial transfer in shake-flask cultures. A combination of RNAseq-based transcriptome analysis and (13)C-(15)N-based flux analysis was used to elucidate the arginase-independent pathway. Isotopic (13)C(15)N-enrichment in γ-aminobutyrate revealed succinate as the entry point in the TCA cycle of the alternative pathway. Transcript analysis combined with enzyme activity measurements indicated increased expression in the Klcar1Δ mutant of a guanidinobutyrase (EC.3.5.3.7), a key enzyme in a new pathway for arginine degradation. Expression of the K. lactis KLLA0F27995g (renamed KlGBU1) encoding guanidinobutyrase enabled S. cerevisiae to use guanidinobutyrate as sole nitrogen source and its deletion in K. lactis almost completely abolish growth on this nitrogen source. Phylogenetic analysis suggests that this enzyme activity is widespread in fungi.
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Affiliation(s)
- G Romagnoli
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 4047, 2600 GA, Delft, The Netherlands
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Mira NP, Münsterkötter M, Dias-Valada F, Santos J, Palma M, Roque FC, Guerreiro JF, Rodrigues F, Sousa MJ, Leão C, Güldener U, Sá-Correia I. The genome sequence of the highly acetic acid-tolerant Zygosaccharomyces bailii-derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant. DNA Res 2014; 21:299-313. [PMID: 24453040 PMCID: PMC4060950 DOI: 10.1093/dnares/dst058] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In this work, it is described the sequencing and annotation of the genome of the yeast strain ISA1307, isolated from a sparkling wine continuous production plant. This strain, formerly considered of the Zygosaccharomyces bailii species, has been used to study Z. bailii physiology, in particular, its extreme tolerance to acetic acid stress at low pH. The analysis of the genome sequence described in this work indicates that strain ISA1307 is an interspecies hybrid between Z. bailii and a closely related species. The genome sequence of ISA1307 is distributed through 154 scaffolds and has a size of around 21.2 Mb, corresponding to 96% of the genome size estimated by flow cytometry. Annotation of ISA1307 genome includes 4385 duplicated genes (∼90% of the total number of predicted genes) and 1155 predicted single-copy genes. The functional categories including a higher number of genes are ‘Metabolism and generation of energy’, ‘Protein folding, modification and targeting’ and ‘Biogenesis of cellular components’. The knowledge of the genome sequence of the ISA1307 strain is expected to contribute to accelerate systems-level understanding of stress resistance mechanisms in Z. bailii and to inspire and guide novel biotechnological applications of this yeast species/strain in fermentation processes, given its high resilience to acidic stress. The availability of the ISA1307 genome sequence also paves the way to a better understanding of the genetic mechanisms underlying the generation and selection of more robust hybrid yeast strains in the stressful environment of wine fermentations.
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Affiliation(s)
- Nuno P Mira
- IBB-Institute for Biotechnology and Bioengineering, Center for Biological and Chemical Engineering, Instituto Superior Técnico, Department of Bioengineering, Universidade de Lisboa, Avenida Rovisco Pais, Lisbon 1049-001, Portugal
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, Neuherberg D-85764, Germany
| | - Filipa Dias-Valada
- IBB-Institute for Biotechnology and Bioengineering, Center for Biological and Chemical Engineering, Instituto Superior Técnico, Department of Bioengineering, Universidade de Lisboa, Avenida Rovisco Pais, Lisbon 1049-001, Portugal
| | - Júlia Santos
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal ICVS/3B's-PT Government Associate Laboratory, Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal
| | - Margarida Palma
- IBB-Institute for Biotechnology and Bioengineering, Center for Biological and Chemical Engineering, Instituto Superior Técnico, Department of Bioengineering, Universidade de Lisboa, Avenida Rovisco Pais, Lisbon 1049-001, Portugal
| | - Filipa C Roque
- IBB-Institute for Biotechnology and Bioengineering, Center for Biological and Chemical Engineering, Instituto Superior Técnico, Department of Bioengineering, Universidade de Lisboa, Avenida Rovisco Pais, Lisbon 1049-001, Portugal
| | - Joana F Guerreiro
- IBB-Institute for Biotechnology and Bioengineering, Center for Biological and Chemical Engineering, Instituto Superior Técnico, Department of Bioengineering, Universidade de Lisboa, Avenida Rovisco Pais, Lisbon 1049-001, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal ICVS/3B's-PT Government Associate Laboratory, Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal
| | - Maria João Sousa
- Centre of Molecular and Environmental Biology (CBMA)/Department of Biology, University of Minho, Braga 4710-057, Portugal
| | - Cecília Leão
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal ICVS/3B's-PT Government Associate Laboratory, Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal
| | - Ulrich Güldener
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, Neuherberg D-85764, Germany
| | - Isabel Sá-Correia
- IBB-Institute for Biotechnology and Bioengineering, Center for Biological and Chemical Engineering, Instituto Superior Técnico, Department of Bioengineering, Universidade de Lisboa, Avenida Rovisco Pais, Lisbon 1049-001, Portugal
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Huerta-Cepas J, Capella-Gutiérrez S, Pryszcz LP, Marcet-Houben M, Gabaldón T. PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res 2013; 42:D897-902. [PMID: 24275491 PMCID: PMC3964985 DOI: 10.1093/nar/gkt1177] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.
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Affiliation(s)
- Jaime Huerta-Cepas
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88. 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A. Protein Expansion Is Primarily due to Indels in Intrinsically Disordered Regions. Mol Biol Evol 2013; 30:2645-53. [DOI: 10.1093/molbev/mst157] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Maguire SL, ÓhÉigeartaigh SS, Byrne KP, Schröder MS, O’Gaora P, Wolfe KH, Butler G. Comparative genome analysis and gene finding in Candida species using CGOB. Mol Biol Evol 2013; 30:1281-91. [PMID: 23486613 PMCID: PMC3649674 DOI: 10.1093/molbev/mst042] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Candida Gene Order Browser (CGOB) was developed as a tool to visualize and analyze synteny relationships in multiple Candida species, and to provide an accurate, manually curated set of orthologous Candida genes for evolutionary analyses. Here, we describe major improvements to CGOB. The underlying structure of the database has been changed significantly. Genomic features are now based directly on genome annotations rather than on protein sequences, which allows non-protein features such as centromere locations in Candida albicans and tRNA genes in all species to be included. The data set has been expanded to 13 species, including genomes of pathogens (C. albicans, C. parapsilosis, C. tropicalis, and C. orthopsilosis), and those of xylose-degrading species with important biotechnological applications (C. tenuis, Scheffersomyces stipitis, and Spathaspora passalidarum). Updated annotations of C. parapsilosis, C. dubliniensis, and Debaryomyces hansenii have been incorporated. We discovered more than 1,500 previously unannotated genes among the 13 genomes, ranging in size from 29 to 3,850 amino acids. Poorly conserved and rapidly evolving genes were also identified. Re-analysis of the mating type loci of the xylose degraders suggests that C. tenuis is heterothallic, whereas both Spa. passalidarum and S. stipitis are homothallic. As well as hosting the browser, the CGOB website (http://cgob.ucd.ie) gives direct access to all the underlying genome annotations, sequences, and curated orthology data.
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Affiliation(s)
- Sarah L. Maguire
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | | | - Kevin P. Byrne
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Markus S. Schröder
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Peadar O’Gaora
- UCD School of Medicine and Medical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Kenneth H. Wolfe
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Geraldine Butler
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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Siso MIG, Becerra M, Maceiras ML, Vázquez ÁV, Cerdán ME. The yeast hypoxic responses, resources for new biotechnological opportunities. Biotechnol Lett 2012; 34:2161-73. [DOI: 10.1007/s10529-012-1039-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/14/2012] [Indexed: 10/27/2022]
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